NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958686853|ref|XP_006252699|]
View 

LIM domain-binding protein 3 isoform X1 [Rattus norvegicus]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
49-127 2.56e-50

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


:

Pssm-ID: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 170.40  E-value: 2.56e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06753     1 SVTLSGPAPWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79
LIM1_ZASP_Cypher cd09454
The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP ...
595-646 2.30e-36

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


:

Pssm-ID: 188838 [Multi-domain]  Cd Length: 52  Bit Score: 130.48  E-value: 2.30e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
LIM3_ZASP_Cypher cd09460
The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP ...
713-767 2.36e-34

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


:

Pssm-ID: 188844  Cd Length: 55  Bit Score: 124.77  E-value: 2.36e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09460     1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
LIM2_Enigma_like cd09362
The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The ...
654-705 1.70e-31

The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


:

Pssm-ID: 188748 [Multi-domain]  Cd Length: 52  Bit Score: 116.42  E-value: 1.70e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
DUF4749 pfam15936
Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. ...
240-342 8.68e-23

Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643).


:

Pssm-ID: 464948 [Multi-domain]  Cd Length: 98  Bit Score: 93.26  E-value: 8.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 240 YNNPIGLYSAETLREMAQMYQMSLRGKASGaGLLGGSLPVKDLAVDSASPVYQAVIKTQSKPEDEAdewarrssnlQSRS 319
Cdd:pfam15936   7 YNSPIGLYSSENIQDALSGQLSGLAGSSEG-GKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR----------QSGS 75
                          90       100
                  ....*....|....*....|...
gi 1958686853 320 FRILAQMTGTEYMQDPDEEALRR 342
Cdd:pfam15936  76 FRVLQEILETEYLQPPEEELNRP 98
PHA03247 super family cl33720
large tegument protein UL36; Provisional
426-576 1.10e-09

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 62.26  E-value: 1.10e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  426 TSYSEGPAAPAPKPRVVT-TASIRPsvyqPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSP--APTYSPSPA 502
Cdd:PHA03247  2677 SSPPQRPRRRAARPTVGSlTSLADP----PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPpaVPAGPATPG 2752
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853  503 ----PAYTPSPAPNYNPTPSAAYSGGPSESASRPPwVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLA 576
Cdd:PHA03247  2753 gparPARPPTTAGPPAPAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP 2829
 
Name Accession Description Interval E-value
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
49-127 2.56e-50

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 170.40  E-value: 2.56e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06753     1 SVTLSGPAPWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79
LIM1_ZASP_Cypher cd09454
The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP ...
595-646 2.30e-36

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188838 [Multi-domain]  Cd Length: 52  Bit Score: 130.48  E-value: 2.30e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
LIM3_ZASP_Cypher cd09460
The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP ...
713-767 2.36e-34

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188844  Cd Length: 55  Bit Score: 124.77  E-value: 2.36e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09460     1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
LIM2_Enigma_like cd09362
The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The ...
654-705 1.70e-31

The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188748 [Multi-domain]  Cd Length: 52  Bit Score: 116.42  E-value: 1.70e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
DUF4749 pfam15936
Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. ...
240-342 8.68e-23

Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643).


Pssm-ID: 464948 [Multi-domain]  Cd Length: 98  Bit Score: 93.26  E-value: 8.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 240 YNNPIGLYSAETLREMAQMYQMSLRGKASGaGLLGGSLPVKDLAVDSASPVYQAVIKTQSKPEDEAdewarrssnlQSRS 319
Cdd:pfam15936   7 YNSPIGLYSSENIQDALSGQLSGLAGSSEG-GKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR----------QSGS 75
                          90       100
                  ....*....|....*....|...
gi 1958686853 320 FRILAQMTGTEYMQDPDEEALRR 342
Cdd:pfam15936  76 FRVLQEILETEYLQPPEEELNRP 98
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
46-126 2.85e-18

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 80.12  E-value: 2.85e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853   46 MSYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:smart00228   1 EPRLVELEkGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT 80

                   ..
gi 1958686853  125 LQ 126
Cdd:smart00228  81 VL 82
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
712-765 1.06e-17

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 77.42  E-value: 1.06e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  712 KCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
653-704 1.80e-15

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 70.88  E-value: 1.80e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  653 ICAKCNTKIMG--EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKD 704
Cdd:smart00132   1 KCAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
54-126 2.13e-15

PDZ domain; PDZ domains are found in diverse signaling proteins.


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 71.54  E-value: 2.13e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  54 GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:pfam00595   8 GRGGLGFSLKGGSDQgDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
654-709 3.68e-15

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 70.05  E-value: 3.68e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLF 709
Cdd:pfam00412   1 CAGCNRPIYDrELVRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
713-765 2.11e-13

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 65.05  E-value: 2.11e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:pfam00412   1 CAGCNRPIYDRELVR-ALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHD 52
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
595-645 1.10e-12

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 63.17  E-value: 1.10e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853  595 CGHCNNVIRG--PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
595-650 3.70e-12

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 61.58  E-value: 3.70e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFF 650
Cdd:pfam00412   1 CAGCNRPIYDRELVrALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57
PHA03247 PHA03247
large tegument protein UL36; Provisional
426-576 1.10e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 62.26  E-value: 1.10e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  426 TSYSEGPAAPAPKPRVVT-TASIRPsvyqPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSP--APTYSPSPA 502
Cdd:PHA03247  2677 SSPPQRPRRRAARPTVGSlTSLADP----PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPpaVPAGPATPG 2752
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853  503 ----PAYTPSPAPNYNPTPSAAYSGGPSESASRPPwVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLA 576
Cdd:PHA03247  2753 gparPARPPTTAGPPAPAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP 2829
TALPID3 pfam15324
Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for ...
434-593 1.46e-06

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.


Pssm-ID: 434634 [Multi-domain]  Cd Length: 1288  Bit Score: 52.20  E-value: 1.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  434 APAPKPRVVTTASIRPSVYQPVPASPYSPSP---GANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTysPSPAPAYTPSP 509
Cdd:pfam15324  986 TPVPTPQPTPPCSPPSPLKEPSPVKTPDSSPcvsEHDFFPVKEIPPEKGADTgPAVSLVITPTVTPI--ATPPPAATPTP 1063
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  510 apnynPTPSAAYSGGPSESASRP-PWVTDD---------SFSQKFAPGKSTTSVSKQTLPRGA--PAYNPTGPQVTPLAR 577
Cdd:pfam15324 1064 -----PLSENSIDKLKSPSPELPkPWEDSDlpleeenpnSEQEELHPRAVVMSVARDEEPESVvlPASPPEPKPLAPPPL 1138
                          170
                   ....*....|....*.
gi 1958686853  578 GTfqraeRFPASSRTP 593
Cdd:pfam15324 1139 GA-----APPSPPQSP 1149
ZM smart00735
ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ...
234-259 5.47e-06

ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.


Pssm-ID: 128974  Cd Length: 26  Bit Score: 43.36  E-value: 5.47e-06
                           10        20
                   ....*....|....*....|....*.
gi 1958686853  234 PSQPRLYNNPIGLYSAETLREMAQMY 259
Cdd:smart00735   1 RVVHKQYNSPIGLYSSENIAETLQGQ 26
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
438-511 1.14e-05

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 48.35  E-value: 1.14e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 438 KPRVVTTASIRPSvyqPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPApTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:TIGR00601  76 KPKTGTGKVAPPA---ATPTSAPTPTPSPPASPAS-GMSAAPASAVEEK-SPSEESATATAPESPSTSVPSSGS 144
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
36-137 1.92e-05

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 47.56  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  36 PEEATAVGTSMSYSVTLTGpgpwgFRLQGGKDFnmpLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 115
Cdd:COG0793    45 PEEYEDFQESTSGEFGGLG-----AELGEEDGK---VVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLR 116
                          90       100
                  ....*....|....*....|....*
gi 1958686853 116 SAS-YNLSLTLQK--SKRPIPISTT 137
Cdd:COG0793   117 GKAgTKVTLTIKRpgEGEPITVTLT 141
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
425-543 5.16e-03

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 40.12  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 425 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSP------APTYTPSPAPTYS 498
Cdd:COG3469    91 STSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTtvsgteTATGGTTTTSTTT 170
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958686853 499 PSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQK 543
Cdd:COG3469   171 TTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLPKH 215
 
Name Accession Description Interval E-value
PDZ_PDLIM-like cd06753
PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density ...
49-127 2.56e-50

PDZ domain of PDZ-LIM family proteins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467235 [Multi-domain]  Cd Length: 79  Bit Score: 170.40  E-value: 2.56e-50
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06753     1 SVTLSGPAPWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79
LIM1_ZASP_Cypher cd09454
The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP ...
595-646 2.30e-36

The first LIM domain of ZASP/Cypher family; The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188838 [Multi-domain]  Cd Length: 52  Bit Score: 130.48  E-value: 2.30e-36
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
LIM3_ZASP_Cypher cd09460
The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP ...
713-767 2.36e-34

The third LIM domain of ZASP/Cypher family; The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188844  Cd Length: 55  Bit Score: 124.77  E-value: 2.36e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09460     1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
LIM3_Enigma_like cd09363
The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The ...
713-766 3.11e-34

The third LIM domain of Enigma-like family; The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188749 [Multi-domain]  Cd Length: 54  Bit Score: 124.47  E-value: 3.11e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 766
Cdd:cd09363     1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNHA 54
LIM3_ENH cd09459
The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma ...
713-767 7.61e-34

The third LIM domain of the Enigma Homolog (ENH) family; The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188843 [Multi-domain]  Cd Length: 55  Bit Score: 123.54  E-value: 7.61e-34
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09459     1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55
LIM2_Enigma_like cd09362
The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The ...
654-705 1.70e-31

The second LIM domain of Enigma-like family; The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188748 [Multi-domain]  Cd Length: 52  Bit Score: 116.42  E-value: 1.70e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
LIM1_Enigma_like cd09361
The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The ...
595-646 6.06e-30

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188747 [Multi-domain]  Cd Length: 52  Bit Score: 112.07  E-value: 6.06e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09361     1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
PDZ_ZASP52-like cd23068
PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), ...
57-127 4.71e-29

PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467281 [Multi-domain]  Cd Length: 82  Bit Score: 110.70  E-value: 4.71e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958686853  57 PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd23068    12 PWGFRLQGGADFGQPLSIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82
LIM3_Enigma cd09458
The third LIM domain of Enigma; The third LIM domain of Enigma: Enigma was initially ...
713-766 5.84e-27

The third LIM domain of Enigma; The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188842  Cd Length: 55  Bit Score: 103.97  E-value: 5.84e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 766
Cdd:cd09458     1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSHA 54
LIM1_ENH cd09453
The first LIM domain of the Enigma Homolog (ENH) family; The first LIM domain of the Enigma ...
595-646 1.25e-25

The first LIM domain of the Enigma Homolog (ENH) family; The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188837 [Multi-domain]  Cd Length: 52  Bit Score: 100.09  E-value: 1.25e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09453     1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
LIM2_Enigma cd09456
The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially ...
654-705 1.16e-24

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188840 [Multi-domain]  Cd Length: 52  Bit Score: 96.99  E-value: 1.16e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
LIM2_ENH cd09457
The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma ...
654-705 9.79e-24

The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188841 [Multi-domain]  Cd Length: 52  Bit Score: 94.32  E-value: 9.79e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09457     1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
DUF4749 pfam15936
Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. ...
240-342 8.68e-23

Domain of unknown function (DUF4749); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643).


Pssm-ID: 464948 [Multi-domain]  Cd Length: 98  Bit Score: 93.26  E-value: 8.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 240 YNNPIGLYSAETLREMAQMYQMSLRGKASGaGLLGGSLPVKDLAVDSASPVYQAVIKTQSKPEDEAdewarrssnlQSRS 319
Cdd:pfam15936   7 YNSPIGLYSSENIQDALSGQLSGLAGSSEG-GKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR----------QSGS 75
                          90       100
                  ....*....|....*....|...
gi 1958686853 320 FRILAQMTGTEYMQDPDEEALRR 342
Cdd:pfam15936  76 FRVLQEILETEYLQPPEEELNRP 98
PDZ_SYNPO2-like cd10820
PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related ...
50-126 8.67e-21

PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467264 [Multi-domain]  Cd Length: 78  Bit Score: 86.98  E-value: 8.67e-21
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  50 VTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd10820     2 VTLTGGAPWGFRLQGGSEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDTLQLLIK 78
LIM3_Enigma_like_1 cd09461
The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an ...
713-766 1.97e-20

The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188845  Cd Length: 54  Bit Score: 85.30  E-value: 1.97e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 766
Cdd:cd09461     1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLHA 54
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
654-705 1.01e-18

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 259829 [Multi-domain]  Cd Length: 53  Bit Score: 80.05  E-value: 1.01e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd08368     1 CAGCGKPIEGrELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53
LIM1_Enigma_like_1 cd09455
The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an ...
595-646 1.48e-18

The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188839  Cd Length: 54  Bit Score: 79.81  E-value: 1.48e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCA--YCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCEYCF 54
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
46-126 2.85e-18

Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.


Pssm-ID: 214570 [Multi-domain]  Cd Length: 85  Bit Score: 80.12  E-value: 2.85e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853   46 MSYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:smart00228   1 EPRLVELEkGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT 80

                   ..
gi 1958686853  125 LQ 126
Cdd:smart00228  81 VL 82
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
712-765 1.06e-17

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 77.42  E-value: 1.06e-17
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  712 KCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
50-126 6.97e-17

canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467153 [Multi-domain]  Cd Length: 81  Bit Score: 76.04  E-value: 6.97e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  50 VTLTGP--GPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd00136     2 VTLEKDpgGGLGFSIRGGKDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGVSLEGLTHEEAVELLKSAGGEVTLTVR 81
LIM1_Paxillin_like cd09336
The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin ...
654-705 7.56e-17

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 259830 [Multi-domain]  Cd Length: 53  Bit Score: 74.73  E-value: 7.56e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52
LIM2_Paxillin_like cd09337
The second LIM domain of the paxillin like protein family; The second LIM domain of the ...
654-705 1.79e-16

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188723 [Multi-domain]  Cd Length: 52  Bit Score: 73.96  E-value: 1.79e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
LIM1_Enigma cd09452
The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially ...
595-646 1.93e-16

The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188836 [Multi-domain]  Cd Length: 52  Bit Score: 73.68  E-value: 1.93e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
713-766 5.27e-16

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 259829 [Multi-domain]  Cd Length: 53  Bit Score: 72.35  E-value: 5.27e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 766
Cdd:cd08368     1 CAGCGKPIE-GRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53
PDZ_shroom2_3_4-like cd06750
PDZ domain of shroom2, shroom3, shroom4, and related domains; PDZ (PSD-95 (Postsynaptic ...
49-127 1.46e-15

PDZ domain of shroom2, shroom3, shroom4, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of shroom2, shroom3, shroom4, and related domains. Shroom family proteins shroom2 (also known as apical-like protein; protein APXL), shroom3 (also known as shroom-related protein), and shroom4 (also known as second homolog of apical protein) are essential regulators of cell morphology during animal development; they regulate cell architecture by directing the subcellular distribution and activation of Rho kinase (ROCK), which results in the localized activation of non-muscle myosin. The interaction between shroom and ROCK is mediated by the shroom domain 2 (SD2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This shroom2,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467232 [Multi-domain]  Cd Length: 82  Bit Score: 72.37  E-value: 1.46e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMtHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06750     4 EVQLQGGAPWGFTLKGGLEHGEPLVISKIEEGGKAAsVGKLQVGDEVVNINGVPLSGS-RQEAIQLVKGSHKTLKLVVRR 82
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
653-704 1.80e-15

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 70.88  E-value: 1.80e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  653 ICAKCNTKIMG--EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKD 704
Cdd:smart00132   1 KCAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
54-126 2.13e-15

PDZ domain; PDZ domains are found in diverse signaling proteins.


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 71.54  E-value: 2.13e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  54 GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:pfam00595   8 GRGGLGFSLKGGSDQgDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
595-646 3.63e-15

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 259829 [Multi-domain]  Cd Length: 53  Bit Score: 70.04  E-value: 3.63e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd08368     1 CAGCGKPIEGRELLrALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
654-709 3.68e-15

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 70.05  E-value: 3.68e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLF 709
Cdd:pfam00412   1 CAGCNRPIYDrELVRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57
LIM1_Leupaxin cd09406
The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
654-705 1.00e-13

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188790 [Multi-domain]  Cd Length: 55  Bit Score: 66.05  E-value: 1.00e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
LIM3_Paxillin_like cd09338
The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin ...
654-705 1.89e-13

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188724 [Multi-domain]  Cd Length: 53  Bit Score: 65.05  E-value: 1.89e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
713-765 2.11e-13

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 65.05  E-value: 2.11e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:pfam00412   1 CAGCNRPIYDRELVR-ALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHD 52
PDZ5_MAGI-1_3-like cd06735
PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, ...
48-127 2.14e-13

PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467217 [Multi-domain]  Cd Length: 84  Bit Score: 66.06  E-value: 2.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  48 YSVTLT-GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06735     2 YSVELErGPKGFGFSIRGGREYnNMPLYVLRLAEDGPAQRDgRLRVGDQILEINGESTQGMTHAQAIELIRSGGSVVRLL 81

                  ...
gi 1958686853 125 LQK 127
Cdd:cd06735    82 LRR 84
PDZ_PTPN3-4-like cd06706
PDZ domain of tyrosine-protein phosphatase non-receptor type 3 (PTPN3), tyrosine-protein ...
56-117 3.27e-13

PDZ domain of tyrosine-protein phosphatase non-receptor type 3 (PTPN3), tyrosine-protein phosphatase non-receptor type 4 (PTNP4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PTPN3, PTPN4 and related domains. PTPN3 (also known as protein-tyrosine phosphatase H1, PTP-H1) has a tumor-suppressive or a tumor-promoting role in many cancers. It serves as a specific phosphatase for the MAP kinase p38gamma; the two interact via their PDZ domains and cooperate to promote Ras-induced oncogenesis. Interaction partners of the PTPN3 PDZ domain include p38gamma and human papillomavirus E6 oncoprotein. PTPN4 (also known as protein-tyrosine phosphatase MEG1) plays a role in immunity, learning, synaptic plasticity or cell homeostasis. p38gamma is also an interaction partner of the PTPN4 PDZ domain: PTPN4 regulates neuronal cell homeostasis by protecting neurons against apoptosis; binding of the C terminus of p38gamma to the PDZ domain of PTPN4, antagonizes the catalytic autoinhibition of PTPN4, leading to cell apoptosis. Other interaction partners of the PTPN4 PDZ domain include glutamate receptor subunit GluN2A, and RABV strain G protein, among others. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467190 [Multi-domain]  Cd Length: 90  Bit Score: 65.80  E-value: 3.27e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  56 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQ--LSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06706    14 GRFGFNVKGGVDQKMPVIVSRVAPGTPADLCIprLNEGDQVLLINGRDISEHTHDQVVMFIKAS 77
LIM1_Paxillin_like cd09336
The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin ...
595-646 4.26e-13

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 259830 [Multi-domain]  Cd Length: 53  Bit Score: 64.33  E-value: 4.26e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
595-645 1.10e-12

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.


