NCBI Conserved Domain Search

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: 9.64e-51

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06753     1 SVTLSGPAPWGFRLQGGKDFNQPLTISRVTPGGKAAQANLRPGDVILAINGESTEGMTHLEAQNKIKAATGSLSLTLER 79

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: 1.44e-36

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

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: 123.61 E-value: 4.44e-34

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09460     1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55

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: 123.70 E-value: 4.45e-34

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 662
Cdd:cd09363     1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNHA 54

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: 123.15 E-value: 6.66e-34

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09459     1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55

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: 116.04 E-value: 2.16e-31

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

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: 116.75 E-value: 4.38e-31

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 193 TIIHAQYNTPISMYSQDAIMDAIAGQAQAQGSDFSGASPLASLPVKDLAVDSASPVYQAVIKTQSKPEDEAdewarrssn 272
Cdd:pfam15936   1 KVVHAQYNSPIGLYSSENIQDALSGQLSGLAGSSEGGKPPPSRPPKKPVVDADSEVYKMLQENQEPKEPPR--------- 71

                          90       100
                  ....*....|....*....|....*...
gi 1958687005 273 lQSRSFRILAQMTGTEYMQDPDEEALRR 300
Cdd:pfam15936  72 -QSGSFRVLQEILETEYLQPPEEELNRP 98

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: 4.98e-30

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09361     1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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: 3.91e-29

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958687005  57 PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd23068    12 PWGFRLQGGADFGQPLSIQKVNPGSPADKAGLRRGDVILRINGTDTSNLTHKQAQDLIKRAGNDLQLTVQR 82

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: 103.19 E-value: 9.12e-27

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 662
Cdd:cd09458     1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSHA 54

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: 8.84e-26

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09453     1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

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: 96.60 E-value: 1.48e-24

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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: 1.09e-23

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09457     1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

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: 7.45e-21

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  50 VTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd10820     2 VTLTGGAPWGFRLQGGSEQKKPLQVAKIRKKSKAALAGLCEGDELLSINGKPCADLSHSEAMDLIDSSGDTLQLLIK 78

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: 84.91 E-value: 1.84e-20

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 662
Cdd:cd09461     1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLHA 54

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: 1.28e-18

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCA--YCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCEYCF 54

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: 79.67 E-value: 1.34e-18

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gi 1958687005 550 CAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd08368     1 CAGCGKPIEGrELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

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: 2.45e-18

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gi 1958687005   46 MSYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:smart00228   1 EPRLVELEkGGGGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGKVTLT 80


                   ..
gi 1958687005  125 LQ 126
Cdd:smart00228  81 VL 82

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: 77.04 E-value: 1.17e-17

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                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  608 KCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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: 75.12 E-value: 5.87e-17

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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: 5.99e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  50 VTLTGP--GPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd00136     2 VTLEKDpgGGLGFSIRGGKDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGVSLEGLTHEEAVELLKSAGGEVTLTVR 81

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: 1.48e-16

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

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: 73.58 E-value: 1.83e-16

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

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: 71.97 E-value: 6.79e-16

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 662
Cdd:cd08368     1 CAGCGKPIE-GRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

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: 1.25e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMtHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06750     4 EVQLQGGAPWGFTLKGGLEHGEPLVISKIEEGGKAAsVGKLQVGDEVVNINGVPLSGS-RQEAIQLVKGSHKTLKLVVRR 82

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

Pssm-ID: 395476 [Multi-domain] Cd Length: 81 Bit Score: 71.54 E-value: 1.84e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  54 GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:pfam00595   8 GRGGLGFSLKGGSDQgDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVENMTHEEAVLALKGSGGKVTLTIL 81

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: 1.98e-15

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  549 ICAKCNTKIMG--EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKD 600
Cdd:smart00132   1 KCAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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: 69.65 E-value: 4.55e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd08368     1 CAGCGKPIEGRELLrALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 69.67 E-value: 5.03e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 550 CAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLF 605
Cdd:pfam00412   1 CAGCNRPIYDrELVRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

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: 8.65e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

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: 65.43 E-value: 1.62e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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: 1.84e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  48 YSVTLT-GPGPWGFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06735     2 YSVELErGPKGFGFSIRGGREYnNMPLYVLRLAEDGPAQRDgRLRVGDQILEINGESTQGMTHAQAIELIRSGGSVVRLL 81


                  ...
gi 1958687005 125 LQK 127
Cdd:cd06735    82 LRR 84

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 64.66 E-value: 2.78e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:pfam00412   1 CAGCNRPIYDRELVR-ALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHD 52

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: 2.81e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  56 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQ--LSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06706    14 GRFGFNVKGGVDQKMPVIVSRVAPGTPADLCIprLNEGDQVLLINGRDISEHTHDQVVMFIKAS 77

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: 3.34e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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: 9.61e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 549 ICAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

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: 62.79 E-value: 1.20e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005  491 CGHCNNVIRG--PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:smart00132   2 CAGCGKPIYGteRVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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: 3.15e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 61.19 E-value: 4.86e-12

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 491 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFF 546
Cdd:pfam00412   1 CAGCNRPIYDRELVrALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYKLF 57

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: 1.98e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09338     1 CGGCNKPIL--ENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53

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: 59.27 E-value: 2.28e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 538 CERCYEQFfAPicakcNTKIM---GEVmhalrqtWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLFS 606
Cdd:cd09331     1 CERCREGF-EP-----DEKIVnsnGEL-------YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

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: 3.57e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958687005  49 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 116
Cdd:cd06763     3 TVELEkGSAGLGFSLEGGKGSplgDRPLTIKRIFKGGAAEQSgVLQVGDEILQINGTSLQGLTRFEAWNIIKS 75

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: 58.50 E-value: 3.93e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

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: 9.62e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

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: 56.98 E-value: 1.37e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 548 PICAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

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: 56.50 E-value: 1.77e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

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: 3.12e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  53 TGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06737    10 RGPESLGFSVRGGLEHGCGLFVSHVSPGSQADNKGLRVGDEIVRINGYSISQCTHEEVINLIKTKKT 76

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: 4.06e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 601
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYFE-KDGKLYCRKDY 52

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: 5.89e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  49 SVTLTGPG---PWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTL 125
Cdd:cd06755     2 TVTLTRPSresPLHFSLLGGSEKGFGIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRNNTH-LSITV 80

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: 6.65e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKpfgnsLFHME----DGEPYCEKDY 601
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGK-----VLTGEymgkDGKPYCERDY 52

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: 6.96e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 489 PLCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09334     1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

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: 7.64e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  58 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYnLSLTLQ 126
Cdd:cd10834    15 LGFNIRGGSEYGLGIYVSKVDPGGLAEQNGIKVGDQILAVNGVSFEDITHSKAVEVLKSQTH-LMLTIK 82

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: 9.38e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 61.88 E-value: 1.21e-09

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  292 DPDEEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTP 371
Cdd:PHA03247  2703 PPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRR 2782

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  372 SPAPA--------------YTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVtddsfs 437
Cdd:PHA03247  2783 LTRPAvaslsesreslpspWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSV------ 2856

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 1958687005  438 qkfAPGKsttSVSKQTLPRGAPAY--NPTGPQVTPLARGTFQRA-ERFP 483
Cdd:PHA03247  2857 ---APGG---DVRRRPPSRSPAAKpaAPARPPVRRLARPAVSRStESFA 2899

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: 1.32e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09345     1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVP 52

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: 1.62e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 490 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09405     1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

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: 53.80 E-value: 1.80e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09327     1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

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: 2.12e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

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: 53.55 E-value: 2.39e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09336     1 CAACNKPI-VG-QVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDYH 53

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: 53.20 E-value: 2.58e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIMGEVM--HALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09351     1 CVKCGEKVLGEGSgcTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

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: 3.23e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  59 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06801    14 GISIKGGAEHKMPILISKIFKGQAADQTgQLFVGDAILSVNGENLEDATHDEAVQALKNAGDEVTLTVK 82

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: 6.15e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPY 596
Cdd:cd09396     1 CAGCKSEIGhGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48

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: 51.06 E-value: 9.60e-09

                           10        20
                   ....*....|....*....|....*.
gi 1958687005  193 TIIHAQYNTPISMYSQDAIMDAIAGQ 218
Cdd:smart00735   1 RVVHKQYNSPIGLYSSENIAETLQGQ 26

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 58.35 E-value: 9.84e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 210 AIMDAIAGQAQAQGSDFSGA-SPLASLPVKdLAVDSASPvyqaviktQSKPED--EADEWARRSSNLQSRSFRILAQMTG 286
Cdd:PRK12323  267 AALLAIADEMAGRSLSFAGAlQDLASLLQK-IALAQVVP--------AAVQDDwpEADDIRRLAGRFDAQEVQLFYQIAN 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 287 T---EYMQDPDEEA------LR----------------------RSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKP 335
Cdd:PRK12323  338 LgrsELALAPDEYAgftmtlLRmlafrpgqsgggagpataaaapVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAAR 417

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 336 RVVTTASIRPSVYQPVPASPYSPS--PGANYSPTPyTPSPAPAYTPSPA---PTYTPSPAPTYSPSPAPAYTPSPAPNYN 410
Cdd:PRK12323  418 AVAAAPARRSPAPEALAAARQASArgPGGAPAPAP-APAAAPAAAARPAaagPRPVAAAAAAAPARAAPAAAPAPADDDP 496

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 411 PtpsaAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQR-AERFPASSRTP 489
Cdd:PRK12323  497 P----PWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVvAPRPPRASASG 572


                  .
gi 1958687005 490 L 490
Cdd:PRK12323  573 L 573

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: 51.75 E-value: 9.97e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

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: 1.06e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 489 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 543
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

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: 1.22e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  59 GFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06752    14 GFNIRGGKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTA 72

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: 51.38 E-value: 1.37e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

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: 50.89 E-value: 1.70e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHM-EDGEPYCEKDY 601
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVdEQNEVYCLDDY 53

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: 50.72 E-value: 1.93e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

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: 2.07e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09344     1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

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: 50.50 E-value: 2.43e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

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: 3.96e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 548 PICAKCNTKIM-GEVMHALRQTWHTTCFICAACkkpfGNSLFHM---EDGEPYCEKDY 601
Cdd:cd09462    20 PVCASCGQSIYdGQYLQALNSDWHADCFRCCEC----GASLSHWyyeKDGRLFCKKDY 73

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: 4.31e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  59 GFRLQGGKDFNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06796    15 GFNVMGGKEQNSPIYISRIIPGGVAdRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAQGSVKLV 81

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 56.15 E-value: 5.78e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIRPSVYQ---PVPASPYSPSPGANYSPTPYTPSPAPAYTPS--PAPTYTPSPAPTYSPSPAPAYT 402
Cdd:PRK07764  408 AAPAPAAAAPAAAAAPAPAAAPqpaPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSaqPAPAPAAAPEPTAAPAPAPPAA 487

                          90       100
                  ....*....|....*....|....*....
gi 1958687005 403 PSPAPNYNPTPSAAYSGGPSESAS-RPPW 430
Cdd:PRK07764  488 PAPAAAPAAPAAPAAPAGADDAATlRERW 516

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: 49.65 E-value: 5.95e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09401     1 CPKCGKPVyFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

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: 6.01e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGE-----PYCEKDY 601
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDtseqvPLCETDY 57

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: 49.34 E-value: 6.57e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYC 538
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFaVDEQNEVYC 49

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: 6.99e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEK 599
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFpPGDRVTFNGKECLCQK 54

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: 48.89 E-value: 8.53e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSL-ADVCFVEEQNNVYCERCY 542
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFgPNDSYYEHEGKIYCHYHY 53

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: 48.84 E-value: 9.06e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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: 48.87 E-value: 1.12e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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: 1.20e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  49 SVTLT-GPGPWGFRLQGGKdfnmPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlSLTLQ 126
Cdd:cd06712     3 TVHLTkEEGGFGFTLRGDS----PVQVASVDPGSCAAEAGLKEGDYIVSVGGVDCKWSKHSEVVKLLKSAGEE-GLELQ 76

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: 1.25e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYCERCY 542
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFtVDVENNIYCVKDY 53

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 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09334     3 CGACRRPIE--GRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETH 53

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: 1.72e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09347     1 CAACTKPITGlgGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPE 54

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: 2.35e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09396     1 CAGCKSEIgHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

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: 2.70e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  48 YSVTLT---GPGpWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06734     2 YDVTLTrreNEG-FGFVIISSVNKKSGSKIGRIIPGSPADRCgQLKVGDRILAVNGISILNLSHGDIVNLIKDSGLSVTL 80


                  ....
gi 1958687005 124 TLQK 127
Cdd:cd06734    81 TIVP 84

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: 47.34 E-value: 3.03e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFG-NSLFHMEDGEPYCEKDY 601
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCY 53

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: 47.43 E-value: 3.12e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIMG--EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09352     1 CVKCGKGVYGasQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 53.79 E-value: 3.67e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  299 RRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPrvvTTASIRPSVYQPVPASPYSP-----SPGANYSPTPYTPSP 373
Cdd:PHA03247  2795 RESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPP---TSAQPTAPPPPPGPPPPSLPlggsvAPGGDVRRRPPSRSP 2871

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  374 APAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTddsfSQKFAPGKSTTSVSKQT 453
Cdd:PHA03247  2872 AAKPAAPARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQ----PPPPPPPRPQPPLAPTT 2947

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1958687005  454 LPRGAPAYNPT--GPQVTPLARGTFQrAERFPASSRTP 489
Cdd:PHA03247  2948 DPAGAGEPSGAvpQPWLGALVPGRVA-VPRFRVPQPAP 2984

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: 3.93e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  71 PLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLT 124
Cdd:cd06675    29 PVFIAMIQPNGVAAQTGkLKVGDRIVSINGQSTDGLTHSEAVNLLKNASGTIILQ 83

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: 53.35 E-value: 4.08e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  330 APAPKPRVVTTASIRPSVYQPVPASPYSPSP---GANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTysPSPAPAYTPSP 405
Cdd:pfam15324  986 TPVPTPQPTPPCSPPSPLKEPSPVKTPDSSPcvsEHDFFPVKEIPPEKGADTgPAVSLVITPTVTPI--ATPPPAATPTP 1063

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  406 apnynPTPSAAYSGGPSESASRP-PWVTDD---------SFSQKFAPGKSTTSVSKQTLPRGA--PAYNPTGPQVTPLAR 473
Cdd:pfam15324 1064 -----PLSENSIDKLKSPSPELPkPWEDSDlpleeenpnSEQEELHPRAVVMSVARDEEPESVvlPASPPEPKPLAPPPL 1138

                          170
                   ....*....|....*.
gi 1958687005  474 GTfqraeRFPASSRTP 489
Cdd:pfam15324 1139 GA-----APPSPPQSP 1149