Pssm-ID: 214528 [Multi-domain]  Cd Length: 54  Bit Score: 63.17  E-value: 1.10e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853  595 CGHCNNVIRG--PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
LIM1_Paxillin cd09405
The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor ...
653-705 1.19e-12

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188789 [Multi-domain]  Cd Length: 54  Bit Score: 63.10  E-value: 1.19e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 653 ICAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
LIM4_Paxillin_like cd09339
The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the ...
595-646 3.24e-12

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188725 [Multi-domain]  Cd Length: 52  Bit Score: 61.59  E-value: 3.24e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
595-650 3.70e-12

LIM domain; This family represents two copies of the LIM structural domain.


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 61.58  E-value: 3.70e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFF 650
Cdd:pfam00412   1 CAGCNRPIYDRELVrALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57
LIM1_PINCH cd09331
The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an ...
642-710 1.81e-11

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188717  Cd Length: 59  Bit Score: 59.65  E-value: 1.81e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 642 CERCYEQFfAPicakcNTKIM---GEVmhalrqtWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLFS 710
Cdd:cd09331     1 CERCREGF-EP-----DEKIVnsnGEL-------YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
LIM3_Paxillin_like cd09338
The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin ...
713-767 2.31e-11

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188724 [Multi-domain]  Cd Length: 53  Bit Score: 59.27  E-value: 2.31e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09338     1 CGGCNKPIL--ENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53
LIM2_PINCH cd09332
The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a ...
595-645 3.60e-11

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188718 [Multi-domain]  Cd Length: 52  Bit Score: 58.89  E-value: 3.60e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
PDZ7_PDZD2-PDZ4_hPro-IL-16-like cd06763
PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 ...
49-116 4.15e-11

PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467244 [Multi-domain]  Cd Length: 86  Bit Score: 59.55  E-value: 4.15e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958686853  49 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 116
Cdd:cd06763     3 TVELEkGSAGLGFSLEGGKGSplgDRPLTIKRIFKGGAAEQSgVLQVGDEILQINGTSLQGLTRFEAWNIIKS 75
LIM2_Leupaxin cd09408
The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a ...
654-705 1.05e-10

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188792 [Multi-domain]  Cd Length: 52  Bit Score: 57.52  E-value: 1.05e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
LIM4_PINCH cd09334
The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a ...
652-705 1.34e-10

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.


Pssm-ID: 188720 [Multi-domain]  Cd Length: 54  Bit Score: 57.36  E-value: 1.34e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 652 PICAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
LIM2_Paxillin cd09407
The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor ...
654-705 1.80e-10

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188791 [Multi-domain]  Cd Length: 52  Bit Score: 56.89  E-value: 1.80e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
PDZ1_harmonin cd06737
PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
53-119 3.63e-10

PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467219 [Multi-domain]  Cd Length: 85  Bit Score: 56.88  E-value: 3.63e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  53 TGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06737    10 RGPESLGFSVRGGLEHGCGLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTKKT 76
LIM1_LIMK cd09364
The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain ...
654-705 4.70e-10

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188750 [Multi-domain]  Cd Length: 53  Bit Score: 55.57  E-value: 4.70e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 705
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYFE-KDGKLYCRKDY 52
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
49-125 6.85e-10

PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RapGEF2 and RapGEF6 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467237 [Multi-domain]  Cd Length: 83  Bit Score: 56.12  E-value: 6.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  49 SVTLTGPG---PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTL 125
Cdd:cd06755     2 TVTLTRPSresPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTH-LSITV 80
LIM4_PINCH cd09334
The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a ...
593-646 6.95e-10

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.


Pssm-ID: 188720 [Multi-domain]  Cd Length: 54  Bit Score: 55.05  E-value: 6.95e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 593 PLCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
LIM3_abLIM cd09329
The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin ...
654-705 7.12e-10

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188715 [Multi-domain]  Cd Length: 52  Bit Score: 55.02  E-value: 7.12e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKpfgnsLFHME----DGEPYCEKDY 705
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGK-----VLTGEymgkDGKPYCERDY 52
PDZ2_PDZD7-like cd10834
PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
58-126 8.90e-10

PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467270 [Multi-domain]  Cd Length: 85  Bit Score: 55.86  E-value: 8.90e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  58 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTLQ 126
Cdd:cd10834    15 LGFNIRGGSEYGLGIYVSKVDPGGLAEQNGIKVGDQILAVNGVSFEDITHSKAVEVLKSQTH-LMLTIK 82
LIM2_Paxillin_like cd09337
The second LIM domain of the paxillin like protein family; The second LIM domain of the ...
595-646 9.46e-10

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188723 [Multi-domain]  Cd Length: 52  Bit Score: 54.70  E-value: 9.46e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
PHA03247 PHA03247
large tegument protein UL36; Provisional
426-576 1.10e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 62.26  E-value: 1.10e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  426 TSYSEGPAAPAPKPRVVT-TASIRPsvyqPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSP--APTYSPSPA 502
Cdd:PHA03247  2677 SSPPQRPRRRAARPTVGSlTSLADP----PPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPpaVPAGPATPG 2752
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853  503 ----PAYTPSPAPNYNPTPSAAYSGGPSESASRPPwVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLA 576
Cdd:PHA03247  2753 gparPARPPTTAGPPAPAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP 2829
LIM2_FHL cd09345
The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of ...
713-764 1.40e-09

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188731 [Multi-domain]  Cd Length: 54  Bit Score: 54.22  E-value: 1.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09345     1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVP 52
LIM1_abLIM cd09327
The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin ...
654-705 1.50e-09

The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188713 [Multi-domain]  Cd Length: 52  Bit Score: 54.18  E-value: 1.50e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09327     1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
LIM1_Paxillin cd09405
The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor ...
594-646 2.03e-09

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188789 [Multi-domain]  Cd Length: 54  Bit Score: 53.86  E-value: 2.03e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 594 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
LIM1_Leupaxin cd09406
The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
595-646 2.45e-09

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188790 [Multi-domain]  Cd Length: 55  Bit Score: 53.72  E-value: 2.45e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
PHA03247 PHA03247
large tegument protein UL36; Provisional
405-593 2.70e-09

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 61.11  E-value: 2.70e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  405 PRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGA------------------ 466
Cdd:PHA03247  2712 PHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAapaagpprrltrpavasl 2791
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  467 ----NYSPTPYTPSPAPAYTPSPAPTY-------TPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGP--SESASRPP 533
Cdd:PHA03247  2792 sesrESLPSPWDPADPPAAVLAPAAALppaaspaGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDvrRRPPSRSP 2871
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  534 WVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERFPASSRTP 593
Cdd:PHA03247  2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQP 2931
LIM1_LPP cd09351
The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma ...
654-705 2.90e-09

The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188737 [Multi-domain]  Cd Length: 54  Bit Score: 53.58  E-value: 2.90e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIMGEVM--HALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09351     1 CVKCGEKVLGEGSgcTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
LIM1_Paxillin_like cd09336
The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin ...
713-767 3.05e-09

The first LIM domain of the paxillin like protein family; The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 259830 [Multi-domain]  Cd Length: 53  Bit Score: 53.16  E-value: 3.05e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09336     1 CAACNKPI-VG-QVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDYH 53
PDZ_syntrophin-like cd06801
PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), ...
59-126 3.76e-09

PDZ domain of syntrophins, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntrophin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467262 [Multi-domain]  Cd Length: 83  Bit Score: 54.12  E-value: 3.76e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  59 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06801    14 GISIKGGAEHKMPILISKIFKGQAADQTgQLFVGDAILSVNGENLEDATHDEAVQALKNAGDEVTLTVK 82
LIM_DA1 cd09396
The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain ...
654-700 7.26e-09

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188782 [Multi-domain]  Cd Length: 53  Bit Score: 52.26  E-value: 7.26e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPY 700
Cdd:cd09396     1 CAGCKSEIGhGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
LIM2_Testin_like cd09341
The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This ...
593-647 1.14e-08

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188727  Cd Length: 56  Bit Score: 51.84  E-value: 1.14e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 593 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 647
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
59-117 1.42e-08

PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467234 [Multi-domain]  Cd Length: 83  Bit Score: 52.32  E-value: 1.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  59 GFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06752    14 GFNIRGGKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTA 72
LIM2_FBLP-1 cd09372
The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of ...
654-705 1.51e-08

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188758 [Multi-domain]  Cd Length: 53  Bit Score: 51.27  E-value: 1.51e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHM-EDGEPYCEKDY 705
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVdEQNEVYCLDDY 53
LIM3_Leupaxin cd09410
The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
654-705 1.68e-08

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188794 [Multi-domain]  Cd Length: 53  Bit Score: 51.36  E-value: 1.68e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52
LIM3_Paxillin cd09409
The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor ...
654-705 1.82e-08

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188793 [Multi-domain]  Cd Length: 53  Bit Score: 51.00  E-value: 1.82e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
LIM1_FHL1 cd09344
The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four ...
713-764 1.95e-08

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188730  Cd Length: 54  Bit Score: 50.91  E-value: 1.95e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09344     1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52
LIM4_Paxillin cd09411
The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor ...
595-646 2.05e-08

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188795 [Multi-domain]  Cd Length: 52  Bit Score: 51.10  E-value: 2.05e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52
LIM4_Leupaxin cd09412
The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a ...
595-646 3.66e-08

The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188796 [Multi-domain]  Cd Length: 52  Bit Score: 50.12  E-value: 3.66e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
LIM1_LIMK1 cd09462
The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain ...
652-705 4.42e-08

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188846 [Multi-domain]  Cd Length: 74  Bit Score: 50.65  E-value: 4.42e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 652 PICAKCNTKIM-GEVMHALRQTWHTTCFICAACkkpfGNSLFHM---EDGEPYCEKDY 705
Cdd:cd09462    20 PVCASCGQSIYdGQYLQALNSDWHADCFRCCEC----GASLSHWyyeKDGRLFCKKDY 73
PDZ_Lin-7-like cd06796
PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), ...
59-124 5.02e-08

PDZ domain of protein Lin-7 and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467258 [Multi-domain]  Cd Length: 86  Bit Score: 50.90  E-value: 5.02e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  59 GFRLQGGKDFNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06796    15 GFNVMGGKEQNSPIYISRIIPGGVAdRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAQGSVKLV 81
LIM2_Lrg1p_like cd09392
The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM ...
595-646 5.82e-08

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188778 [Multi-domain]  Cd Length: 53  Bit Score: 49.66  E-value: 5.82e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSL-ADVCFVEEQNNVYCERCY 646
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFgPNDSYYEHEGKIYCHYHY 53
LIM2_FBLP-1 cd09372
The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of ...
595-642 5.84e-08

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1); The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188758 [Multi-domain]  Cd Length: 53  Bit Score: 49.73  E-value: 5.84e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYC 642
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFaVDEQNEVYC 49
LIM1_Lrg1p_like cd09391
The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM ...
654-705 6.50e-08

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188777  Cd Length: 57  Bit Score: 49.61  E-value: 6.50e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGE-----PYCEKDY 705
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDtseqvPLCETDY 57
LIM_TLP_like cd09401
The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like ...
654-705 7.17e-08

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188785 [Multi-domain]  Cd Length: 53  Bit Score: 49.26  E-value: 7.17e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09401     1 CPKCGKPVyFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
LIM2_Enigma cd09456
The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially ...
595-646 8.37e-08

The second LIM domain of Enigma; The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188840 [Multi-domain]  Cd Length: 52  Bit Score: 49.23  E-value: 8.37e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
LIM2_abLIM cd09328
The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin ...
654-703 1.00e-07

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188714  Cd Length: 56  Bit Score: 49.27  E-value: 1.00e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEK 703
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFpPGDRVTFNGKECLCQK 54
LIM3_Paxillin_like cd09338
The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin ...
595-646 1.32e-07

The third LIM domain of the paxillin like protein family; The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188724 [Multi-domain]  Cd Length: 53  Bit Score: 48.49  E-value: 1.32e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
LIM2_Ajuba_like cd09355
The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: ...
595-646 1.35e-07

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188741 [Multi-domain]  Cd Length: 53  Bit Score: 48.49  E-value: 1.35e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYCERCY 646
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFtVDVENNIYCVKDY 53
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
49-126 1.40e-07

PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467196 [Multi-domain]  Cd Length: 78  Bit Score: 49.51  E-value: 1.40e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  49 SVTLT-GPGPWGFRLQGGKdfnmPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlSLTLQ 126
Cdd:cd06712     3 TVHLTkEEGGFGFTLRGDS----PVQVASVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKSAGEE-GLELQ 76
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
405-594 1.50e-07

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 54.88  E-value: 1.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 405 PRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPS--PGANYSPTPyTPSPAPAYT 482
Cdd:PRK12323  383 AQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASArgPGGAPAPAP-APAAAPAAA 461
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 483 PSPA---PTYTPSPAPTYSPSPAPAYTPSPAPNYNPtpsaAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLP 559
Cdd:PRK12323  462 ARPAaagPRPVAAAAAAAPARAAPAAAPAPADDDPP----PWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDA 537
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1958686853 560 RGAPAYNPTGPQVTPLARGTFQR-AERFPASSRTPL 594
Cdd:PRK12323  538 FETLAPAPAAAPAPRAAAATEPVvAPRPPRASASGL 573
LIM4_PINCH cd09334
The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a ...
713-765 1.55e-07

The fourth LIM domain of protein PINCH; The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes.


Pssm-ID: 188720 [Multi-domain]  Cd Length: 54  Bit Score: 48.51  E-value: 1.55e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09334     3 CGACRRPIE--GRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETH 53
LIM4_FHL cd09347
The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of ...
713-764 2.29e-07

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188733  Cd Length: 56  Bit Score: 48.11  E-value: 2.29e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09347     1 CAACTKPITGlgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPE 54
LIM_DA1 cd09396
The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain ...
595-646 2.78e-07

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188782 [Multi-domain]  Cd Length: 53  Bit Score: 47.63  E-value: 2.78e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09396     1 CAGCKSEIgHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
LIM5_PINCH cd09335
The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays ...
654-705 2.86e-07

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188721 [Multi-domain]  Cd Length: 54  Bit Score: 47.73  E-value: 2.86e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFG-NSLFHMEDGEPYCEKDY 705
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCY 53
LIM1_Ajuba_like cd09352
The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: ...
654-705 2.86e-07

The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188738  Cd Length: 54  Bit Score: 47.81  E-value: 2.86e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIMG--EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09352     1 CVKCGKGVYGasQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
PDZ4_MAGI-1_3-like cd06734
PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, ...
48-127 3.14e-07

PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467216 [Multi-domain]  Cd Length: 84  Bit Score: 48.76  E-value: 3.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  48 YSVTLT---GPGpWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06734     2 YDVTLTrreNEG-FGFVIISSVNKKSGSKIGRIIPGSPADRCgQLKVGDRILAVNGISILNLSHGDIVNLIKDSGLSVTL 80

                  ....
gi 1958686853 124 TLQK 127
Cdd:cd06734    81 TIVP 84
LIM2_FHL1 cd09424
The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain ...
713-762 4.31e-07

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188808  Cd Length: 58  Bit Score: 47.45  E-value: 4.31e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09424     1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50
PDZ12_MUPP1-like cd06675
PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight ...
71-124 4.58e-07

PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F


Pssm-ID: 467163 [Multi-domain]  Cd Length: 86  Bit Score: 48.13  E-value: 4.58e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  71 PLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06675    29 PVFIAMIQPNGVAAQTGkLKVGDRIVSINGQSTDGLTHSEAVNLLKNASGTIILQ 83
LIM2_Leupaxin cd09408
The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a ...
595-644 5.92e-07

The second LIM domain of Leupaxin; The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188792 [Multi-domain]  Cd Length: 52  Bit Score: 46.74  E-value: 5.92e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCER 644
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50
LIM3_Fhl2 cd09431
The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of ...
654-710 7.40e-07

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188815  Cd Length: 57  Bit Score: 46.91  E-value: 7.40e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLFS 710
Cdd:cd09431     1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
LIM1_LIMK2 cd09463
The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain ...
654-705 7.86e-07

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188847 [Multi-domain]  Cd Length: 53  Bit Score: 46.40  E-value: 7.86e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 705
Cdd:cd09463     1 CTGCGGRIQdSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYE-KDGKLYCHKHY 52
LIM1_Zyxin cd09349
The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of ...
713-763 9.13e-07

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188735 [Multi-domain]  Cd Length: 87  Bit Score: 47.54  E-value: 9.13e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09349    34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCE 84
LIM3_LIMPETin cd09421
The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin ...
709-762 1.08e-06

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188805  Cd Length: 59  Bit Score: 46.41  E-value: 1.08e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 709 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09421     1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54
LIM1_LPP cd09351
The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma ...
713-763 1.15e-06

The first LIM domain of lipoma preferred partner (LPP); The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188737 [Multi-domain]  Cd Length: 54  Bit Score: 45.88  E-value: 1.15e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09351     1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCE 51
PDZ2_DLG5-like cd06765
PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density ...
62-129 1.16e-06

PDZ domain 2 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467246 [Multi-domain]  Cd Length: 77  Bit Score: 46.96  E-value: 1.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958686853  62 LQGGKDFNMPLT----ISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 129
Cdd:cd06765     4 LSGQKDSGISLEngvfISRIVPGSPAAkEGSLTVGDRIIAINGIALDNKSLSECEALLRSCRDSLSLSLMKVF 76
LIM3_PINCH cd09333
The third LIM domain of protein PINCH; The third LIM domain of protein PINCH: PINCH plays ...
595-646 1.20e-06

The third LIM domain of protein PINCH; The third LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188719  Cd Length: 51  Bit Score: 45.83  E-value: 1.20e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCfVEEQNNVYCERCY 646
Cdd:cd09333     1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLRCH 51
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
438-520 1.34e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 51.70  E-value: 1.34e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 438 KPRVVTTASIRPSVYQpvPASPYSPSPGANYSPTP---YTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYN 514
Cdd:PRK14971  370 SGGRGPKQHIKPVFTQ--PAAAPQPSAAAAASPSPsqsSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAV 447

                  ....*.
gi 1958686853 515 PTPSAA 520
Cdd:PRK14971  448 RPAQFK 453
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
433-593 1.36e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 52.16  E-value: 1.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 433 AAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPT------YTPSPAPTYSPSPAPAY 505
Cdd:PRK07003  379 AVPAPGARAAAAVGASAVPAVtAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATadrgddAADGDAPVPAKANARAS 458
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 506 TPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKqtlPRGAPAYNPTGPQVTPLARGTFQRAER 585
Cdd:PRK07003  459 ADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVP---DARAPAAASREDAPAAAAPPAPEARPP 535

                  ....*...
gi 1958686853 586 FPASSRTP 593
Cdd:PRK07003  536 TPAAAAPA 543
PDZ2_GRIP1-2-like cd06681
PDZ domain 2 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
50-124 1.41e-06

PDZ domain 2 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467169 [Multi-domain]  Cd Length: 89  Bit Score: 46.84  E-value: 1.41e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  50 VTLT-GPGPWGFRLQGG----KDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06681     5 VTLEkEGNSFGFVIRGGahedRNKSRPLTVTHVRPGGPADrEGTIKPGDRLLSVDGISLHGATHAEAMSILKQCGQEATL 84

                  .
gi 1958686853 124 T 124
Cdd:cd06681    85 L 85
TALPID3 pfam15324
Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for ...
434-593 1.46e-06

Hedgehog signalling target; TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.


Pssm-ID: 434634 [Multi-domain]  Cd Length: 1288  Bit Score: 52.20  E-value: 1.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  434 APAPKPRVVTTASIRPSVYQPVPASPYSPSP---GANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTysPSPAPAYTPSP 509
Cdd:pfam15324  986 TPVPTPQPTPPCSPPSPLKEPSPVKTPDSSPcvsEHDFFPVKEIPPEKGADTgPAVSLVITPTVTPI--ATPPPAATPTP 1063
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  510 apnynPTPSAAYSGGPSESASRP-PWVTDD---------SFSQKFAPGKSTTSVSKQTLPRGA--PAYNPTGPQVTPLAR 577
Cdd:pfam15324 1064 -----PLSENSIDKLKSPSPELPkPWEDSDlpleeenpnSEQEELHPRAVVMSVARDEEPESVvlPASPPEPKPLAPPPL 1138
                          170
                   ....*....|....*.
gi 1958686853  578 GTfqraeRFPASSRTP 593
Cdd:pfam15324 1139 GA-----APPSPPQSP 1149
PDZ4_LNX1_2-like cd06680
PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ ...
49-124 1.52e-06

PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467168 [Multi-domain]  Cd Length: 89  Bit Score: 46.96  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  49 SVTL--TGPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06680     2 DITLrrSSSGSLGFSIVGGYEEshgNQPFFVKSIVPGTPAYNDgRLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGRVT 81

                  ..
gi 1958686853 123 LT 124
Cdd:cd06680    82 LT 83
PDZ2-PTPN13_FRMPD2-like cd06792
PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and ...
48-127 1.69e-06

PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467254 [Multi-domain]  Cd Length: 87  Bit Score: 46.44  E-value: 1.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  48 YSVTLT-GPGPWGFRLQGGKDFNMPLT---ISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06792     3 FEVELSkKDGSLGISVTGGINTSVRHGgiyVKSLVPGGAAEQDgRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVT 82

                  ....*
gi 1958686853 123 LTLQK 127
Cdd:cd06792    83 LVLER 87
LIM1_Lmx1b cd09371
The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein ...
713-764 1.90e-06

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188757 [Multi-domain]  Cd Length: 53  Bit Score: 45.45  E-value: 1.90e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFYskKDKPL-CKK 764
Cdd:cd09371     1 CAGCQRPIS--DRYLlRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLyCKQ 50
LIM1_FHL cd09343
The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of ...
709-762 2.23e-06

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188729  Cd Length: 59  Bit Score: 45.51  E-value: 2.23e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 709 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09343     1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLC 54
LIM4_FHL cd09347
The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of ...
595-645 2.48e-06

The fourth LIM domain of Four and a half LIM domains protein (FHL); The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188733  Cd Length: 56  Bit Score: 45.03  E-value: 2.48e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRGP----FLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09347     1 CAACTKPITGLggakFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
PHA03378 PHA03378
EBNA-3B; Provisional
444-593 2.65e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 51.22  E-value: 2.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 444 TASIRPSVYQP----VPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSA 519
Cdd:PHA03378  654 PPQVEITPYKPtwtqIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGR 733
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 520 AYSGGPSESASRPPWVTDDSFSQkfaPGKSTTSVSKQTLPRGAPAYNPTgPQVTPLARgtfQRAERFPASSRTP 593
Cdd:PHA03378  734 ARPPAAAPGRARPPAAAPGRARP---PAAAPGRARPPAAAPGAPTPQPP-PQAPPAPQ---QRPRGAPTPQPPP 800
LIM_ALP_like cd09360
The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM ...
595-643 2.68e-06

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188746 [Multi-domain]  Cd Length: 52  Bit Score: 45.06  E-value: 2.68e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVC--FVEEQnnVYCE 643
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGyfFIEDE--LYCE 49
LIM2_FHL cd09345
The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of ...
654-705 2.84e-06

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188731 [Multi-domain]  Cd Length: 54  Bit Score: 44.98  E-value: 2.84e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09345     1 CKACGKAIMPGSkkMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
LIM3_Leupaxin cd09410
The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
595-646 3.44e-06

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188794 [Multi-domain]  Cd Length: 53  Bit Score: 44.81  E-value: 3.44e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52
PHA03247 PHA03247
large tegument protein UL36; Provisional
405-593 3.45e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 3.45e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  405 PRPQASAYSPAAATSPAPAAHTSYSegPAAPAPKPrvvTTASIRPSVYQPVPASPYSP-----SPGANYSPTPYTPSPAP 479
Cdd:PHA03247  2799 PSPWDPADPPAAVLAPAAALPPAAS--PAGPLPPP---TSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSPAA 2873
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  480 AYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTddsfSQKFAPGKSTTSVSKQTLP 559
Cdd:PHA03247  2874 KPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ----PPPPPPPRPQPPLAPTTDP 2949
                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1958686853  560 RGAPAYNPT--GPQVTPLARGTFQrAERFPASSRTP 593
Cdd:PHA03247  2950 AGAGEPSGAvpQPWLGALVPGRVA-VPRFRVPQPAP 2984
LIM6_LIMPETin cd09432
The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin ...
595-645 3.77e-06

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188816  Cd Length: 56  Bit Score: 44.77  E-value: 3.77e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09432     1 CAACGKPITGiggtKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
406-537 3.82e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 50.48  E-value: 3.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 406 RPQASAyspaaATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANySPTPYTPSPAPAYTPSP 485
Cdd:PRK14951  365 KPAAAA-----EAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAA-PPAPVAAPAAAAPAAAP 438
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 486 APTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTD 537
Cdd:PRK14951  439 AAAPAAVALAPAPPAQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTP 490
LIM4_FHL2 cd09433
The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain ...
713-762 4.07e-06

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188817  Cd Length: 58  Bit Score: 44.60  E-value: 4.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09433     1 CAGCTNPISGlgGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILC 52
LIM_N_RAP cd09446
The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein ...
713-765 4.11e-06

The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188830  Cd Length: 53  Bit Score: 44.52  E-value: 4.11e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09446     1 CARCGYGVYPAEK-INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52
LIM1_Testin_like cd09340
The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This ...
654-705 4.14e-06

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188726  Cd Length: 58  Bit Score: 44.51  E-value: 4.14e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKI-MGEV-----MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09340     1 CEKCKEPInPGEVavfaeRAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
LIM1_Enigma_like cd09361
The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The ...
713-765 4.32e-06

The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188747 [Multi-domain]  Cd Length: 52  Bit Score: 44.27  E-value: 4.32e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09361     1 CAHCNQVIR--GPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51
LIM2_PINCH cd09332
The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a ...
654-703 4.53e-06

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188718 [Multi-domain]  Cd Length: 52  Bit Score: 44.25  E-value: 4.53e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 703
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50
LIM2_Paxillin cd09407
The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor ...
595-646 4.66e-06

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188791 [Multi-domain]  Cd Length: 52  Bit Score: 44.18  E-value: 4.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
LIM1_UF1 cd09397
LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing ...
654-705 4.84e-06

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188783 [Multi-domain]  Cd Length: 58  Bit Score: 44.56  E-value: 4.84e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 654 CAKCNTKIMGEVMH----ALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEKDY 705
Cdd:cd09397     1 CRKCGLEIEGKSISskdgELSGQWHRECFVCTTCGCPFqFSVPCYVLDDKPYCQQHY 57
LIM3_FHL cd09346
The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of ...
654-705 4.98e-06

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188732  Cd Length: 52  Bit Score: 44.24  E-value: 4.98e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKI-MGEVMHAlRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09346     1 CAKCKKAItSGGVTYR-DQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
LIM2_FHL3 cd09427
The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain ...
710-762 4.99e-06

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188811  Cd Length: 58  Bit Score: 44.46  E-value: 4.99e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 710 STKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09427     1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53
LIM3_FHL cd09346
The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of ...
734-762 5.28e-06

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188732  Cd Length: 52  Bit Score: 44.24  E-value: 5.28e-06
                          10        20
                  ....*....|....*....|....*....
gi 1958686853 734 WHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09346    20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48
ZM smart00735
ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ...
234-259 5.47e-06

ZASP-like motif; Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.


Pssm-ID: 128974  Cd Length: 26  Bit Score: 43.36  E-value: 5.47e-06
                           10        20
                   ....*....|....*....|....*.
gi 1958686853  234 PSQPRLYNNPIGLYSAETLREMAQMY 259
Cdd:smart00735   1 RVVHKQYNSPIGLYSSENIAETLQGQ 26
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
454-578 5.48e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 49.71  E-value: 5.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 454 PVPASPYSPSPganysPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 533
Cdd:PRK14951  373 AAPAEKKTPAR-----PEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVAL 447
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958686853 534 WVTDDSFSQKfAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARG 578
Cdd:PRK14951  448 APAPPAQAAP-ETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPT 491
LIM1_Leupaxin cd09406
The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
713-767 5.50e-06

The first LIM domain of Leupaxin; The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188790 [Multi-domain]  Cd Length: 55  Bit Score: 44.09  E-value: 5.50e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09406     3 CASCQKPI-AG-QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
54-125 5.57e-06

PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467249 [Multi-domain]  Cd Length: 80  Bit Score: 44.74  E-value: 5.57e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853  54 GPGPWGFRLQGGKD----FnmpltISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd06768     8 GPEGYGFNLHAEKGrpghF-----IREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQVVEKIKASGNQVTLLV 78
LIM2_Prickle cd09418
The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three ...
652-701 5.67e-06

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188802  Cd Length: 56  Bit Score: 44.34  E-value: 5.67e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 652 PICAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09418     1 PRCSACDEIIFAdECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
LIM1_FHL2 cd09422
The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of ...
709-762 5.81e-06

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188806  Cd Length: 62  Bit Score: 44.51  E-value: 5.81e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 709 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09422     1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54
LIM3_Leupaxin cd09410
The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton ...
713-767 6.02e-06

The third LIM domain of Leupaxin; The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188794 [Multi-domain]  Cd Length: 53  Bit Score: 44.04  E-value: 6.02e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09410     1 CSGCGRPVK--ENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53
LIM3_Paxillin cd09409
The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor ...
713-767 6.30e-06

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188793 [Multi-domain]  Cd Length: 53  Bit Score: 44.06  E-value: 6.30e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09409     1 CGGCARAIL--ENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53
LIM1_LIMPETin cd09414
The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin ...
595-646 6.39e-06

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188798 [Multi-domain]  Cd Length: 58  Bit Score: 43.93  E-value: 6.39e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 595 CGHCNNVI-RGPFLVAMGRS-----WHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09414     1 CGGCSEPLkYGELAVTAPKFgesllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
428-579 6.52e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 49.91  E-value: 6.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 428 YSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTP 507
Cdd:pfam05109 421 FSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTE 500
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 508 SPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKsTTSVSKQTLPRgAPAYNPTGPQVTPLARGT 579
Cdd:pfam05109 501 SKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGK-TSPTSAVTTPT-PNATSPTPAVTTPTPNAT 570
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
433-530 6.58e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 49.42  E-value: 6.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 433 AAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPApn 512
Cdd:PRK14950  362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHT---PESAPKLTRAAI-- 436
                          90
                  ....*....|....*...
gi 1958686853 513 ynPTPSAAYSGGPSESAS 530
Cdd:PRK14950  437 --PVDEKPKYTPPAPPKE 452
LIM_TLP_like cd09401
The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like ...
608-646 6.66e-06

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188785 [Multi-domain]  Cd Length: 53  Bit Score: 43.87  E-value: 6.66e-06
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958686853 608 VAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09401    15 TSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
LIM1_Lhx3b cd09467
The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein ...
652-705 6.78e-06

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188851 [Multi-domain]  Cd Length: 55  Bit Score: 43.77  E-value: 6.78e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 652 PICAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHMEDGePYCEKDY 705
Cdd:cd09467     2 PLCAGCNQHIVDRfILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDS-VYCKDDF 55
LIM1_Ajuba_like cd09352
The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: ...
713-764 7.07e-06

The first LIM domain of Ajuba-like proteins; The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188738  Cd Length: 54  Bit Score: 43.96  E-value: 7.07e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09352     1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEE 52
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
402-533 7.57e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 49.46  E-value: 7.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 402 VENPRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPyTPSPAPAY 481
Cdd:PRK07003  380 VPAPGARAAAAVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVP-AKANARAS 458
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 482 TPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 533
Cdd:PRK07003  459 ADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDA 510
LIM2_CRP2 cd09840
The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine ...
595-646 7.80e-06

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188871 [Multi-domain]  Cd Length: 54  Bit Score: 43.94  E-value: 7.80e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09840     1 CSRCGDsVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
431-574 8.89e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.21  E-value: 8.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 431 GPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPA 510
Cdd:PRK07764  637 AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADD 716
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 511 PNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAynPTGPQVTP 574
Cdd:PRK07764  717 PAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAP--AAAPPPSP 778
LIM1_AWH cd09373
The first LIM domain of Arrowhead (AWH); The first LIM domain of Arrowhead (AWH): Arrowhead ...
713-763 8.95e-06

The first LIM domain of Arrowhead (AWH); The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188759 [Multi-domain]  Cd Length: 54  Bit Score: 43.52  E-value: 8.95e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPF-YSKKDKPLCK 763
Cdd:cd09373     1 CTGCGEPIT--DRFLlKVSGRSWHVSCLRCCVCQTPLERQPScFTRDRQIYCK 51
PDZ_SYNJ2BP-like cd06709
PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 ...
50-126 9.40e-06

PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467193 [Multi-domain]  Cd Length: 86  Bit Score: 44.59  E-value: 9.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  50 VTLT-GPGPWGFRLQGGKDfnMPLT-------ISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYN 120
Cdd:cd06709     3 ITLKrGPSGLGFNIVGGTD--QPYIpndsgiyVAKIKEdGAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRNAGED 80

                  ....*.
gi 1958686853 121 LSLTLQ 126
Cdd:cd06709    81 VKLKVQ 86
PDZ3_PDZD2-PDZ1_hPro-IL-16-like cd06759
PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 ...
59-116 9.85e-06

PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467240 [Multi-domain]  Cd Length: 87  Bit Score: 44.57  E-value: 9.85e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958686853  59 GFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 116
Cdd:cd06759    15 GFSIVGGRDSprgPMGIYVKTIFPGGAAAEDgRLKEGDEILEVNGESLQGLTHQEAIQKFKQ 76
LIM4_FHL1 cd09348
The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain ...
595-645 9.90e-06

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188734  Cd Length: 64  Bit Score: 43.60  E-value: 9.90e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 595 CGHCNNVI----RGPFLVAM-GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09348     5 CSGCQNPItgfgKGTNVVNYeGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
LIM1_LIMK cd09364
The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain ...
713-765 9.92e-06

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188750 [Multi-domain]  Cd Length: 53  Bit Score: 43.25  E-value: 9.92e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQpfYSKKDKPL-CKKH 765
Cdd:cd09364     1 CAGCRGKILDSQ-YVQALNQDWHCDCFRCSVCSDSLSNW--YFEKDGKLyCRKD 51
LIM1_Lhx2_Lhx9 cd09369
The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: ...
654-705 9.93e-06

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188755 [Multi-domain]  Cd Length: 54  Bit Score: 43.48  E-value: 9.93e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 654 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFG--NSLFhMEDGEPYCEKDY 705
Cdd:cd09369     1 CAGCGEKIQDRfYLLAVDRQWHASCLKCCECRLPLDseLSCF-SRDGNIYCKEDY 54
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
654-701 1.03e-05

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188813  Cd Length: 53  Bit Score: 43.26  E-value: 1.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
LIM2_abLIM cd09328
The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin ...
711-753 1.04e-05

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188714  Cd Length: 56  Bit Score: 43.49  E-value: 1.04e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958686853 711 TKCHGCDFPVEagDKFIEALGHTWHDTCFICAVChvnleGQPF 753
Cdd:cd09328     2 TKCDSCQDFVE--GEVVSALGKTYHPKCFVCSVC-----RQPF 37
LIM2_Lhx1_Lhx5 cd09375
The second LIM domain of Lhx1 (also known as Lim1) and Lhx5; The second LIM domain of Lhx1 ...
654-705 1.10e-05

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5; The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188761  Cd Length: 56  Bit Score: 43.50  E-value: 1.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 654 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSLFHMEDGEPYCEKDY 705
Cdd:cd09375     1 CAGCDQGISPNdlVRRARDKVFHLNCFTCMVCRKQLstGEELYILDENKFICKEDY 56
LIM1_LIMK cd09364
The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain ...
595-646 1.14e-05

The first LIM domain of LIMK (LIM domain Kinase ); The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188750 [Multi-domain]  Cd Length: 53  Bit Score: 43.25  E-value: 1.14e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCERCY 646
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRKDY 52
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
438-511 1.14e-05

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 48.35  E-value: 1.14e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 438 KPRVVTTASIRPSvyqPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPApTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:TIGR00601  76 KPKTGTGKVAPPA---ATPTSAPTPTPSPPASPAS-GMSAAPASAVEEK-SPSEESATATAPESPSTSVPSSGS 144
LIM1_Lhx3b cd09467
The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein ...
593-643 1.18e-05

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188851 [Multi-domain]  Cd Length: 55  Bit Score: 43.39  E-value: 1.18e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 593 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 643
Cdd:cd09467     2 PLCAGCNQHIVDRFILkVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52
LIM4_FHL3 cd09434
The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain ...
713-763 1.20e-05

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188818  Cd Length: 56  Bit Score: 43.21  E-value: 1.20e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09434     1 CAACNKPITGfgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCR 53
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
432-603 1.22e-05

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 49.01  E-value: 1.22e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  432 PAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSP----SPAPAYTP 507
Cdd:PHA03307   139 RPVGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPprrsSPISASAS 218
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  508 SPAPnyNPTPSAAYSGGPSESASRPPWVTD-DSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERF 586
Cdd:PHA03307   219 SPAP--APGRSAADDAGASSSDSSSSESSGcGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSP 296
                          170
                   ....*....|....*..
gi 1958686853  587 PASSRTPLCGHCNNVIR 603
Cdd:PHA03307   297 SPSPSSPGSGPAPSSPR 313
LIM2_Zyxin cd09353
The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of ...
595-652 1.35e-05

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188739 [Multi-domain]  Cd Length: 60  Bit Score: 43.38  E-value: 1.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNV-YCERCYEQFFAP 652
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQpHCVNDYHRRYAP 59
PHA03269 PHA03269
envelope glycoprotein C; Provisional
435-558 1.46e-05

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 48.57  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 435 PAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYT---PSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:PHA03269   25 NIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAAsrkPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQL 104
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 512 NYNPTPSAAYSGGPSESASRPPWVTDDS-FSQKFAPGKSTTSVSKQTL 558
Cdd:PHA03269  105 AAAPKPDAAEAFTSAAQAHEAPADAGTSaASKKPDPAAHTQHSPPPFA 152
LIM2_Testin_like cd09341
The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This ...
652-701 1.52e-05

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188727  Cd Length: 56  Bit Score: 42.98  E-value: 1.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 652 PICAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51
LIM2_Zyxin cd09353
The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of ...
713-753 1.55e-05