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: 47.06 E-value: 4.48e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09424     1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50

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: 5.32e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCER 540
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50

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: 6.02e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09349    34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCE 84

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: 46.52 E-value: 6.51e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLFS 606
Cdd:cd09431     1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 52.76 E-value: 7.33e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 340 TASIRPSVYQP----VPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSA 415
Cdd:PHA03378  654 PPQVEITPYKPtwtqIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAPPGRAQRPAAATGRARPPAAAPGR 733

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 416 AYSGGPSESASRPPWVTDDSFSQkfaPGKSTTSVSKQTLPRGAPAYNPTgPQVTPLARgtfQRAERFPASSRTP 489
Cdd:PHA03378  734 ARPPAAAPGRARPPAAAPGRARP---PAAAPGRARPPAAAPGAPTPQPP-PQAPPAPQ---QRPRGAPTPQPPP 800

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 52.54 E-value: 8.38e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 329 AAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPT------YTPSPAPTYSPSPAPAY 401
Cdd:PRK07003  379 AVPAPGARAAAAVGASAVPAVtAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATadrgddAADGDAPVPAKANARAS 458

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 402 TPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKqtlPRGAPAYNPTGPQVTPLARGTFQRAER 481
Cdd:PRK07003  459 ADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVP---DARAPAAASREDAPAAAAPPAPEARPP 535


                  ....*...
gi 1958687005 482 FPASSRTP 489
Cdd:PRK07003  536 TPAAAAPA 543

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 52.02 E-value: 9.48e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 248 VYQAVIKTQSKPED-EADEWARRSSNLQSRSFRILAQMT---GTEYMQDPDEEA------LR--RSRPQASAyspaaATS 315
Cdd:PRK14951  299 VLQAVPQAAAAATDpEAAEVARLAALMPADETQLLYSIClhgRAELGLAPDEYAaltmvlLRllAFKPAAAA-----EAA 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 316 PAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSP 395
Cdd:PRK14951  374 APAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAA-PPAPVAAPAAAAPAAAPAAAPAAVALAPAPP 452

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1958687005 396 SPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTD 433
Cdd:PRK14951  453 AQAAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTP 490

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: 9.94e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958687005  62 LQGGKDFNMPLT----ISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 129
Cdd:cd06765     4 LSGQKDSGISLEngvfISRIVPGSPAAkEGSLTVGDRIIAINGIALDNKSLSECEALLRSCRDSLSLSLMKVF 76

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: 46.02 E-value: 9.95e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 601
Cdd:cd09463     1 CTGCGGRIQdSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYE-KDGKLYCHKHY 52

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: 1.05e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09351     1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCE 51

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: 1.08e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCfVEEQNNVYCERCY 542
Cdd:cd09333     1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADA-RELKGELYCLRCH 51

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: 1.21e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  50 VTLT-GPGPWGFRLQGG----KDFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06681     5 VTLEkEGNSFGFVIRGGahedRNKSRPLTVTHVRPGGPADrEGTIKPGDRLLSVDGISLHGATHAEAMSILKQCGQEATL 84


                  .
gi 1958687005 124 T 124
Cdd:cd06681    85 L 85

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 51.70 E-value: 1.26e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 334 KPRVVTTASIRPSVYQpvPASPYSPSPGANYSPTP---YTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYN 410
Cdd:PRK14971  370 SGGRGPKQHIKPVFTQ--PAAAPQPSAAAAASPSPsqsSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAPQAV 447


                  ....*.
gi 1958687005 411 PTPSAA 416
Cdd:PRK14971  448 RPAQFK 453

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: 1.28e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  49 SVTL--TGPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06680     2 DITLrrSSSGSLGFSIVGGYEEshgNQPFFVKSIVPGTPAYNDgRLKCGDIILAVNGVSTVGMSHAALVPLLKEQRGRVT 81


                  ..
gi 1958687005 123 LT 124
Cdd:cd06680    82 LT 83

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: 46.02 E-value: 1.28e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 605 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09421     1 FANQCEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYC 54

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: 1.45e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  48 YSVTLT-GPGPWGFRLQGGKDFNMPLT---ISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06792     3 FEVELSkKDGSLGISVTGGINTSVRHGgiyVKSLVPGGAAEQDgRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVT 82


                  ....*
gi 1958687005 123 LTLQK 127
Cdd:cd06792    83 LVLER 87

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 50.24 E-value: 1.74e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 344 RPSVYQPVPASPYSPSPgANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTYSP--------SPAPAYTPS-----PAPNY 409
Cdd:PHA02682   75 RPSGQSPLAPSPACAAP-APACPACAPAAPAPAVTcPAPAPACPPATAPTCPPpavcpapaRPAPACPPStrqcpPAPPL 153

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1958687005 410 nPTPSAAYSGGPS---ESASRPPWVTDDSFSQKFAPGKS 445
Cdd:PHA02682  154 -PTPKPAPAAKPIflhNQLPPPDYPAASCPTIETAPAAS 191

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 51.48 E-value: 1.77e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  328 PAAPAPKPrVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPtyspsPAPAYTPSPAP 407
Cdd:PHA03247  2554 PLPPAAPP-AAPDRSVPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSP-----LPPDTHAPDPP 2627

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  408 NYNPTPSAAYSGGPSESASRPPWVTDDSfsqkFAPGKSTTSVSKQTLPRGAPAYNPTG---PQVTPLARGTFQRAERFPA 484
Cdd:PHA03247  2628 PPSPSPAANEPDPHPPPTVPPPERPRDD----PAPGRVSRPRRARRLGRAAQASSPPQrprRRAARPTVGSLTSLADPPP 2703


                   ....*
gi 1958687005  485 SSRTP 489
Cdd:PHA03247  2704 PPPTP 2708

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: 45.41 E-value: 1.92e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRGP----FLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09347     1 CAACTKPITGLggakFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

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: 51.07 E-value: 2.16e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 324 YSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTP 403
Cdd:pfam05109 421 FSKAPESTTTSPTLNTTGFAAPNTTTGLPSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTE 500

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 404 SPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKsTTSVSKQTLPRgAPAYNPTGPQVTPLARGT 475
Cdd:pfam05109 501 SKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGK-TSPTSAVTTPT-PNATSPTPAVTTPTPNAT 570

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: 45.06 E-value: 2.16e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFYskKDKPL-CKK 660
Cdd:cd09371     1 CAGCQRPIS--DRYLlRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLyCKQ 50

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: 45.20 E-value: 2.23e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 52

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: 2.31e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVC--FVEEQnnVYCE 539
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGyfFIEDE--LYCE 49

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: 45.12 E-value: 2.41e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 605 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09343     1 FANTCEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLC 54

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: 2.55e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09345     1 CKACGKAIMPGSkkMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

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: 44.98 E-value: 2.88e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09433     1 CAGCTNPISGlgGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILC 52

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: 2.92e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09432     1 CAACGKPITGiggtKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55

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: 44.84 E-value: 3.37e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 606 STKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09427     1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 50.10 E-value: 3.69e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 350 PVPASPYSPSPganysPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:PRK14951  373 AAPAEKKTPAR-----PEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVAL 447

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958687005 430 WVTDDSFSQKfAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARG 474
Cdd:PRK14951  448 APAPPAQAAP-ETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPT 491

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: 44.43 E-value: 3.72e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09410     1 CSGCGRPVK--ENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53

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: 3.74e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09361     1 CAHCNQVIR--GPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51

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: 4.30e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKI-MGEVMHAlRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09346     1 CAKCKKAItSGGVTYR-DQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

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: 4.39e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKI-MGEV-----MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09340     1 CEKCKEPInPGEVavfaeRAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

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: 4.44e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09407     1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

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: 4.47e-06

                          10        20
                  ....*....|....*....|....*....
gi 1958687005 630 WHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09346    20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48

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: 4.58e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 599
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

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: 4.65e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09409     1 CGGCARAIL--ENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53

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: 4.75e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09406     3 CASCQKPI-AG-QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55

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: 4.78e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005  54 GPGPWGFRLQGGKD----FnmpltISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd06768     8 GPEGYGFNLHAEKGrpghF-----IREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQVVEKIKASGNQVTLLV 78

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: 44.14 E-value: 4.86e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09446     1 CARCGYGVYPAEK-INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 49.81 E-value: 4.92e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 329 AAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPApn 408
Cdd:PRK14950  362 PVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHT---PESAPKLTRAAI-- 436

                          90
                  ....*....|....*...
gi 1958687005 409 ynPTPSAAYSGGPSESAS 426
Cdd:PRK14950  437 --PVDEKPKYTPPAPPKE 452

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: 43.96 E-value: 4.99e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 548 PICAKCNTKIMG-EVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09418     1 PRCSACDEIIFAdECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

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: 44.18 E-value: 5.13e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 550 CAKCNTKIMGEVMH----ALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEKDY 601
Cdd:cd09397     1 CRKCGLEIEGKSISskdgELSGQWHRECFVCTTCGCPFqFSVPCYVLDDKPYCQQHY 57

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: 5.46e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 491 CGHCNNVI-RGPFLVAMGRS-----WHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09414     1 CGGCSEPLkYGELAVTAPKFgesllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

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: 5.64e-06

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1958687005 504 VAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09401    15 TSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

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: 5.85e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 548 PICAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHMEDGePYCEKDY 601
Cdd:cd09467     2 PLCAGCNQHIVDRfILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDS-VYCKDDF 55

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 49.49 E-value: 5.91e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIrPSVYQPVPAS--------PYSPSPGANYSPTPYTPSPAPA---YTPSPAPTYTPSPAPTYSPS 396
Cdd:PRK12323  464 PAAAGPRPVAAAAAAA-PARAAPAAAPapadddppPWEELPPEFASPAPAQPDAAPAgwvAESIPDPATADPDDAFETLA 542

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1958687005 397 PAPAYTPSPAPNYNPTPSAAySGGPSESASRPPWVTD 433
Cdd:PRK12323  543 PAPAAAPAPRAAAATEPVVA-PRPPRASASGLPDMFD 578

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: 6.05e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09840     1 CSRCGDsVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

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: 44.13 E-value: 6.34e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 605 FSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09422     1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54

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: 48.74 E-value: 6.65e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 334 KPRVVTTASIRPSvyqPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPApTYTPSPAPTYSPSPAPAYTPSPAP 407
Cdd:TIGR00601  76 KPKTGTGKVAPPA---ATPTSAPTPTPSPPASPAS-GMSAAPASAVEEK-SPSEESATATAPESPSTSVPSSGS 144

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: 43.87 E-value: 7.09e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958687005 607 TKCHGCDFPVEagDKFIEALGHTWHDTCFICAVChvnleGQPF 649
Cdd:cd09328     2 TKCDSCQDFVE--GEVVSALGKTYHPKCFVCSVC-----RQPF 37

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: 7.21e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPF-YSKKDKPLCK 659
Cdd:cd09373     1 CTGCGEPIT--DRFLlKVSGRSWHVSCLRCCVCQTPLERQPScFTRDRQIYCK 51

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 48.96 E-value: 7.48e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPAPKPRVVTTASIRPSVyqpVPASPYSPSPGANYSPTPYT---PSPAPAYTPSPAPTYTPSPAPTY--SP 395
Cdd:PHA03269   32 HTSAATQKPDPAPAPHQAASRAPDPAV---APTSAASRKPDLAQAPTPAAsekFDPAPAPHQAASRAPDPAVAPQLaaAP 108

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1958687005 396 SPAPAYTPSPAPNYNPTPSAAysggPSESASRPP 429
Cdd:PHA03269  109 KPDAAEAFTSAAQAHEAPADA----GTSAASKKP 138

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: 43.58 E-value: 7.58e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09352     1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEE 52

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: 8.07e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  50 VTLT-GPGPWGFRLQGGKDfnMPLT-------ISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYN 120
Cdd:cd06709     3 ITLKrGPSGLGFNIVGGTD--QPYIpndsgiyVAKIKEdGAAAIDGRLQEGDKILEINGQSLENLTHQDAVELFRNAGED 80


                  ....*.
gi 1958687005 121 LSLTLQ 126
Cdd:cd06709    81 VKLKVQ 86

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: 8.45e-06

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005  59 GFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKS 116
Cdd:cd06759    15 GFSIVGGRDSprgPMGIYVKTIFPGGAAAEDgRLKEGDEILEVNGESLQGLTHQEAIQKFKQ 76

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: 8.56e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQpfYSKKDKPL-CKKH 661
Cdd:cd09364     1 CAGCRGKILDSQ-YVQALNQDWHCDCFRCSVCSDSLSNW--YFEKDGKLyCRKD 51

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: 43.60 E-value: 8.58e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09434     1 CAACNKPITGfgGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCR 53

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 49.21 E-value: 8.96e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 327 GPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTytpsPAPTYSPSPAPAYTPSPA 406
Cdd:PRK07764  637 AEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPA----GAAPAQPAPAPAATPPAG 712

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 407 PNYNPTPSAAysgGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERFPA 484
Cdd:PRK07764  713 QADDPAAQPP---QAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAE 787

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: 9.43e-06

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

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: 9.51e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 550 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSLFHMEDGEPYCEKDY 601
Cdd:cd09375     1 CAGCDQGISPNdlVRRARDKVFHLNCFTCMVCRKQLstGEELYILDENKFICKEDY 56

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 48.57 E-value: 9.52e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 331 PAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYT---PSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 407
Cdd:PHA03269   25 NIPIPELHTSAATQKPDPAPAPHQAASRAPDPAVAPTSAAsrkPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAVAPQL 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 408 NYNPTPSAAYSGGPSESASRPPWVTDDS-FSQKFAPGKSTTSVSKQTL 454
Cdd:PHA03269  105 AAAPKPDAAEAFTSAAQAHEAPADAGTSaASKKPDPAAHTQHSPPPFA 152

conjugal transfer pilus assembly protein TraB; Provisional

Pssm-ID: 184281 [Multi-domain] Cd Length: 475 Bit Score: 48.67 E-value: 9.69e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 329 AAPAPKPRVVTTASirpsvyQPVPASPySPSPGANYSPtpyTPSPAPAYTPSPAPTYTPSPAPTYspsPAPAYTPSPAPN 408
Cdd:PRK13729  119 QVKALGANPVTATG------EPVPQMP-ASPPGPEGEP---QPGNTPVSFPPQGSVAVPPPTAFY---PGNGVTPPPQVT 185

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1958687005 409 YNPTP------SAAYSGGPSESASRPPWVTDDSFS 437
Cdd:PRK13729  186 YQSVPvpnriqRKTFTYNEGKKGPSLPYIPSGSFA 220

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 49.17 E-value: 9.73e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  350 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAP----AYTPSPAPNYNPTPSAAYSGGPSESA 425
Cdd:PHA03247   389 RHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPATPLPSAepgsDDGPAPPPERQPPAPATEPAPDDPDD 468