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188739 [Multi-domain]  Cd Length: 60  Bit Score: 43.00  E-value: 1.55e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 753
Cdd:cd09353     1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLEGESF 39
PHA03269 PHA03269
envelope glycoprotein C; Provisional
427-519 1.60e-05

envelope glycoprotein C; Provisional


Pssm-ID: 165527 [Multi-domain]  Cd Length: 566  Bit Score: 48.19  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 427 SYSEGPAAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPG-ANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPS--PA 502
Cdd:PHA03269   46 PHQAASRAPDPAVAPTSAASRKPDLAQaPTPAASEKFDPApAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQahEA 125
                          90
                  ....*....|....*..
gi 1958686853 503 PAYTPSPAPNYNPTPSA 519
Cdd:PHA03269  126 PADAGTSAASKKPDPAA 142
PRK13729 PRK13729
conjugal transfer pilus assembly protein TraB; Provisional
433-541 1.63e-05

conjugal transfer pilus assembly protein TraB; Provisional


Pssm-ID: 184281 [Multi-domain]  Cd Length: 475  Bit Score: 48.28  E-value: 1.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 433 AAPAPKPRVVTTASirpsvyQPVPASPySPSPGANYSPtpyTPSPAPAYTPSPAPTYTPSPAPTYspsPAPAYTPSPAPN 512
Cdd:PRK13729  119 QVKALGANPVTATG------EPVPQMP-ASPPGPEGEP---QPGNTPVSFPPQGSVAVPPPTAFY---PGNGVTPPPQVT 185
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1958686853 513 YNPTP------SAAYSGGPSESASRPPWVTDDSFS 541
Cdd:PRK13729  186 YQSVPvpnriqRKTFTYNEGKKGPSLPYIPSGSFA 220
LIM4_LIMPETin cd09425
The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin ...
713-762 1.64e-05

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188809  Cd Length: 54  Bit Score: 42.81  E-value: 1.64e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09425     1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
36-137 1.92e-05

C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440556 [Multi-domain]  Cd Length: 341  Bit Score: 47.56  E-value: 1.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  36 PEEATAVGTSMSYSVTLTGpgpwgFRLQGGKDFnmpLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 115
Cdd:COG0793    45 PEEYEDFQESTSGEFGGLG-----AELGEEDGK---VVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLR 116
                          90       100
                  ....*....|....*....|....*
gi 1958686853 116 SAS-YNLSLTLQK--SKRPIPISTT 137
Cdd:COG0793   117 GKAgTKVTLTIKRpgEGEPITVTLT 141
LIM2_Lrg1p_like cd09392
The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM ...
654-705 1.94e-05

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188778 [Multi-domain]  Cd Length: 53  Bit Score: 42.73  E-value: 1.94e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFG-NSLFHMEDGEPYCEKDY 705
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGpNDSYYEHEGKIYCHYHY 53
PRK10263 PRK10263
DNA translocase FtsK; Provisional
432-574 2.06e-05

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 48.16  E-value: 2.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  432 PAAPAPKPRVVTTASIRPSV-YQPVPAsPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY-TPSP 509
Cdd:PRK10263   339 PVTQTPPVASVDVPPAQPTVaWQPVPG-PQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAeQPAQ 417
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  510 APNYNPTPSAA-----YSGGPSESASRPPWVTDDSFS-----QKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTP 574
Cdd:PRK10263   418 QPYYAPAPEQPaqqpyYAPAPEQPVAGNAWQAEEQQStfapqSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEP 492
LIM1_Lhx4 cd09468
The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein ...
654-705 2.12e-05

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188852  Cd Length: 52  Bit Score: 42.65  E-value: 2.12e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 705
Cdd:cd09468     1 CAGCNQHILDKfILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52
LIM2_Testin_like cd09341
The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This ...
713-762 2.19e-05

The second LIM domain of Testin-like family; The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188727  Cd Length: 56  Bit Score: 42.59  E-value: 2.19e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCD---FpveaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09341     3 CAACDeliF----SGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51
PHA03247 PHA03247
large tegument protein UL36; Provisional
454-532 2.22e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.40  E-value: 2.22e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  454 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAP----AYTPSPAPNYNPTPSAAYSGGPSESA 529
Cdd:PHA03247   389 RHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPATPLPSAepgsDDGPAPPPERQPPAPATEPAPDDPDD 468

                   ...
gi 1958686853  530 SRP 532
Cdd:PHA03247   469 ATR 471
PDZ1_GRIP1-2-like cd06687
PDZ domain 1 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
57-123 2.24e-05

PDZ domain 1 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467175 [Multi-domain]  Cd Length: 83  Bit Score: 43.17  E-value: 2.24e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853  57 PWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06687    12 TLGLTVSGGIDKDGKPRVSNLRPGGIAARSdQLNVGDYIKSVNGIRTTKLRHDEIISLLKNVGERVVL 79
LIM1_Enigma_like_1 cd09455
The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an ...
654-702 2.42e-05

The first LIM domain of an Enigma subfamily with unknown function; The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188839  Cd Length: 54  Bit Score: 42.44  E-value: 2.42e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICA--ACKKPFGNSLFHMEDGEPYCE 702
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCE 51
PDZ3_PDZD7-like cd06751
PDZ domain 3 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
59-134 2.44e-05

PDZ domain 3 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of the Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa and can also form homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the third PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467233 [Multi-domain]  Cd Length: 89  Bit Score: 43.58  E-value: 2.44e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  59 GFRLQGGKDF-NMPLT-ISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlsltlqKSKRPIPI 134
Cdd:cd06751    14 GISISGGIESkVQPVVkIEKIFPGGAAALSGnLKAGYELVSVDGESLQQVTHQQAVDIIRRAYSN------KSKEPMEI 86
LIM_ALP cd09450
This family represents the LIM domain of ALP, actinin-associated LIM protein; This family ...
654-702 2.71e-05

This family represents the LIM domain of ALP, actinin-associated LIM protein; This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188834 [Multi-domain]  Cd Length: 53  Bit Score: 42.20  E-value: 2.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 702
Cdd:cd09450     1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49
PDZ3_Dlg1-2-4-like cd06795
PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg) ...
50-126 2.90e-05

PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467257 [Multi-domain]  Cd Length: 91  Bit Score: 43.11  E-value: 2.90e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  50 VTLT-GPGPWGFRLQGGKDfNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06795     5 IVLHkGSTGLGFNIVGGED-GEGIFISFILAGGPADLSgELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTIIAQ 82
LIM6_LIMPETin cd09432
The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin ...
713-762 3.00e-05

The sixth LIM domain of protein LIMPETin; The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188816  Cd Length: 56  Bit Score: 42.08  E-value: 3.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09432     1 CAACGKPITGigGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52
LIM2_Lhx2_Lhx9 cd09377
The second LIM domain of Lhx2 and Lhx9 family; The second LIM domain of Lhx2 and Lhx9 family: ...
654-705 3.00e-05

The second LIM domain of Lhx2 and Lhx9 family; The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188763  Cd Length: 59  Bit Score: 42.26  E-value: 3.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 654 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEKDY 705
Cdd:cd09377     5 CARCHLGISASelVMRARDLVFHLNCFTCATCNKPLtKGDHFGMRDGLVYCRLHY 59
LIM_CRP_like cd09326
The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich ...
654-701 3.03e-05

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188712  Cd Length: 53  Bit Score: 41.81  E-value: 3.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 654 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09326     1 CPRCGKSVyAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYC 49
LIM2_Paxillin_like cd09337
The second LIM domain of the paxillin like protein family; The second LIM domain of the ...
713-764 3.06e-05

The second LIM domain of the paxillin like protein family; The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188723 [Multi-domain]  Cd Length: 52  Bit Score: 41.99  E-value: 3.06e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09337     1 CAYCNGPIL--DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCRE 50
LIM5_LIMPETin cd09430
The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin ...
731-762 3.24e-05

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188814  Cd Length: 52  Bit Score: 42.08  E-value: 3.24e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958686853 731 GHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09430    17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
LIM2_Prickle cd09418
The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three ...
593-647 3.52e-05

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188802  Cd Length: 56  Bit Score: 42.03  E-value: 3.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 593 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 647
Cdd:cd09418     1 PRCSACDEIIFADECTeAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56
LIM2_LIMK2 cd09465
The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM ...
594-646 3.61e-05

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188849 [Multi-domain]  Cd Length: 59  Bit Score: 41.85  E-value: 3.61e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 594 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSL--ADVCFVEEQNNVYCERCY 646
Cdd:cd09465     5 LCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIedGDTYALVQHTTLYCGKCH 59
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
405-533 3.64e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 47.29  E-value: 3.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 405 PRPQASAYSPAAATSPAPAAH---TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAY 481
Cdd:PRK07764  636 PAEASAAPAPGVAAPEHHPKHvavPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQAD 715
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 482 TPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 533
Cdd:PRK07764  716 DPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPA 767
LIM1_Enigma cd09452
The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially ...
654-705 3.67e-05

The first LIM domain of Enigma; The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188836 [Multi-domain]  Cd Length: 52  Bit Score: 41.71  E-value: 3.67e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
LIM_LASP_like cd09359
The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 ...
713-765 3.68e-05

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188745  Cd Length: 53  Bit Score: 41.87  E-value: 3.68e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09359     1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAH 52
LIM2_CRP3 cd09482
The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine ...
642-705 3.75e-05

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188866 [Multi-domain]  Cd Length: 54  Bit Score: 41.92  E-value: 3.75e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 642 CERCYEQFFAPicakcnTKIMGEvmhalRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09482     1 CPRCGKSVYAA------EKVMGG-----GKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
LIM2_FHL2 cd09426
The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain ...
654-701 3.79e-05

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188810  Cd Length: 57  Bit Score: 41.96  E-value: 3.79e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09426     1 CSECKKTIMpgTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50
LIM1_TRIP6 cd09350
The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain ...
654-705 4.03e-05

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188736  Cd Length: 54  Bit Score: 41.62  E-value: 4.03e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09350     1 CGRCGENVVGEGtgCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
LIM1_Lmx1a cd09370
The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein ...
595-646 4.30e-05

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188756 [Multi-domain]  Cd Length: 52  Bit Score: 41.68  E-value: 4.30e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIRGPFLVAMGRS-WHPEEFNCAYCKTSLADVCFVEEQnNVYCERCY 646
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52
PDZ1_Scribble-like cd06704
PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
55-127 4.34e-05

PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467188 [Multi-domain]  Cd Length: 87  Bit Score: 42.65  E-value: 4.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  55 PGPWGFRLQGGKDfNMP-------LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06704     9 TGGLGISIAGGKG-STPykgddegIFISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDADHHEAVEALKNSGNTVTMVVLR 87
PDZ3_Scribble-like cd06702
PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
56-127 4.45e-05

PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467186 [Multi-domain]  Cd Length: 89  Bit Score: 42.63  E-value: 4.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  56 GPWGFRLQGGKD-----F--NMP-LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06702    10 GPLGLSIVGGSDhsshpFgvDEPgIFISKVIPDGAAAKSGLRIGDRILSVNGKDLRHATHQEAVSALLSPGQEIKLLVRH 89
LIM5_LIMPETin cd09430
The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin ...
595-646 4.57e-05

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188814  Cd Length: 52  Bit Score: 41.31  E-value: 4.57e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
LIM_DA1 cd09396
The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain ...
713-760 4.58e-05

The Lim domain of DA1; The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188782 [Multi-domain]  Cd Length: 53  Bit Score: 41.47  E-value: 4.58e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 713 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKP 760
Cdd:cd09396     1 CAGCKSEIGHGR-FLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47
PDZ2_ZO1-like_ds cd06728
PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form ...
48-127 4.59e-05

PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467210 [Multi-domain]  Cd Length: 79  Bit Score: 42.21  E-value: 4.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  48 YSVTLTGPGP---WGFRLqGGKDFnmpltISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06728     1 LKVTLTKSRKndeYGLRL-GSRIF-----VKEITPDSLAAKDgNLQEGDIILKINGTPVENLSLSEAKKLIEKSKDKLQL 74

                  ....
gi 1958686853 124 TLQK 127
Cdd:cd06728    75 VVLR 78
LIM_ALP_like cd09360
The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM ...
654-703 4.67e-05

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188746 [Multi-domain]  Cd Length: 52  Bit Score: 41.59  E-value: 4.67e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 703
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCET 50
LIM5_LIMPETin cd09430
The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin ...
654-701 4.75e-05

The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188814  Cd Length: 52  Bit Score: 41.31  E-value: 4.75e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
304-568 4.77e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 46.79  E-value: 4.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 304 EADEWARRSSNLQSRSFRILAQMTGT---EYMQDPDEE-----------ALRRSSTPIEHAPVCTSQATSPLLPASAPSP 369
Cdd:PRK12323  313 EADDIRRLAGRFDAQEVQLFYQIANLgrsELALAPDEYagftmtllrmlAFRPGQSGGGAGPATAAAAPVAQPAPAAAAP 392
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 370 AAASPIAASPTLATAAAAHAVAASAAGPASSPVENPRPQASAYSPAAATSPapaahtsySEGPAAPAPKPRVVTTASIRP 449
Cdd:PRK12323  393 AAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARG--------PGGAPAPAPAPAAAPAAAARP 464
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 450 SVYQPVPASPYSPSPganysptpyTPSPAPAYTPSPAPTYTP--SPAPTYSPSPAPaYTPSPAPNYNPTPSAAYSGGPSE 527
Cdd:PRK12323  465 AAAGPRPVAAAAAAA---------PARAAPAAAPAPADDDPPpwEELPPEFASPAP-AQPDAAPAGWVAESIPDPATADP 534
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1958686853 528 SASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPT 568
Cdd:PRK12323  535 DDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPD 575
LIM4_Paxillin cd09411
The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor ...
654-702 4.81e-05

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188795 [Multi-domain]  Cd Length: 52  Bit Score: 41.47  E-value: 4.81e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 702
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49
LIM2_CRP2 cd09840
The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine ...
654-705 5.05e-05

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188871 [Multi-domain]  Cd Length: 54  Bit Score: 41.63  E-value: 5.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09840     1 CSRCGDSVyAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
LIM3_Testin_like cd09342
The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This ...
713-762 5.17e-05

The third LIM domain of Testin-like family; The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188728  Cd Length: 57  Bit Score: 41.61  E-value: 5.17e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWH--DTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09342     1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52
LIM4_FHL1 cd09348
The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain ...
712-762 5.46e-05

The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188734  Cd Length: 64  Bit Score: 41.67  E-value: 5.46e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 712 KCHGCDFPVEA---GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09348     4 KCSGCQNPITGfgkGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57
LIM4_Leupaxin cd09412
The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a ...
654-701 6.41e-05

The fourth LIM domain of Leupaxin; The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188796 [Multi-domain]  Cd Length: 52  Bit Score: 41.26  E-value: 6.41e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48
PDZ_tamalin_CYTIP-like cd06713
PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ ...
56-123 6.60e-05

PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This tamalin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467197 [Multi-domain]  Cd Length: 91  Bit Score: 42.23  E-value: 6.60e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  56 GPWGFRLQ----GGKDFN---MPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06713    14 ETFGFEIQtyglHHKNSNeveMCTYVCRVHEDSPAYLAGLTAGDVILSVNGVSVEGASHQEIVELIRSSGNTLRL 88
LIM1_Testin_like cd09340
The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This ...
713-765 7.15e-05

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188726  Cd Length: 58  Bit Score: 41.05  E-value: 7.15e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegQPFYsKKDKPLCKKH 765
Cdd:cd09340     1 CEKCKEPINPGEVavFAERAGEdaCWHPGCFVCETCNellVDL--IYFY-HDGKIYCGRH 57
2A1904 TIGR00927
K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...
402-491 7.23e-05

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 273344 [Multi-domain]  Cd Length: 1096  Bit Score: 46.53  E-value: 7.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  402 VENPRPQASAYSPAAATSPAPAAHTSYSEGPAAPA-PKPRVVTTASIRPS-VYQPVPASPYSPSPGANYSPTPYTPSPAP 479
Cdd:TIGR00927  347 IRNPLSRTSAPAVRIASATFRGLEKNPSTAPSTPAtPRVRAVLTTQVHHCvVVKPAPAVPTTPSPSLTTALFPEAPSPSP 426
                           90
                   ....*....|..
gi 1958686853  480 AYTPSPAPTYTP 491
Cdd:TIGR00927  427 SALPPGQPDLHP 438
LIM3_abLIM cd09329
The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin ...
713-764 7.62e-05

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188715 [Multi-domain]  Cd Length: 52  Bit Score: 40.77  E-value: 7.62e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKK 764
Cdd:cd09329     1 CAGCGQEIKNGQALL-ALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCER 50
LIM1_TRIP6 cd09350
The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain ...
713-763 7.63e-05

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188736  Cd Length: 54  Bit Score: 40.85  E-value: 7.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09350     1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCE 51
LIM1_FHL cd09343
The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of ...
612-646 7.66e-05

The first LIM domain of Four and a half LIM domains protein (FHL); The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188729  Cd Length: 59  Bit Score: 40.88  E-value: 7.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 612 RSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09343    24 RHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
LIM3_FHL cd09346
The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of ...
595-646 8.11e-05

The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188732  Cd Length: 52  Bit Score: 40.77  E-value: 8.11e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09346     1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
PDZ3_PTPN13_FRMPD2-like cd06695
PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ ...
48-131 9.02e-05

PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467181 [Multi-domain]  Cd Length: 90  Bit Score: 41.86  E-value: 9.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  48 YSVTLT-GPGPWGFRLQGGK------DFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06695     2 FEVKLTkGSSGLGFSFLGGEnnspedPFSGLVRIKKLFPGQPAAESgLIQEGDVILAVNGEPLKGLSYQEVLSLLRGAPP 81
                          90
                  ....*....|..
gi 1958686853 120 NLSLTLqksKRP 131
Cdd:cd06695    82 EVTLLL---CRP 90
LIM3_abLIM cd09329
The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin ...
595-646 9.18e-05

The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188715 [Multi-domain]  Cd Length: 52  Bit Score: 40.77  E-value: 9.18e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 595 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLAdvcfvEE---QNNV-YCERCY 646
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGKVLT-----GEymgKDGKpYCERDY 52
LIM5_PINCH cd09335
The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays ...
595-647 9.37e-05

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188721 [Multi-domain]  Cd Length: 54  Bit Score: 40.79  E-value: 9.37e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLA-DVCFVEEQNNVYCERCYE 647
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCYD 54
LIM4_LIMPETin cd09425
The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin ...
611-646 9.43e-05

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188809  Cd Length: 54  Bit Score: 40.50  E-value: 9.43e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09425    19 GQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
LIM2_FHL2 cd09426
The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain ...
713-762 9.64e-05

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188810  Cd Length: 57  Bit Score: 40.80  E-value: 9.64e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09426     1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50
LIM1_Lhx4 cd09468
The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein ...
595-643 1.02e-04

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188852  Cd Length: 52  Bit Score: 40.72  E-value: 1.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 643
Cdd:cd09468     1 CAGCNQHILDKFILkVLDRHWHSSCLKCADCQMQLAERCF-SRAGNVYCK 49
LIM_Mical_like cd09358
The LIM domain of Mical (molecule interacting with CasL) like family; The LIM domain of Mical ...
713-765 1.15e-04

The LIM domain of Mical (molecule interacting with CasL) like family; The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188744 [Multi-domain]  Cd Length: 53  Bit Score: 40.33  E-value: 1.15e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 713 CHGCD---FPVEagdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09358     1 CAVCGktvYPME----RLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPH 52
LIM1_FHL1 cd09344
The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four ...
611-645 1.23e-04

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188730  Cd Length: 54  Bit Score: 40.51  E-value: 1.23e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09344    19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
LIM1_Lmx1b cd09371
The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein ...
595-647 1.31e-04

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188757 [Multi-domain]  Cd Length: 53  Bit Score: 40.05  E-value: 1.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQnNVYCERCYE 647
Cdd:cd09371     1 CAGCQRPISDRYLLrVNERSWHEECLQCSVCQQPLTTSCYFRDR-KLYCKQDYQ 53
LIM1_FHL1 cd09344
The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four ...
654-703 1.36e-04

The first LIM domain of Four and a half LIM domains protein 1; The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188730  Cd Length: 54  Bit Score: 40.12  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 703
Cdd:cd09344     1 CAECRKPIGADSkeLHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52
LIM1_PINCH cd09331
The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an ...
713-763 1.50e-04

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188717  Cd Length: 59  Bit Score: 40.39  E-value: 1.50e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09331     1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCE 51
LIM2_LPP cd09354
The second LIM domain of lipoma preferred partner (LPP); The second LIM domain of lipoma ...
595-652 1.51e-04

The second LIM domain of lipoma preferred partner (LPP); The second LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188740 [Multi-domain]  Cd Length: 60  Bit Score: 40.22  E-value: 1.51e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYCERCYEQFFAP 652
Cdd:cd09354     1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFtVDATNQIHCIEDFHKKFAP 59
LIM2_FHL3 cd09427
The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain ...
671-701 1.52e-04

The second LIM domain of Four and a half LIM domains protein 3 (FHL3); The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188811  Cd Length: 58  Bit Score: 40.22  E-value: 1.52e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958686853 671 QTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09427    23 QTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53
LIM2_LIMK2 cd09465
The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM ...
650-714 1.58e-04

The second LIM domain of LIMK2 (LIM domain Kinase 2); The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188849 [Multi-domain]  Cd Length: 59  Bit Score: 40.30  E-value: 1.58e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 650 FAPICAKCNTKIMGEVMHALRQTWHTTCFICAACKkpfgnslFHMEDGEPYCEKDYINLFSTKCH 714
Cdd:cd09465     2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCK-------VIIEDGDTYALVQHTTLYCGKCH 59
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
72-115 1.58e-04

circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467623 [Multi-domain]  Cd Length: 88  Bit Score: 40.93  E-value: 1.58e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958686853  72 LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 115
Cdd:cd06782    16 LVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLR 59
LIM1_Paxillin cd09405
The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor ...
713-767 1.69e-04

The first LIM domain of paxillin; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188789 [Multi-domain]  Cd Length: 54  Bit Score: 39.99  E-value: 1.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 767
Cdd:cd09405     2 CGACKKPI-AG-QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54
LIM_LASP_like cd09359
The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 ...
654-705 1.74e-04

The LIM domain of LIM and SH3 Protein (LASP)-like proteins; The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188745  Cd Length: 53  Bit Score: 39.94  E-value: 1.74e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09359     1 CARCGKIVYpTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53
PDZ13_MUPP1-like cd06676
PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 ...
49-125 1.86e-04

PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ13 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467164 [Multi-domain]  Cd Length: 83  Bit Score: 40.79  E-value: 1.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  49 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06676     1 TITLErGSDGLGFSIVGGFGSphgDLPIYVKTVFEKGAAAEDgRLKRGDQILAVNGESLEGVTHEEAVNILKKTKGTVTL 80

                  ..
gi 1958686853 124 TL 125
Cdd:cd06676    81 TV 82
LIM2_LIMK cd09365
The second LIM domain of LIMK (LIM domain Kinase ); The second LIM domain of LIMK (LIM domain ...
595-646 1.86e-04

The second LIM domain of LIMK (LIM domain Kinase ); The second LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188751 [Multi-domain]  Cd Length: 54  Bit Score: 39.66  E-value: 1.86e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLAD---VCFVeEQNNVYCERCY 646
Cdd:cd09365     1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIGDgdsYALV-ERSKLYCGVCY 54
LIM2_Ajuba_like cd09355
The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: ...
654-705 1.86e-04

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188741 [Multi-domain]  Cd Length: 53  Bit Score: 39.63  E-value: 1.86e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHME-DGEPYCEKDY 705
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDvENNIYCVKDY 53
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
432-507 1.93e-04

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 44.06  E-value: 1.93e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 432 PAAPAPKPRVVTTASIRPSV--YQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSpAPTYSPSPAPAYTP 507
Cdd:PLN02983  142 PQPPPPAPVVMMQPPPPHAMppASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHPPLKSPM-AGTFYRSPAPGEPP 218
LIM2_FHL1 cd09424
The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain ...
611-650 1.93e-04

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188808  Cd Length: 58  Bit Score: 39.74  E-value: 1.93e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFF 650
Cdd:cd09424    19 GNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
454-592 1.97e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 1.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 454 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTySPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 533
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGA-AAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDG 668
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 534 WVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERFPASSRT 592
Cdd:PRK07764  669 WPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQG 727
LIM4_LIMPETin cd09425
The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin ...
671-705 2.01e-04

The fourth LIM domain of protein LIMPETin; The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188809  Cd Length: 54  Bit Score: 39.73  E-value: 2.01e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 671 QTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09425    20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
LIM_LASP cd09447
The LIM domain of LIM and SH3 Protein (LASP); The LIM domain of LIM and SH3 Protein (LASP): ...
654-705 2.07e-04

The LIM domain of LIM and SH3 Protein (LASP); The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188831  Cd Length: 53  Bit Score: 39.67  E-value: 2.07e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCN-TKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09447     1 CARCGkTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53
LIM2_ENH cd09457
The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma ...
727-763 2.07e-04

The second LIM domain of the Enigma Homolog (ENH) family; The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188841 [Multi-domain]  Cd Length: 52  Bit Score: 39.63  E-value: 2.07e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1958686853 727 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09457    13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCE 49
LIM_like_1 cd09400
LIM domain in proteins of unknown function; LIM domain in proteins of unknown function: LIM ...
712-762 2.10e-04

LIM domain in proteins of unknown function; LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. The LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).


Pssm-ID: 188784  Cd Length: 61  Bit Score: 39.72  E-value: 2.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 712 KCHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09400     4 PCASCGLPVFLAER-LLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53
PHA02682 PHA02682
ORF080 virion core protein; Provisional
449-549 2.15e-04

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 44.08  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 449 PSVYQPVPASPySPSPGAnYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPS-----PAPNYnPTPSAAYSG 523
Cdd:PHA02682   86 PACAAPAPACP-ACAPAA-PAPAVTCPAPAPACPPATAPTCPPPAVCPAPARPAPACPPStrqcpPAPPL-PTPKPAPAA 162
                          90       100
                  ....*....|....*....|....*....
gi 1958686853 524 GPS---ESASRPPWVTDDSFSQKFAPGKS 549
Cdd:PHA02682  163 KPIflhNQLPPPDYPAASCPTIETAPAAS 191
PHA03247 PHA03247
large tegument protein UL36; Provisional
426-579 2.18e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.93  E-value: 2.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  426 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPS-------PAPTYTPSPAPT-- 496
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSltsladpPPPPPTPEPAPHal 2715
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  497 -----YSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPwvtddsfsqkfaPGKSTTSVSKQTLPRGAPAYNP---- 567
Cdd:PHA03247  2716 vsatpLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARP------------ARPPTTAGPPAPAPPAAPAAGPprrl 2783
                          170
                   ....*....|..
gi 1958686853  568 TGPQVTPLARGT 579
Cdd:PHA03247  2784 TRPAVASLSESR 2795
PHA03378 PHA03378
EBNA-3B; Provisional
430-517 2.24e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 44.67  E-value: 2.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 430 EGPAAPAPKPRVVTT---------ASIRPSVYQPVPASPYSPSPGANYSPTPY-TPSPAPAYTP-SPAPTYTPSPAPTYS 498
Cdd:PHA03378  708 AAPPGRAQRPAAATGrarppaaapGRARPPAAAPGRARPPAAAPGRARPPAAApGRARPPAAAPgAPTPQPPPQAPPAPQ 787
                          90
                  ....*....|....*....
gi 1958686853 499 PSPAPAYTPSPAPNYNPTP 517
Cdd:PHA03378  788 QRPRGAPTPQPPPQAGPTS 806
LIM4_FHL2 cd09433
The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain ...
595-645 2.24e-04

The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2); The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188817  Cd Length: 58  Bit Score: 39.59  E-value: 2.24e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09433     1 CAGCTNPISGlggtKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
452-532 2.38e-04

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 44.88  E-value: 2.38e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  452 YQPvPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASR 531
Cdd:PRK12270    36 YGP-GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVE 114

                   .
gi 1958686853  532 P 532
Cdd:PRK12270   115 D 115
LIM2_Zyxin cd09353
The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of ...
654-705 2.41e-04

The second LIM domain of Zyxin; The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188739 [Multi-domain]  Cd Length: 60  Bit Score: 39.91  E-value: 2.41e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDG-EPYCEKDY 705
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAnQPHCVNDY 53
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
405-534 2.42e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.59  E-value: 2.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 405 PRPQASAYSPAAATSpapaaHTSYSEGPAAPAPkprvvttasirpsvyQPVPASPYSPSPGANYSPTPYTPSPAPAYTPS 484
Cdd:PRK07764  408 AAPAPAAAAPAAAAA-----PAPAAAPQPAPAP---------------APAPAPPSPAGNAPAGGAPSPPPAAAPSAQPA 467
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 485 PAPTYTPSPAPTYSPSPAPAYTPSPAPNyNPTPSAAYSGGPSESASRPPW 534
Cdd:PRK07764  468 PAPAAAPEPTAAPAPAPPAAPAPAAAPA-APAAPAAPAGADDAATLRERW 516
LIM_TLP_like cd09401
The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like ...
713-764 2.48e-04

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188785 [Multi-domain]  Cd Length: 53  Bit Score: 39.25  E-value: 2.48e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09401     1 CPKCGKPVYFAEK-KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51
LIM1_Lhx3_Lhx4 cd09368
The first LIM domain of Lhx3 and Lhx4 family; The first LIM domain of Lhx3-Lhx4 family: Lhx3 ...
595-643 2.53e-04

The first LIM domain of Lhx3 and Lhx4 family; The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188754  Cd Length: 52  Bit Score: 39.33  E-value: 2.53e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 595 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 643
Cdd:cd09368     1 CGGCQEHILDRFiLKVLDRTWHAKCLKCNDCGAQLTDKCF-ARNGHVYCK 49
LIM2_Lhx3_Lhx4 cd09376
The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and ...
713-764 2.63e-04

The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188762  Cd Length: 56  Bit Score: 39.64  E-value: 2.63e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPL-CKK 764
Cdd:cd09376     1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLEtGDEFYLMEDDRLvCKK 54
LIM1_Zyxin cd09349
The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of ...
654-705 2.65e-04

The first LIM domain of Zyxin; The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188735 [Multi-domain]  Cd Length: 87  Bit Score: 40.61  E-value: 2.65e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09349    34 CGICGQPLSrtQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
LIM2_Lhx3_Lhx4 cd09376
The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and ...
654-705 2.90e-04

The second LIM domain of Lhx3-Lhx4 family; The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188762  Cd Length: 56  Bit Score: 39.26  E-value: 2.90e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 654 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSLFHMEDGEPYCEKDY 705
Cdd:cd09376     1 CAGCDEGIPPTqvVRRAQDNVYHLECFACFMCKRQLetGDEFYLMEDDRLVCKKDY 56
LIM2_Testin cd09416
The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three ...
712-763 2.93e-04

The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188800  Cd Length: 56  Bit Score: 39.46  E-value: 2.93e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 712 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09416     2 RCAGCDELIFS-NEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 52
LIM2_AWH cd09379
The second LIM domain of Arrowhead (AWH); The second LIM domain of Arrowhead (AWH): Arrowhead ...
713-765 2.97e-04

The second LIM domain of Arrowhead (AWH); The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188765  Cd Length: 55  Bit Score: 39.33  E-value: 2.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPLCKKH 765
Cdd:cd09379     1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLStGEEFALIEDRVLCKAH 54
LIM2_Paxillin cd09407
The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor ...
713-764 3.19e-04

The second LIM domain of paxillin; The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188791 [Multi-domain]  Cd Length: 52  Bit Score: 39.17  E-value: 3.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09407     1 CYYCNGPIL--DKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRK 50
motB PRK12799
flagellar motor protein MotB; Reviewed
454-577 3.20e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 43.94  E-value: 3.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 454 PVPASPYSPSPGANYSPTPYTPS-PAPAYTPSPAPtyTPSPAPTYSPSPA-PAYTPSPAPNYNPTPSAAYSGGPSESASR 531
Cdd:PRK12799  300 PVAAVTPSSAVTQSSAITPSSAAiPSPAVIPSSVT--TQSATTTQASAVAlSSAGVLPSDVTLPGTVALPAAEPVNMQPQ 377
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1958686853 532 PPWVTDdsfSQKFAPGKSTTSVSKQT--LPrGAPAYNPTgpqVTPLAR 577
Cdd:PRK12799  378 PMSTTE---TQQSSTGNITSTANGPTtsLP-AAPASNIP---VSPTSR 418
LIM2_TRIP6 cd09356
The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain ...
713-753 3.32e-04

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188742  Cd Length: 53  Bit Score: 39.08  E-value: 3.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 753
Cdd:cd09356     1 CSVCSKPIM--ERILRATGKAYHPHCFTCVVCHRSLDGIPF 39
PDZ6_PDZD2-PDZ3_hPro-IL-16-like cd06762
PDZ domain 6 of PDZ domain containing 2 (PDZD2), PDZ domain 3 of human pro-interleukin-16 ...
59-117 3.45e-04

PDZ domain 6 of PDZ domain containing 2 (PDZD2), PDZ domain 3 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the third PDZ domain (PDZ3) of human pro-interleukin-16 (isoform 1, also known as nPro-IL-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467243 [Multi-domain]  Cd Length: 86  Bit Score: 39.94  E-value: 3.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958686853  59 GFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06762    15 GFSLAGGSDLeNKSITVHRVFPSGLAAQEgTIQKGDRILSINGKSLKGVTHGDALSVLKQA 75
PHA03291 PHA03291
envelope glycoprotein I; Provisional
432-531 3.46e-04

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 43.79  E-value: 3.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 432 PAAPAPKPRVVTTasirpSVYQPV--PASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSP 509
Cdd:PHA03291  188 PALPLSAPRLGPA-----DVFVPAtpRPTPRTTASPETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPAPPTP 262
                          90       100
                  ....*....|....*....|..
gi 1958686853 510 APNYNPTPSAaysgGPSESASR 531
Cdd:PHA03291  263 GGGEAPPANA----TPAPEASR 280
LIM1_LIMK1 cd09462
The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain ...
715-765 3.57e-04

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188846 [Multi-domain]  Cd Length: 74  Bit Score: 39.48  E-value: 3.57e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 715 GCDFPVEAG-------DKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKKH 765
Cdd:cd09462    16 GNVLPVCAScgqsiydGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKD 72
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
431-564 3.58e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 44.07  E-value: 3.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 431 GPAAPAPKPRVVTTASirPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPA 510
Cdd:PRK07003  404 GAAGAALAPKAAAAAA--ATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPA 481
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 511 PNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPA 564
Cdd:PRK07003  482 SDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPP 535
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
443-511 3.68e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 43.96  E-value: 3.68e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 443 TTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPtyspsPAPAYTPSPAP 511
Cdd:PRK14965  381 APAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP-----PARSADPAAAA 444
PRK10905 PRK10905
cell division protein DamX; Validated
432-524 3.83e-04

cell division protein DamX; Validated


Pssm-ID: 236792 [Multi-domain]  Cd Length: 328  Bit Score: 43.39  E-value: 3.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 432 PAAPAPKPRVVTT------ASIRPSVYQPVPASPYSPSPGanyspTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY 505
Cdd:PRK10905  142 TAKTQTAERPATTrparkqAVIEPKKPQATAKTEPKPVAQ-----TPKRTEPAAPVASTKAPAATSTPAPKETATTAPVQ 216
                          90
                  ....*....|....*....
gi 1958686853 506 TPSPAPNYNPTPSAAYSGG 524
Cdd:PRK10905  217 TASPAQTTATPAAGGKTAG 235
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
460-533 3.87e-04

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 44.11  E-value: 3.87e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  460 YSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 533
Cdd:PRK12270    36 YGPGSTAA-PTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAP 108
PDZ1_FL-whirlin cd06740
PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
58-117 3.95e-04

PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467222 [Multi-domain]  Cd Length: 82  Bit Score: 39.65  E-value: 3.95e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  58 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06740    15 LGFSIRGGAEHGVGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKVTHAEAVKILRVS 74
PDZ2_FL-whirlin cd06741
PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
49-125 4.03e-04

PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467223 [Multi-domain]  Cd Length: 84  Bit Score: 39.94  E-value: 4.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSaSYNLSLTL 125
Cdd:cd06741     5 NLVVEDGQSLGLMIRGGAEYGLGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITHDEAVKILKS-SKHLIMTV 80
PHA03247 PHA03247
large tegument protein UL36; Provisional
426-593 4.08e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.16  E-value: 4.08e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  426 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPA-PTYSPSPAPA 504
Cdd:PHA03247  2583 TSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-DPPPPSPSPAANEPDPHPPPTVPPPErPRDDPAPGRV 2661
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  505 YTPSPAPNYN-PTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGksttsvskqtlPRGAPAYNPTGPqVTPLARGTFQRA 583
Cdd:PHA03247  2662 SRPRRARRLGrAAQASSPPQRPRRRAARPTVGSLTSLADPPPPP-----------PTPEPAPHALVS-ATPLPPGPAAAR 2729
                          170
                   ....*....|
gi 1958686853  584 ERFPASSRTP 593
Cdd:PHA03247  2730 QASPALPAAP 2739
PDZ2_Scribble-like cd06703
PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
59-127 4.21e-04

PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467187 [Multi-domain]  Cd Length: 92  Bit Score: 39.94  E-value: 4.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853  59 GFRLQGGK------DFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06703    15 GFSIAGGKgstpfrDGDEGIFISRITEGGAADrDGKLQVGDRVLSINGVDVTEARHDQAVALLTSSSPTITLVVER 90
LIM1_Testin cd09413
The first LIM domain of Testin; The first LIM domain of Testin: Testin contains three ...
713-765 4.24e-04

The first LIM domain of Testin; The first LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188797  Cd Length: 58  Bit Score: 38.98  E-value: 4.24e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 713 CHGCDFPVEAGDK--FIEALGHT--WHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09413     1 CYCCKQPMKEGDPavYAERAGYDklWHPACFVCSTCGELLVDMIYFWKNGKLYCGRH 57
PRK09752 PRK09752
AIDA-I family autotransporter YfaL;
471-507 4.71e-04