                   ...
gi 1958687005  426 SRP 428
Cdd:PHA03247   469 ATR 471

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: 9.83e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCERCY 542
Cdd:cd09364     1 CAGCRGKILdSQYVQALNQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRKDY 52

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 48.57 E-value: 9.94e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 323 SYSEGPAAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPG-ANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPS--PA 398
Cdd:PHA03269   46 PHQAASRAPDPAVAPTSAASRKPDLAQaPTPAASEKFDPApAPHQAASRAPDPAVAPQLAAAPKPDAAEAFTSAAQahEA 125

                          90
                  ....*....|....*..
gi 1958687005 399 PAYTPSPAPNYNPTPSA 415
Cdd:PHA03269  126 PADAGTSAASKKPDPAA 142

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: 1.01e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 489 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 539
Cdd:cd09467     2 PLCAGCNQHIVDRFILkVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

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: 43.10 E-value: 1.03e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 550 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFG--NSLFhMEDGEPYCEKDY 601
Cdd:cd09369     1 CAGCGEKIQDRfYLLAVDRQWHASCLKCCECRLPLDseLSCF-SRDGNIYCKEDY 54

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: 1.06e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 491 CGHCNNVI----RGPFLVAM-GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09348     5 CSGCQNPItgfgKGTNVVNYeGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60

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: 1.14e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNV-YCERCYEQFFAP 548
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQpHCVNDYHRRYAP 59

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 48.93 E-value: 1.17e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  328 PAAPAPKPRVVTTASIRPSV-YQPVPAsPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY-TPSP 405
Cdd:PRK10263   339 PVTQTPPVASVDVPPAQPTVaWQPVPG-PQTGEPVIAPAPEGYPQQSQYAQPAVQYNEPLQQPVQPQQPYYAPAAeQPAQ 417

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  406 APNYNPTPSAA-----YSGGPSESASRPPWVTDDSFS-----QKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTP 470
Cdd:PRK10263   418 QPYYAPAPEQPaqqpyYAPAPEQPVAGNAWQAEEQQStfapqSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEP 492

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: 1.34e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 649
Cdd:cd09353     1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLEGESF 39

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: 1.44e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 548 PICAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09341     1 PRCAACDELIfSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

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: 1.56e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09425     1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50

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: 1.59e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  36 PEEATAVGTSMSYSVTLTGpgpwgFRLQGGKDFnmpLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 115
Cdd:COG0793    45 PEEYEDFQESTSGEFGGLG-----AELGEEDGK---VVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDDAVKLLR 116

                          90       100
                  ....*....|....*....|....*
gi 1958687005 116 SAS-YNLSLTLQK--SKRPIPISTT 137
Cdd:COG0793   117 GKAgTKVTLTIKRpgEGEPITVTLT 141

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: 1.83e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 601
Cdd:cd09468     1 CAGCNQHILDKfILKVLDRHWHSSCLKCADCQMQLAERCFS-RAGNVYCKEDF 52

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: 1.93e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005  57 PWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06687    12 TLGLTVSGGIDKDGKPRVSNLRPGGIAARSdQLNVGDYIKSVNGIRTTKLRHDEIISLLKNVGERVVL 79

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: 42.21 E-value: 2.09e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCD---FpveaGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09341     3 CAACDeliF----SGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYC 51

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: 2.09e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  59 GFRLQGGKDF-NMPLT-ISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNlsltlqKSKRPIPI 134
Cdd:cd06751    14 GISISGGIESkVQPVVkIEKIFPGGAAALSGnLKAGYELVSVDGESLQQVTHQQAVDIIRRAYSN------KSKEPMEI 86

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: 2.11e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICA--ACKKPFGNSLFHMEDGEPYCE 598
Cdd:cd09455     1 CESCNQQIRGPFITALGKIWCPDHFICAnaSCRRPLQDIGFVEEKGQLYCE 51

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: 2.32e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09432     1 CAACGKPITGigGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52

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: 2.34e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 598
Cdd:cd09450     1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49

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: 2.48e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  50 VTLT-GPGPWGFRLQGGKDfNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06795     5 IVLHkGSTGLGFNIVGGED-GEGIFISFILAGGPADLSgELRRGDQILSVNGVDLRNATHEQAAAALKNAGQTVTIIAQ 82

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: 41.96 E-value: 2.53e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFG-NSLFHMEDGEPYCEKDY 601
Cdd:cd09392     1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGpNDSYYEHEGKIYCHYHY 53

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: 2.56e-05

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958687005 627 GHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09430    17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

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: 2.58e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 538 CERCYEQFFAPicakcnTKIMGEvmhalRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09482     1 CPRCGKSVYAA------EKVMGG-----GKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

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: 2.64e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 550 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF-GNSLFHMEDGEPYCEKDY 601
Cdd:cd09377     5 CARCHLGISASelVMRARDLVFHLNCFTCATCNKPLtKGDHFGMRDGLVYCRLHY 59

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: 2.64e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 550 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09326     1 CPRCGKSVyAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYC 49

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: 42.23 E-value: 2.66e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 490 LCGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSL--ADVCFVEEQNNVYCERCY 542
Cdd:cd09465     5 LCHGCSLLMTGPAMVAGEYKYHPECFACMSCKVIIedGDTYALVQHTTLYCGKCH 59

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: 2.85e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09337     1 CAYCNGPIL--DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCRE 50

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: 2.96e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09426     1 CSECKKTIMpgTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

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: 2.99e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

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: 3.07e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 489 PLCGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 543
Cdd:cd09418     1 PRCSACDEIIFADECTeAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56

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: 3.18e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09350     1 CGRCGENVVGEGtgCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

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: 41.69 E-value: 3.72e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

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: 3.73e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  55 PGPWGFRLQGGKDfNMP-------LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06704     9 TGGLGISIAGGKG-STPykgddegIFISRVTEGGPAAKAGVRVGDKLLEVNGVDLVDADHHEAVEALKNSGNTVTMVVLR 87

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: 3.80e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09840     1 CSRCGDSVyAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

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: 3.82e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  56 GPWGFRLQGGKD-----F--NMP-LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06702    10 GPLGLSIVGGSDhsshpFgvDEPgIFISKVIPDGAAAKSGLRIGDRILSVNGKDLRHATHQEAVSALLSPGQEIKLLVRH 89

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: 3.91e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 609 CHGCDFPVEAGDkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKP 656
Cdd:cd09396     1 CAGCKSEIGHGR-FLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47

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: 3.92e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWH--DTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09342     1 CDACGEPIGPDVQRVAHNGQHWHatEECFCCSNCKKSLLGQPFLPKNGQIFC 52

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 46.90 E-value: 3.94e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 280 ILAQMTGT----EYMQDPDEEALRRSRPQASAyspaAATSPAPAAHTSYSEGPAAPA-PKPRVVTTASIRPSVYQPVPAS 354
Cdd:PRK07764  573 ALAEELGGdwqvEAVVGPAPGAAGGEGPPAPA----SSGPPEEAARPAAPAAPAAPAaPAPAGAAAAPAEASAAPAPGVA 648

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 355 PYSPSPGANYSPTPY-TPSPAPAYTPSPAPTyTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAySGGPSESASRPPWVTD 433
Cdd:PRK07764  649 APEHHPKHVAVPDASdGGDGWPAKAGGAAPA-APPPAPAPAAPAAPAGAAPAQPAPAPAATPP-AGQADDPAAQPPQAAQ 726

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 434 DSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTfQRAERFPASSRTP 489
Cdd:PRK07764  727 GASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPAPAA-APAAAPPPSPPSE 781

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: 3.94e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  48 YSVTLTGPGP---WGFRLqGGKDFnmpltISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06728     1 LKVTLTKSRKndeYGLRL-GSRIF-----VKEITPDSLAAKDgNLQEGDIILKINGTPVENLSLSEAKKLIEKSKDKLQL 74


                  ....
gi 1958687005 124 TLQK 127
Cdd:cd06728    75 VVLR 78

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: 3.94e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09430     1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48

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: 4.03e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 599
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCET 50

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: 41.48 E-value: 4.40e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09359     1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAH 52

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: 4.42e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48

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: 41.29 E-value: 4.43e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIRGPFLVAMGRS-WHPEEFNCAYCKTSLADVCFVEEQnNVYCERCY 542
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52

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: 4.54e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 598
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCH 49

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: 42.25 E-value: 5.55e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  48 YSVTLT-GPGPWGFRLQGGK------DFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06695     2 FEVKLTkGSSGLGFSFLGGEnnspedPFSGLVRIKKLFPGQPAAESgLIQEGDVILAVNGEPLKGLSYQEVLSLLRGAPP 81

                          90
                  ....*....|..
gi 1958687005 120 NLSLTLqksKRP 131
Cdd:cd06695    82 EVTLLL---CRP 90

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: 41.29 E-value: 5.62e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 608 KCHGCDFPVEA---GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09348     4 KCSGCQNPITGfgkGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57

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: 5.66e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  56 GPWGFRLQ----GGKDFN---MPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06713    14 ETFGFEIQtyglHHKNSNeveMCTYVCRVHEDSPAYLAGLTAGDVILSVNGVSVEGASHQEIVELIRSSGNTLRL 88

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: 41.23 E-value: 5.74e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09350     1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCE 51

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 46.38 E-value: 6.04e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 300 RSRPQASAYSPAAATSPAPAAHTSYSEGP-AAPAPK---PRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPyTPSPAP 375
Cdd:PRK07003  378 GAVPAPGARAAAAVGASAVPAVTAVTGAAgAALAPKaaaAAAATRAEAPPAAPAPPATADRGDDAADGDAPVP-AKANAR 456

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 376 AYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:PRK07003  457 ASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDA 510

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: 6.51e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKK 660
Cdd:cd09329     1 CAGCGQEIKNGQALL-ALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCER 50

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: 7.00e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09346     1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 46.47 E-value: 7.27e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  322 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPS-------PAPTYTPSPAPT-- 392
Cdd:PHA03247  2636 NEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSltsladpPPPPPTPEPAPHal 2715

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  393 -----YSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPwvtddsfsqkfaPGKSTTSVSKQTLPRGAPAYNP---- 463
Cdd:PHA03247  2716 vsatpLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARP------------ARPPTTAGPPAPAPPAAPAAGPprrl 2783

                          170
                   ....*....|..
gi 1958687005  464 TGPQVTPLARGT 475
Cdd:PHA03247  2784 TRPAVASLSESR 2795

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 46.21 E-value: 7.37e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 326 EGPAAPAPKPRVVTT---------ASIRPSVYQPVPASPYSPSPGANYSPTPY-TPSPAPAYTP-SPAPTYTPSPAPTYS 394
Cdd:PHA03378  708 AAPPGRAQRPAAATGrarppaaapGRARPPAAAPGRARPPAAAPGRARPPAAApGRARPPAAAPgAPTPQPPPQAPPAPQ 787

                          90
                  ....*....|....*....
gi 1958687005 395 PSPAPAYTPSPAPNYNPTP 413
Cdd:PHA03378  788 QRPRGAPTPQPPPQAGPTS 806

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: 7.46e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09426     1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50

ORF080 virion core protein; Provisional

Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 45.24 E-value: 7.61e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPrvvttASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTY-SPSPAPAYTPS-- 404
Cdd:PHA02682   93 PACPACAP-----AAPAPAVTCPAPAPACPPATAPTCPPPAVCPAPARPAPACPPSTRQCPPAPPLpTPKPAPAAKPIfl 167

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1958687005 405 ----PAPNYNPTPSAAYSGGPSESASRPPWVTD 433
Cdd:PHA02682  168 hnqlPPPDYPAASCPTIETAPAASPVLEPRIPD 200

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 44.83 E-value: 7.76e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 328 PAAPAPKPRVVTTASIRPSV--YQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSpAPTYSPSPAPAYTP 403
Cdd:PLN02983  142 PQPPPPAPVVMMQPPPPHAMppASPPAAQPAPSAPASSPPPTPASPPPAKAPKSSHPPLKSPM-AGTFYRSPAPGEPP 218

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: 7.89e-05

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 508 RSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09343    24 RHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

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: 40.66 E-value: 7.97e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegQPFYsKKDKPLCKKH 661
Cdd:cd09340     1 CEKCKEPINPGEVavFAERAGEdaCWHPGCFVCETCNellVDL--IYFY-HDGKIYCGRH 57

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: 40.38 E-value: 8.49e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 491 CGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLAdvcfvEE---QNNV-YCERCY 542
Cdd:cd09329     1 CAGCGQEIKnGQALLALDKQWHVWCFKCKECGKVLT-----GEymgKDGKpYCERDY 52

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: 8.81e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 491 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 539
Cdd:cd09468     1 CAGCNQHILDKFILkVLDRHWHSSCLKCADCQMQLAERCF-SRAGNVYCK 49

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: 8.98e-05

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09425    19 GQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

envelope glycoprotein I; Provisional

Pssm-ID: 223033 [Multi-domain] Cd Length: 401 Bit Score: 45.33 E-value: 9.52e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTasirpSVYQPV--PASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSP 405
Cdd:PHA03291  188 PALPLSAPRLGPA-----DVFVPAtpRPTPRTTASPETTPTPSTTTSPPSTTIPAPSTTIAAPQAGTTPEAEGTPAPPTP 262

                          90       100
                  ....*....|....*....|..
gi 1958687005 406 APNYNPTPSAaysgGPSESASR 427
Cdd:PHA03291  263 GGGEAPPANA----TPAPEASR 280

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: 40.41 E-value: 9.84e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLA-DVCFVEEQNNVYCERCYE 543
Cdd:cd09335     1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTlKSKFYEFDMKPVCKKCYD 54

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: 40.60 E-value: 1.05e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958687005 567 QTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09427    23 QTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

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: 1.19e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 546 FAPICAKCNTKIMGEVMHALRQTWHTTCFICAACKkpfgnslFHMEDGEPYCEKDYINLFSTKCH 610
Cdd:cd09465     2 FGELCHGCSLLMTGPAMVAGEYKYHPECFACMSCK-------VIIEDGDTYALVQHTTLYCGKCH 59

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: 39.94 E-value: 1.27e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 609 CHGCD---FPVEagdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09358     1 CAVCGktvYPME----RLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPH 52

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 45.55 E-value: 1.27e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  327 GPAAPAPKPRVVTTASIRPSVYQPV-PASPYSPSPGANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTYSPSPAPAYTPS 404
Cdd:PHA03307    74 GPGTEAPANESRSTPTWSLSTLAPAsPAREGSPTPPGPSSPDPPPPTPPPASPpPSPAPDLSEMLRPVGSPGPPPAASPP 153