AIDA-I family autotransporter YfaL;


Pssm-ID: 182059 [Multi-domain]  Cd Length: 1250  Bit Score: 43.89  E-value: 4.71e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1958686853  471 TPYTPsPAPAYTPSPAPTytPSPAPTYSPSPAPAYTP 507
Cdd:PRK09752   919 TPPSP-PDPDPTPDPDPT--PDPDPTPDPEPTPAYQP 952
LIM1_LIMPETin cd09414
The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin ...
654-705 4.78e-04

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188798 [Multi-domain]  Cd Length: 58  Bit Score: 38.92  E-value: 4.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKI----MGEVMHALRQT--WHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09414     1 CGGCSEPLkygeLAVTAPKFGESllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
453-535 4.85e-04

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 42.90  E-value: 4.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 453 QPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPA--PNYNPTPSAAY-SGGPSEsa 529
Cdd:PLN02983  143 QPPPPAPVVMMQPPPPHAMP-PASPPAAQPAPSAPASSPPPTP---ASPPPAKAPKSShpPLKSPMAGTFYrSPAPGE-- 216

                  ....*.
gi 1958686853 530 srPPWV 535
Cdd:PLN02983  217 --PPFV 220
LIM1_Lmx1b cd09371
The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein ...
654-706 4.96e-04

The first LIM domain of Lmx1b; The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188757 [Multi-domain]  Cd Length: 53  Bit Score: 38.51  E-value: 4.96e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFhMEDGEPYCEKDYI 706
Cdd:cd09371     1 CAGCQRPISDRyLLRVNERSWHEECLQCSVCQQPLTTSCY-FRDRKLYCKQDYQ 53
LIM2_PINCH cd09332
The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a ...
713-764 5.23e-04

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188718 [Multi-domain]  Cd Length: 52  Bit Score: 38.47  E-value: 5.23e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGC-DFPVeagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09332     1 CGKCgEFVI---GRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50
PDZ4_GRIP1-2-like cd06686
PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
50-126 5.40e-04

PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467174 [Multi-domain]  Cd Length: 99  Bit Score: 40.02  E-value: 5.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  50 VTLTGP--GPWGFRLQGGKDFNMPLT----ISRITPGSKAAQSQLSQ-GDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06686    10 VILRGDplKGFGIQLQGGVFATETLSspplISFIEPDSPAERCGVLQvGDRVLSINGIPTEDRTLEEANQLLRDSASKVT 89

                  ....
gi 1958686853 123 LTLQ 126
Cdd:cd06686    90 LEIE 93
LIM2_Ajuba_like cd09355
The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: ...
723-753 5.50e-04

The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188741 [Multi-domain]  Cd Length: 53  Bit Score: 38.48  E-value: 5.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958686853 723 GDKFIEALGHTWHDTCFICAVCHVNLEGQPF 753
Cdd:cd09355     9 MEMILQALGKSYHPGCFRCCVCNECLDGVPF 39
LIM2_LIMPETin_like cd09417
The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of ...
593-647 5.52e-04

The second LIM domain of protein LIMPETin and related proteins; The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188801  Cd Length: 56  Bit Score: 38.67  E-value: 5.52e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 593 PLCGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 647
Cdd:cd09417     1 DRSVQCDELIFsGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56
LIM2_FHL5 cd09428
The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain ...
713-762 5.56e-04

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188812  Cd Length: 54  Bit Score: 38.67  E-value: 5.56e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09428     1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50
dnaA PRK14086
chromosomal replication initiator protein DnaA;
425-577 5.66e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 43.28  E-value: 5.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 425 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPganysptpyTPSPA-PAYTPSPAPTYTPSPAPTYSPSPAP 503
Cdd:PRK14086  101 HARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLP---------TARPAyPAYQQRPEPGAWPRAADDYGWQQQR 171
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 504 AYTPSPAPnynPTPSAAYSggPSESASRPPwvtddsfsqkFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLAR 577
Cdd:PRK14086  172 LGFPPRAP---YASPASYA--PEQERDREP----------YDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPE 230
LIM2_CRP3 cd09482
The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine ...
593-646 5.95e-04

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188866 [Multi-domain]  Cd Length: 54  Bit Score: 38.46  E-value: 5.95e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 593 PLCGhcNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09482     2 PRCG--KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
LIM1_LIMPETin cd09414
The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin ...
713-765 5.99e-04

The first LIM domain of protein LIMPETin; The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188798 [Multi-domain]  Cd Length: 58  Bit Score: 38.53  E-value: 5.99e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 713 CHGCDFPVEAGD------KFIEALGhtWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 765
Cdd:cd09414     1 CGGCSEPLKYGElavtapKFGESLL--WHPACFRCSTCEELLVDLTYCVHDDQIYCERH 57
PDZ_GOPC-like cd06800
PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and ...
59-110 6.19e-04

PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467261 [Multi-domain]  Cd Length: 83  Bit Score: 39.28  E-value: 6.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853  59 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEA 110
Cdd:cd06800    14 GISITGGKEHGVPILISEIHEGQPADRCgGLYVGDAILSVNGIDLRDAKHKEA 66
LIM2_CRP2 cd09840
The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine ...
713-763 6.27e-04

The second LIM domain of Cysteine Rich Protein 2 (CRP2); The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188871 [Multi-domain]  Cd Length: 54  Bit Score: 38.55  E-value: 6.27e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09840     1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
457-564 6.50e-04

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 43.34  E-value: 6.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  457 ASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAysgGPSESASRPPwvt 536
Cdd:PRK12270    34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPA---APPAAAAAAA--- 107
                           90       100
                   ....*....|....*....|....*...
gi 1958686853  537 ddsfsqkfaPGKSTTSVSKQTLpRGAPA 564
Cdd:PRK12270   108 ---------PAAAAVEDEVTPL-RGAAA 125
LIM2_Prickle cd09418
The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three ...
712-762 6.61e-04

The second LIM domain of Prickle; The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188802  Cd Length: 56  Bit Score: 38.18  E-value: 6.61e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 712 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09418     2 RCSACDEIIFA-DECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
PDZ3_MAGI-1_3-like cd06733
PDZ domain 3 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, ...
59-107 6.64e-04

PDZ domain 3 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467215 [Multi-domain]  Cd Length: 85  Bit Score: 39.13  E-value: 6.64e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853  59 GFRLQGGKDFNMPLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTH 107
Cdd:cd06733    14 GFRILGGTEEGSQVSIGAIVPGGAADLDGrLRTGDELLSVDGVNVVGASH 63
LIM1_LIMK2 cd09463
The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain ...
713-765 6.65e-04

The first LIM domain of LIMK2 (LIM domain Kinase 2); The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188847 [Multi-domain]  Cd Length: 53  Bit Score: 38.31  E-value: 6.65e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEAGdKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKKH 765
Cdd:cd09463     1 CTGCGGRIQDS-FHYRVVQEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKH 51
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
454-583 6.78e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 43.05  E-value: 6.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 454 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTysPSPAPAYTPSP-APNYNPTPSAAYSGGPSESASRP 532
Cdd:PRK07764  392 GAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPA--PAPAPAPPSPAgNAPAGGAPSPPPAAAPSAQPAPA 469
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 533 PWVTDDSFSqkfAPGKSTTSVSKQTLPRGAPAynPTGPQVTPLARGTFQRA 583
Cdd:PRK07764  470 PAAAPEPTA---APAPAPPAAPAPAAAPAAPA--APAAPAGADDAATLRER 515
LIM1_UF1 cd09397
LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing ...
734-767 6.79e-04

LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188783 [Multi-domain]  Cd Length: 58  Bit Score: 38.40  E-value: 6.79e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 734 WHDTCFICAVCHVNLEGQ-PFYSKKDKPLCKKHAH 767
Cdd:cd09397    24 WHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHYH 58
LIM1_LMO2 cd09384
The first LIM domain of LMO2 (LIM domain only protein 2); The first LIM domain of LMO2 (LIM ...
713-764 7.00e-04

The first LIM domain of LMO2 (LIM domain only protein 2); The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188770  Cd Length: 56  Bit Score: 38.29  E-value: 7.00e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVeaGDK-FIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKK 764
Cdd:cd09384     1 CGGCQQNI--GDRyFLKAIDQYWHEDCLSCDLCGCRLGevGRRLYYKLGRKLCRR 53
PDZ6_GRIP1-2-like cd06683
PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
45-127 7.01e-04

PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467171 [Multi-domain]  Cd Length: 85  Bit Score: 39.21  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  45 SMSYSVTLT--GpGPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNL 121
Cdd:cd06683     1 AIIYTVELKryG-GPLGITISGTEEPFDPIVISGLTEGGLAERTgAIHVGDRILAINGESLRGKPLSEAIHLLQNAGDTV 79

                  ....*.
gi 1958686853 122 SLTLQK 127
Cdd:cd06683    80 TLKISR 85
LIM2_LMO4 cd09387
The second LIM domain of LMO4 (LIM domain only protein 4); The second LIM domain of LMO4 (LIM ...
654-704 7.04e-04

The second LIM domain of LMO4 (LIM domain only protein 4); The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188773  Cd Length: 55  Bit Score: 38.23  E-value: 7.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIMGE--VMHALRQTWHTTCFICAACkkpfGNSL-----FHMEDGEPYCEKD 704
Cdd:cd09387     1 CSACGQSIPASelVMRAQGNVYHLKCFTCSTC----HNQLvpgdrFHYVNGSLFCEHD 54
LIM3_LIMPETin cd09421
The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin ...
595-647 7.26e-04

The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188805  Cd Length: 59  Bit Score: 38.32  E-value: 7.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVI--RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 647
Cdd:cd09421     5 CEECSKIIgiDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59
PRK14954 PRK14954
DNA polymerase III subunits gamma and tau; Provisional
455-568 7.36e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184918 [Multi-domain]  Cd Length: 620  Bit Score: 43.01  E-value: 7.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 455 VPASPYSPSPGANYSPTPytPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPS---PAPNYNPTPSAAYSGGPSESASR 531
Cdd:PRK14954  380 VAPSPAGSPDVKKKAPEP--DLPQPDRHPGPAKPEAPGARPAELPSPASAPTPEqqpPVARSAPLPPSPQASAPRNVASG 457
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1958686853 532 PPWVTDDSFSQKFApGKSTTSVSKQTL------PRGAPAYNPT 568
Cdd:PRK14954  458 KPGVDLGSWQGKFM-NFTRNGSRKQPVqasssdAAQTGVFEGV 499
PDZ_RGS3-like cd06711
PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 ...
69-125 7.37e-04

PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467195 [Multi-domain]  Cd Length: 77  Bit Score: 38.91  E-value: 7.37e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  69 NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd06711    19 DSPVRVQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKCVELAHAIRNCPSEIILLV 75
DUF3432 pfam11914
Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. ...
464-520 7.71e-04

Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with pfam00096. This domain has two conserved sequence motifs: YPSPV and PSP.


Pssm-ID: 403204 [Multi-domain]  Cd Length: 98  Bit Score: 39.32  E-value: 7.71e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 464 PGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 520
Cdd:pfam11914   5 PASAVSSISSYSSSVTTSYPSPITTSYPSPVSTSYSSPVPSSYPSPVHTSFPSPSIA 61
LIM_CRP_like cd09326
The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich ...
713-763 7.71e-04

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188712  Cd Length: 53  Bit Score: 37.96  E-value: 7.71e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09326     1 CPRCGKSVYAAEEVI-AAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50
Neisseria_TspB pfam05616
Neisseria meningitidis TspB protein; This family consists of several Neisseria meningitidis ...
470-593 7.78e-04

Neisseria meningitidis TspB protein; This family consists of several Neisseria meningitidis TspB virulence factor proteins.


Pssm-ID: 283306 [Multi-domain]  Cd Length: 517  Bit Score: 42.77  E-value: 7.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 470 PTP-YTPSPAPAYTPSPAPTYTPSPAPTYSPSP--APAYTPSPAP--NYNPTPSAAYSGGPSESASRP--PWVT------ 536
Cdd:pfam05616 326 PRPdLTPASAEAPHAQPLPEVSPAENPANNPDPdeNPGTRPNPEPdpDLNPDANPDTDGQPGTRPDSPavPDRPngrdgk 405
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 537 ------DDSFSQKFAPgkSTTSVSKQTLPRGAPAYNPTGPQVTplARGTFQRAERFPASSRTP 593
Cdd:pfam05616 406 dgkdgeDGGLLCDFFP--DILACDELGKPEDNMAEDINIPQET--DDKEFQKHGFFPDNAQCP 464
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
449-528 7.83e-04

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 42.96  E-value: 7.83e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  449 PSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTyTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSES 528
Cdd:PRK12270    39 GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA-APAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEV 117
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
713-762 7.95e-04

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188813  Cd Length: 53  Bit Score: 37.87  E-value: 7.95e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09429     1 CVKCNKPITSGG--VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
LIM1_PINCH cd09331
The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an ...
611-651 8.23e-04

The first LIM domain of protein PINCH; The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188717  Cd Length: 59  Bit Score: 38.08  E-value: 8.23e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFFA 651
Cdd:cd09331    19 GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
LIM4_FHL3 cd09434
The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain ...
595-645 8.30e-04

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3); The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188818  Cd Length: 56  Bit Score: 38.20  E-value: 8.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 645
Cdd:cd09434     1 CAACNKPITGfgggKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
LIM5_PINCH cd09335
The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays ...
713-764 8.49e-04

The fifth LIM domain of protein PINCH; The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188721 [Multi-domain]  Cd Length: 54  Bit Score: 38.10  E-value: 8.49e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEaGDkFIEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDKPLCKK 764
Cdd:cd09335     1 CYHCNQVIE-GD-VVSALNKTWCVDHFSCSFCDTKLTLKsKFYEFDMKPVCKK 51
LIM3_Prickle cd09420
The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three ...
731-764 8.95e-04

The third LIM domain of Prickle; The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188804  Cd Length: 59  Bit Score: 38.19  E-value: 8.95e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853 731 GHTWH--DTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09420    21 GQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCSR 56
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
425-511 9.10e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 42.52  E-value: 9.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 425 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPAS-PYSPSPGAnysptpyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAP 503
Cdd:PRK14963  343 GGAPSEGVAAVAPPAPAPADLTQRLNRLEKEVRSlRSAPTAAA-------TAAGAPLPDFDPRPRGPPAPEPARSAEAPP 415

                  ....*...
gi 1958686853 504 AYTPSPAP 511
Cdd:PRK14963  416 LVAPAAAP 423
LIM3_Fhl2 cd09431
The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of ...
713-762 9.47e-04

The third LIM domain of Four and a half LIM domains protein 2 (FHL2); The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188815  Cd Length: 57  Bit Score: 38.05  E-value: 9.47e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09431     1 CVQCKKPITTGG--VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYC 48
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
595-647 9.78e-04

The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188813  Cd Length: 53  Bit Score: 37.87  E-value: 9.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 647
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
LIM2_CRP3 cd09482
The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine ...
713-763 1.03e-03

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188866 [Multi-domain]  Cd Length: 54  Bit Score: 37.69  E-value: 1.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09482     1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50
LIM4_Paxillin_like cd09339
The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the ...
654-705 1.04e-03

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188725 [Multi-domain]  Cd Length: 52  Bit Score: 37.70  E-value: 1.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
LIM2_CRP cd09403
The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich ...
642-705 1.06e-03

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188787  Cd Length: 54  Bit Score: 37.56  E-value: 1.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 642 CERCYEQFFAPicakcnTKIMGEvmhalRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09403     1 CPRCGKSVYAA------EKIIGA-----GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
LIM1_Lhx1_Lhx5 cd09367
The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also ...
713-763 1.07e-03

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188753 [Multi-domain]  Cd Length: 52  Bit Score: 37.79  E-value: 1.07e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDKPLCK 763
Cdd:cd09367     1 CAGCDRPIL--DKFLlNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCR 49
PRK07994 PRK07994
DNA polymerase III subunits gamma and tau; Validated
448-510 1.09e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236138 [Multi-domain]  Cd Length: 647  Bit Score: 42.55  E-value: 1.09e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 448 RPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPA 510
Cdd:PRK07994  360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQL 422
PDZ5_GRIP1-2-like cd06682
PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related ...
41-127 1.11e-03

PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family domain PDZ5 is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467170 [Multi-domain]  Cd Length: 85  Bit Score: 38.48  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  41 AVGTSMSYSVTLTGPGPwgfRLQGGkdfnmPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06682     6 PKRSGVGLGITISAPKN---RKPGD-----PLIISDVKKGSVAHRTgTLEPGDKLLAIDNIRLDNCSMEDAAQILQQAED 77

                  ....*...
gi 1958686853 120 NLSLTLQK 127
Cdd:cd06682    78 IVKLKIRK 85
LIM1_Lrg1p_like cd09391
The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM ...
595-646 1.21e-03

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188777  Cd Length: 57  Bit Score: 37.67  E-value: 1.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVY-----CERCY 646
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSeqvplCETDY 57
LIM2_CRP cd09403
The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich ...
595-646 1.22e-03

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188787  Cd Length: 54  Bit Score: 37.56  E-value: 1.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09403     1 CPRCGKsVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
PRK05641 PRK05641
putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
470-510 1.25e-03

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated


Pssm-ID: 235540 [Multi-domain]  Cd Length: 153  Bit Score: 40.23  E-value: 1.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958686853 470 PTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAytPSPA 510
Cdd:PRK05641   44 DLSAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPA--PASA 82
LIM1_Lmx1a cd09370
The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein ...
654-705 1.26e-03

The first LIM domain of Lmx1a; The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188756 [Multi-domain]  Cd Length: 52  Bit Score: 37.44  E-value: 1.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGEVMHALRQT-WHTTCFICAACKKPFGNSLFhMEDGEPYCEKDY 705
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCF-YRDKKLYCKEDY 52
FAP pfam07174
Fibronectin-attachment protein (FAP); This family contains bacterial fibronectin-attachment ...
444-511 1.26e-03

Fibronectin-attachment protein (FAP); This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix.


Pssm-ID: 429334  Cd Length: 301  Bit Score: 41.45  E-value: 1.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 444 TASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:pfam07174  36 VAHADPEPAPPPPSTATAPPAPPPPPPAPAAPAPPPPPAAPNAPNAPPPPADPNAPPPPPADPNAPPP 103
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
453-532 1.26e-03

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 42.57  E-value: 1.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  453 QPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRP 532
Cdd:PRK12270    40 STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119
PDZ5_PTPN13-like cd06697
PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related ...
50-123 1.29e-03

PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), Protein-tyrosine phosphatase 1E (PTP-E1), and Protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467183 [Multi-domain]  Cd Length: 87  Bit Score: 38.48  E-value: 1.29e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853  50 VTLT-GPGPWGFRLQGGKDFNMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06697     6 ITLTcHPGQLGLKLTGGSDSKYQvIYVLEIVPGSAAAEEgSLQPLDIIHYINGVSTQGMTLEDAVRALEASLPTVVL 82
LIM1_Isl cd09366
The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl ...
654-705 1.29e-03

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188752 [Multi-domain]  Cd Length: 55  Bit Score: 37.32  E-value: 1.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 654 CAKCNTKIMGEVMhaLR----QTWHTTCFICAACKKPFGNS--LFhMEDGEPYCEKDY 705
Cdd:cd09366     1 CVGCGGKIHDQYI--LRvapdLEWHAACLKCAECGQYLDETctCF-VRDGKTYCKRDY 55
LIM2_FHL5 cd09428
The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain ...
654-701 1.42e-03

The second LIM domain of Four and a half LIM domains protein 5 (FHL5); The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188812  Cd Length: 54  Bit Score: 37.51  E-value: 1.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09428     1 CFHCKKTIMpgSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50
LIM1_Prickle_1 cd09483
The first LIM domain of Prickle 1; The first LIM domain of Prickle 1. Prickle contains three ...
654-701 1.43e-03

The first LIM domain of Prickle 1; The first LIM domain of Prickle 1. Prickle contains three C-terminal LIM domains and a N-terminal PET domain Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in mainly expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. In addition, Prickle 1 regulates cell movements during gastrulation and neuronal migration through interaction with the noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188867  Cd Length: 59  Bit Score: 37.59  E-value: 1.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 654 CAKCNTKI-MGEV-MHALRQ----TWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09483     1 CEQCGIKInGGEVaVFASRAgpgvCWHPSCFVCFTCNELLVDLIYFYQDGKIHC 54
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
469-527 1.44e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 41.80  E-value: 1.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 469 SPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY---TPSPAPNYNPTPSAAYSGGPSE 527
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVeekSPSEESATATAPESPSTSVPSS 142
LIM2_FHL cd09345
The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of ...
611-646 1.56e-03

The second LIM domain of Four and a half LIM domains protein (FHL); The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188731 [Multi-domain]  Cd Length: 54  Bit Score: 37.27  E-value: 1.56e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09345    19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
LIM1_CRP3 cd09481
The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine ...
654-705 1.61e-03

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188865  Cd Length: 54  Bit Score: 37.43  E-value: 1.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09481     2 CGACEKTVYhAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
LIM2_abLIM cd09328
The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin ...
595-645 1.70e-03

The second LIM domain on actin binding LIM (abLIM) proteins; The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188714  Cd Length: 56  Bit Score: 37.33  E-value: 1.70e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLAD---VCFVEeqNNVYCERC 645
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPgdrVTFNG--KECLCQKC 55
PHA03379 PHA03379
EBNA-3A; Provisional
402-587 1.72e-03

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 41.97  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 402 VENPRPQAsayspaaatspAPAAHTSYSEGPAApAPKPRVVTTASIRPSVYQPVPAspysPSPGANYSPTPYTPS----- 476
Cdd:PHA03379  420 VEKPRPEV-----------PQSLETATSHGSAQ-VPEPPPVHDLEPGPLHDQHSMA----PCPVAQLPPGPLQDLepgdq 483
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 477 -PAPAYTPSPAPTYTPSPA-PTYSP-SPAPAYTPSPAP-NYNPTPSA-AYSGGPSESASRPpwvTDDSFSQKFAPGKSTT 551
Cdd:PHA03379  484 lPGVVQDGRPACAPVPAPAgPIVRPwEASLSQVPGVAFaPVMPQPMPvEPVPVPTVALERP---VCPAPPLIAMQGPGET 560
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1958686853 552 SVSKQTLPRGAPA-YNPTGPQ-VTP------LARGtfqRAERFP 587
Cdd:PHA03379  561 SGIVRVRERWRPApWTPNPPRsPSQmsvrdrLARL---RAEAQP 601
PLN02983 PLN02983
biotin carboxyl carrier protein of acetyl-CoA carboxylase
472-533 1.75e-03

biotin carboxyl carrier protein of acetyl-CoA carboxylase


Pssm-ID: 215533 [Multi-domain]  Cd Length: 274  Bit Score: 40.98  E-value: 1.75e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 472 PYTPSPAPAYT---PSPAPTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAysggPSESASRPP 533
Cdd:PLN02983  142 PQPPPPAPVVMmqpPPPHAMPPASPPAAQPAPSAPASSPPPTP---ASPPPA----KAPKSSHPP 199
LIM1_Lhx1_Lhx5 cd09367
The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also ...
654-705 1.75e-03

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188753 [Multi-domain]  Cd Length: 52  Bit Score: 37.02  E-value: 1.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 705
Cdd:cd09367     1 CAGCDRPILDKfLLNVLDRAWHAKCVQCCDCKCPLTEKCFS-REGKLYCRNDF 52
PDHac_trf_long TIGR01348
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
470-526 1.83e-03

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]


Pssm-ID: 273566 [Multi-domain]  Cd Length: 546  Bit Score: 41.78  E-value: 1.83e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958686853 470 PTPYTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPAPNYNPTPSAAYSGGPS 526
Cdd:TIGR01348 197 ATAPAPASAQPAAQSPAATQPEPAAA---PAAAKAQAPAPQQAGTQNPAKVDHAAPA 250
LIM2_FHL1 cd09424
The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain ...
673-709 1.84e-03

The second LIM domain of Four and a half LIM domains protein 1 (FHL1); The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188808  Cd Length: 58  Bit Score: 37.05  E-value: 1.84e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1958686853 673 WHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLF 709
Cdd:cd09424    22 WHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
LIM4_Paxillin_like cd09339
The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the ...
713-764 1.88e-03

The fourth LIM domain of the Paxillin-like protein family; The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188725 [Multi-domain]  Cd Length: 52  Bit Score: 36.93  E-value: 1.88e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 764
Cdd:cd09339     1 CAGCGKPITGR--CITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHP 50
LIM3_Paxillin cd09409
The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor ...
595-646 1.91e-03

The third LIM domain of paxillin; The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188793 [Multi-domain]  Cd Length: 53  Bit Score: 37.13  E-value: 1.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
KAR9 pfam08580
Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal ...
438-590 1.92e-03

Yeast cortical protein KAR9; The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase.


Pssm-ID: 430088 [Multi-domain]  Cd Length: 684  Bit Score: 41.74  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 438 KPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAP---TYSPSPAPAYTP------- 507
Cdd:pfam08580 508 PSNTATSETPTPALRPPSRPQPPPPGNRPRWNASTNTNDLDVGHNFKPLTLTTPSPTPsrsSRSSSTLPPVSPlsrdksr 587
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 508 SPAPNYNPTPSAAY---SGGPSESAS---RPPWVTDDSFSqkfapgKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQ 581
Cdd:pfam08580 588 SPAPTCRSVSRASRrraSRKPTRIGSpnsRTSLLDEPPYP------KLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661

                  ....*....
gi 1958686853 582 RAERfPASS 590
Cdd:pfam08580 662 PQTR-PGTS 669
LIM1_FHL2 cd09422
The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of ...
612-646 1.99e-03

The first LIM domain of Four and a half LIM domains protein 2 (FHL2); The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188806  Cd Length: 62  Bit Score: 37.19  E-value: 1.99e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 612 RSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09422    24 RHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58
PRK04654 PRK04654
sec-independent translocase; Provisional
460-556 2.02e-03

sec-independent translocase; Provisional


Pssm-ID: 135173 [Multi-domain]  Cd Length: 214  Bit Score: 40.57  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 460 YSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAY-SGGPSESASRPPwvTDD 538
Cdd:PRK04654  119 LSASAQVD-AAAGAEPGAGQAHTPVPAPAPVIAQAQPIAPAPHQTLVPAPHDTIVPAPHAAHlPSAPATPVSVAP--VDA 195
                          90
                  ....*....|....*...
gi 1958686853 539 SFSQKFAPGKSTTSVSKQ 556
Cdd:PRK04654  196 GTSASPTPSEPTKIQEKQ 213
LIM4_Paxillin cd09411
The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor ...
713-762 2.04e-03

The fourth LIM domain of Paxillin; The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188795 [Multi-domain]  Cd Length: 52  Bit Score: 36.85  E-value: 2.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEAgdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09411     1 CSGCQKPITG--RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
442-533 2.14e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 41.33  E-value: 2.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 442 VTTASIRPsVYQPVPASPYSPSPGANY-SPTPYT-PSPAPAYTPSPAPTYT-PSPAPTYSPSPAPAYTPSPAPNYNPTPS 518
Cdd:PRK14950  355 VIEALLVP-VPAPQPAKPTAAAPSPVRpTPAPSTrPKAAAAANIPPKEPVReTATPPPVPPRPVAPPVPHTPESAPKLTR 433
                          90
                  ....*....|....*
gi 1958686853 519 AAYSGGPSESASRPP 533
Cdd:PRK14950  434 AAIPVDEKPKYTPPA 448
LIM2_CRP cd09403
The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich ...
713-763 2.16e-03

The second LIM domain of Cysteine Rich Protein (CRP); The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188787  Cd Length: 54  Bit Score: 36.78  E-value: 2.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 713 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 763
Cdd:cd09403     1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50
PRK14948 PRK14948
DNA polymerase III subunit gamma/tau;
436-513 2.23e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237862 [Multi-domain]  Cd Length: 620  Bit Score: 41.49  E-value: 2.23e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 436 APKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNY 513
Cdd:PRK14948  363 AFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLN 440
rad23 TIGR00601
UV excision repair protein Rad23; All proteins in this family for which functions are known ...
474-541 2.24e-03

UV excision repair protein Rad23; All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273167 [Multi-domain]  Cd Length: 378  Bit Score: 41.03  E-value: 2.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 474 TPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAyTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFS 541
Cdd:TIGR00601  82 GKVAPPAATPTSAPTPTPSPPASPASGMSAA-PASAVEEKSPSEESATATAPESPSTSVPSSGSDAAS 148
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
430-504 2.26e-03

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 41.41  E-value: 2.26e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  430 EGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA 504
Cdd:PRK12270    40 STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAA-PPKPAAAAAAAAAPAAPPAAAAAAAPAAAAV 113
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
456-539 2.28e-03

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 41.41  E-value: 2.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  456 PASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTySPSPAPAYTPSPAPnynPTPSAAYSGGPSESASRPPWV 535
Cdd:PRK12270    38 PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA-APAAPPKPAAAAAA---AAAPAAPPAAAAAAAPAAAAV 113

                   ....
gi 1958686853  536 TDDS 539
Cdd:PRK12270   114 EDEV 117
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
407-533 2.33e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 41.37  E-value: 2.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 407 PQASAYSPAAATSPAPAAHTSYSEGPAA-PAPKPRVVTTASIRPSVYQPVPASPySPSPGANYSPTPYTPSPAPAYTPSP 485
Cdd:PRK07003  417 AAAATRAEAPPAAPAPPATADRGDDAADgDAPVPAKANARASADSRCDERDAQP-PADSGSASAPASDAPPDAAFEPAPR 495
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 486 APTYTPSPAPTYSPSPAPAYTPS---PAPNYNPTPSAAysgGPSESASRPP 533
Cdd:PRK07003  496 AAAPSAATPAAVPDARAPAAASRedaPAAAAPPAPEAR---PPTPAAAAPA 543
PDZ1_PDZD7-like cd10833
PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
56-106 2.42e-03

PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467269 [Multi-domain]  Cd Length: 84  Bit Score: 37.41  E-value: 2.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853  56 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMT 106
Cdd:cd10833    12 GSLGFSVRGGSEHGLGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENIT 62
PDZ3_LNX1_2-like cd06679
PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ ...
64-126 2.42e-03

PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467167 [Multi-domain]  Cd Length: 88  Bit Score: 37.62  E-value: 2.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853  64 GGKDFNMPLTISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06679    22 GSRRGDLPIYVTNVQPdGCLGRDGRIKKGDVLLSINGISLTNLSHSEAVAVLKASAASSSIVLK 85
LIM1_CRP2 cd09480
The first LIM domain of Cysteine Rich Protein 2 (CRP2); The first LIM domain of Cysteine Rich ...
654-705 2.59e-03

The first LIM domain of Cysteine Rich Protein 2 (CRP2); The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188864  Cd Length: 55  Bit Score: 36.51  E-value: 2.59e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 705
Cdd:cd09480     2 CGACGRTVYhAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54
LIM1_MLP84B_like cd09404
The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A ...
712-749 2.64e-03

The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188788  Cd Length: 54  Bit Score: 36.70  E-value: 2.64e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958686853 712 KCHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLE 749
Cdd:cd09404     1 KCPKCGKSVYAAEERL-AGGYKWHKMCFKCGMCNKLLD 37
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
425-573 2.81e-03

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 41.21  E-value: 2.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 425 HTSYSEGPAAPApKPRVVTTASIRPSVYQP----VPASPYSPSpganySPTPYTPSPAPAYTPSPA-PTYTPSPAPTYSP 499
Cdd:PTZ00449  587 HPKDPEEPKKPK-RPRSAQRPTRPKSPKLPelldIPKSPKRPE-----SPKSPKRPPPPQRPSSPErPEGPKIIKSPKPP 660
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 500 SpapaytpSPAPNYNPTPSAAYSGGPSESASRP-----PWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVT 573
Cdd:PTZ00449  661 K-------SPKPPFDPKFKEKFYDDYLDAAAKSketktTVVLDESFESILKETLPETPGTPFTTPRPLPPKLPRDEEFP 732
PDZ1_PTPN13-like cd23072
PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related ...
59-129 2.82e-03

PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467285 [Multi-domain]  Cd Length: 92  Bit Score: 37.47  E-value: 2.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  59 GFRLQGGKD---FNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 129
Cdd:cd23072    16 GFQIVGGEKsgrLDLGIFISSITPGGPAdLDGRLKPGDRLISVNDVSLEGLSHDAAVEILQNAPEDVTLVVSQPK 90
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
461-559 3.03e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 40.91  E-value: 3.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 461 SPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAytPSPAPNYNPTPSAAySGGPSESASRPPWVTddsf 540
Cdd:PRK14971  370 SGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSA--PQSATQPAGTPPTV-SVDPPAAVPVNPPST---- 442
                          90
                  ....*....|....*....
gi 1958686853 541 sqkfAPGKSTTSVSKQTLP 559
Cdd:PRK14971  443 ----APQAVRPAQFKEEKK 457
LIM_CLP36 cd09448
This family represents the LIM domain of CLP36; This family represents the LIM domain of CLP36. ...
595-644 3.16e-03

This family represents the LIM domain of CLP36; This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188832  Cd Length: 52  Bit Score: 36.43  E-value: 3.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADV--CFVEEQnnVYCER 644
Cdd:cd09448     1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKghFFVEDQ--IYCEK 50
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
431-534 3.17e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 431 GPAAPAPKPRVVTTASIRPSvYQPVPASPYSPSPGANYSPTPYTPSPAPAytPSPAPTYTPSPAPTYSPSPAPAYTPSPA 510
Cdd:PRK07764  609 PEEAARPAAPAAPAAPAAPA-PAGAAAAPAEASAAPAPGVAAPEHHPKHV--AVPDASDGGDGWPAKAGGAAPAAPPPAP 685
                          90       100
                  ....*....|....*....|....
gi 1958686853 511 PnyNPTPSAAYSGGPSESASRPPW 534
Cdd:PRK07764  686 A--PAAPAAPAGAAPAQPAPAPAA 707
LIM1_TRIP6 cd09350
The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain ...
595-646 3.18e-03

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188736  Cd Length: 54  Bit Score: 36.23  E-value: 3.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 595 CGHCNN--VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09350     1 CGRCGEnvVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
431-562 3.19e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 40.82  E-value: 3.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 431 GPAAPAPKPRVVTTASIRP-SVYQPVPASPYSPSPGANYSPT-PYTPSPaPAYTPSPAPTYTPSPAPTYSPSPAPAYTPS 508
Cdd:PRK14959  392 GGAATIPTPGTQGPQGTAPaAGMTPSSAAPATPAPSAAPSPRvPWDDAP-PAPPRSGIPPRPAPRMPEASPVPGAPDSVA 470
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 509 PAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQ-KFAPGKSTTSVSKQTLPRGA 562
Cdd:PRK14959  471 SASDAPPTLGDPSDTAEHTPSGPRTWDGFLEFCQgRNGQGGRLATVLRQATPEHA 525
PRK10856 PRK10856
cytoskeleton protein RodZ;
453-530 3.23e-03

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 40.39  E-value: 3.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 453 QPVP-------ASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGP 525
Cdd:PRK10856  160 QSVPldtstttDPATTPAPAAPVDTTP-TNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLP 238

                  ....*
gi 1958686853 526 SESAS 530
Cdd:PRK10856  239 TDQAG 243
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
322-536 3.31e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.12  E-value: 3.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 322 ILAQMTGT----EYMQDPDEEALRRSSTPIEHAPVCTSQATSPLLPASAPSPAAASPIAASPTLATAAAAHAVAASAAGP 397
Cdd:PRK07764  573 ALAEELGGdwqvEAVVGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEH 652
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 398 ASSPVENPRPQASAYSPAAATSpapaahtsySEGPAAPAPKP-RVVTTASIRPSVYQPVPASPYSPSPGAnySPTPYTPS 476
Cdd:PRK07764  653 HPKHVAVPDASDGGDGWPAKAG---------GAAPAAPPPAPaPAAPAAPAGAAPAQPAPAPAATPPAGQ--ADDPAAQP 721
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 477 PAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVT 536
Cdd:PRK07764  722 PQAAQGASAPSPAADDPVP---LPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSP 778
PDHac_trf_long TIGR01348
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model ...
445-502 3.39e-03

pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form; This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase]


Pssm-ID: 273566 [Multi-domain]  Cd Length: 546  Bit Score: 40.63  E-value: 3.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 445 ASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPA 502
Cdd:TIGR01348 193 GSTPATAPAPASAQPAAQSPAATQPEPAAAPAAAKAQAPAPQQAGTQNPAKVDHAAPA 250
PDZ5_DrPTPN13-like cd23060
PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and ...
50-125 3.41e-03

PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467273 [Multi-domain]  Cd Length: 80  Bit Score: 36.94  E-value: 3.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853  50 VTLTGP--GPWGFRLQGGKDFNmPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd23060     2 IELEKPanGGLGFSLVGGEGGS-GIFVKSISPGGVADRDgRLQVGDRLLQVNGESVIGLSHSKAVNILRKAKGTVQLTV 79
LIM2_TRIP6 cd09356
The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain ...
595-642 3.56e-03

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6); The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188742  Cd Length: 53  Bit Score: 36.38  E-value: 3.56e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 595 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYC 642
Cdd:cd09356     1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFtVDATGQIHC 49
LIM1_Isl cd09366
The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl ...
595-646 3.57e-03

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188752 [Multi-domain]  Cd Length: 55  Bit Score: 36.17  E-value: 3.57e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 595 CGHCNNVIRGPFL--VAMGRSWHPEEFNCAYCKTSLAD--VCFVEEqNNVYCERCY 646
Cdd:cd09366     1 CVGCGGKIHDQYIlrVAPDLEWHAACLKCAECGQYLDEtcTCFVRD-GKTYCKRDY 55
LIM1_Lhx2_Lhx9 cd09369
The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: ...
595-646 3.64e-03