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  405 PAPNyNPTPSAAYSGGPSESAsrPPWVTDDSFSQKFAPGKSTTSVSKQT--LPRGAPAYNPTGPQVTPLARGTFQRAERF 482
Cdd:PHA03307   154 AAGA-SPAAVASDAASSRQAA--LPLSSPEETARAPSSPPAEPPPSTPPaaASPRPPRRSSPISASASSPAPAPGRSAAD 230


                   ....
gi 1958687005  483 PASS 486
Cdd:PHA03307   231 DAGA 234

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: 1.28e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYCERCYEQFFAP 548
Cdd:cd09354     1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFtVDATNQIHCIEDFHKKFAP 59

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: 1.30e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09344    19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53

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: 1.36e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958687005  72 LTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIK 115
Cdd:cd06782    16 LVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMSLDEVVKLLR 59

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: 1.38e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVeAGdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 663
Cdd:cd09405     2 CGACKKPI-AG-QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 45.31 E-value: 1.43e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  322 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPA-PTYSPSPAPA 400
Cdd:PHA03247  2583 TSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAP-DPPPPSPSPAANEPDPHPPPTVPPPErPRDDPAPGRV 2661

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  401 YTPSPAPNYN-PTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGksttsvskqtlPRGAPAYNPTGPqVTPLARGTFQRA 479
Cdd:PHA03247  2662 SRPRRARRLGrAAQASSPPQRPRRRAARPTVGSLTSLADPPPPP-----------PTPEPAPHALVS-ATPLPPGPAAAR 2729

                          170
                   ....*....|
gi 1958687005  480 ERFPASSRTP 489
Cdd:PHA03247  2730 QASPALPAAP 2739

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: 1.44e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 491 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEQnNVYCERCYE 543
Cdd:cd09371     1 CAGCQRPISDRYLLrVNERSWHEECLQCSVCQQPLTTSCYFRDR-KLYCKQDYQ 53

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: 1.46e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEV--MHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 599
Cdd:cd09344     1 CAECRKPIGADSkeLHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52

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: 40.01 E-value: 1.50e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09331     1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCE 51

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: 40.04 E-value: 1.53e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLAD---VCFVeEQNNVYCERCY 542
Cdd:cd09365     1 CHGCSQIITGPVMVAGDHKFHPECFSCSSCKAFIGDgdsYALV-ERSKLYCGVCY 54

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: 40.10 E-value: 1.55e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 608 KCHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09400     4 PCASCGLPVFLAER-LLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

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: 39.97 E-value: 1.59e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09433     1 CAGCTNPISGlggtKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55

flagellar motor protein MotB; Reviewed

Pssm-ID: 183756 [Multi-domain] Cd Length: 421 Bit Score: 44.71 E-value: 1.59e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 350 PVPASPYSPSPGANYSPTPYTPS-PAPAYTPSPAPtyTPSPAPTYSPSPA-PAYTPSPAPNYNPTPSAAYSGGPSESASR 427
Cdd:PRK12799  300 PVAAVTPSSAVTQSSAITPSSAAiPSPAVIPSSVT--TQSATTTQASAVAlSSAGVLPSDVTLPGTVALPAAEPVNMQPQ 377

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 428 PPWVTDdsfSQKFAPGKSTTSVSKQT--LPrGAPAYNPTgpqVTPLAR 473
Cdd:PRK12799  378 PMSTTE---TQQSSTGNITSTANGPTtsLP-AAPASNIP---VSPTSR 418

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: 1.60e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  49 SVTLT-GPGPWGFRLQGGKDF---NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06676     1 TITLErGSDGLGFSIVGGFGSphgDLPIYVKTVFEKGAAAEDgRLKRGDQILAVNGESLEGVTHEEAVNILKKTKGTVTL 80


                  ..
gi 1958687005 124 TL 125
Cdd:cd06676    81 TV 82

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 44.06 E-value: 1.60e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 349 QPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPA--PNYNPTPSAAY-SGGPSEsa 425
Cdd:PLN02983  143 QPPPPAPVVMMQPPPPHAMP-PASPPAAQPAPSAPASSPPPTP---ASPPPAKAPKSShpPLKSPMAGTFYrSPAPGE-- 216


                  ....*.
gi 1958687005 426 srPPWV 431
Cdd:PLN02983  217 --PPFV 220

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: 41.24 E-value: 1.65e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 360 PGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 416
Cdd:pfam11914   5 PASAVSSISSYSSSVTTSYPSPITTSYPSPVSTSYSSPVPSSYPSPVHTSFPSPSIA 61

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: 1.74e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHME-DGEPYCEKDY 601
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDvENNIYCVKDY 53

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: 1.80e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09349    34 CGICGQPLSrtQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.93 E-value: 1.83e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  325 SEGPAAPAPKPRvvTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPA---------------YTPSPAPTYTPSP 389
Cdd:PHA03247  2608 PRGPAPPSPLPP--DTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPApgrvsrprrarrlgrAAQASSPPQRPRR 2685

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  390 ---APTYSP------SPAPAYTPSPAP----NYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPR 456
Cdd:PHA03247  2686 raaRPTVGSltsladPPPPPPTPEPAPhalvSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAG 2765

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1958687005  457 GAPAYNPTGPQVTPLARGTfqRAERFPASSRTP 489
Cdd:PHA03247  2766 PPAPAPPAAPAAGPPRRLT--RPAVASLSESRE 2796

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: 1.84e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFF 546
Cdd:cd09424    19 GNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

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: 1.91e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCN-TKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09447     1 CARCGkTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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: 1.92e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  348 YQPvPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASR 427
Cdd:PRK12270    36 YGP-GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVE 114


                   .
gi 1958687005  428 P 428
Cdd:PRK12270   115 D 115

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: 1.95e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1958687005 623 IEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09457    13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCE 49

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: 1.97e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 567 QTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09425    20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

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: 2.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDG-EPYCEKDY 601
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAnQPHCVNDY 53

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: 39.56 E-value: 2.08e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09359     1 CARCGKIVYpTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

cell division protein DamX; Validated

Pssm-ID: 236792 [Multi-domain] Cd Length: 328 Bit Score: 43.77 E-value: 2.11e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTT------ASIRPSVYQPVPASPYSPSPGanyspTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY 401
Cdd:PRK10905  142 TAKTQTAERPATTrparkqAVIEPKKPQATAKTEPKPVAQ-----TPKRTEPAAPVASTKAPAATSTPAPKETATTAPVQ 216

                          90
                  ....*....|....*....
gi 1958687005 402 TPSPAPNYNPTPSAAYSGG 420
Cdd:PRK10905  217 TASPAQTTATPAAGGKTAG 235

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: 2.16e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09401     1 CPKCGKPVYFAEK-KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 44.78 E-value: 2.18e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  322 TSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGAnySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY 401
Cdd:PHA03307    64 RFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREG--SPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRPV 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  402 TPSPAPNYNPTPSAAYSGGPSESASRPPWvtDDSFSQKFAPGKSTTSVSKQTLPRGAPAynPTGPQVTPLARGtfqRAER 481
Cdd:PHA03307   142 GSPGPPPAASPPAAGASPAAVASDAASSR--QAALPLSSPEETARAPSSPPAEPPPSTP--PAAASPRPPRRS---SPIS 214


                   ....*....
gi 1958687005  482 FPASSRTPL 490
Cdd:PHA03307   215 ASASSPAPA 223

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: 2.18e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 491 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCE 539
Cdd:cd09368     1 CGGCQEHILDRFiLKVLDRTWHAKCLKCNDCGAQLTDKCF-ARNGHVYCK 49

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

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 44.60 E-value: 2.24e-04

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  325 SEGPAAPA-PKPRVVTTASIRPS-VYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTP 387
Cdd:TIGR00927  374 STAPSTPAtPRVRAVLTTQVHHCvVVKPAPAVPTTPSPSLTTALFPEAPSPSPSALPPGQPDLHP 438

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: 2.53e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPL-CKK 660
Cdd:cd09376     1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLEtGDEFYLMEDDRLvCKK 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.54 E-value: 2.53e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  328 PAAPA--PKPRVVTTASIRPSVYQPVPASPYSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPtySPSPAPAYTPSP 405
Cdd:PHA03247  2875 PAAPArpPVRRLARPAVSRSTESFALPPDQPERPPQPQ-APPPPQPQPQPPPPPQPQPPPPPPPRP--QPPLAPTTDPAG 2951

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005  406 APNYNPTPSAAYSGG--PSESASrPPWVTDDSFSQKFAPGKSTTSVSKQTLPR 456
Cdd:PHA03247  2952 AGEPSGAVPQPWLGAlvPGRVAV-PRFRVPQPAPSREAPASSTPPLTGHSLSR 3003

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: 2.56e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLE-GQPFYSKKDKPLCKKH 661
Cdd:cd09379     1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLStGEEFALIEDRVLCKAH 54

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237871 [Multi-domain] Cd Length: 576 Bit Score: 43.96 E-value: 2.64e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 339 TTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPtyspsPAPAYTPSPAP 407
Cdd:PRK14965  381 APAPPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP-----PARSADPAAAA 444

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 43.97 E-value: 2.64e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 305 ASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPA-SPYSPSPGANYSPTPYTPSPAPAYTPSPAP 383
Cdd:COG3469    88 AATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSgASATSSAGSTTTTTTVSGTETATGGTTTTS 167

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1958687005 384 TYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:COG3469   168 TTTTTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLP 213

chromosomal replication initiator protein DnaA;

Pssm-ID: 237605 [Multi-domain] Cd Length: 617 Bit Score: 44.05 E-value: 2.85e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPganysptpyTPSPA-PAYTPSPAPTYTPSPAPTYSPSPAP 399
Cdd:PRK14086  101 HARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLP---------TARPAyPAYQQRPEPGAWPRAADDYGWQQQR 171

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 400 AYTPSPAPnynPTPSAAYSggPSESASRPPwvtddsfsqkFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLAR 473
Cdd:PRK14086  172 LGFPPRAP---YASPASYA--PEQERDREP----------YDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDRPE 230

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 44.54 E-value: 2.90e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  350 PVPASPYSPSPGANYSptpyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:PHA03247  2552 PPPLPPAAPPAAPDRS----VPPPRPAPRPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPP 2627

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  430 wvtddSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTfqRAERFPASSRTP 489
Cdd:PHA03247  2628 -----PPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRAR--RLGRAAQASSPP 2680

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: 39.07 E-value: 2.93e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 608 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09416     2 RCAGCDELIFS-NEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 52

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: 2.96e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958687005  59 GFRLQGGKDF-NMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06762    15 GFSLAGGSDLeNKSITVHRVFPSGLAAQEgTIQKGDRILSINGKSLKGVTHGDALSVLKQA 75

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: 2.96e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 550 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSLFHMEDGEPYCEKDY 601
Cdd:cd09376     1 CAGCDEGIPPTqvVRRAQDNVYHLECFACFMCKRQLetGDEFYLMEDDRLVCKKDY 56

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: 2.98e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPF 649
Cdd:cd09356     1 CSVCSKPIM--ERILRATGKAYHPHCFTCVVCHRSLDGIPF 39

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: 3.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09407     1 CYYCNGPIL--DKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRK 50

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: 3.13e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 611 GCDFPVEAG-------DKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKKH 661
Cdd:cd09462    16 GNVLPVCAScgqsiydGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKD 72

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: 3.15e-04

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  356 YSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:PRK12270    36 YGPGSTAA-PTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAP 108

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.82 E-value: 3.34e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 350 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTysPSPAPAYTPSP-APNYNPTPSAAYSGGPSESASRP 428
Cdd:PRK07764  392 GAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPA--PAPAPAPPSPAgNAPAGGAPSPPPAAAPSAQPAPA 469

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 429 PWVTDDSFSqkfAPGKSTTSVSKQTLPRGAPAynPTGPQVTPLARGTFQRA 479
Cdd:PRK07764  470 PAAAPEPTA---APAPAPPAAPAPAAAPAAPA--APAAPAGADDAATLRER 515

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: 3.39e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  58 WGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06740    15 LGFSIRGGAEHGVGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFEKVTHAEAVKILRVS 74

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: 3.46e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  49 SVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSaSYNLSLTL 125
Cdd:cd06741     5 NLVVEDGQSLGLMIRGGAEYGLGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFLDITHDEAVKILKS-SKHLIMTV 80

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: 3.61e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005  59 GFRLQGGK------DFNMPLTISRITPGSKAA-QSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQK 127
Cdd:cd06703    15 GFSIAGGKgstpfrDGDEGIFISRITEGGAADrDGKLQVGDRVLSINGVDVTEARHDQAVALLTSSSPTITLVVER 90

AIDA-I family autotransporter YfaL;

Pssm-ID: 182059 [Multi-domain] Cd Length: 1250 Bit Score: 43.89 E-value: 3.90e-04

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1958687005  367 TPYTPsPAPAYTPSPAPTytPSPAPTYSPSPAPAYTP 403
Cdd:PRK09752   919 TPPSP-PDPDPTPDPDPT--PDPDPTPDPEPTPAYQP 952

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: 4.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKI----MGEVMHALRQT--WHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09414     1 CGGCSEPLkygeLAVTAPKFGESllWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

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: 4.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09428     1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

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: 4.15e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 609 CHGCDFPVEAGDK--FIEALGHT--WHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09413     1 CYCCKQPMKEGDPavYAERAGYDklWHPACFVCSTCGELLVDMIYFWKNGKLYCGRH 57

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: 38.84 E-value: 4.17e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 489 PLCGhcNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09482     2 PRCG--KSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

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: 43.54 E-value: 4.24e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 366 PTP-YTPSPAPAYTPSPAPTYTPSPAPTYSPSP--APAYTPSPAP--NYNPTPSAAYSGGPSESASRP--PWVT------ 432
Cdd:pfam05616 326 PRPdLTPASAEAPHAQPLPEVSPAENPANNPDPdeNPGTRPNPEPdpDLNPDANPDTDGQPGTRPDSPavPDRPngrdgk 405

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 433 ------DDSFSQKFAPgkSTTSVSKQTLPRGAPAYNPTGPQVTplARGTFQRAERFPASSRTP 489
Cdd:pfam05616 406 dgkdgeDGGLLCDFFP--DILACDELGKPEDNMAEDINIPQET--DDKEFQKHGFFPDNAQCP 464

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: 4.62e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  50 VTLTGP--GPWGFRLQGGKDFNMPLT----ISRITPGSKAAQSQLSQ-GDLVVAIDGVNTDTMTHLEAQNKIKSASYNLS 122
Cdd:cd06686    10 VILRGDplKGFGIQLQGGVFATETLSspplISFIEPDSPAERCGVLQvGDRVLSINGIPTEDRTLEEANQLLRDSASKVT 89


                  ....
gi 1958687005 123 LTLQ 126
Cdd:cd06686    90 LEIE 93

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: 4.76e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09840     1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 43.62 E-value: 4.97e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  328 PAAPAPKPrvvttASIRPSVYQPV-----------PASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPS 396
Cdd:PHA03307   123 PASPPPSP-----APDLSEMLRPVgspgpppaaspPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPST 197

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  397 PAPAYTPSPAPNYNPTPSAAYSGGPS---ESASRPPWVTDDSFS----------QKFAPGKSTTSVSKQTLPRGAPAYNP 463
Cdd:PHA03307   198 PPAAASPRPPRRSSPISASASSPAPApgrSAADDAGASSSDSSSsessgcgwgpENECPLPRPAPITLPTRIWEASGWNG 277

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 1958687005  464 TGPQVTPLARGTFQRAERFPASSRTPLCGHCNNVIR 499
Cdd:PHA03307   278 PSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPR 313

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: 5.08e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958687005 619 GDKFIEALGHTWHDTCFICAVCHVNLEGQPF 649
Cdd:cd09355     9 MEMILQALGKSYHPGCFRCCVCNECLDGVPF 39

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: 5.17e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 609 CHGCDFPVEAGD------KFIEALGhtWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 661
Cdd:cd09414     1 CGGCSEPLKYGElavtapKFGESLL--WHPACFRCSTCEELLVDLTYCVHDDQIYCERH 57

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: 5.20e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  353 ASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAysgGPSESASRPPwvt 432
Cdd:PRK12270    34 ADYGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPA---APPAAAAAAA--- 107

                           90       100
                   ....*....|....*....|....*...
gi 1958687005  433 ddsfsqkfaPGKSTTSVSKQTLpRGAPA 460
Cdd:PRK12270   108 ---------PAAAAVEDEVTPL-RGAAA 125

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 1958687005 609 CHGC-DFPVeagDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09332     1 CGKCgEFVI---GRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHP 50

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: 5.32e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005  59 GFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEA 110
Cdd:cd06800    14 GISITGGKEHGVPILISEIHEGQPADRCgGLYVGDAILSVNGIDLRDAKHKEA 66

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: 5.32e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFhMEDGEPYCEKDYI 602
Cdd:cd09371     1 CAGCQRPISDRyLLRVNERSWHEECLQCSVCQQPLTTSCY-FRDRKLYCKQDYQ 53

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

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 41.00 E-value: 5.33e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958687005 366 PTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAytPSPA 406
Cdd:PRK05641   44 DLSAVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPA--PASA 82

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184927 [Multi-domain] Cd Length: 504 Bit Score: 42.90 E-value: 5.36e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPAS-PYSPSPGAnysptpyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAP 399
Cdd:PRK14963  343 GGAPSEGVAAVAPPAPAPADLTQRLNRLEKEVRSlRSAPTAAA-------TAAGAPLPDFDPRPRGPPAPEPARSAEAPP 415


                  ....*...
gi 1958687005 400 AYTPSPAP 407
Cdd:PRK14963  416 LVAPAAAP 423

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: 5.70e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005  59 GFRLQGGKDFNMPLTISRITPGSKAAQSQ-LSQGDLVVAIDGVNTDTMTH 107
Cdd:cd06733    14 GFRILGGTEEGSQVSIGAIVPGGAADLDGrLRTGDELLSVDGVNVVGASH 63

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: 5.70e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 608 KCHGCDFPVEAgDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09418     2 RCSACDEIIFA-DECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

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: 42.61 E-value: 5.72e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 340 TASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAP 407
Cdd:pfam07174  36 VAHADPEPAPPPPSTATAPPAPPPPPPAPAAPAPPPPPAAPNAPNAPPPPADPNAPPPPPADPNAPPP 103

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: 38.28 E-value: 5.91e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 489 PLCGHCNNVIR-GPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 543
Cdd:cd09417     1 DRSVQCDELIFsGEYTKAMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56

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: 5.92e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  69 NMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd06711    19 DSPVRVQAVDPGGPAEQAGLQQGDTVLQINGQPVERSKCVELAHAIRNCPSEIILLV 75

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184918 [Multi-domain] Cd Length: 620 Bit Score: 43.01 E-value: 6.01e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 351 VPASPYSPSPGANYSPTPytPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPS---PAPNYNPTPSAAYSGGPSESASR 427
Cdd:PRK14954  380 VAPSPAGSPDVKKKAPEP--DLPQPDRHPGPAKPEAPGARPAELPSPASAPTPEqqpPVARSAPLPPSPQASAPRNVASG 457

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1958687005 428 PPWVTDDSFSQKFApGKSTTSVSKQTL------PRGAPAYNPT 464
Cdd:PRK14954  458 KPGVDLGSWQGKFM-NFTRNGSRKQPVqasssdAAQTGVFEGV 499

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: 6.02e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIMGE--VMHALRQTWHTTCFICAACkkpfGNSL-----FHMEDGEPYCEKD 600
Cdd:cd09387     1 CSACGQSIPASelVMRAQGNVYHLKCFTCSTC----HNQLvpgdrFHYVNGSLFCEHD 54

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: 6.02e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  45 SMSYSVTLT--GpGPWGFRLQGGKDFNMPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNL 121
Cdd:cd06683     1 AIIYTVELKryG-GPLGITISGTEEPFDPIVISGLTEGGLAERTgAIHVGDRILAINGESLRGKPLSEAIHLLQNAGDTV 79


                  ....*.
gi 1958687005 122 SLTLQK 127
Cdd:cd06683    80 TLKISR 85

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: 6.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVeaGDK-FIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKK 660
Cdd:cd09384     1 CGGCQQNI--GDRyFLKAIDQYWHEDCLSCDLCGCRLGevGRRLYYKLGRKLCRR 53

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: 6.06e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRG----PFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERC 541
Cdd:cd09434     1 CAACNKPITGfgggKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.05 E-value: 6.18e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 291 QDPDEEALRRSRPQASAyspaaATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYT 370
Cdd:PRK07764  634 AAPAEASAAPAPGVAAP-----EHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAAT 708

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 371 PSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSE-------SASRPPWVTDDSFSQKFAP 442
Cdd:PRK07764  709 PPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPpapapaaAPAAAPPPSPPSEEEEMAE 787

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: 6.27e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  345 PSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTyTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSES 424
Cdd:PRK12270    39 GSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA-APAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEV 117

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: 6.53e-04

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005 627 GHTWH--DTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09420    21 GQHWHatEKCFCCAQCKKSLLGRPFLPKQGQIYCSR 56

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: 6.72e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09326     1 CPRCGKSVYAAEEVI-AAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

biotin carboxyl carrier protein of acetyl-CoA carboxylase

Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 42.13 E-value: 6.80e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 368 PYTPSPAPAYT---PSPAPTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAysggPSESASRPP 429
Cdd:PLN02983  142 PQPPPPAPVVMmqpPPPHAMPPASPPAAQPAPSAPASSPPPTP---ASPPPA----KAPKSSHPP 199

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: 38.01 E-value: 6.92e-04

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 630 WHDTCFICAVCHVNLEGQ-PFYSKKDKPLCKKHAH 663
Cdd:cd09397    24 WHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHYH 58

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: 7.28e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09429     1 CVKCNKPITSGG--VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

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: 38.07 E-value: 7.32e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09482     1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

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: 37.93 E-value: 8.11e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEAGdKFIEALGHTWHDTCFICAVCHVNLEGQpFYSKKDKPLCKKH 661
Cdd:cd09463     1 CTGCGGRIQDS-FHYRVVQEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKH 51

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: 8.33e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAGDkfIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09431     1 CVQCKKPITTGG--VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYC 48

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: 8.36e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 543
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

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: 37.94 E-value: 8.49e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 538 CERCYEQFFAPicakcnTKIMGEvmhalRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09403     1 CPRCGKSVYAA------EKIIGA-----GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

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: 8.56e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQFFA 547
Cdd:cd09331    19 GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 42.55 E-value: 9.07e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 344 RPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPA 406
Cdd:PRK07994  360 HPAAPLPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQL 422

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: 42.19 E-value: 9.08e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 365 SPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY---TPSPAPNYNPTPSAAYSGGPSE 423
Cdd:TIGR00601  81 TGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASAVeekSPSEESATATAPESPSTSVPSS 142

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: 37.71 E-value: 9.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEaGDkFIEALGHTWHDTCFICAVCHVNLEGQ-PFYSKKDKPLCKK 660
Cdd:cd09335     1 CYHCNQVIE-GD-VVSALNKTWCVDHFSCSFCDTKLTLKsKFYEFDMKPVCKK 51

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: 37.93 E-value: 9.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVI--RGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYE 543
Cdd:cd09421     5 CEECSKIIgiDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59

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: 42.51 E-value: 9.21e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 334 KPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAP---TYSPSPAPAYTP------- 403
Cdd:pfam08580 508 PSNTATSETPTPALRPPSRPQPPPPGNRPRWNASTNTNDLDVGHNFKPLTLTTPSPTPsrsSRSSSTLPPVSPlsrdksr 587

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 404 SPAPNYNPTPSAAY---SGGPSESAS---RPPWVTDDSFSqkfapgKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQ 477
Cdd:pfam08580 588 SPAPTCRSVSRASRrraSRKPTRIGSpnsRTSLLDEPPYP------KLTLSKGLPRTPRNRQSYAGTSPSRSVSVSSGLG 661


                  ....*....
gi 1958687005 478 RAERfPASS 486
Cdd:pfam08580 662 PQTR-PGTS 669

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: 9.43e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

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: 9.54e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  41 AVGTSMSYSVTLTGPGPwgfRLQGGkdfnmPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASY 119
Cdd:cd06682     6 PKRSGVGLGITISAPKN---RKPGD-----PLIISDVKKGSVAHRTgTLEPGDKLLAIDNIRLDNCSMEDAAQILQQAED 77


                  ....*...
gi 1958687005 120 NLSLTLQK 127
Cdd:cd06682    78 IVKLKIRK 85

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: 9.75e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 491 CGHCNN-VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09403     1 CPRCGKsVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53

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: 1.02e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKIM--GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09428     1 CFHCKKTIMpgSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50

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: 1.05e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  349 QPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRP 428
Cdd:PRK12270    40 STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVEDEVTP 119

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: 37.41 E-value: 1.05e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDKPLCK 659
Cdd:cd09367     1 CAGCDRPIL--DKFLlNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCR 49

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: 1.10e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005  50 VTLT-GPGPWGFRLQGGKDFNMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSL 123
Cdd:cd06697     6 ITLTcHPGQLGLKLTGGSDSKYQvIYVLEIVPGSAAAEEgSLQPLDIIHYINGVSTQGMTLEDAVRALEASLPTVVL 82

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 40.95 E-value: 1.13e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 356 YSPSPGANySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAY-SGGPSESASRPPwvTDD 434
Cdd:PRK04654  119 LSASAQVD-AAAGAEPGAGQAHTPVPAPAPVIAQAQPIAPAPHQTLVPAPHDTIVPAPHAAHlPSAPATPVSVAP--VDA 195

                          90
                  ....*....|....*...
gi 1958687005 435 SFSQKFAPGKSTTSVSKQ 452
Cdd:PRK04654  196 GTSASPTPSEPTKIQEKQ 213

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: 1.14e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVY-----CERCY 542
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPDTSeqvplCETDY 57

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: 1.17e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLAD---VCFVEeqNNVYCERC 541
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPgdrVTFNG--KECLCQKC 55

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: 40.93 E-value: 1.19e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIRPSVYQ-PVPASPYSPSPGANYSPTPYTPspapaYTPSPAPTYTPSPAPTYSPSpAPAYTPSPA 406
Cdd:pfam07117  17 CLGGGGNMAMARPMSLPLPPGQePEPPRPEEEEGQGGGGGTFPFP-----GSPEPEPGGGGSGPMPMSAS-APEPEPAKA 90

                          90       100
                  ....*....|....*....|..
gi 1958687005 407 PNYNPTPSAA---YSGGPSESA 425
Cdd:pfam07117  91 KPQRPAPAQGhghGGGGDSDSS 112

104 kDa microneme/rhoptry antigen; Provisional

Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 42.37 E-value: 1.19e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPApKPRVVTTASIRPSVYQP----VPASPYSPSpganySPTPYTPSPAPAYTPSPA-PTYTPSPAPTYSP 395
Cdd:PTZ00449  587 HPKDPEEPKKPK-RPRSAQRPTRPKSPKLPelldIPKSPKRPE-----SPKSPKRPPPPQRPSSPErPEGPKIIKSPKPP 660

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 396 SpapaytpSPAPNYNPTPSAAYSGGPSESASRP-----PWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVT 469
Cdd:PTZ00449  661 K-------SPKPPFDPKFKEKFYDDYLDAAAKSketktTVVLDESFESILKETLPETPGTPFTTPRPLPPKLPRDEEFP 732

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: 1.23e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 550 CAKCNTKI-MGEV-MHALRQ----TWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09483     1 CEQCGIKInGGEVaVFASRAgpgvCWHPSCFVCFTCNELLVDLIYFYQDGKIHC 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 42.23 E-value: 1.25e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  299 RRSRPQASAYSPAAATSPA--------PAAHTSYSEGPAAPAPKPRVVTTAS---------------------------- 342
Cdd:PHA03247  2605 RGDPRGPAPPSPLPPDTHApdppppspSPAANEPDPHPPPTVPPPERPRDDPapgrvsrprrarrlgraaqassppqrpr 2684

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  343 ---IRPSVYQ-------PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSP--APTYSPSPA----PAYTPSPA 406
Cdd:PHA03247  2685 rraARPTVGSltsladpPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPpaVPAGPATPGgparPARPPTTA 2764

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005  407 PNYNPTPSAAYSGGPSESASRPPwVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLA 472
Cdd:PHA03247  2765 GPPAPAPPAAPAAGPPRRLTRPA-VASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLP 2829

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: 1.26e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 366 PTPYTPSPAPAYTPSPAPTYTPSPAPtysPSPAPAYTPSPAPNYNPTPSAAYSGGPS 422
Cdd:TIGR01348 197 ATAPAPASAQPAAQSPAATQPEPAAA---PAAAKAQAPAPQQAGTQNPAKVDHAAPA 250

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: 37.06 E-value: 1.28e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGEVMHALRQT-WHTTCFICAACKKPFGNSLFhMEDGEPYCEKDY 601
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSlWHERCLQCASCKEPLETTCF-YRDKKLYCKEDY 52

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 41.97 E-value: 1.29e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 250 QAVIKTQSKPEDEADEWARRSSNLQSRSFRILAQMTgteymqdpdEEALRRSRpqasayspaaatspapaahTSYSEGPA 329
Cdd:PRK14959  300 EAALASLDLPEDEARQWLGWAKRFEPAHIHACWQMT---------LEGQRRVL-------------------TSLEPAMA 351

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 330 AP------APKPRVVTTASIRPSVYQPVPAS-PYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYT 402
Cdd:PRK14959  352 LEllllnlAMLPRLMPVESLRPSGGGASAPSgSAAEGPASGGAATIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPS 431

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 403 PS-PAPNYNPTPSAaySGGPSESASRPPWVTDdsfsqkfAPGK--STTSVSKQTLPRGAPA----YNPTGPQ 467
Cdd:PRK14959  432 PRvPWDDAPPAPPR--SGIPPRPAPRMPEASP-------VPGApdSVASASDAPPTLGDPSdtaeHTPSGPR 494

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.08 E-value: 1.31e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  329 AAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTyTPSPAPTYSPSPAPAYTPSPAPN 408
Cdd:PHA03307   254 ECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAP-SSPRASSSSSSSRESSSSSTSSS 332

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  409 YNPTPSAAYSGGPSesASRPPWVTDDSFSqkfAPGKSTtsvskqtlPRGAPAYNPTGPQVTPLARGTFQRAERFPASSRT 488
Cdd:PHA03307   333 SESSRGAAVSPGPS--PSRSPSPSRPPPP---ADPSSP--------RKRPRPSRAPSSPAASAGRPTRRRARAAVAGRAR 399


                   .
gi 1958687005  489 P 489
Cdd:PHA03307   400 R 400

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: 1.38e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09345    19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.08 E-value: 1.42e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  223 GSDFSGASPLASLPVKDLAVDSASPVYQAVIKTQSKPEDEADEWARRSSNLQSRSFRILAQMTGTEYMQDPDEEALRRSR 302
Cdd:PHA03307   190 PAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRI 269

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  303 PQASAYSPAAATSPAPAAHTSYSE-GPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSP 381
Cdd:PHA03307   270 WEASGWNGPSSRPGPASSSSSPRErSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSR 349

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  382 APTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAysgGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTlPRGAPAY 461
Cdd:PHA03307   350 SPSPSRPPPPADPSSPRKRPRPSRAP---SSPAAS---AGRPTRRRARAAVAGRARRRDATGRFPAGRPRPS-PLDAGAA 422

                          250
                   ....*....|
gi 1958687005  462 NPTGPQVTPL 471
Cdd:PHA03307   423 SGAFYARYPL 432

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 184923 [Multi-domain] Cd Length: 624 Bit Score: 41.97 E-value: 1.43e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 327 GPAAPAPKPRVVTTASIRP-SVYQPVPASPYSPSPGANYSPT-PYTPSPaPAYTPSPAPTYTPSPAPTYSPSPAPAYTPS 404
Cdd:PRK14959  392 GGAATIPTPGTQGPQGTAPaAGMTPSSAAPATPAPSAAPSPRvPWDDAP-PAPPRSGIPPRPAPRMPEASPVPGAPDSVA 470

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 405 PAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQ-KFAPGKSTTSVSKQTLPRGA 458
Cdd:PRK14959  471 SASDAPPTLGDPSDTAEHTPSGPRTWDGFLEFCQgRNGQGGRLATVLRQATPEHA 525

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: 1.46e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 550 CAKCNTKIMGEVMhaLR----QTWHTTCFICAACKKPFGNS--LFhMEDGEPYCEKDY 601
Cdd:cd09366     1 CVGCGGKIHDQYI--LRvapdLEWHAACLKCAECGQYLDETctCF-VRDGKTYCKRDY 55

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 41.72 E-value: 1.46e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 338 VTTASIRPsVYQPVPASPYSPSPGANY-SPTPYT-PSPAPAYTPSPAPTYT-PSPAPTYSPSPAPAYTPSPAPNYNPTPS 414
Cdd:PRK14950  355 VIEALLVP-VPAPQPAKPTAAAPSPVRpTPAPSTrPKAAAAANIPPKEPVReTATPPPVPPRPVAPPVPHTPESAPKLTR 433

                          90
                  ....*....|....*
gi 1958687005 415 AAYSGGPSESASRPP 429
Cdd:PRK14950  434 AAIPVDEKPKYTPPA 448

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 41.76 E-value: 1.46e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 303 PQASAYSPAAATSPAPAAHTSYSEGPAA-PAPKPRVVTTASIRPSVYQPVPASPySPSPGANYSPTPYTPSPAPAYTPSP 381
Cdd:PRK07003  417 AAAATRAEAPPAAPAPPATADRGDDAADgDAPVPAKANARASADSRCDERDAQP-PADSGSASAPASDAPPDAAFEPAPR 495

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 382 APTYTPSPAPTYSPSPAPAYTPS---PAPNYNPTPSAAysgGPSESASRPP 429
Cdd:PRK07003  496 AAAPSAATPAAVPDARAPAAASRedaPAAAAPPAPEAR---PPTPAAAAPA 543

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: 41.42 E-value: 1.47e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 370 TPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAyTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFS 437
Cdd:TIGR00601  82 GKVAPPAATPTSAPTPTPSPPASPASGMSAA-PASAVEEKSPSEESATATAPESPSTSVPSSGSDAAS 148

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: 1.52e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09409     1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 41.68 E-value: 1.58e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 327 GPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAP----AYTPSPAPTYTPSPAPTYSPSPAPAyt 402
Cdd:pfam03154 179 GAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPhtliQQTPTLHPQRLPSPHPPLQPMTQPP-- 256

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 403 PSPAPNYNPTPSAAYSG----GPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTP 470
Cdd:pfam03154 257 PPSQVSPQPLPQPSLHGqmppMPHSLQTGPSHMQHPVPPQPFPLTPQSSQSQVPPGPSPAAPGQSQQRIHTP 328

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: 41.83 E-value: 1.62e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSP-----SPAPAYT 402
Cdd:pfam05109 449 PSSTHVPTNLTAPASTGPTVSTADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPtpnatSPTPAVT 528

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 403 pSPAPN-YNPT-----PSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRgAPAYNPTGPQVTPLARGT 475
Cdd:pfam05109 529 -TPTPNaTSPTlgktsPTSAVTTPTPNATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPT-PNATSPTVGETSPQANTT 605

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: 37.04 E-value: 1.67e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09481     2 CGACEKTVYhAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

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: 1.70e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPFGNSLFHmEDGEPYCEKDY 601
Cdd:cd09367     1 CAGCDRPILDKfLLNVLDRAWHAKCVQCCDCKCPLTEKCFS-REGKLYCRNDF 52

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 41.49 E-value: 1.72e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 332 APKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNY 409
Cdd:PRK14948  363 AFISEIANASAPANPTPAPNPSPPPAPIQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLN 440

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: 1.72e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGdkFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09339     1 CAGCGKPITGR--CITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHP 50

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: 1.78e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 609 CHGCDFPVEAGDKFIEAlGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCK 659
Cdd:cd09403     1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

probable pectinesterase/pectinesterase inhibitor

Pssm-ID: 215130 [Multi-domain] Cd Length: 670 Bit Score: 41.61 E-value: 1.80e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 343 IRPSVYQPVPASPYSP-----SPGANYSpTPyTPSPAPAYTP----SPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTP 413
Cdd:PLN02217  544 IQGDAWIPGKGVPYIPglfagNPGSTNS-TP-TGSAASSNTTfssdSPSTVVAPSTSPPAGHLGSPPATPSKIVSPSTSP 621

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1958687005 414 SAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQT 453
Cdd:PLN02217  622 PASHLGSPSTTPSSPESSIKVASTETASPESSIKVASTES 661

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: 1.82e-03

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1958687005 569 WHTTCFICAACKKPFGNSLFHMEDGEPYCEKDYINLF 605
Cdd:cd09424    22 WHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

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

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.80 E-value: 1.85e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  326 EGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA 400
Cdd:PRK12270    40 STAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAA-PPKPAAAAAAAAAPAAPPAAAAAAAPAAAAV 113

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

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.80 E-value: 1.85e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  352 PASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTySPSPAPAYTPSPAPnynPTPSAAYSGGPSESASRPPWV 431
Cdd:PRK12270    38 PGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAA-APAAPPKPAAAAAA---AAAPAAPPAAAAAAAPAAAAV 113


                   ....
gi 1958687005  432 TDDS 435
Cdd:PRK12270   114 EDEV 117

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 41.40 E-value: 1.88e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 302 RPQASAYSPAAATSPAPAahtSYSEGPAAPAPKPRVVTTASIRPsvyqPVPASPYSPSPGANYSPTPYTPSPAPAYTPSP 381
Cdd:PRK12323  463 RPAAAGPRPVAAAAAAAP---ARAAPAAAPAPADDDPPPWEELP----PEFASPAPAQPDAAPAGWVAESIPDPATADPD 535

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1958687005 382 APTYTPSPAPTYSPSPAPAYTPSPAPNYNPtPSAAYSGGPSESASRPP 429
Cdd:PRK12323  536 DAFETLAPAPAAAPAPRAAAATEPVVAPRP-PRASASGLPDMFDGDWP 582

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: 1.91e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEAgdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09411     1 CSGCQKPITG--RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48

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: 36.81 E-value: 2.03e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 508 RSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09422    24 RHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 58

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: 2.07e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005  56 GPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMT 106
Cdd:cd10833    12 GSLGFSVRGGSEHGLGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENIT 62

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: 2.08e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  64 GGKDFNMPLTISRITP-GSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQ 126
Cdd:cd06679    22 GSRRGDLPIYVTNVQPdGCLGRDGRIKKGDVLLSINGISLTNLSHSEAVAVLKASAASSSIVLK 85

sec-independent translocase; Provisional

Pssm-ID: 135173 [Multi-domain] Cd Length: 214 Bit Score: 40.18 E-value: 2.17e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 329 AAPAPKPRVVTTASIRPSVYQPVPASPyspSPGANYSPTPyTPSPAP----AYTPSPAPTYTPSPAP--TYSPSPAPAYT 402
Cdd:PRK04654  105 ATPVATPLELAHADLSASAQVDAAAGA---EPGAGQAHTP-VPAPAPviaqAQPIAPAPHQTLVPAPhdTIVPAPHAAHL 180

                          90       100
                  ....*....|....*....|....*
gi 1958687005 403 PS-PAPNYNPTP-SAAYSGGPSESA 425
Cdd:PRK04654  181 PSaPATPVSVAPvDAGTSASPTPSE 205

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 2.20e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  291 QDPDEEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPK---PRVVTTASIRPSVYQPVPASPYSPSPGANYSPT 367
Cdd:PHA03307   798 RPGRLRRSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAaarPPPARSSESSKSKPAAAGGRARGKNGRRRPRPP 877

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958687005  368 PYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAY 417
Cdd:PHA03307   878 EPRARPGAAAPPKAAAAAPPAGAPAPRPRPAPRVKLGPMPPGGPDPRGGF 927

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: 2.23e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEKDY 601
Cdd:cd09480     2 CGACGRTVYhAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54

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: 2.30e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958687005 608 KCHGCDFPVEAGDKFIeALGHTWHDTCFICAVCHVNLE 645
Cdd:cd09404     1 KCPKCGKSVYAAEERL-AGGYKWHKMCFKCGMCNKLLD 37

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: 2.42e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  59 GFRLQGGKD---FNMPLTISRITPGSKA-AQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKSK 129
Cdd:cd23072    16 GFQIVGGEKsgrLDLGIFISSITPGGPAdLDGRLKPGDRLISVNDVSLEGLSHDAAVEILQNAPEDVTLVVSQPK 90

cytoskeleton protein RodZ;

Pssm-ID: 236776 [Multi-domain] Cd Length: 331 Bit Score: 40.39 E-value: 2.43e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 349 QPVP-------ASPYSPSPGANYSPTPyTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGP 421
Cdd:PRK10856  160 QSVPldtstttDPATTPAPAAPVDTTP-TNSQTPAVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLP 238


                  ....*
gi 1958687005 422 SESAS 426
Cdd:PRK10856  239 TDQAG 243

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: 36.61 E-value: 2.44e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 491 CGHCNN--VIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09350     1 CGRCGEnvVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

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

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 39.08 E-value: 2.50e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005 372 SPAPAYTPSPAPTytPSPAPTYSPSPAPAYTPSPAP 407
Cdd:PRK05641   46 SAVQEQVPTPAPA--PAPAVPSAPTPVAPAAPAPAP 79

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: 41.01 E-value: 2.50e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 341 ASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPA 398
Cdd:TIGR01348 193 GSTPATAPAPASAQPAAQSPAATQPEPAAAPAAAKAQAPAPQQAGTQNPAKVDHAAPA 250

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 41.29 E-value: 2.59e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIRPSVY----------QPVPASPYSP---------SPGANYSPTPYTPSPAPAYTPSPAPTYTP- 387
Cdd:pfam03154 391 PPPPALKPLSSLSTHHPPSAHppplqlmpqsQQLPPPPAQPpvltqsqslPPPAASHPPTSGLHQVPSQSPFPQHPFVPg 470

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1958687005 388 SPAPTYSPSPAPAYTPSPAPNYNPTPSAAYS-GGP---SESASRPP 429
Cdd:pfam03154 471 GPPPITPPSGPPTSTSSAMPGIQPPSSASVSsSGPvpaAVSCPLPP 516

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: 2.73e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADV--CFVEEQnnVYCER 540
Cdd:cd09448     1 CDKCGSGIVGVFVKIRDKPRHPECYVCTDCGTNLKQKghFFVEDQ--IYCEK 50

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 41.08 E-value: 2.77e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  355 PYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:PHA03247   376 KRASLPTRKRRSARHAATPFARGPGGDDQTRPAAPVPASVPTPAPTPVPASAPPPPATPLPSAEPGSDDGPAPPP 450

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 40.91 E-value: 2.82e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 357 SPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAytPSPAPNYNPTPSAAySGGPSESASRPPWVTddsf 436
Cdd:PRK14971  370 SGGRGPKQHIKPVFTQPAAAPQPSAAAAASPSPSQSSAAAQPSA--PQSATQPAGTPPTV-SVDPPAAVPVNPPST---- 442

                          90
                  ....*....|....*....
gi 1958687005 437 sqkfAPGKSTTSVSKQTLP 455
Cdd:PRK14971  443 ----APQAVRPAQFKEEKK 457

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: 2.93e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005  50 VTLTGP--GPWGFRLQGGKDFNmPLTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTL 125
Cdd:cd23060     2 IELEKPanGGLGFSLVGGEGGS-GIFVKSISPGGVADRDgRLQVGDRLLQVNGESVIGLSHSKAVNILRKAKGTVQLTV 79

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 40.74 E-value: 2.95e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 292 DPDEEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSP--GANYSPTPY 369
Cdd:PRK07764  664 DGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSpaADDPVPLPP 743

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 370 TPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGP 421
Cdd:PRK07764  744 EPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDD 795

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 40.84 E-value: 2.99e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  210 AIMDAIAGQAQAQGSDFSGASPLASLPVKDlavdsaSPVYQAVIKTQSKPEDEADE--WARRSSNLQSRSFRILAQMTGT 287
Cdd:PRK10263   321 AVAAAATTATQSWAAPVEPVTQTPPVASVD------VPPAQPTVAWQPVPGPQTGEpvIAPAPEGYPQQSQYAQPAVQYN 394

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  288 EYMQDP------DEEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPkprvvTTASIRPSVYQPVP-ASPYSPSP 360
Cdd:PRK10263   395 EPLQQPvqpqqpYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNA-----WQAEEQQSTFAPQStYQTEQTYQ 469

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  361 GANYSPTPYTPSPA----PAYTPSPAPTYT-PSPAPTY------------SPSPAPAYTPSPAPNYNPTPSAAySGGPSE 423
Cdd:PRK10263   470 QPAAQEPLYQQPQPveqqPVVEPEPVVEETkPARPPLYyfeeveekrareREQLAAWYQPIPEPVKEPEPIKS-SLKAPS 548

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958687005  424 SASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTG-----PQV 468
Cdd:PRK10263   549 VAAVPPVEAAAAVSPLASGVKKATLATGAAATVAAPVFSLANsggprPQV 598

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: 36.00 E-value: 3.23e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 491 CGHCNNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCF-VEEQNNVYC 538
Cdd:cd09356     1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFtVDATGQIHC 49

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: 3.36e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 550 CAKCNTKIMGE--VMHALRQTWHTTCFICAACKKPF--GNSlFHMEDGEPYCEKDY 601
Cdd:cd09378     1 CSGCLEKIAPSelVMRALENVYHLRCFCCCVCERQLqkGDE-FVLKEGQLLCKSDY 55

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: 38.57 E-value: 3.37e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 344 RPSVYQPVPASPYSPS------------PGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPnYNP 411
Cdd:pfam12868  49 RDYYEDPYSPSPYPPSpagpyasqgqyyPETNYFPPPPGSTPQPPVDPQPNAPPPPYNPADYPPPPGAAPPPQPYQ-YPP 127

                          90
                  ....*....|....*..
gi 1958687005 412 TPsaaysgGPSESASRP 428
Cdd:pfam12868 128 PP------GPDPYAPRP 138

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: 3.46e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 549 ICAKCNTKIMGEVMHALRQ-TWHTTCFICAACKKPFGNSLF-HMEDGEPYCEKDY 601
Cdd:cd09381     1 VCSSCGLEIVDKYLLKVNDlCWHVRCLSCSVCRTSLGRHTScYIKDKDIFCKLDY 55

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: 3.46e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 491 CGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLAD--VCFVEEqNNVYCERCY 542
Cdd:cd09369     1 CAGCGEKIQDRFyLLAVDRQWHASCLKCCECRLPLDSelSCFSRD-GNIYCKEDY 54

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: 3.57e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958687005 507 GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCYEQ 544
Cdd:cd09426    19 GNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56

flagellar motor protein MotB; Reviewed

Pssm-ID: 183756 [Multi-domain] Cd Length: 421 Bit Score: 40.47 E-value: 3.58e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 373 PAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPApnynPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQ 452
Cdd:PRK12799  300 PVAAVTPSSAVTQSSAITPSSAAIPSPAVIPSSV----TTQSATTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQ 375

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958687005 453 TLPRGAPAYNPTGP-QVTPLARGTFQRAERFPASSRTP 489
Cdd:PRK12799  376 PQPMSTTETQQSSTgNITSTANGPTTSLPAAPASNIPV 413

Chitinase [Carbohydrate transport and metabolism];

Pssm-ID: 442692 [Multi-domain] Cd Length: 534 Bit Score: 40.51 E-value: 3.62e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSP------APTYTPSPAPTYS 394
Cdd:COG3469    91 STSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTTTSGASATSSAGSTTTTTtvsgteTATGGTTTTSTTT 170

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1958687005 395 PSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQK 439
Cdd:COG3469   171 TTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGLPKH 215

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 40.52 E-value: 3.70e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 325 SEGPAAPAPKPRVVTT-ASIRPSVYQPVPASPYSPSPGAnysPTPYTPSPAPAYTPSPAPtytPSPAPTYSPSPAPAYTP 403
Cdd:pfam03154 143 STSPSIPSPQDNESDSdSSAQQQILQTQPPVLQAQSGAA---SPPSPPPPGTTQAATAGP---TPSAPSVPPQGSPATSQ 216

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 404 SPAPNYNP-TPSAAYSGGPSESASRPPwvTDDSFSQKFAPGKSTTSVSKQTLPRgAPAYNPTGPQVTPLARG 474
Cdd:pfam03154 217 PPNQTQSTaAPHTLIQQTPTLHPQRLP--SPHPPLQPMTQPPPPSQVSPQPLPQ-PSLHGQMPPMPHSLQTG 285

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: 3.71e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958687005 609 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLEGQ 647
Cdd:cd09369     1 CAGCGEKIQ--DRFyLLAVDRQWHASCLKCCECRLPLDSE 38

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: 3.72e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFySKKDKPLCK 659
Cdd:cd09467     4 CAGCNQHIV--DRFIlKVLDRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCK 52

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: 35.78 E-value: 3.83e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 491 CGHCNNVIRGPFL--VAMGRSWHPEEFNCAYCKTSLAD--VCFVEEqNNVYCERCY 542
Cdd:cd09366     1 CVGCGGKIHDQYIlrVAPDLEWHAACLKCAECGQYLDEtcTCFVRD-GKTYCKRDY 55

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: 38.22 E-value: 3.86e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 350 PVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTyTPSPAPTySPSPAPAYTPSPAPNYNPTPSAAYS 418
Cdd:COG3147     1 PAEEAAAAPAAAAAPAAPAAAAAPAPAAAAAAAAP-KPAAKPA-APKPAAAAAAAPAAKAAAPAGGGWV 67

flagellar biosynthesis protein FlhF;

Pssm-ID: 237182 [Multi-domain] Cd Length: 559 Bit Score: 40.36 E-value: 3.91e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 330 APAPKPrVVTTASIRPSVYQPVPASPYSPSPGANYSpTPYTPSPAPAYTPSPAPTytpsPAPTYSPSPAPAYTPSPAPNY 409
Cdd:PRK12727  124 APAAAP-VRAASIPSPAAQALAHAAAVRTAPRQEHA-LSAVPEQLFADFLTTAPV----PRAPVQAPVVAAPAPVPAIAA 197

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958687005 410 NPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGP 466
Cdd:PRK12727  198 ALAAHAAYAQDDDEQLDDDGFDLDDALPQILPPAALPPIVVAPAAPAALAAVAAAAP 254

envelope glycoprotein C; Provisional

Pssm-ID: 165527 [Multi-domain] Cd Length: 566 Bit Score: 40.10 E-value: 4.10e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 293 PDEEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVyqpVPASPYSPSPGANYSPTPY-TP 371
Cdd:PHA03269   46 PHQAASRAPDPAVAPTSAASRKPDLAQAPTPAASEKFDPAPAPHQAASRAPDPAV---APQLAAAPKPDAAEAFTSAaQA 122

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1958687005 372 SPAPAYTPSPAPTYTPSPAPTYSPSPAP-AYTPS 404
Cdd:PHA03269  123 HEAPADAGTSAASKKPDPAAHTQHSPPPfAYTRS 156

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: 4.17e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005  73 TISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHL 108
Cdd:pfam17820   1 VVTAVVPGSPAERAGLRVGDVILAVNGKPVRSLEDV 36

EBNA-3A; Provisional

Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 40.43 E-value: 4.18e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVT---TASIRPSVYQPVPASPY-------------SPSPGANYSPTPYTPS------PAPAYTPSPAPTY 385
Cdd:PHA03379  418 PPVEKPRPEVPQsleTATSHGSAQVPEPPPVHdlepgplhdqhsmAPCPVAQLPPGPLQDLepgdqlPGVVQDGRPACAP 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 386 TPSPA-PTYSP-SPAPAYTPSPAP-NYNPTPSA-AYSGGPSESASRPpwvTDDSFSQKFAPGKSTTSVSKQTLPRGAPA- 460
Cdd:PHA03379  498 VPAPAgPIVRPwEASLSQVPGVAFaPVMPQPMPvEPVPVPTVALERP---VCPAPPLIAMQGPGETSGIVRVRERWRPAp 574

                         170       180       190
                  ....*....|....*....|....*....|
gi 1958687005 461 YNPTGPQ-VTP------LARGtfqRAERFP 483
Cdd:PHA03379  575 WTPNPPRsPSQmsvrdrLARL---RAEAQP 601

60S ribosomal protein L19-like protein; Provisional

Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 39.93 E-value: 4.27e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 295 EEALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPA 374
Cdd:PTZ00436  186 ERARREDAAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 265

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 375 PAYTPsPAPTYTPSPAPTYSPSPAPAytpspAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTL 454
Cdd:PTZ00436  266 KAAAP-PAKAAAPPAKAAAPPAKAAA-----PPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAA 339

                         170
                  ....*....|...
gi 1958687005 455 PRGAPAYNPTGPQ 467
Cdd:PTZ00436  340 PPAKAAAAPVGKK 352

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: 4.27e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 489 PLCGHCNNVI-RGPFLVAMGRSWHPEEFNCAYCKTSLADVcFVEEQNNVYCERCY 542
Cdd:cd09462    20 PVCASCGQSIyDGQYLQALNSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73

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

Pssm-ID: 235540 [Multi-domain] Cd Length: 153 Bit Score: 38.30 E-value: 4.28e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1958687005 365 SPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA 400
Cdd:PRK05641   47 AVQEQVPTPAPAPAPAVPSAPTPVAPAAPAPAPASA 82

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: 4.48e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 550 CAKCNTKIMGEVMHALRQT-WHTTCFICAACKKPFG-NSLF-HMEDGEPYC 597
Cdd:cd09394     1 CVGCKESITEGHAYELGGDrWHIHCFKCYKCDKKLScDSNFlVLGDGSLIC 51

Cornifin (SPRR) family; SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteriztic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high.

Pssm-ID: 280537 [Multi-domain] Cd Length: 135 Bit Score: 38.11 E-value: 4.48e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 350 PVPASPYSPSPGANYSPTPYTPS-PAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASR- 427
Cdd:pfam02389  38 PEPCCPKVPEPCCPKVPEPCCPKvPEPCCPKVPEPCYPKVPEPCSPKVPEPCHPKAPEPCHPKVPEPCYPKAPEPCQPKv 117

                          90
                  ....*....|....*.
gi 1958687005 428 ----PPWVTDDSFSQK 439
Cdd:pfam02389 118 pepcPSTVTPGPAQQK 133

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237871 [Multi-domain] Cd Length: 576 Bit Score: 40.11 E-value: 4.49e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 358 PSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAYSGGPS 422
Cdd:PRK14965  384 PPSAAWGAPTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAP---PARSADPAAAAS 445

Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning];

Pssm-ID: 442497 [Multi-domain] Cd Length: 455 Bit Score: 39.83 E-value: 4.59e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 225 DFSGASPLASLPVKDLAVDSASPVYQAVIKTQSKPEDEADEWARRSSNLQSRSFRILAQMTGTEYMQDPDEEALRRSRPQ 304
Cdd:COG3266   162 LLLLALQDIQGTLQALGAVAALLGLRKAEEALALRAGSAAADALALLLLLLASALGEAVAAAAELAALALLAAGAAEVLT 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 305 ASAYSPAAATSPAPAahtSYSEGPAAPAPKPrVVTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPT 384
Cdd:COG3266   242 ARLVLLLLIIGSALK---APSQASSASAPAT-TSLGEQQEVSLPPAVAAQPAAAAAAQPSAVALPAAPAAAAAAAAPAEA 317

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 385 YTPSPAP--------TYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:COG3266   318 AAPQPTAakpvvtetAAPAAPAPEAAAAAAAPAAPAVAKKLAADEQWLASQPA 370

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: 4.59e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958687005 616 VEAGDKFIealghtwHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHA 662
Cdd:cd09360    13 VKARDKNR-------HPECFVCADCGLNLKNKGYFFIEDELYCETHA 52

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: 35.91 E-value: 4.69e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 489 PLCGHCNNVIRGPF-LVAMGRSWHPEEFNCAYCKTSLADVCFvEEQNNVYCErcyEQFF 546
Cdd:cd09466     2 PKCAGCDHPIFDRFiLKVQDKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCK---EDFF 56

EBNA-3A; Provisional

Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 40.43 E-value: 4.71e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 334 KPRVVTTASIRPSVYQPVPASPYSPSPganysptpyTPSPAPAYTPSPAPTYTPSPAPTYSPSpapAYTPSPAPNYNPTP 413
Cdd:PHA03379  407 KASEPTYGTPRPPVEKPRPEVPQSLET---------ATSHGSAQVPEPPPVHDLEPGPLHDQH---SMAPCPVAQLPPGP 474

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 414 SaaysggpsesasrppwvtddsfsQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERFPASSR 487
Cdd:PHA03379  475 L-----------------------QDLEPGDQLPGVVQDGRPACAPVPAPAGPIVRPWEASLSQVPGVAFAPVM 525

cell division protein DedD; Provisional

Pssm-ID: 236940 [Multi-domain] Cd Length: 226 Bit Score: 39.22 E-value: 4.95e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 345 PSVYQPVPASP--------YSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 416
Cdd:PRK11633   57 PAATQALPTQPpegaaeavRAGDAAAPSLDPATVAPPNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPKPEPK 136

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 4.96e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  336 RVVTTASIRPSVyqPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAP----------TYSPSPAPAYTPSP 405
Cdd:PHA03247   241 RVVISHPLRGDI--AAPAPPPVVGEGADRAPETARGATGPPPPPEAAAPNGAAAPPdgvwgaalagAPLALPAPPDPPPP 318

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  406 APNYN-----------------PTPSAAYSGGPSESaSRPPW-----VTDDSFSQKFAPGKSTTSVSKQTLPRGApaynp 463
Cdd:PHA03247   319 APAGDaeeeddedgamevvsplPRPRQHYPLGFPKR-RRPTWtppssLEDLSAGRHHPKRASLPTRKRRSARHAA----- 392

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1958687005  464 tgpqvTPLARGT-----FQRAERFPASSRTP 489
Cdd:PHA03247   393 -----TPFARGPggddqTRPAAPVPASVPTP 418

cytoskeleton protein RodZ;

Pssm-ID: 236776 [Multi-domain] Cd Length: 331 Bit Score: 39.62 E-value: 4.99e-03

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 339 TTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYT-PSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAA 416
Cdd:PRK10856  171 DPATTPAPAAPVDTTPTNSQTPAVATAPAPAVDPQQNAVVaPSQANVDTAATPAPAAPATPDGAAPLPTDQAGVSTPAA 249

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: 39.52 E-value: 5.01e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 366 PTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPP 429
Cdd:pfam07174  32 ALPAVAHADPEPAPPPPSTATAPPAPPPPPPAPAAPAPPPPPAAPNAPNAPPPPADPNAPPPPP 95

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: 35.66 E-value: 5.05e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKIM-GEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 598
Cdd:cd09446     1 CARCGYGVYpAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50

septation protein SepH; Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments.

Pssm-ID: 468676 [Multi-domain] Cd Length: 346 Bit Score: 39.75 E-value: 5.20e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVVTTASIR---PSVYQPVPASPYS---PSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAY 401
Cdd:NF040712  230 DSDPAEAGTPDDLASARrrrAGVEQPEDEPVGPgaaPAAEPDEATRDAGEPPAPGAAETPEAAEPPAPAPAAPAAPAAPE 309

                          90       100
                  ....*....|....*....|....*....
gi 1958687005 402 TPSPAPNYNPTPSAAysGGPSESASRPPW 430
Cdd:NF040712  310 AEEPARPEPPPAPKP--KRRRRRASVPSW 336

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: 5.22e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEAGDKfIEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKKH 661
Cdd:cd09439     1 CYFCKKRVYVMER-LSAEGLFFHRSCFKCSYCGTTLRlgAYAFDRDDGKFYCKPH 54

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: 5.32e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1958687005 550 CAKCNTKIMGEVMHALRQTWHTTCFICAACKKPF---------GNSLFHmedgePYCEK 599
Cdd:cd09330     1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMFgegeemylqGSEIWH-----PDCRQ 54

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: 5.37e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  59 GFRLQGGKDF----NMP-LTISRITPGSKAAQS-QLSQGDLVVAIDGVNTDTMTHLEAQNKIKSA 117
Cdd:cd06723    14 GFSIAGGTDNphigDDPsIYITKIIPGGAAAADgRLRVNDIILRVNDVDVRNVTHSVAVEALKEA 78

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: 5.40e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958687005 564 ALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCE 598
Cdd:cd09461    17 ALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51

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: 5.41e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958687005 609 CHGCDFPVEAGDK--FIEALGH--TWHDTCFICAVCH---VNLegqpFYSKKD-KPLCKKHaHA 664
Cdd:cd09415     1 CEQCGEQISGGDIavFASRAGPgaCWHPACFVCSTCKellVDL----IYFYQDgKVYCGRH-HA 59

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.

Pssm-ID: 467780 [Multi-domain] Cd Length: 424 Bit Score: 39.85 E-value: 5.57e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 322 TSYSEGPAAPA----PKPRVVTTASIRPSVYQP---------VPASPYS--PSPGANYSPTPYTPSPAPAYTPSPAPTYT 386
Cdd:cd23959   103 PDESLGPFRAArvpnPFSASSSTQRETHKTAQVappkaepqtAPVTPFGqlPMFGQHPPPAKPLPAAAAAQQSSASPGEV 182

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1958687005 387 PSP--APTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPS 422
Cdd:cd23959   183 ASPfaSGTVSASPFATATDTAPSSGAPDGFPAEASAPS 220

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: 5.83e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 550 CAKCNTKI--MGEVMhALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYC 597
Cdd:cd09445     1 CRSCGKPVykMEEII-AEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49

Spumavirus gag protein;

Pssm-ID: 460872 [Multi-domain] Cd Length: 614 Bit Score: 39.73 E-value: 6.06e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 283 QMTGTEYMQDPDEEALRR-----------SRPQASAYSPAAATSPAPAAHTSYSEGP---AAPAPKPRVVTTASIRPSVY 348
Cdd:pfam03276 156 QEIELLALREQEAEALRIglaeispgaqgGIPPGASFSGLPSLPAIGGIHLPAIPGIharAPPGNIARSLGDDIMPSLGD 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 349 QPVPASPYSPSPGANYSPTPYTPsPAPAYTPSP----------APTYTPSPAPTYSPSPAPAYTPSPAPnynPTPSAAYS 418
Cdd:pfam03276 236 AGMPQPRFAFHPGNPFAEAEGHP-FAEAEGERPrdiprapridAPSAPAIPAIQPIAPPMIPPIGAPIP---IPHGASIP 311

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958687005 419 GGPSESASR-PPWvtddsfsqkfapgksttsvskqtLPRGAPAYNPTGPQVTP 470
Cdd:pfam03276 312 GEHIRNPREePIR-----------------------LGREAPAIDGRFAPAID 341

capsid maturational protease; Provisional

Pssm-ID: 223061 [Multi-domain] Cd Length: 663 Bit Score: 39.60 E-value: 6.45e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 328 PAAPAPKPRVV----TTASIRP-SVYQPVPASPYSPSPgaNYSPTPYTPSPAPAYTPSPAPTYTPSPaptyspsPAPAYT 402
Cdd:PHA03369  359 VLAAAAKVAVIaapqTHTGPADrQRPQRPDGIPYSVPA--RSPMTAYPPVPQFCGDPGLVSPYNPQS-------PGTSYG 429

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958687005 403 PSPAPNYNPTPSAaysggpsesasrpPWVTDDSFSQKFAPGKSTTSVSKQ 452
Cdd:PHA03369  430 PEPVGPVPPQPTN-------------PYVMPISMANMVYPGHPQEHGHER 466

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: 6.46e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1958687005 609 CHGCDFPVEagDKFI-EALGHTWHDTCFICAVCHVNLEGQPFY 650
Cdd:cd09468     1 CAGCNQHIL--DKFIlKVLDRHWHSSCLKCADCQMQLAERCFS 41

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: 6.57e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1958687005  74 ISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQ 111
Cdd:COG0265   205 VARVEPGSPAAKAGLRPGDVILAVDGKPVTSARDLQRL 242

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 39.77 E-value: 6.66e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  325 SEGPAAPAPKPRVVTTASIRPSVYQPVPA-------------SPYSPSPGANYSPTPYTP--SPAPAYTPSPAPTYTPSP 389
Cdd:PHA03307   197 TPPAAASPRPPRRSSPISASASSPAPAPGrsaaddagasssdSSSSESSGCGWGPENECPlpRPAPITLPTRIWEASGWN 276

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  390 APTYSPSPAPAYTPSPAPNYNPTPSAAYSGGPSESASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVT 469
Cdd:PHA03307   277 GPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRSPSPSRP 356

                          170       180
                   ....*....|....*....|
gi 1958687005  470 PLARGTFQRAERFPASSRTP 489
Cdd:PHA03307   357 PPPADPSSPRKRPRPSRAPS 376

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: 35.33 E-value: 6.68e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958687005 550 CAKCNTKI-MGEVMHALRQTWHTTCFICAACKKPFGNSLFHMEDGEPYCEK 599
Cdd:cd09476     1 CPRCDKTVyFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 39.92 E-value: 6.68e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  297 ALRRSRPQASAYSPAAATSPAPAAHTSYSEGPAAPAPKPRVVTTASIRPSV-YQPVPASPYSPSPGANYSPTPYTPSPAP 375
Cdd:PHA03247  2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPpPPPRPQPPLAPTTDPAGAGEPSGAVPQP 2962

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005  376 ---AYTPSPAP---TYTPSPAPtysPSPAPAyTPSPAPNYNPTP---SAAYSGGPSESASRPP-------WVTDD 434
Cdd:PHA03247  2963 wlgALVPGRVAvprFRVPQPAP---SREAPA-SSTPPLTGHSLSrvsSWASSLALHEETDPPPvslkqtlWPPDD 3033

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

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 39.59 E-value: 6.87e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005  325 SEGPAAPAPKprvVTTASIRPSVYQPVPASPYSPSPGANYSPTP-----YTPSPAPAYTPSPAPTYTPSPAPTySPSPAP 399
Cdd:TIGR00927  351 LSRTSAPAVR---IASATFRGLEKNPSTAPSTPATPRVRAVLTTqvhhcVVVKPAPAVPTTPSPSLTTALFPE-APSPSP 426

                           90
                   ....*....|..
gi 1958687005  400 AYTPSPAPNYNP 411
Cdd:TIGR00927  427 SALPPGQPDLHP 438

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: 7.10e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958687005 491 CGHCNNVIRGPFLV-AMGRSWHPEEFNCAYCKTSLADVCFVEEqNNVYC 538
Cdd:cd09367     1 CAGCDRPILDKFLLnVLDRAWHAKCVQCCDCKCPLTEKCFSRE-GKLYC 48

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.

Pssm-ID: 465521 [Multi-domain] Cd Length: 506 Bit Score: 39.56 E-value: 7.14e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 321 HTSYSEGPAAPApkprvvTTASIRPSVYQPVPASPYSPSPGANYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPA 400
Cdd:pfam17823  90 HTPHGTDLSEPA------TREGAADGAASRALAAAASSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANASAAPRAAIA 163

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 401 YTPSPAPNYNPTPSAAYSGGPSES---ASRPPWVTDDSFSQKFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQ 477
Cdd:pfam17823 164 AASAPHAASPAPRTAASSTTAASSttaASSAPTTAASSAPATLTPARGISTAATATGHPAAGTALAAVGNSSPAAGTVTA 243

                         170       180       190
                  ....*....|....*....|....*....|
gi 1958687005 478 RAERFPASSRTPLCGHCNNVIRGPFLVAMG 507
Cdd:pfam17823 244 AVGTVTPAALATLAAAAGTVASAAGTINMG 273

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: 7.29e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 550 CAKCNTKIMGE-VMHALRQTWHTTCFICAACKKPF---GNSLFhMEDGEPYCEKDY 601
Cdd:cd09386     1 CAGCGGKIVDRfLLHALDRYWHNGCLKCSCCQAQLgeiGSSCY-TKGGMILCKNDY 55

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: 7.30e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958687005 609 CHGCDFPVEagDKF-IEALGHTWHDTCFICAVCHVNLE--GQPFYSKKDKPLCKK 660
Cdd:cd09388     1 CAGCNRKIK--DRYlLKALDQYWHEDCLKCACCDCRLGevGSTLYTKANLILCRR 53

PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification];

Pssm-ID: 444064 [Multi-domain] Cd Length: 548 Bit Score: 39.28 E-value: 7.59e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 325 SEGPAAPAPKPRVVTTASIRPSVYQPVPASPYSPSPGA--NYSPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYT 402
Cdd:COG5180   286 GSEPQSDAPEAETARPIDVKGVASAPPATRPVRPPGGArdPGTPRPGQPTERPAGVPEAASDAGQPPSAYPPAEEAVPGK 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 403 PSPApnynPTPSAAYSGGPSESasrppwvtddsfsqkFAPGKSTTSVSKQTLPRGAPAYNPTGPQVTPLARGTFQRAERF 482
Cdd:COG5180   366 PLEQ----GAPRPGSSGGDGAP---------------FQPPNGAPQPGLGRRGAPGPPMGAGDLVQAALDGGGRETASLG 426


                  ....
gi 1958687005 483 PASS 486
Cdd:COG5180   427 GAAG 430

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: 35.24 E-value: 7.74e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005 491 CGHCNNVIRGPFLV------AMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCER 540
Cdd:cd09841     1 CQQCGRQICGGDIAvfasraGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGR 56

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: 7.83e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAGDKFIEALGHTWHDT--CFICAVCHVNLEGQPFYSKKDKPLC 658
Cdd:cd09419     1 CQGCHNAIDPEVQRVSYNNFHWHAEpeCFLCSCCSKCLIGQKFMPVEGMVFC 52

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: 35.16 E-value: 8.11e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1958687005 609 CHGCDFPVEAgdKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 660
Cdd:cd09452     1 CAQCNKIIRG--RYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPK 50

cell division protein DedD; Provisional

Pssm-ID: 236940 [Multi-domain] Cd Length: 226 Bit Score: 38.45 E-value: 8.29e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 326 EGpAAPAPKPRVVTTASIRPSVYQPvpaspyspspganySPTPYTPSPAPAYTPSPAPTYTPSPAPTYSPSPAPAYTPSP 405
Cdd:PRK11633   69 EG-AAEAVRAGDAAAPSLDPATVAP--------------PNTPVEPEPAPVEPPKPKPVEKPKPKPKPQQKVEAPPAPKP 133


                  ..
gi 1958687005 406 AP 407
Cdd:PRK11633  134 EP 135

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: 34.88 E-value: 8.90e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958687005 491 CGHCNNVIRG--PFLVAM----GRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09340     1 CEKCKEPINPgeVAVFAErageDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

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 1958687005 491 CGHC-NNVIRGPFLVAMGRSWHPEEFNCAYCKTSLADVCFVEEQNNVYCERCY 542
Cdd:cd09481     2 CGACeKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.

Pssm-ID: 312941 [Multi-domain] Cd Length: 732 Bit Score: 39.22 E-value: 9.18e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958687005 345 PSVYQPVPASPYSPSPGANYSPTPYTPSPAPaytpspaPTYTPSPAPTYSPSPAPAYTPSPAPNYNPTPSA-----AYSG 419
Cdd:pfam09606 376 PSPVPGQQVRQVTPNQFMRQSPQPSVPSPQG-------PGSQPPQSHPGGMIPSPALIPSPSPQMSQQPAQqrtigQDSP 448


                  ...
gi 1958687005 420 GPS 422
Cdd:pfam09606 449 GGS 451

Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription];

Pssm-ID: 440513 [Multi-domain] Cd Length: 349 Bit Score: 38.91 E-value: 9.45e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1958687005  65 GKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHL 108
Cdd:COG0750   123 GVPVLTPPVVGEVVPGSPAAKAGLQPGDRIVAINGQPVTSWDDL 166

circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains; Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in 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 beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus.

Pssm-ID: 467638 [Multi-domain] Cd Length: 83 Bit Score: 35.63 E-value: 9.54e-03

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958687005  73 TISRITPGSKAAQSQLSQGDLVVAIDGVNTDT 104
Cdd:cd23081     2 VVGEVVANSPAAEAGLKPGDRILKIDGQKVRT 33

PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. 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 RGS12-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: 467194 [Multi-domain] Cd Length: 76 Bit Score: 35.30 E-value: 9.67e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958687005  54 GPGPWGFRLQGgkdfNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTH 107
Cdd:cd06710     8 GRAGYGFTISG----QAPCVLSCVVRGSPADVAGLKAGDQILAVNGINVSKASH 57

PDZ domain 1 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 1 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 PDZ1 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: 467213 [Multi-domain] Cd Length: 85 Bit Score: 35.65 E-value: 9.96e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958687005  47 SYSVTLT-GPGPWGFRLQGGKDFNMPLTISRITPGSKAAQ-SQLSQGDLVVAIDGVNTDTMTHLEA 110
Cdd:cd06731     1 LIRTSLKkSARGFGFTIIGGDEPDEFLQIKSVVPDGPAALdGKLRTGDVLVSVNDTCVLGYTHADV 66