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188755 [Multi-domain]  Cd Length: 54  Bit Score: 36.16  E-value: 3.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 595 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLAD--VCFVEEqNNVYCERCY 646
Cdd:cd09369     1 CAGCGEKIQDRFyLLAVDRQWHASCLKCCECRLPLDSelSCFSRD-GNIYCKEDY 54
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
426-519 3.70e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 40.56  E-value: 3.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 426 TSYSEGPAAPAPKPrvvttaSIRPSVYQPVPASPYSPSPGanySPTPYTPSPAPAYTPSPAPtytPSPAPTYSPSPAPAY 505
Cdd:PRK14950  372 TAAAPSPVRPTPAP------STRPKAAAAANIPPKEPVRE---TATPPPVPPRPVAPPVPHT---PESAPKLTRAAIPVD 439
                          90
                  ....*....|....
gi 1958686853 506 TPSPAPNYNPTPSA 519
Cdd:PRK14950  440 EKPKYTPPAPPKEE 453
LIM1_Lhx2_Lhx9 cd09369
The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: ...
713-751 3.75e-03

The first LIM domain of Lhx2 and Lhx9 family; The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188755 [Multi-domain]  Cd Length: 54  Bit Score: 36.16  E-value: 3.75e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958686853 713 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLEGQ 751
Cdd:cd09369     1 CAGCGEKIQ--DRFyLLAVDRQWHASCLKCCECRLPLDSE 38
LIM2_Lmx1a_Lmx1b cd09378
The second LIM domain of Lmx1a and Lmx1b; The second LIM domain of Lmx1a and Lmx1b: Lmx1a and ...
654-705 3.89e-03

The second LIM domain of Lmx1a and Lmx1b; The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188764  Cd Length: 55  Bit Score: 36.27  E-value: 3.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 654 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSlFHMEDGEPYCEKDY 705
Cdd:cd09378     1 CSGCLEKIAPSelVMRALENVYHLRCFCCCVCERQLqkGDE-FVLKEGQLLCKSDY 55
PRK04654 PRK04654
sec-independent translocase; Provisional
433-530 3.92e-03

sec-independent translocase; Provisional


Pssm-ID: 135173 [Multi-domain]  Cd Length: 214  Bit Score: 39.41  E-value: 3.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 433 AAPAPKPRVVTTASIRPSVYQPVPASPyspSPGANYSPTPyTPSPAP----AYTPSPAPTYTPSPAPTYSPSPAPAYTPS 508
Cdd:PRK04654  105 ATPVATPLELAHADLSASAQVDAAAGA---EPGAGQAHTP-VPAPAPviaqAQPIAPAPHQTLVPAPHDTIVPAPHAAHL 180
                          90       100
                  ....*....|....*....|..
gi 1958686853 509 PAPNYNPTPSAAYSGGPSESAS 530
Cdd:PRK04654  181 PSAPATPVSVAPVDAGTSASPT 202
LIM1_Lhx3a cd09466
The first LIM domain of Lhx3a; The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein ...
593-650 4.01e-03

The first LIM domain of Lhx3a; The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188850 [Multi-domain]  Cd Length: 56  Bit Score: 36.29  E-value: 4.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 593 PLCGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCErcyEQFF 650
Cdd:cd09466     2 PKCAGCDHPIFDRFiLKVQDKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCK---EDFF 56
LIM1_Lhx7_Lhx8 cd09381
The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 ...
653-705 4.01e-03

The first LIM domain of Lhx7 and Lhx8; The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188767 [Multi-domain]  Cd Length: 56  Bit Score: 36.11  E-value: 4.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 653 ICAKCNTKIMGEVMHALRQ-TWHTTCFICAACKKPFGNSLF-HMEDGEPYCEKDY 705
Cdd:cd09381     1 VCSSCGLEIVDKYLLKVNDlCWHVRCLSCSVCRTSLGRHTScYIKDKDIFCKLDY 55
LIM1_Lhx3b cd09467
The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein ...
713-763 4.31e-03

The first LIM domain of Lhx3b; The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188851 [Multi-domain]  Cd Length: 55  Bit Score: 36.07  E-value: 4.31e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDKPLCK 763
Cdd:cd09467     4 CAGCNQHIV--DRFIlKVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52
LIM_N_RAP cd09446
The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein ...
654-702 4.53e-03

The LIM domain of N-RAP; The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188830  Cd Length: 53  Bit Score: 36.05  E-value: 4.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 702
Cdd:cd09446     1 CARCGYGVYpAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50
LIM2_FHL2 cd09426
The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain ...
611-648 4.57e-03

The second LIM domain of Four and a half LIM domains protein 2 (FHL2); The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes.


Pssm-ID: 188810  Cd Length: 57  Bit Score: 36.18  E-value: 4.57e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958686853 611 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQ 648
Cdd:cd09426    19 GNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56
LIM1_LIMK1 cd09462
The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain ...
593-646 4.82e-03

The first LIM domain of LIMK1 (LIM domain Kinase 1); The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188846 [Multi-domain]  Cd Length: 74  Bit Score: 36.40  E-value: 4.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 593 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVcFVEEQNNVYCERCY 646
Cdd:cd09462    20 PVCASCGQSIyDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
73-108 4.83e-03

PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 35.97  E-value: 4.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853  73 TISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHL 108
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDV 36
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
429-593 4.97e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 40.54  E-value: 4.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  429 SEGPAAPAPKPRVVTTASIRPSVYQPVPA-------------SPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPA- 494
Cdd:PHA03307   197 TPPAAASPRPPRRSSPISASASSPAPAPGrsaaddagasssdSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWn 276
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  495 -PTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVT 573
Cdd:PHA03307   277 gPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRP 356
                          170       180
                   ....*....|....*....|
gi 1958686853  574 PLARGTFQRAERFPASSRTP 593
Cdd:PHA03307   357 PPPADPSSPRKRPRPSRAPS 376
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
425-543 5.16e-03

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 40.12  E-value: 5.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 425 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSP------APTYTPSPAPTYS 498
Cdd:COG3469    91 STSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTtvsgteTATGGTTTTSTTT 170
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958686853 499 PSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQK 543
Cdd:COG3469   171 TTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLPKH 215
LIM_Mical cd09439
The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule ...
713-765 5.16e-03

The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188823 [Multi-domain]  Cd Length: 55  Bit Score: 35.73  E-value: 5.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKKH 765
Cdd:cd09439     1 CYFCKKRVYVMER-LSAEGLFFHRSCFKCSYCGTTLRlgAYAFDRDDGKFYCKPH 54
LIM1_Rga cd09394
The first LIM domain of Rga GTPase-Activating Proteins; The first LIM domain of Rga ...
654-701 5.19e-03

The first LIM domain of Rga GTPase-Activating Proteins; The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188780  Cd Length: 55  Bit Score: 35.80  E-value: 5.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 654 CAKCNTKIMGEVMHALRQT-WHTTCFICAACKKPFG-NSLF-HMEDGEPYC 701
Cdd:cd09394     1 CVGCKESITEGHAYELGGDrWHIHCFKCYKCDKKLScDSNFlVLGDGSLIC 51
DedD COG3147
Cell division protein DedD (periplasmic protein involved in septation) [Cell cycle control, ...
454-522 5.24e-03

Cell division protein DedD (periplasmic protein involved in septation) [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442381 [Multi-domain]  Cd Length: 140  Bit Score: 37.83  E-value: 5.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 454 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTyTPSPAPTySPSPAPAYTPSPAPNYNPTPSAAYS 522
Cdd:COG3147     1 PAEEAAAAPAAAAAPAAPAAAAAPAPAAAAAAAAP-KPAAKPA-APKPAAAAAAAPAAKAAAPAGGGWV 67
LIM_ALP_like cd09360
The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM ...
720-766 5.32e-03

The LIM domain of ALP (actinin-associated LIM protein) family; This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188746 [Multi-domain]  Cd Length: 52  Bit Score: 35.81  E-value: 5.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958686853 720 VEAGDKFIealghtwHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 766
Cdd:cd09360    13 VKARDKNR-------HPECFVCADCGLNLKNKGYFFIEDELYCETHA 52
LIM1_Prickle cd09415
The first LIM domain of Prickle; The first LIM domain of Prickle: Prickle contains three ...
713-768 5.52e-03

The first LIM domain of Prickle; The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188799  Cd Length: 59  Bit Score: 35.70  E-value: 5.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958686853 713 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegqpFYSKKD-KPLCKKHaHA 768
Cdd:cd09415     1 CEQCGEQISGGDIavFASRAGPgaCWHPACFVCSTCKellVDL----IYFYQDgKVYCGRH-HA 59
PRK05641 PRK05641
putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
476-511 5.59e-03

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated


Pssm-ID: 235540 [Multi-domain]  Cd Length: 153  Bit Score: 38.30  E-value: 5.59e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853 476 SPAPAYTPSPAPTytPSPAPTYSPSPAPAYTPSPAP 511
Cdd:PRK05641   46 SAVQEQVPTPAPA--PAPAVPSAPTPVAPAAPAPAP 79
motB PRK12799
flagellar motor protein MotB; Reviewed
477-593 5.75e-03

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 39.70  E-value: 5.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 477 PAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPApnynPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQ 556
Cdd:PRK12799  300 PVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSV----TTQSATTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQ 375
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958686853 557 TLPRGAPAYNPTGP-QVTPLARGTFQRAERFPASSRTP 593
Cdd:PRK12799  376 PQPMSTTETQQSSTgNITSTANGPTTSLPAAPASNIPV 413
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
432-529 6.06e-03

Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 39.01  E-value: 6.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 432 PAAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPGANYSPTPYTPspapaYTPSPAPTYTPSPAPTYSPSpAPAYTPSPA 510
Cdd:pfam07117  17 CLGGGGNMAMARPMSLPLPPGQePEPPRPEEEEGQGGGGGTFPFP-----GSPEPEPGGGGSGPMPMSAS-APEPEPAKA 90
                          90       100
                  ....*....|....*....|..
gi 1958686853 511 PNYNPTPSAA---YSGGPSESA 529
Cdd:pfam07117  91 KPQRPAPAQGhghGGGGDSDSS 112
LIM3_Enigma_like_1 cd09461
The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an ...
668-702 6.20e-03

The third LIM domain of an Enigma subfamily with unknown function; The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188845  Cd Length: 54  Bit Score: 35.60  E-value: 6.20e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958686853 668 ALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 702
Cdd:cd09461    17 ALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
PDZ1_Dlg1-2-4-like cd06723
PDZ domain 1 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg) ...
59-117 6.26e-03

PDZ domain 1 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F.


Pssm-ID: 467206 [Multi-domain]  Cd Length: 89  Bit Score: 36.52  E-value: 6.26e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853  59 GFRLQGGKDF----NMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06723    14 GFSIAGGTDNphigDDPsIYITKIIPGGAAAADgRLRVNDIILRVNDVDVRNVTHSVAVEALKEA 78
PHA03247 PHA03247
large tegument protein UL36; Provisional
432-533 6.33e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.31  E-value: 6.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  432 PAAPAPKPRVvTTASIRPSVYQPVPASPysPSPGANYSPTPYTPSPAPAyTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:PHA03247   389 RHAATPFARG-PGGDDQTRPAAPVPASV--PTPAPTPVPASAPPPPATP-LPSAEPGSDDGPAPPPERQPPAPATEPAPD 464
                           90       100
                   ....*....|....*....|..
gi 1958686853  512 NYNPTPSAAYSGGPSESASRPP 533
Cdd:PHA03247   465 DPDDATRKALDALRERRPPEPP 486
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
462-526 6.39e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 39.72  E-value: 6.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 462 PSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAYSGGPS 526
Cdd:PRK14965  384 PPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP---PARSADPAAAAS 445
PRK10856 PRK10856
cytoskeleton protein RodZ;
443-520 6.62e-03

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 39.62  E-value: 6.62e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 443 TTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 520
Cdd:PRK10856  171 DPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVaPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249
LIM4_abLIM cd09330
The fourth LIM domain of actin binding LIM (abLIM) proteins; The fourth LIM domain of actin ...
654-703 6.74e-03

The fourth LIM domain of actin binding LIM (abLIM) proteins; The fourth LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188716  Cd Length: 56  Bit Score: 35.41  E-value: 6.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958686853 654 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPF---------GNSLFHmedgePYCEK 703
Cdd:cd09330     1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFgegeemylqGSEIWH-----PDCRQ 54
LIM_Mical_like_2 cd09445
This domain belongs to the LIM domain family which are found on Mical (molecule interacting ...
654-701 6.75e-03

This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins; The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188829 [Multi-domain]  Cd Length: 53  Bit Score: 35.52  E-value: 6.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958686853 654 CAKCNTKI--MGEVMhALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 701
Cdd:cd09445     1 CRSCGKPVykMEEII-AEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
432-521 6.80e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 40.15  E-value: 6.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  432 PAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 511
Cdd:PHA03307   838 PPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAGAPAPRPRPAPRVKLGPMP 917
                           90
                   ....*....|
gi 1958686853  512 NYNPTPSAAY 521
Cdd:PHA03307   918 PGGPDPRGGF 927
PHA03247 PHA03247
large tegument protein UL36; Provisional
427-558 7.43e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 39.92  E-value: 7.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  427 SYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA-- 504
Cdd:PHA03247  2897 SFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVpr 2976
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853  505 -YTPSPAPNyNPTPSAAYSGGPSESASR-PPWVTDDSFSQKFAPGKSTTsvsKQTL 558
Cdd:PHA03247  2977 fRVPQPAPS-REAPASSTPPLTGHSLSRvSSWASSLALHEETDPPPVSL---KQTL 3028
LIM1_Lhx1_Lhx5 cd09367
The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also ...
595-642 7.45e-03

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5; The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188753 [Multi-domain]  Cd Length: 52  Bit Score: 35.10  E-value: 7.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958686853 595 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEqNNVYC 642
Cdd:cd09367     1 CAGCDRPILDKFLLnVLDRAWHAKCVQCCDCKCPLTEKCFSRE-GKLYC 48
LIM1_Lhx4 cd09468
The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein ...
713-754 7.48e-03

The first LIM domain of Lhx4; The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.


Pssm-ID: 188852  Cd Length: 52  Bit Score: 35.33  E-value: 7.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958686853 713 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFY 754
Cdd:cd09468     1 CAGCNQHIL--DKFIlKVLDRHWHSSCLKCADCQMQLAERCFS 41
LIM1_Prickle_3 cd09841
The first LIM domain of Prickle 3; The first LIM domain of Prickle 3/LIM domain only 6 (LM06): ...
595-644 7.51e-03

The first LIM domain of Prickle 3; The first LIM domain of Prickle 3/LIM domain only 6 (LM06): Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188872  Cd Length: 59  Bit Score: 35.62  E-value: 7.51e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 595 CGHCNNVIRGPFLV------AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCER 644
Cdd:cd09841     1 CQQCGRQICGGDIAvfasraGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGR 56
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
74-111 7.83e-03

Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440035 [Multi-domain]  Cd Length: 274  Bit Score: 38.98  E-value: 7.83e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958686853  74 ISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQ 111
Cdd:COG0265   205 VARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRL 242
DUF3824 pfam12868
Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It ...
448-532 7.99e-03

Domain of unknwon function (DUF3824); This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known.


Pssm-ID: 372351 [Multi-domain]  Cd Length: 145  Bit Score: 37.41  E-value: 7.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 448 RPSVYQPVPASPYSPS------------PGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPnYNP 515
Cdd:pfam12868  49 RDYYEDPYSPSPYPPSpagpyasqgqyyPETNYFPPPPGSTPQPPVDPQPNAPPPPYNPADYPPPPGAAPPPQPYQ-YPP 127
                          90
                  ....*....|....*..
gi 1958686853 516 TPsaaysgGPSESASRP 532
Cdd:pfam12868 128 PP------GPDPYAPRP 138
LIM1_LMO1_LMO3 cd09388
The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3); The first LIM domain ...
713-764 8.46e-03

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3); The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188774  Cd Length: 55  Bit Score: 35.22  E-value: 8.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958686853 713 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKK 764
Cdd:cd09388     1 CAGCNRKIK--DRYlLKALDQYWHEDCLKCACCDCRLGevGSTLYTKANLILCRR 53
PRK05641 PRK05641
putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
469-504 8.71e-03

putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated


Pssm-ID: 235540 [Multi-domain]  Cd Length: 153  Bit Score: 37.53  E-value: 8.71e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958686853 469 SPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA 504
Cdd:PRK05641   47 AVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPASA 82
LIM1_LMO4 cd09386
The first LIM domain of LMO4 (LIM domain only protein 4); The first LIM domain of LMO4 (LIM ...
654-705 8.88e-03

The first LIM domain of LMO4 (LIM domain only protein 4); The first LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188772 [Multi-domain]  Cd Length: 55  Bit Score: 35.09  E-value: 8.88e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958686853 654 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPF---GNSLFhMEDGEPYCEKDY 705
Cdd:cd09386     1 CAGCGGKIVDRfLLHALDRYWHNGCLKCSCCQAQLgeiGSSCY-TKGGMILCKNDY 55
LIM1_CRP3 cd09481
The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine ...
595-646 8.95e-03

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188865  Cd Length: 54  Bit Score: 35.12  E-value: 8.95e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958686853 595 CGHC-NNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09481     2 CGACeKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
LIM1_TLP cd09476
The first LIM domain of thymus LIM protein (TLP); The first LIM domain of thymus LIM protein ...
654-703 9.06e-03

The first LIM domain of thymus LIM protein (TLP); The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188860  Cd Length: 54  Bit Score: 34.94  E-value: 9.06e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958686853 654 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 703
Cdd:cd09476     1 CPRCDKTVyFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51
LIM3_Testin cd09419
The third LIM domain of Testin; The third LIM domain of Testin: Testin contains three ...
713-762 9.18e-03

The third LIM domain of Testin; The third LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers at cell-cell-contact areas and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188803  Cd Length: 59  Bit Score: 35.25  E-value: 9.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958686853 713 CHGCDFPVEAGDKFIEALGHTWHDT--CFICAVCHVNLEGQPFYSKKDKPLC 762
Cdd:cd09419     1 CQGCHNAIDPEVQRVSYNNFHWHAEpeCFLCSCCSKCLIGQKFMPVEGMVFC 52
PRK11633 PRK11633
cell division protein DedD; Provisional
449-520 9.24e-03

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 38.45  E-value: 9.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853 449 PSVYQPVPASP--------YSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 520
Cdd:PRK11633   57 PAATQALPTQPpegaaeavRAGDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPKPEPK 136
LIM1_Testin_like cd09340
The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This ...
595-646 9.26e-03

The first LIM domain of Testin-like family; The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.


Pssm-ID: 188726  Cd Length: 58  Bit Score: 35.27  E-value: 9.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958686853 595 CGHCNNVIRG--PFLVAM----GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 646
Cdd:cd09340     1 CEKCKEPINPgeVAVFAErageDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
403-591 9.80e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 39.38  E-value: 9.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  403 ENPRPQASaysPAAATSPAPAAHTSYSEGPAAPAPKPRvvttASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYT 482
Cdd:PHA03307   254 ECPLPRPA---PITLPTRIWEASGWNGPSSRPGPASSS----SSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSS 326
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958686853  483 PSPAPTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGA 562
Cdd:PHA03307   327 SSTSSSSESSRGAAVSPGPSPSRSPSPSR---PPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRARAAVAGRARRRDA 403
                          170       180       190
                   ....*....|....*....|....*....|
gi 1958686853  563 PAYNPTG-PQVTPLARGtfQRAERFPASSR 591
Cdd:PHA03307   404 TGRFPAGrPRPSPLDAG--AASGAFYARYP 431
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH