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Conserved domains on  [gi|568988041|ref|XP_006519251|]
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LIM domain only protein 7 isoform X40 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CH_LMO7 cd21277
calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 ...
14-129 2.78e-74

calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 (LMO-7), also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. It contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


:

Pssm-ID: 409126 [Multi-domain]  Cd Length: 116  Bit Score: 242.05  E-value: 2.78e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277     1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568988041   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277    81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116
DUF4757 pfam15949
Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. ...
242-401 1.90e-57

Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with pfam00412. There are two completely conserved residues (W and L) that may be functionally important.


:

Pssm-ID: 464950  Cd Length: 170  Bit Score: 196.12  E-value: 1.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   242 MSYRRISAIEPKSALPFNRFLPNKSKQPSYVPAPLRKKRPDKHEDNRRSW-----ASPVYTETDGTFSRLFQKIYGENGS 316
Cdd:pfam15949    1 MLARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQRLFQKVSDDLGS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   317 KSMSDVSAEDV-QNLRQVRYEEMQKIKSQLKEQDQKWQDDLAKWKNRRKSYTSDLQKKKEEREEIEKQALEKS----DRS 391
Cdd:pfam15949   81 KSMSDIRCEEEaQPLSQVRYEELQKIRNQLKEEEDKWQDDLARWKSRRRSASQDLIKKEEERKKIEKLMSGEGgdsnRRK 160
                          170
                   ....*....|
gi 568988041   392 SKTFREMLQD 401
Cdd:pfam15949  161 SKTFKEMVEE 170
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
1323-1381 1.77e-11

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: 60.41  E-value: 1.77e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041 1323 CSYCNN-ILGKgaaMIIETLGLSYHLHCFKCVSCGCDLGGSSSGaevrIRNHQLYCNDCY 1381
Cdd:cd08368     1 CAGCGKpIEGR---ELLRALGKKWHPECFKCAECGKPLGGDSFY----EKDGKPYCEKCY 53
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
715-783 2.79e-09

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: 55.08  E-value: 2.79e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041    715 FGFTI---KWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKkwEEVMANAQETGNLVMDVRR 783
Cdd:smart00228   14 LGFSLvggKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHL--EAVDLLKKAGGKVTLTVLR 83
 
Name Accession Description Interval E-value
CH_LMO7 cd21277
calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 ...
14-129 2.78e-74

calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 (LMO-7), also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. It contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409126 [Multi-domain]  Cd Length: 116  Bit Score: 242.05  E-value: 2.78e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277     1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568988041   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277    81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116
DUF4757 pfam15949
Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. ...
242-401 1.90e-57

Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with pfam00412. There are two completely conserved residues (W and L) that may be functionally important.


Pssm-ID: 464950  Cd Length: 170  Bit Score: 196.12  E-value: 1.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   242 MSYRRISAIEPKSALPFNRFLPNKSKQPSYVPAPLRKKRPDKHEDNRRSW-----ASPVYTETDGTFSRLFQKIYGENGS 316
Cdd:pfam15949    1 MLARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQRLFQKVSDDLGS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   317 KSMSDVSAEDV-QNLRQVRYEEMQKIKSQLKEQDQKWQDDLAKWKNRRKSYTSDLQKKKEEREEIEKQALEKS----DRS 391
Cdd:pfam15949   81 KSMSDIRCEEEaQPLSQVRYEELQKIRNQLKEEEDKWQDDLARWKSRRRSASQDLIKKEEERKKIEKLMSGEGgdsnRRK 160
                          170
                   ....*....|
gi 568988041   392 SKTFREMLQD 401
Cdd:pfam15949  161 SKTFKEMVEE 170
CH smart00033
Calponin homology domain; Actin binding domains present in duplicate at the N-termini of ...
17-98 1.53e-13

Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.


Pssm-ID: 214479 [Multi-domain]  Cd Length: 101  Bit Score: 67.73  E-value: 1.53e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041     17 EAQRWVEAVTEKNFE--TTDFRASLENGVLLCDLINKLKPGVV--KKINRLSTPIAGLDNINVFLRACEQIGLKEaQLFH 92
Cdd:smart00033    2 TLLRWVNSLLAEYDKppVTNFSSDLKDGVALCALLNSLSPGLVdkKKVAASLSRFKKIENINLALSFAEKLGGKV-VLFE 80

                    ....*.
gi 568988041     93 PGDLQD 98
Cdd:smart00033   81 PEDLVE 86
CH pfam00307
Calponin homology (CH) domain; The CH domain is found in both cytoskeletal proteins and signal ...
20-130 2.49e-12

Calponin homology (CH) domain; The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin have only a single copy.


Pssm-ID: 425596 [Multi-domain]  Cd Length: 109  Bit Score: 64.62  E-value: 2.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041    20 RWVEAVTEKNFET---TDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQ-IGLKEAQLfhpgD 95
Cdd:pfam00307    9 RWINSHLAEYGPGvrvTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKLENINLALDVAEKkLGVPKVLI----E 84
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 568988041    96 LQDLsnrvtvkqeeTDRRLKNVLITLYWLGRKAQS 130
Cdd:pfam00307   85 PEDL----------VEGDNKSVLTYLASLFRRFQA 109
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
1323-1381 1.77e-11

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: 60.41  E-value: 1.77e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041 1323 CSYCNN-ILGKgaaMIIETLGLSYHLHCFKCVSCGCDLGGSSSGaevrIRNHQLYCNDCY 1381
Cdd:cd08368     1 CAGCGKpIEGR---ELLRALGKKWHPECFKCAECGKPLGGDSFY----EKDGKPYCEKCY 53
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
1322-1380 1.76e-09

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: 54.70  E-value: 1.76e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041   1322 VCSYCNNILGkGAAMIIETLGLSYHLHCFKCVSCGCDLGGSssgaEVRIRNHQLYCNDC 1380
Cdd:smart00132    1 KCAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPLSGD----TFFEKDGKLYCKDC 54
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
715-783 2.79e-09

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: 55.08  E-value: 2.79e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041    715 FGFTI---KWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKkwEEVMANAQETGNLVMDVRR 783
Cdd:smart00228   14 LGFSLvggKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHL--EAVDLLKKAGGKVTLTVLR 83
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
1323-1385 7.90e-08

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


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 50.02  E-value: 7.90e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568988041  1323 CSYCNN-ILGKGAAMIietLGLSYHLHCFKCVSCGCDLGGSSSgaevRIRNHQLYCNDCYLRFK 1385
Cdd:pfam00412    1 CAGCNRpIYDRELVRA---LGKVWHPECFRCAVCGKPLTTGDF----YEKDGKLYCKHDYYKLF 57
SCP1 COG5199
Calponin [Cytoskeleton];
17-139 5.02e-07

Calponin [Cytoskeleton];


Pssm-ID: 227526 [Multi-domain]  Cd Length: 178  Bit Score: 51.46  E-value: 5.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFETT-DFRASLENGVLLCDLINKLKPGVVKkINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:COG5199    17 EVTLWIETVLGEKFEPPgDLLSLLKDGVRLCRILNEASPLDIK-YKESKMPFVQMENISSFINGLKKLRVPEYELFQTND 95
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 568988041   96 LQDLSNrvtvkqeetdrrLKNVLITLYWLGRKAQSNPYYNGPYL 139
Cdd:COG5199    96 LFEAKD------------LRQVVICLYSLSRYAQKERMFSGPFL 127
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
708-786 5.50e-07

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 54.06  E-value: 5.50e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041  708 TPGNKPVFGFTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSykdTKKWEEVMANAQETGNLVMDVRRYGK 786
Cdd:COG3975   478 APSLKPSLGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVT---ADNLDDALAAYKPGDPIELLVFRRDE 553
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
715-757 1.22e-06

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 47.66  E-value: 1.22e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 568988041   715 FGFTIK----WDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFS 757
Cdd:pfam00595   12 LGFSLKggsdQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVE 58
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
715-754 2.12e-06

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: 46.77  E-value: 2.12e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 568988041  715 FGFTI---KWDISGIFVASVEQGSPAEFS-QLQVDDEILAINNT 754
Cdd:cd00136    12 LGFSIrggKDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGV 55
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
684-783 1.09e-04

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 46.45  E-value: 1.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   684 RGSPLREVSRSLDQFSDmrvsiNQTPGNKPVFGFT-------------IKWDISGIFVASVEQGSPAEFSQLQVDDEILA 750
Cdd:TIGR02037  314 RKGKEKTITVTLGASPE-----EQASSSNPFLGLTvanlspeirkelrLKGDVKGVVVTKVVSGSPAARAGLQPGDVILS 388
                           90       100       110
                   ....*....|....*....|....*....|...
gi 568988041   751 INNTkfSYKDTKKWEEVMANAQETGNLVMDVRR 783
Cdd:TIGR02037  389 VNQQ--PVSSVAELRKVLARAKKGGRVALLILR 419
 
Name Accession Description Interval E-value
CH_LMO7 cd21277
calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 ...
14-129 2.78e-74

calponin homology (CH) domain found in LIM domain only protein 7; LIM domain only protein 7 (LMO-7), also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. It contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409126 [Multi-domain]  Cd Length: 116  Bit Score: 242.05  E-value: 2.78e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277     1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568988041   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277    81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116
CH_LMO7-like cd21208
calponin homology (CH) domain found in LIM domain only protein 7 and similar proteins; This ...
14-129 2.18e-62

calponin homology (CH) domain found in LIM domain only protein 7 and similar proteins; This family includes LIM domain only protein 7 (LMO-7) and LIM and calponin homology domains-containing protein 1 (LIMCH1), and similar proteins. LMO-7, also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. LIMCH1 acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. Members of this family contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409057 [Multi-domain]  Cd Length: 119  Bit Score: 207.96  E-value: 2.18e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21208     1 ALKEARTWIEAVTGKKFPSDDFRESLEDGILLCELINAIKPGSIKKINRLPTPIAGLDNLNLFLKACEDLGLKDSQLFDP 80
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 568988041   94 GDLQDLSNRVT---VKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21208    81 TDLQDLSNRRIathVRKKEDERRLKNVAITLYWLGRAAR 119
DUF4757 pfam15949
Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. ...
242-401 1.90e-57

Domain of unknown function (DUF4757); This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with pfam00412. There are two completely conserved residues (W and L) that may be functionally important.


Pssm-ID: 464950  Cd Length: 170  Bit Score: 196.12  E-value: 1.90e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   242 MSYRRISAIEPKSALPFNRFLPNKSKQPSYVPAPLRKKRPDKHEDNRRSW-----ASPVYTETDGTFSRLFQKIYGENGS 316
Cdd:pfam15949    1 MLARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQRLFQKVSDDLGS 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   317 KSMSDVSAEDV-QNLRQVRYEEMQKIKSQLKEQDQKWQDDLAKWKNRRKSYTSDLQKKKEEREEIEKQALEKS----DRS 391
Cdd:pfam15949   81 KSMSDIRCEEEaQPLSQVRYEELQKIRNQLKEEEDKWQDDLARWKSRRRSASQDLIKKEEERKKIEKLMSGEGgdsnRRK 160
                          170
                   ....*....|
gi 568988041   392 SKTFREMLQD 401
Cdd:pfam15949  161 SKTFKEMVEE 170
CH_LIMCH1 cd21278
calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1; ...
14-130 1.35e-54

calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1; LIM and calponin homology domains-containing protein 1 (LIMCH1) acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. LIMCH1 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409127 [Multi-domain]  Cd Length: 118  Bit Score: 185.84  E-value: 1.35e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21278     1 AFTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDP 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 568988041   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQS 130
Cdd:cd21278    81 GDLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANS 117
CH_SF cd00014
calponin homology (CH) domain superfamily; CH domains are actin filament (F-actin) binding ...
16-126 1.88e-23

calponin homology (CH) domain superfamily; CH domains are actin filament (F-actin) binding motifs, which may be present as a single copy or in tandem repeats (which increase binding affinity). They either function as autonomous actin binding motifs or serve a regulatory function. CH domains are found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, as well as proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).


Pssm-ID: 409031 [Multi-domain]  Cd Length: 103  Bit Score: 96.25  E-value: 1.88e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNF--ETTDFRASLENGVLLCDLINKLKPGVVKKINRLS-TPIAGLDNINVFLRACEQIGLKEAQLFH 92
Cdd:cd00014     2 EELLKWINEVLGEELpvSITDLFESLRDGVLLCKLINKLSPGSIPKINKKPkSPFKKRENINLFLNACKKLGLPELDLFE 81
                          90       100       110
                  ....*....|....*....|....*....|....
gi 568988041   93 PGDLQDlsnrvtvkqeetDRRLKNVLITLYWLGR 126
Cdd:cd00014    82 PEDLYE------------KGNLKKVLGTLWALAL 103
CH_dMP20-like cd21207
calponin homology (CH) domain found in Drosophila melanogaster muscle-specific protein 20 ...
16-126 3.28e-23

calponin homology (CH) domain found in Drosophila melanogaster muscle-specific protein 20 (dMP20) and similar domains; This subfamily contains Drosophila melanogaster muscle-specific protein 20 (dMP20), Echinococcus granulosus myophilin, Dictyostelium discoideum Rac guanine nucleotide exchange factor B (also called Trix), and similar proteins. dMP20 is present only in the synchronous muscles of D. melanogaster. It may be involved in the system linking the nerve impulse with the contraction or the relaxation process. Trix is involved in the regulation of the late steps of the endocytic pathway. dMP20 contains a single copy of the CH domain, while Trix (triple CH-domain array exchange factor) contains three, two type 3 CH domains which are included in this model, and one type 1 CH domain that is not included in this subfamily, but is part of the superfamily. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409056 [Multi-domain]  Cd Length: 107  Bit Score: 95.45  E-value: 3.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFET-TDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPG 94
Cdd:cd21207     8 AEALDWIEAVTGEKLDDgKDYEDVLKDGVILCKLINILKPGSVKKINTSKMAFKLMENIENFLTACKGYGVPKTDLFQTV 87
                          90       100       110
                  ....*....|....*....|....*....|..
gi 568988041   95 DLQDLSNrvtvkqeetdrrLKNVLITLYWLGR 126
Cdd:cd21207    88 DLYEKKN------------IPQVTNCLFALGR 107
CH_SCP1-like cd21210
calponin homology (CH) domain found in Saccharomyces cerevisiae transgelin (SCP1) and similar ...
16-126 1.84e-17

calponin homology (CH) domain found in Saccharomyces cerevisiae transgelin (SCP1) and similar proteins; The family includes transgelins from Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are also called SCP1 and STG1, respectively. Transgelin, also called calponin homolog 1, has actin-binding and actin-bundling activity. It stabilizes actin filaments against disassembly. Transgelin contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409059 [Multi-domain]  Cd Length: 101  Bit Score: 78.95  E-value: 1.84e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21210     3 QEAREWIEEVLGEKLAQGDLLDALKDGVVLCKLANRILPADIRKYKESKMPFVQMENISAFLNAARKLGVPENDLFQTVD 82
                          90       100       110
                  ....*....|....*....|....*....|.
gi 568988041   96 LQDlsnrvtvkqeetDRRLKNVLITLYWLGR 126
Cdd:cd21210    83 LFE------------RKNPAQVLQCLHALSR 101
CH_CNN cd21211
calponin homology (CH) domain found in the calponin family; Calponin is an actin ...
16-106 6.24e-15

calponin homology (CH) domain found in the calponin family; Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and many types of non-muscle cells. There are three calponin isoforms, calponin-1, -2, -3. All of them are actin-binding proteins with functions in inhibiting actin-activated myosin ATPase and stabilizing the actin cytoskeleton. Calponin-1 is specifically expressed in smooth muscle cells and plays a role in fine-tuning smooth muscle contractility. Calponin-2 is expressed in both smooth muscle and non-muscle cells and regulates multiple actin cytoskeleton-based functions. Calponin-3 is expressed in the brain and participates in actin cytoskeleton-based activities in embryonic development and myogenesis. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409060 [Multi-domain]  Cd Length: 108  Bit Score: 71.96  E-value: 6.24e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21211     6 AELRTWIEGVTGLSI-GPNFQKGLKDGIILCELINKLQPGSVKKINESMQNWHQLENIGNFIKAIVSYGMKPHDIFEAND 84
                          90
                  ....*....|.
gi 568988041   96 LQDLSNRVTVK 106
Cdd:cd21211    85 LFENGNMTQVQ 95
CH_CNN2 cd21283
calponin homology (CH) domain found in calponin-2; Calponin-2 (CNN2), also called neutral ...
16-106 7.43e-15

calponin homology (CH) domain found in calponin-2; Calponin-2 (CNN2), also called neutral calponin, or smooth muscle calponin H2, is an actin cytoskeleton-associated regulatory protein that inhibits the activity of myosin-ATPase and cytoskeleton dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409132 [Multi-domain]  Cd Length: 109  Bit Score: 71.89  E-value: 7.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21283     6 AELRTWIEGLTGRSI-GPDFQKGLKDGVILCELMNKLQPGSVPKINRSMQNWHQLENLSNFIKAMVSYGMKPVDLFEAND 84
                          90
                  ....*....|.
gi 568988041   96 LQDLSNRVTVK 106
Cdd:cd21283    85 LFESGNMTQVQ 95
CH_CNN1 cd21282
calponin homology (CH) domain found in calponin-1 and similar proteins; Calponin-1 (CNN1), ...
16-106 2.90e-14

calponin homology (CH) domain found in calponin-1 and similar proteins; Calponin-1 (CNN1), also called basic calponin, or smooth muscle calponin H1, is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C, and tropomyosin. Calponin-1 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409131 [Multi-domain]  Cd Length: 108  Bit Score: 70.29  E-value: 2.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21282     6 EELRVWIEGVTGRRI-GDNFMDGLKDGVILCELINKLQPGSVRKINESTQNWHKLENIGNFIKAIMHYGVKPHDIFEAND 84
                          90
                  ....*....|.
gi 568988041   96 LQDLSNRVTVK 106
Cdd:cd21282    85 LFENTNHTQVQ 95
CH_CNN3 cd21284
calponin homology (CH) domain found in calponin-3; Calponin-3 (CNN3), also called acidic ...
17-106 1.42e-13

calponin homology (CH) domain found in calponin-3; Calponin-3 (CNN3), also called acidic isoform calponin, is an F-actin-binding protein that is expressed in the brain and has been shown to control dendritic spine morphology, density, and plasticity by regulating actin cytoskeletal reorganization and dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409133 [Multi-domain]  Cd Length: 111  Bit Score: 68.39  E-value: 1.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGDL 96
Cdd:cd21284     9 ELRNWIEEVTGMSI-GENFQKGLKDGVILCELINKLQPGSIRKINESKLNWHQLENIGNFIKAIQAYGMKPHDIFEANDL 87
                          90
                  ....*....|
gi 568988041   97 QDLSNRVTVK 106
Cdd:cd21284    88 FENGNMTQVQ 97
CH smart00033
Calponin homology domain; Actin binding domains present in duplicate at the N-termini of ...
17-98 1.53e-13

Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.


Pssm-ID: 214479 [Multi-domain]  Cd Length: 101  Bit Score: 67.73  E-value: 1.53e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041     17 EAQRWVEAVTEKNFE--TTDFRASLENGVLLCDLINKLKPGVV--KKINRLSTPIAGLDNINVFLRACEQIGLKEaQLFH 92
Cdd:smart00033    2 TLLRWVNSLLAEYDKppVTNFSSDLKDGVALCALLNSLSPGLVdkKKVAASLSRFKKIENINLALSFAEKLGGKV-VLFE 80

                    ....*.
gi 568988041     93 PGDLQD 98
Cdd:smart00033   81 PEDLVE 86
CH_IQGAP cd21206
calponin homology (CH) domain found in the IQ motif containing GTPase activating protein ...
16-101 5.48e-13

calponin homology (CH) domain found in the IQ motif containing GTPase activating protein family; Members of the IQ motif containing GTPase activating protein (IQGAP) family are associated with the Ras GTP-binding protein and act as essential regulators of cytoskeletal function. There are three known IQGAP family members: IQGAP1, IQGAP2, and IQGAP3. They are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity. It lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP3 regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton.


Pssm-ID: 409055 [Multi-domain]  Cd Length: 118  Bit Score: 66.87  E-value: 5.48e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   16 AEAQRWVEAVTEKNFE-TTDFRASLENGVLLCDLINKLKPGVVKKINrlsTPIAGL-----DNINVFLRACEQIGLKEAQ 89
Cdd:cd21206    11 EEAKQWIEACLNEELPpTTEFEEELRNGVVLAKLANKFAPKLVPLKK---IYDVGLqfrhtDNINHFLRALKKIGLPKIF 87
                          90
                  ....*....|..
gi 568988041   90 LFHPGDLQDLSN 101
Cdd:cd21206    88 HFETTDLYEKKN 99
CH_VAV cd21201
calponin homology (CH) domain found in VAV proteins; VAV proteins function both as cytoplasmic ...
34-101 8.66e-13

calponin homology (CH) domain found in VAV proteins; VAV proteins function both as cytoplasmic guanine nucleotide exchange factors (GEFs) for Rho GTPases and as scaffold proteins, and they play important roles in cell signaling by coupling cell surface receptors to various effector functions. They play key roles in processes that require cytoskeletal reorganization including immune synapse formation, phagocytosis, cell spreading, and platelet aggregation, among others. Vertebrates have three VAV proteins (VAV1, VAV2, and VAV3). VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the CH domain, an actin-binding domain which is present as a single copy in VAV proteins.


Pssm-ID: 409050  Cd Length: 117  Bit Score: 66.12  E-value: 8.66e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKINRLSTP----IAGLDNINVFLRAC-EQIGLKEAQLFHPGDLQDLSN 101
Cdd:cd21201    31 DLAQALRDGVLLCQLLNRLSPGSVDDREINLRPqmsqFLCLKNIRTFLQACrTVFGLRSADLFEPEDLYDVTN 103
CH pfam00307
Calponin homology (CH) domain; The CH domain is found in both cytoskeletal proteins and signal ...
20-130 2.49e-12

Calponin homology (CH) domain; The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin have only a single copy.


Pssm-ID: 425596 [Multi-domain]  Cd Length: 109  Bit Score: 64.62  E-value: 2.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041    20 RWVEAVTEKNFET---TDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQ-IGLKEAQLfhpgD 95
Cdd:pfam00307    9 RWINSHLAEYGPGvrvTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKLENINLALDVAEKkLGVPKVLI----E 84
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 568988041    96 LQDLsnrvtvkqeeTDRRLKNVLITLYWLGRKAQS 130
Cdd:pfam00307   85 PEDL----------VEGDNKSVLTYLASLFRRFQA 109
LIM cd08368
LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains ...
1323-1381 1.77e-11

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: 60.41  E-value: 1.77e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041 1323 CSYCNN-ILGKgaaMIIETLGLSYHLHCFKCVSCGCDLGGSSSGaevrIRNHQLYCNDCY 1381
Cdd:cd08368     1 CAGCGKpIEGR---ELLRALGKKWHPECFKCAECGKPLGGDSFY----EKDGKPYCEKCY 53
CH_PIX cd21202
calponin homology (CH) domain found in the Pak Interactive eXchange factor family; Pak ...
36-96 4.30e-11

calponin homology (CH) domain found in the Pak Interactive eXchange factor family; Pak Interactive eXchange factor (PIX) proteins are Rho guanine nucleotide exchange factors (GEFs), which activate small GTPases by exchanging bound GDP for free GTP. They act as GEFs for both Cdc42 and Rac1, and have been implicated in cell motility, adhesion, neurite outgrowth, and cell polarity. Vertebrates contain two proteins from the PIX family, alpha-PIX and beta-PIX. Alpha-PIX, also called Rho guanine nucleotide exchange factor 6 (ARHGEF6), is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Beta-PIX, also called Rho guanine nucleotide exchange factor 7 (ARHGEF7), plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. Both alpha-PIX and beta-PIX contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409051 [Multi-domain]  Cd Length: 114  Bit Score: 61.39  E-value: 4.30e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568988041   36 RASLENGVLLCDLINKLKPGVVKKInrLSTPIAG---LDNINVFLRACEQIGLKEAQLFHPGDL 96
Cdd:cd21202    31 SESLKNGVVLCRLVNRLKPGTVEKI--YDEPTTEeecLYNFESFLKACQELGILAEEIFDPNDL 92
LIM smart00132
Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM ...
1322-1380 1.76e-09

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: 54.70  E-value: 1.76e-09
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041   1322 VCSYCNNILGkGAAMIIETLGLSYHLHCFKCVSCGCDLGGSssgaEVRIRNHQLYCNDC 1380
Cdd:smart00132    1 KCAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPLSGD----TFFEKDGKLYCKDC 54
PDZ smart00228
Domain present in PSD-95, Dlg, and ZO-1/2; Also called DHR (Dlg homologous region) or GLGF ...
715-783 2.79e-09

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: 55.08  E-value: 2.79e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041    715 FGFTI---KWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKkwEEVMANAQETGNLVMDVRR 783
Cdd:smart00228   14 LGFSLvggKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHL--EAVDLLKKAGGKVTLTVLR 83
LIM pfam00412
LIM domain; This family represents two copies of the LIM structural domain.
1323-1385 7.90e-08

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


Pssm-ID: 395333 [Multi-domain]  Cd Length: 57  Bit Score: 50.02  E-value: 7.90e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568988041  1323 CSYCNN-ILGKGAAMIietLGLSYHLHCFKCVSCGCDLGGSSSgaevRIRNHQLYCNDCYLRFK 1385
Cdd:pfam00412    1 CAGCNRpIYDRELVRA---LGKVWHPECFRCAVCGKPLTTGDF----YEKDGKLYCKHDYYKLF 57
CH_GAS2-like cd21204
calponin homology (CH) domain found in the growth arrest-specific protein 2 family; The growth ...
20-130 7.92e-08

calponin homology (CH) domain found in the growth arrest-specific protein 2 family; The growth arrest-specific protein 2 (GAS-2) family includes GAS-2, and GAS-2 like proteins, GAS2L1-3. GAS-2 may play a role in apoptosis by acting as a cell death substrate for caspases. GAS2L1 (also called GAS2-related protein on chromosome 22 or growth arrest-specific protein 2-like 1) and GAS2L2 (also called GAS2-related protein on chromosome 17 or growth arrest-specific protein 2-like 2) may be involved in the cross-linking of microtubules and microfilaments. GAS2L3, also called GAS2-like protein 3, is a cytoskeletal linker protein that may promote and stabilize the formation of the actin and microtubule network. Members of this family contain a single copy of the CH domain at the N-terminal region. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409053  Cd Length: 131  Bit Score: 52.66  E-value: 7.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   20 RWVEAVTEKNFETTDFRASLENGVLLCDLINKL--------------KPGVVKKI----NRLSTPIAGLDNINVFLRACE 81
Cdd:cd21204    13 EWLNDLLGDDLTPDNFLDELRNGVVLCQLAQKIqeaaekareagkknGPPPSYKLkcneNAKPGSFFARDNVANFLRWCR 92
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 568988041   82 QIGLKEAQLFHPGDLqdlsnrVTVKQEetdrrlKNVLITLYWLGRKAQS 130
Cdd:cd21204    93 KLGVDEVLLFESEDL------VLHKNP------RQVLLCLLELARIAAR 129
CH_LRCH cd21205
calponin homology (CH) domain found in the leucine-rich repeat and calponin homology ...
34-114 1.07e-07

calponin homology (CH) domain found in the leucine-rich repeat and calponin homology domain-containing protein family; The leucine-rich repeat and calponin homology domain-containing protein (LRCH) family includes LRCH1-4. LRCH1, also called calponin homology domain-containing protein 1, or neuronal protein 81 (NP81), acts as a negative regulator of GTPase Cdc42 by sequestering Cdc42-guanine exchange factor DOCK8. LRCH2 may play a role in the organization of the cytoskeleton. LRCH3 is part of the DISP complex and may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. LRCH4, also called leucine-rich repeat neuronal protein 4, or leucine-rich neuronal protein, acts as a novel Toll-like receptor (TLR) accessory protein that regulates the innate immune response. Members of this family contain a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409054 [Multi-domain]  Cd Length: 107  Bit Score: 51.53  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKINRLS------TPIAGLDNINVFLRACEQIGLKEAQLFHPGDLqdLSNRVTVKQ 107
Cdd:cd21205    21 DLGEALMDGVVLCHLANHVRPRSVPSIHVPSpavpklSMAKCRRNVENFLEACRKLGVPEERLCSPGDI--LEEKGLVRV 98

                  ....*..
gi 568988041  108 EETDRRL 114
Cdd:cd21205    99 AVTVQAL 105
CH_AtKIN14-like cd21203
calponin homology (CH) domain found in Arabidopsis thaliana Kinesin-like KIN-14 protein family; ...
34-97 1.49e-07

calponin homology (CH) domain found in Arabidopsis thaliana Kinesin-like KIN-14 protein family; Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. This family includes a group of kinesin-like proteins belonging to KIN-14 protein family. They all contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409052 [Multi-domain]  Cd Length: 112  Bit Score: 51.26  E-value: 1.49e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKI--------NRLSTPIAGLDNINVFLRACEQIGLKeaqLFHPGDLQ 97
Cdd:cd21203    25 EFRLCLRDGVVLCKLLNKLQPGAVPKVvespddpdGAAGSAFQYFENVRNFLVAIEEMGLP---TFEASDLE 93
CH_VAV3 cd21264
calponin homology (CH) domain found in VAV3 protein and similar proteins; VAV3 is ubiquitously ...
25-101 4.13e-07

calponin homology (CH) domain found in VAV3 protein and similar proteins; VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. Its function has been implicated in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and it plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The model corresponds to CH domain, an actin-binding domain which is present as a single copy in VAV3 protein.


Pssm-ID: 409113  Cd Length: 117  Bit Score: 49.96  E-value: 4.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   25 VTEKNFETTDFRASLENGVLLCDLINKLKPGVV--KKIN---RLSTPIAgLDNINVFLRA-CEQIGLKEAQLFHPGDLQD 98
Cdd:cd21264    22 VTWDTAQVFDLAQTLRDGVLLCQLLNNLRPHSInlKEINlrpQMSQFLC-LKNIRTFLSAcCETFGMRKSELFEAFDLFD 100

                  ...
gi 568988041   99 LSN 101
Cdd:cd21264   101 VRD 103
SCP1 COG5199
Calponin [Cytoskeleton];
17-139 5.02e-07

Calponin [Cytoskeleton];


Pssm-ID: 227526 [Multi-domain]  Cd Length: 178  Bit Score: 51.46  E-value: 5.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFETT-DFRASLENGVLLCDLINKLKPGVVKkINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:COG5199    17 EVTLWIETVLGEKFEPPgDLLSLLKDGVRLCRILNEASPLDIK-YKESKMPFVQMENISSFINGLKKLRVPEYELFQTND 95
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 568988041   96 LQDLSNrvtvkqeetdrrLKNVLITLYWLGRKAQSNPYYNGPYL 139
Cdd:COG5199    96 LFEAKD------------LRQVVICLYSLSRYAQKERMFSGPFL 127
COG3975 COG3975
Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];
708-786 5.50e-07

Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only];


Pssm-ID: 443174 [Multi-domain]  Cd Length: 591  Bit Score: 54.06  E-value: 5.50e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041  708 TPGNKPVFGFTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSykdTKKWEEVMANAQETGNLVMDVRRYGK 786
Cdd:COG3975   478 APSLKPSLGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVT---ADNLDDALAAYKPGDPIELLVFRRDE 553
IQG1 COG5261
Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and ...
17-102 5.56e-07

Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms];


Pssm-ID: 227586 [Multi-domain]  Cd Length: 1054  Bit Score: 54.51  E-value: 5.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLST-PIAGLDNINVFLRACEQIGLKEaqLFHpGD 95
Cdd:COG5261    48 EAKIWIEEVIEEALPELCFEDSLRNGVFLAKLTQRFNPDLTTVIFPADKlQFRHTDNINAFLDLIEHVGLPE--SFH-FE 124

                  ....*..
gi 568988041   96 LQDLSNR 102
Cdd:COG5261   125 LQDLYEK 131
PDZ pfam00595
PDZ domain; PDZ domains are found in diverse signaling proteins.
715-757 1.22e-06

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


Pssm-ID: 395476 [Multi-domain]  Cd Length: 81  Bit Score: 47.66  E-value: 1.22e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 568988041   715 FGFTIK----WDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFS 757
Cdd:pfam00595   12 LGFSLKggsdQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVE 58
CH_alphaPIX cd21265
calponin homology (CH) domain found in alpha-Pak Interactive eXchange factor; Alpha-Pak ...
36-96 1.43e-06

calponin homology (CH) domain found in alpha-Pak Interactive eXchange factor; Alpha-Pak Interactive eXchange factor (alpha-PIX), also called PAK-interacting exchange factor alpha, Rho guanine nucleotide exchange factor 6 (ARHGEF6), Rac/Cdc42 guanine nucleotide exchange factor 6, or Cool (Cloned out of Library)-2, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac1, and is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Alpha-PIX contains a single copy of the CH domain at its N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409114  Cd Length: 117  Bit Score: 48.66  E-value: 1.43e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041   36 RASLENGVLLCDLINKLKPGVVKKI-NRLSTPIAGLDNINVFLRACEQIGLkeaQLFHPGDL 96
Cdd:cd21265    32 KSSLKDGVVLCKLIERLLPGSVEKYcLEPKTEADCIGNIKEFLKGCAALKV---ETFEPDDL 90
PDZ_canonical cd00136
canonical PDZ domain; Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs ...
715-754 2.12e-06

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: 46.77  E-value: 2.12e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 568988041  715 FGFTI---KWDISGIFVASVEQGSPAEFS-QLQVDDEILAINNT 754
Cdd:cd00136    12 LGFSIrggKDGGGGIFVSRVEPGGPAARDgRLRVGDRILEVNGV 55
CH_VAV1 cd21262
calponin homology (CH) domain found in VAV1 protein; VAV1 is expressed predominantly in the ...
25-99 2.24e-06

calponin homology (CH) domain found in VAV1 protein; VAV1 is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the CH domain, an actin-binding domain which is present as a single copy in VAV1 protein.


Pssm-ID: 409111  Cd Length: 120  Bit Score: 48.01  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   25 VTEKNFETTDFRASLENGVLLCDLINKLKPGVV--KKIN---RLSTPIAgLDNINVFLRAC-EQIGLKEAQLFHPGDLQD 98
Cdd:cd21262    22 VTWDSAQVCDLAQALRDGVLLCQLLNNLLPHAVnlREINlrpQMSQFLC-LKNIRTFLSTCcEKFGLRKSELFEAFDLFD 100

                  .
gi 568988041   99 L 99
Cdd:cd21262   101 V 101
CH_PLS_FIM_rpt1 cd21217
first calponin homology (CH) domain found in the plastin/fimbrin family; This family includes ...
34-86 2.46e-06

first calponin homology (CH) domain found in the plastin/fimbrin family; This family includes plastin and fimbrin. Plastin has three isoforms, plastin-1, -2, and -3, which are all actin-bundling proteins. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, LC64P, or lymphocyte cytosolic protein 1 (LCP-1), plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Fimbrin has been found in plants and fungi. Arabidopsis thaliana fimbrin (AtFIM) includes fimbrin-1, -2, -3, -4, and -5; they cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Fungal fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409066 [Multi-domain]  Cd Length: 114  Bit Score: 47.57  E-value: 2.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVV--KKINRLS--TPIAGLDNINVFLRACEQIGLK 86
Cdd:cd21217    32 DLFEALRDGVLLCKLINKIVPGTIdeRKLNKKKpkNIFEATENLNLALNAAKKIGCK 88
CH_IQGAP3 cd21276
calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP3; IQ motif ...
17-101 4.09e-06

calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP3; IQ motif containing GTPase activating protein 3 (IQGAP3) associates with Ras GTP-binding proteins. It regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton. It belongs to the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP3 contains a single copy of the CH domain at the N-terminus.


Pssm-ID: 409125 [Multi-domain]  Cd Length: 152  Bit Score: 48.05  E-value: 4.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFET-TDFRASLENGVLLCDLINKLKPGVV--KKI---NRLSTPIAGL-----DNINVFLRACEQIGL 85
Cdd:cd21276    12 EAKRWMEACLKEELPPpTELEESLRNGVYLAKLGHCFAPRVVplKKIydlEQMRYQATGLhfrhtDNINHWRNAMMHIGL 91
                          90
                  ....*....|....*...
gi 568988041   86 keAQLFHP--GDLQDLSN 101
Cdd:cd21276    92 --PSIFHPetTDIYDKKN 107
PDZ2_FL-whirlin cd06741
PDZ domain 2 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
702-785 4.32e-06

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: 46.10  E-value: 4.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041  702 RVSINQTPGNKpvFGFTIKWDIS---GIFVASVEQGSPAEFSQLQVDDEILAINNTKF---SYKDTKKweeVMANAQEtg 775
Cdd:cd06741     3 KVNLVVEDGQS--LGLMIRGGAEyglGIYVTGVDPGSVAENAGLKVGDQILEVNGRSFldiTHDEAVK---ILKSSKH-- 75
                          90
                  ....*....|
gi 568988041  776 nLVMDVRRYG 785
Cdd:cd06741    76 -LIMTVKDVG 84
CH_TAGLN-like cd21209
calponin homology (CH) domain found in the transgelin family; The transgelin (TAGLN) family ...
33-107 4.94e-06

calponin homology (CH) domain found in the transgelin family; The transgelin (TAGLN) family includes transgelin, transgelin-2 and transgelin-3. Transgelin, also called 22 kDa actin-binding protein, protein WS3-10, or smooth muscle protein 22-alpha (SM22-alpha), acts as an actin cross-linking/gelling protein that may be involved in calcium interactions and in regulating contractile properties of the cell. Transgelin-2, also called epididymis tissue protein Li 7e, or SM22-alpha homolog, acts as an actin-binding protein that induces actin gelation and regulates actin cytoskeleton. It may participate in the development and progression of multiple cancers. Transgelin-3, also called neuronal protein 22 (NP22), or neuronal protein NP25, may have a role in alcohol-related adaptations and may mediate regulatory signal transduction pathways in neurons. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409058 [Multi-domain]  Cd Length: 119  Bit Score: 47.12  E-value: 4.94e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568988041   33 TDFRASLENGVLLCDLINKLKP---GVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGDLQDLSNRVTVKQ 107
Cdd:cd21209    28 LGFQKWLKDGTVLCKLINSLYPegsKPVKKIQSSKMAFKQMEQISQFLKAAEDYGVRTTDIFQTVDLWEGKDMAAVQR 105
PDZ_Par6-like cd06718
PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F ...
702-783 5.66e-06

PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. 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 Par6-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: 467202 [Multi-domain]  Cd Length: 84  Bit Score: 45.64  E-value: 5.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041  702 RVSINQTPGnKPvFGFTIK----WD-ISGIFVASVEQGSPAEFSQ-LQVDDEILAINNTKFSYKDTkkwEEVMANAQETG 775
Cdd:cd06718     2 RVELIKPPG-KP-LGFYIRdgngVErVPGIFISRLVLGSLADSTGlLAVGDEILEVNGVEVTGKSL---DDVTDMMVAPT 76

                  ....*...
gi 568988041  776 NLVMDVRR 783
Cdd:cd06718    77 RLIITVKP 84
LIM3_abLIM cd09329
The third LIM domain of actin binding LIM (abLIM) proteins; The third LIM domain of actin ...
1323-1381 1.33e-05

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


Pssm-ID: 188715 [Multi-domain]  Cd Length: 52  Bit Score: 43.85  E-value: 1.33e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041 1323 CSYCNNILGKGAAMIieTLGLSYHLHCFKCVSCGCDLGGSSSGaevriRNHQLYCNDCY 1381
Cdd:cd09329     1 CAGCGQEIKNGQALL--ALDKQWHVWCFKCKECGKVLTGEYMG-----KDGKPYCERDY 52
CH_VAV2 cd21263
calponin homology (CH) domain found in VAV2 protein and similar proteins; VAV2 is widely ...
34-101 1.49e-05

calponin homology (CH) domain found in VAV2 protein and similar proteins; VAV2 is widely expressed and functions as a guanine nucleotide exchange factor (GEF) for RhoA, RhoB and RhoG and also activates Rac1 and Cdc42. It is implicated in many cellular and physiological functions including blood pressure control, eye development, neurite outgrowth and branching, EGFR endocytosis and degradation, and cell cluster morphology, among others. It has been reported to associate with Nek3. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The model corresponds to CH domain, an actin-binding domain which is present as a single copy in VAV2 protein.


Pssm-ID: 409112  Cd Length: 119  Bit Score: 45.72  E-value: 1.49e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVV--KKIN---RLSTPIAgLDNINVFLRAC-EQIGLKEAQLFHPGDLQDLSN 101
Cdd:cd21263    31 DLAQALRDGVLLCQLLHNLSPGSIdlKDINfrpQMSQFLC-LKNIRTFLKVChDKFGLRNSELFDPFDLFDVRD 103
PDZ_rhophilin-like cd06712
PDZ domain of rhophilin-1, rhophilin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
715-782 1.61e-05

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: 44.11  E-value: 1.61e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041  715 FGFTIKWDiSGIFVASVEQGSPAEFSQLQVDDEILAINNtkfsyKDTK--KWEEVMANAQETGNLVMDVR 782
Cdd:cd06712    13 FGFTLRGD-SPVQVASVDPGSCAAEAGLKEGDYIVSVGG-----VDCKwsKHSEVVKLLKSAGEEGLELQ 76
PDZ3_ZO1-like_domain cd06729
PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ ...
725-756 1.62e-05

PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 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 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: 467211 [Multi-domain]  Cd Length: 82  Bit Score: 44.48  E-value: 1.62e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTKF 756
Cdd:cd06729    24 GIFVAGVQEGSPAEKQGLQEGDQILKVNGVDF 55
LIM3_Zyxin_like cd09357
The third LIM domain of Zyxin-like family; The third LIM domain of Zyxin like family: This ...
1323-1380 2.59e-05

The third LIM domain of Zyxin-like family; The third LIM domain of Zyxin like family: This family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and Trip6 LIM proteins. Members of Zyxin family contain three tandem C-terminal LIM domains, and a proline-rich N-terminal region. Zyxin proteins are detected primarily in focal adhesion plaques. They function as scaffolds, participating in the assembly of multiple interactions and signal transduction networks, which regulate cell adhesion, spreading, and motility. They can also shuffle into nucleus. In nucleus, zyxin proteins affect gene transcription by interaction with a variety of nuclear proteins, including several transcription factors, playing regulating roles in cell proliferation, differentiation and apoptosis. 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: 188743  Cd Length: 63  Bit Score: 43.18  E-value: 2.59e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568988041 1323 CSYCNN-IL---GKGAAMIIETLGLSYHLHCFKCVSCGCDLggsSSGAEVR----IRNHqLYCNDC 1380
Cdd:cd09357     1 CSVCGEpIMpepGQDETVRIVALDRSFHVNCYKCEDCGMLL---SSEDEGQgcypLDGH-LLCKSC 62
CH_LRCH3 cd21272
calponin homology (CH) domain found in leucine-rich repeat and calponin homology ...
27-93 3.01e-05

calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 3; Leucine-rich repeat and calponin homology domain-containing protein 3 (LRCH3) is part of the DISP (DOCK7-Induced Septin disPlacement) complex. It may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. LRCH3 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409121  Cd Length: 109  Bit Score: 44.60  E-value: 3.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   27 EKNFET-------TDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLD------NINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21272     7 RKNIESrlkvslpSDLGAALTDGVVLCHLANHVRPRSVPSIHVPSPAVPKLTmakcrrNVENFLEACRRIGVPQEQLCLP 86
CH_LRCH1 cd21270
calponin homology (CH) domain found in leucine-rich repeat and calponin homology ...
34-110 3.31e-05

calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1; Leucine-rich repeat and calponin homology domain-containing protein 1 (LRCH1), also called calponin homology domain-containing protein 1, or neuronal protein 81 (NP81), acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. LRCH1 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409119  Cd Length: 112  Bit Score: 44.46  E-value: 3.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLD------NINVFLRACEQIGLKEAQLFHPGDLQDLSNRVTVKQ 107
Cdd:cd21270    24 DLGAALMDGVVLCHLVNHVRPRSVASIHVPSPAVPKLSmakcrrNVENFLEACRKIGVPEADLCSPYDILQLNLRGIRKT 103

                  ...
gi 568988041  108 EET 110
Cdd:cd21270   104 VET 106
PDZ1_PDZD7-like cd10833
PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
703-785 4.51e-05

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: 43.19  E-value: 4.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041  703 VSINQTPGNKpvFGFTIKWDIS---GIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVManaqeTGN--L 777
Cdd:cd10833     4 VTVEKSPDGS--LGFSVRGGSEhglGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENITMSSAVKVL-----TGSnrL 76

                  ....*...
gi 568988041  778 VMDVRRYG 785
Cdd:cd10833    77 RMVVRRMG 84
PDZ2_harmonin cd06738
PDZ domain 2 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
704-769 7.65e-05

PDZ domain 2 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 2 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 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: 467220 [Multi-domain]  Cd Length: 82  Bit Score: 42.69  E-value: 7.65e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568988041  704 SINQTPGNKPvfgftikwdisGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKkwEEVMA 769
Cdd:cd06738    18 SISSGPTQKP-----------GIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFTNVDHK--EAVMA 70
PDZ_TAX1BP3-like cd10822
PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic ...
705-752 8.87e-05

PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). 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 TAX1BP3-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: 467265 [Multi-domain]  Cd Length: 94  Bit Score: 42.71  E-value: 8.87e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 568988041  705 INQTPGNKPvFGFTIKwdisGIFVASVEQGSPAEFSQLQVDDEILAIN 752
Cdd:cd10822    23 IDQDPSKNP-FSYTDK----GIYVTRVSEGGPAEKAGLQVGDKILQVN 65
CH_IQGAP2 cd21275
calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP2; IQ motif ...
17-101 9.55e-05

calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP2; IQ motif containing GTPase activating protein 2 (IQGAP2) is a member of the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP2 binds to activated Cdc42 and Rac1 but does not seem to stimulate their GTPase activity. It associates with calmodulin. IQGAP2 contains a single copy of the CH domain at the N-terminus.


Pssm-ID: 409124 [Multi-domain]  Cd Length: 156  Bit Score: 44.24  E-value: 9.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   17 EAQRWVEAVTEKNFE-TTDFRASLENGVLLCDLINKLKPGVV--KKI---NRLSTPIAGL-----DNINVFLRACEQIGL 85
Cdd:cd21275    36 EAKQWIEACLNEELPpTTELEEGLRNGVYLVKLAKFFAPKLVseKKIydvDQVRYKRSGLhfrhtDNTVQWLRAMESIGL 115
                          90
                  ....*....|....*...
gi 568988041   86 keAQLFHP--GDLQDLSN 101
Cdd:cd21275   116 --PKIFYPetTDVYDRKN 131
degP_htrA_DO TIGR02037
periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various ...
684-783 1.09e-04

periplasmic serine protease, Do/DeqQ family; This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273938 [Multi-domain]  Cd Length: 428  Bit Score: 46.45  E-value: 1.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   684 RGSPLREVSRSLDQFSDmrvsiNQTPGNKPVFGFT-------------IKWDISGIFVASVEQGSPAEFSQLQVDDEILA 750
Cdd:TIGR02037  314 RKGKEKTITVTLGASPE-----EQASSSNPFLGLTvanlspeirkelrLKGDVKGVVVTKVVSGSPAARAGLQPGDVILS 388
                           90       100       110
                   ....*....|....*....|....*....|...
gi 568988041   751 INNTkfSYKDTKKWEEVMANAQETGNLVMDVRR 783
Cdd:TIGR02037  389 VNQQ--PVSSVAELRKVLARAKKGGRVALLILR 419
CH_TAGLN2 cd21280
calponin homology (CH) domain found in transgelin-2; Transgelin-2, also called epididymis ...
21-107 1.33e-04

calponin homology (CH) domain found in transgelin-2; Transgelin-2, also called epididymis tissue protein Li 7e, or SM22-alpha homolog, acts as an actin-binding protein that induces actin gelation and regulates the actin cytoskeleton. It may participate in the development and progression of multiple cancers. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409129 [Multi-domain]  Cd Length: 137  Bit Score: 43.33  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041   21 WVEAVTEKNFETTD-----FRASLENGVLLCDLINKLKP---GVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFH 92
Cdd:cd21280    16 WITAQCGKQVGRPQpgrenFQNWLKDGTVLCHLINSLYPkgqAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQ 95
                          90
                  ....*....|....*
gi 568988041   93 PGDLQDLSNRVTVKQ 107
Cdd:cd21280    96 TVDLWEGKNMASVQR 110
PDZ_PDZD11-like cd06752
PDZ domain of PDZ domain-containing protein 11, and related domains; PDZ (PSD-95 (Postsynaptic ...
702-784 1.59e-04

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: 41.53  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568988041  702 RVSINQTPGNKPVfGFTI---KWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVMANAQEtgnLV 778
Cdd:cd06752     1 RTVVLKRPPGEQL-GFNIrggKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTARE---IQ 76

                  ....*.
gi 568988041  779 MDVRRY 784
Cdd:cd06752    77 MRVRYF 82
CH_LRCH4 cd21273
calponin homology (CH) domain found in leucine-rich repeat and calponin homology ...
34-96 2.82e-04

calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4; Leucine-rich repeat and calponin homology domain-containing protein 4 (LRCH4), also called leucine-rich repeat neuronal protein 4, or leucine-rich neuronal protein, acts as a novel Toll-like receptor (TLR) accessory protein that regulates the innate immune response. LRCH4 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409122  Cd Length: 109  Bit Score: 41.81  E-value: 2.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLD------NINVFLRACEQIGLKEAQLFHPGDL 96
Cdd:cd21273    24 DLAEALSNGAVLCQLANQLRPRSVSIIHVPSPAVPKLSkakcrkNVENFIEACRKMGVPEVDLCSPSDV 92
RseP COG0750
Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, ...
728-786 3.28e-04

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


Pssm-ID: 440513 [Multi-domain]  Cd Length: 349  Bit Score: 44.69  E-value: 3.28e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568988041  728 VASVEQGSPAEFSQLQVDDEILAINNTKFSYkdtkkWEEVMANAQETGN--LVMDVRRYGK 786
Cdd:COG0750   132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTS-----WDDLVDIIRASPGkpLTLTVERDGE 187
LIM1_Enigma_like cd09361
The first LIM domain of Enigma-like family; The first LIM domain of Enigma-like family: The ...
1323-1381 3.85e-04

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: 39.65  E-value: 3.85e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041 1323 CSYCNNILgKGAAMIieTLGLSYHLHCFKCVSCGCDLggsSSGAEVRIRNHqLYCNDCY 1381
Cdd:cd09361     1 CAHCNQVI-RGPFLV--ALGRSWHPEEFTCSHCHCSL---AEIGFVEEKGS-LYCELCY 52
PDZ1_DLG5-like cd06764
PDZ domain 1 of Discs Large 5 (Dlg5) and related domains; PDZ (PSD-95 (Postsynaptic density ...
724-783 4.11e-04

PDZ domain 1 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 1 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 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: 467245 [Multi-domain]  Cd Length: 95  Bit Score: 40.85  E-value: 4.11e-04
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gi 568988041  724 SGIFVASVEQGSPAEfSQLQVDDEILAINNTKFSYKDTKKWEEVMANAQETGNLVmdVRR 783
Cdd:cd06764    38 CSIFVTKVDKGSIAD-GRLRVNDCLLRINDVDLTNKDKKQAIQAVLNGGGVINMV--VRR 94
LIM4_FHL1 cd09348
The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1); The fourth LIM domain ...
1323-1380 4.62e-04

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: 39.75  E-value: 4.62e-04
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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568988041 1323 CSYCNN-ILGKG-AAMIIETLGLSYHLHCFKCVSCGCDLggsssgAEVR--IRNHQLYCNDC 1380
Cdd:cd09348     5 CSGCQNpITGFGkGTNVVNYEGSSWHDYCFNCKKCSLNL------ANKRfvFHNGQIYCSDC 60
CH_LRCH2 cd21271
calponin homology (CH) domain found in leucine-rich repeat and calponin homology ...
34-93 4.73e-04

calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 2; Leucine-rich repeat and calponin homology domain-containing protein 2 (LRCH2) may play a role in the organization of the cytoskeleton. It contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409120  Cd Length: 111  Bit Score: 41.07  E-value: 4.73e-04
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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568988041   34 DFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLD------NINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21271    25 DLGAALMDGVVLCHLANHIRPRSVGSIHVPSPAVPKLSmakcrrNVENFLDACRKLGVPEDKLCLP 90
LIM5_LIMPETin cd09430
The fifth LIM domain of protein LIMPETin; The fifth LIM domain of protein LIMPETin: LIMPETin ...
1323-1381 4.77e-04

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: 39.38  E-value: 4.77e-04
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gi 568988041 1323 CSYCNNILGKGAamiIETLGLSYHLHCFKCVSCGCDLGGSSSGAevriRNHQLYCNDCY 1381
Cdd:cd09430     1 CSKCNKIINSGG---VTYKNEPWHRECFTCTNCSKSLAGQRFTS----RDEKPYCADCF 52
LIM3_FHL1 cd09429
The third LIM domain of Four and a half LIM domains protein 1 (FHL1); The third LIM domain of ...
1323-1381 4.79e-04

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


Pssm-ID: 188813  Cd Length: 53  Bit Score: 39.41  E-value: 4.79e-04
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gi 568988041 1323 CSYCNNILGKGaamiietlGLSY-----HLHCFKCVSCGCDLGGSSSGAevriRNHQLYCNDCY 1381
Cdd:cd09429     1 CVKCNKPITSG--------GVTYqdqpwHSECFVCSSCSKKLAGQRFTA----VEDQYYCVDCY 52
PDZ3_MUPP1-like cd06791
PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) ...
722-778 5.20e-04

PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and 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 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: 467253 [Multi-domain]  Cd Length: 89  Bit Score: 40.29  E-value: 5.20e-04
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gi 568988041  722 DISGIFVASVEQGSPAEFS-QLQVDDEILAINNTK---FSYKDTKkweEVMANaqeTGNLV 778
Cdd:cd06791    29 ELSGIFVKSIIPGSAADQDgRIQVNDQIIAVDGVNlqgFTNQEAV---EVLRN---TGQVV 83
PDZ_densin_erbin-like cd06749
PDZ domain of densin, erbin, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95) ...
702-783 6.16e-04

PDZ domain of densin, erbin, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of densin, erbin, and related domains. Densin (also known as leucine-rich repeat-containing protein 7, LRRC7, densin-180, protein LAP1) and erbin (also known as densin-180-like protein, Erbb2-interacting protein, protein LAP2) belong to the LAP (leucine-rich repeat and PDZ domain) family of scaffolding proteins that play roles in the maintenance of cell shape and apical-basal polarity. Densin and erbin are components of the excitatory postsynaptic compartment and are regulators of dendritic morphology and postsynaptic structure. The densin PDZ domain binds CaV1.3 alpha1 subunit, delta-catenin, and MAGUIN-1. Binding partners of the erbin PDZ domain include ErbB receptor tyrosine kinase ErbB2, HTLV-1 Tax1, Cav1.3 Ca2+channels, and constituents of the cadherin:catenin cell adhesion complex, in particular delta-catenin, p0071 and ARVCF. The erbin PDZ domain binds Smad3, a transductor of the TGFbeta pathway, possibly by a novel interface of binding. Erbin and two other LAP proteins (scribble and lano) redundantly regulate epithelial polarity and apical adhesion 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 densin and erbin-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: 467231 [Multi-domain]  Cd Length: 87  Bit Score: 40.00  E-value: 6.16e-04
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gi 568988041  702 RVSINQTPGnkpvFGFTIKWDIS-----------GIFVASVEQGSPAEfSQLQVDDEILAINNTKFSYKDTKKWEEVMAN 770
Cdd:cd06749     2 RVRIEKNPG----LGFSISGGIGsqgnpfrpdddGIFVTKVQPDGPAS-KLLQPGDKILEVNGYDFVNIEHGQAVSLLKS 76
                          90
                  ....*....|...
gi 568988041  771 AQETGNLVmdVRR 783
Cdd:cd06749    77 FQNTVDLV--VER 87
PDZ1_harmonin cd06737
PDZ domain 1 of harmonin isoforms a, b, and c, and related domains; PDZ (PSD-95 (Postsynaptic ...
715-785 6.99e-04

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: 39.93  E-value: 6.99e-04
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gi 568988041  715 FGFTIKWDI---SGIFVASVEQGSPAEFSQLQVDDEILAINNtkFSYKDTKKwEEVMANAQETGNLVMDVRRYG 785
Cdd:cd06737    15 LGFSVRGGLehgCGLFVSHVSPGSQADNKGLRVGDEIVRING--YSISQCTH-EEVINLIKTKKTVSLKVRHVG 85
PDZ_NHERF-like cd06768
PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related ...
715-780 7.85e-04

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: 39.73  E-value: 7.85e-04
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gi 568988041  715 FGFTIKWD--ISGIFVASVEQGSPAEFSQLQVDDEILAINNT---KFSYkdtkkwEEVMANAQETGN----LVMD 780
Cdd:cd06768    12 YGFNLHAEkgRPGHFIREVDPGSPAERAGLKDGDRLVEVNGEnveGESH------EQVVEKIKASGNqvtlLVVD 80
LIM1_Isl cd09366
The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl ...
1343-1381 7.88e-04

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: 38.86  E-value: 7.88e-04
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gi 568988041 1343 LSYHLHCFKCVSCGCDLGGSSSgaeVRIRNHQLYCNDCY 1381
Cdd:cd09366    20 LEWHAACLKCAECGQYLDETCT---CFVRDGKTYCKRDY 55
CH_betaPIX cd21266
calponin homology (CH) domain found in beta-Pak Interactive eXchange factor; Beta-Pak ...
35-96 7.98e-04

calponin homology (CH) domain found in beta-Pak Interactive eXchange factor; Beta-Pak Interactive eXchange factor (beta-PIX), also called PAK-interacting exchange factor beta, Rho guanine nucleotide exchange factor 7 (ARHGEF7), p85, or Cool (Cloned out of Library)-1, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac1, and plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. Beta-PIX contains a single copy of the CH domain at its N-terminus. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409115  Cd Length: 112  Bit Score: 40.67  E-value: 7.98e-04
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gi 568988041   35 FRASLENGVLLCDLINKLKPGVVKKI-NRLSTPIAGLDNINVFLRACeqiGLKEAQLFHPGDL 96
Cdd:cd21266    29 LQASLKDGVVLCRLLERLLPGSIDKVyPEPRTESECLSNIREFLRGC---GALRLETFDANDL 88
CH_IQGAP1 cd21274
calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP1; IQ motif ...
17-101 9.99e-04

calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP1; IQ motif containing GTPase activating protein 1 (IQGAP1), also called p195, is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. It plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton. It belongs to the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity. It lacks GAP activity. Both, IQGAP1 and IQGAP2, specifically bind to Cdc42 and Rac1, but not to RhoA. Despite similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP1 contains a single copy of the CH domain at the N-terminus.


Pssm-ID: 409123 [Multi-domain]  Cd Length: 154  Bit Score: 41.13  E-value: 9.99e-04
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gi 568988041   17 EAQRWVEAVTEKNFE-TTDFRASLENGVLLCDLINKLKPGVV--KKI-NRLST--PIAGL-----DNINVFLRACEQIGL 85
Cdd:cd21274    13 EAKRWMEACLGEDLPpTTELEEGLRNGVYLAKLGNFFSPKVVslKKIyDREQTryKATGLhfrhtDNVIQWLNAMDEIGL 92
                          90
                  ....*....|....*...
gi 568988041   86 keAQLFHP--GDLQDLSN 101
Cdd:cd21274    93 --PKIFYPetTDIYDRKN 108
CtpA COG0793
C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, ...
696-752 1.14e-03

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: 42.93  E-value: 1.14e-03
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gi 568988041  696 DQFSDMRVsinQTPGNKPVFGFTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAIN 752
Cdd:COG0793    46 EEYEDFQE---STSGEFGGLGAELGEEDGKVVVVSVIPGSPAEKAGIKPGDIILAID 99
LIM1_UF1 cd09397
LIM domain in proteins of unknown function; The first Lim domain of a LIM domain containing ...
1314-1381 1.19e-03

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


Pssm-ID: 188783 [Multi-domain]  Cd Length: 58  Bit Score: 38.40  E-value: 1.19e-03
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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568988041 1314 NRSVSGKRVCSYCNNILGKgaamiietlglsYHLHCFKCVSCGCDLggsSSGAEVRIRNHQLYCNDCY 1381
Cdd:cd09397     5 GLEIEGKSISSKDGELSGQ------------WHRECFVCTTCGCPF---QFSVPCYVLDDKPYCQQHY 57
LIM2_LIMK1 cd09464
The second LIM domain of LIMK1 (LIM domain Kinase 1); The second LIM domain of LIMK1 (LIM ...
1323-1381 1.25e-03

The second LIM domain of LIMK1 (LIM domain Kinase 1); The second 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: 188848  Cd Length: 55  Bit Score: 38.32  E-value: 1.25e-03
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gi 568988041 1323 CSYCNNILGKGAAMIIETLglSYHLHCFKCVSCGCDLGGSSSGAEVriRNHQLYCNDCY 1381
Cdd:cd09464     1 CHGCSETITTGLVMVAGEQ--KYHPECFSCLRCGAFIGDGDTYALV--EHSKLYCGHCY 55
PDZ_RapGEF2_RapGEF6-like cd06755
PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange ...
725-770 1.29e-03

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: 39.17  E-value: 1.29e-03
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gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVMAN 770
Cdd:cd06755    27 GIFVSKVEKGSKAAEAGLKRGDQILEVNGQNFENITLKKALEILRN 72
PDZ2_PDZD7-like cd10834
PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related ...
725-756 1.33e-03

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: 39.29  E-value: 1.33e-03
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gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTKF 756
Cdd:cd10834    28 GIYVSKVDPGGLAEQNGIKVGDQILAVNGVSF 59
CH_TAGLN3 cd21281
calponin homology (CH) domain found in transgelin-3; Transgelin-3, also called neuronal ...
34-96 1.45e-03

calponin homology (CH) domain found in transgelin-3; Transgelin-3, also called neuronal protein 22 (NP22), or neuronal protein NP25, may have a role in alcohol-related adaptations and may mediate regulatory signal transduction pathways in neurons. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.


Pssm-ID: 409130 [Multi-domain]  Cd Length: 119  Bit Score: 39.95  E-value: 1.45e-03
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gi 568988041   34 DFRASLENGVLLCDLINKLKP---GVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGDL 96
Cdd:cd21281    29 NFQKWLMDGTILCRLINSLYPpgkEPIKKISETKMAFKQMEKISQFLQAAEAYGVITTDIFQTVDL 94
PDZ_MPP-like cd06726
PDZ domain of membrane palmitoylated proteins (MPPs), and related domains; PDZ (PSD-95 ...
716-772 1.54e-03

PDZ domain of membrane palmitoylated proteins (MPPs), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1-7 (also known as MAGUK p55 subfamily members 1-7), and related domains. MPPs comprise a subfamily of a larger group of multidomain proteins, namely, membrane-associated guanylate kinases (MAGUKs). MPPs form diverse protein complexes at the cell membranes, which are involved in a wide range of cellular processes, including establishing proper cell structure, polarity and cell adhesion. MPPs have only one 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 MPP1-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: 467208 [Multi-domain]  Cd Length: 80  Bit Score: 38.79  E-value: 1.54e-03
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gi 568988041  716 GFTIKWDISGIFVASVEQGSPAEFS-QLQVDDEILAINNTKFSYKDTKKWEEVMANAQ 772
Cdd:cd06726    14 GATIKMEEDSVIVARILHGGMAHRSgLLHVGDEILEINGIPVSGKTVDELQKLLSSLS 71
LIM2_SF3 cd09441
The second Lim domain of pollen specific protein SF3; The second Lim domain of pollen specific ...
1323-1377 1.61e-03

The second Lim domain of pollen specific protein SF3; The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. 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: 188825 [Multi-domain]  Cd Length: 61  Bit Score: 38.22  E-value: 1.61e-03
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gi 568988041 1323 CSYCNNILGKGAAMIIEtlGLSYHLHCFKCVSCGCDLGGSSSGAevriRNHQLYC 1377
Cdd:cd09441     1 CVACGKTVYPIEKVTVE--GTSYHKSCFKCSHGGCTISPSNYAA----HEGRLYC 49
cpPDZ2_DegP-like cd23084
circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine ...
717-787 2.07e-03

circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do), and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for the identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for the combining with other DegP monomers to form a stable oligomer structure. 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 DegP family PDZ domain 2 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: 467631 [Multi-domain]  Cd Length: 83  Bit Score: 38.38  E-value: 2.07e-03
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gi 568988041  717 FTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAINNtkfsyKDTKKWEEvMANAQETG--NLVMDVRRYGKS 787
Cdd:cd23084    11 VTDEDGGKGVVVTEVDPGSPAAQSGLKKGDVIIGVNR-----QPVKSIAE-LRKVLKSKpsAVLLQIKRGDSS 77
LIM2_Ajuba_like cd09355
The second LIM domain of Ajuba-like proteins; The second LIM domain of Ajuba-like proteins: ...
1323-1377 2.75e-03

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: 37.32  E-value: 2.75e-03
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gi 568988041 1323 CSYCNNILGKgaaMIIETLGLSYHLHCFKCVSCGCDLGGSSSGAEVrirNHQLYC 1377
Cdd:cd09355     1 CAVCGHLIME---MILQALGKSYHPGCFRCCVCNECLDGVPFTVDV---ENNIYC 49
LIM2_Lhx2_Lhx9 cd09377
The second LIM domain of Lhx2 and Lhx9 family; The second LIM domain of Lhx2 and Lhx9 family: ...
1319-1377 3.02e-03

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: 37.25  E-value: 3.02e-03
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gi 568988041 1319 GKRVCSYCNniLGKGAA-MIIETLGLSYHLHCFKCVSCGCDLggsSSGAEVRIRNHQLYC 1377
Cdd:cd09377     1 SVKRCARCH--LGISASeLVMRARDLVFHLNCFTCATCNKPL---TKGDHFGMRDGLVYC 55
PDZ1_FL-whirlin cd06740
PDZ domain 1 of the full-length isoform of whirlin and related domains; PDZ (PSD-95 ...
716-757 3.10e-03

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: 38.11  E-value: 3.10e-03
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gi 568988041  716 GFTIK--WDIS-GIFVASVEQGSPAEFSQLQVDDEILAINNTKFS 757
Cdd:cd06740    16 GFSIRggAEHGvGIYVSLVEPGSLAEKEGLRVGDQILRVNDVSFE 60
PDZ3_Scribble-like cd06702
PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains; PDZ (PSD-95 ...
725-783 3.25e-03

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: 38.01  E-value: 3.25e-03
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gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNtkfsyKDTKKW---EEVMANAQETGNLVMDVRR 783
Cdd:cd06702    33 GIFISKVIPDGAAAKSGLRIGDRILSVNG-----KDLRHAthqEAVSALLSPGQEIKLLVRH 89
PDZ2-PTPN13_FRMPD2-like cd06792
PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and ...
715-780 3.32e-03

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: 37.96  E-value: 3.32e-03
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gi 568988041  715 FGFTI------KWDISGIFVASVEQGSPAEFS-QLQVDDEILAINNTKFSYKDTKKWEEVMANAQETGNLVMD 780
Cdd:cd06792    14 LGISVtggintSVRHGGIYVKSLVPGGAAEQDgRIQKGDRLLEVNGVSLEGVTHKQAVECLKNAGQVVTLVLE 86
LIM3_Lrg1p_like cd09393
The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third LIM ...
1345-1380 3.50e-03

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein; The third 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: 188779  Cd Length: 56  Bit Score: 36.91  E-value: 3.50e-03
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gi 568988041 1345 YHLHCFKCVSCGCDLGGSSSGAEVRIRNHQLYCNDC 1380
Cdd:cd09393    20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
LIM3_FHL cd09346
The third LIM domain of Four and a half LIM domains protein (FHL); The third LIM domain of ...
1323-1381 3.54e-03

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: 36.92  E-value: 3.54e-03
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gi 568988041 1323 CSYCNNILGKGaamiietlGLSY-----HLHCFKCVSCGCDLGGSSSGAevriRNHQLYCNDCY 1381
Cdd:cd09346     1 CAKCKKAITSG--------GVTYrdqpwHKECFVCTGCKKQLAGQRFTS----RDEYPYCVDCF 52
LIM1_abLIM cd09327
The first LIM domain of actin binding LIM (abLIM) proteins; The first LIM domain of actin ...
1345-1381 3.65e-03

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: 36.85  E-value: 3.65e-03
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gi 568988041 1345 YHLHCFKCVSCGCDLggSSSGAEVriRNHQLYCNDCY 1381
Cdd:cd09327    20 FHIKCFTCKVCGCDL--AQGGFFV--KEGEYYCTDDY 52
PDZ_RGS3-like cd06711
PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains; PDZ (PSD-95 ...
715-753 4.02e-03

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: 37.37  E-value: 4.02e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 568988041  715 FGFTIKWDiSGIFVASVEQGSPAEFSQLQVDDEILAINN 753
Cdd:cd06711    12 FGFTICDD-SPVRVQAVDPGGPAEQAGLQQGDTVLQING 49
LIM3_LIMPETin cd09421
The third LIM domain of protein LIMPETin; The third LIM domain of protein LIMPETin: LIMPETin ...
1323-1381 4.31e-03

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: 36.78  E-value: 4.31e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568988041 1323 CSYCNNILGkgaamiIETLGLSY-----HLHCFKCVSCGCDLGGSSSGAevriRNHQLYCNDCY 1381
Cdd:cd09421     5 CEECSKIIG------IDSKDLSYkdkhwHEACFLCSKCKISLVDKPFGS----KADRIYCGNCY 58
DegQ COG0265
Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational ...
725-755 5.64e-03

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


Pssm-ID: 440035 [Multi-domain]  Cd Length: 274  Bit Score: 40.52  E-value: 5.64e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTK 755
Cdd:COG0265   202 GVLVARVEPGSPAAKAGLRPGDVILAVDGKP 232
PDZ_RGS12-like cd06710
PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains; PDZ (PSD-95 ...
715-760 5.99e-03

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: 36.84  E-value: 5.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 568988041  715 FGFTIkwdiSG---IFVASVEQGSPAEFSQLQVDDEILAINNT---KFSYKD 760
Cdd:cd06710    12 YGFTI----SGqapCVLSCVVRGSPADVAGLKAGDQILAVNGInvsKASHED 59
cpPDZ_CPP-like cd06782
circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, ...
722-760 6.06e-03

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: 37.46  E-value: 6.06e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 568988041  722 DISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKD 760
Cdd:cd06782    12 DDGYLVVVSPIPGGPAEKAGIKPGDVIVAVDGESVRGMS 50
PDZ_6 pfam17820
PDZ domain; This entry represents the PDZ domain from a wide variety of proteins.
727-783 6.40e-03

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


Pssm-ID: 436067 [Multi-domain]  Cd Length: 54  Bit Score: 36.35  E-value: 6.40e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 568988041   727 FVASVEQGSPAEFSQLQVDDEILAINNTkfSYKDTKKWEEVMANAQETgNLVMDVRR 783
Cdd:pfam17820    1 VVTAVVPGSPAERAGLRVGDVILAVNGK--PVRSLEDVARLLQGSAGE-SVTLTVRR 54
cpPDZ1_DegP-like cd10839
circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine ...
725-755 6.76e-03

circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. 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 DegP family PDZ domain 1 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: 467630 [Multi-domain]  Cd Length: 91  Bit Score: 37.08  E-value: 6.76e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTK 755
Cdd:cd10839    26 GALVAQVLPDSPAAKAGLKAGDVILSLNGKP 56
LIM_CRP_like cd09326
The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich ...
1342-1381 6.77e-03

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: 36.03  E-value: 6.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568988041 1342 GLSYHLHCFKCVSCGCDLgGSSSGAEvriRNHQLYCNDCY 1381
Cdd:cd09326    18 GKSWHKSCFTCAVCNKRL-DSTTLAE---HDGEIYCKSCY 53
cpPDZ_Deg_HtrA-like cd06779
permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping ...
722-787 7.18e-03

permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini 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 Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus.


Pssm-ID: 467621 [Multi-domain]  Cd Length: 91  Bit Score: 37.27  E-value: 7.18e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568988041  722 DISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDtkKWEEVMANAQETGNLVMDVRRYGKS 787
Cdd:cd06779    23 VNRGVLVAEVIPGSPAAKAGLKEGDVILSVNGKPVTSFN--DLRAALDTKKPGDSLNLTILRDGKT 86
LIM2_LIMK cd09365
The second LIM domain of LIMK (LIM domain Kinase ); The second LIM domain of LIMK (LIM domain ...
1323-1381 7.30e-03

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: 36.19  E-value: 7.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041 1323 CSYCNNILgKGAAMIIETLglSYHLHCFKCVSCGCDLGGSSSGAEVriRNHQLYCNDCY 1381
Cdd:cd09365     1 CHGCSQII-TGPVMVAGDH--KFHPECFSCSSCKAFIGDGDSYALV--ERSKLYCGVCY 54
LIM2_Lmx1a_Lmx1b cd09378
The second LIM domain of Lmx1a and Lmx1b; The second LIM domain of Lmx1a and Lmx1b: Lmx1a and ...
1323-1381 7.51e-03

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


Pssm-ID: 188764  Cd Length: 55  Bit Score: 35.89  E-value: 7.51e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041 1323 CSYCNNILGKgAAMIIETLGLSYHLHCFKCVSCGCDLggsSSGAEVRIRNHQLYCNDCY 1381
Cdd:cd09378     1 CSGCLEKIAP-SELVMRALENVYHLRCFCCCVCERQL---QKGDEFVLKEGQLLCKSDY 55
LIM_Ltd-1 cd09443
The LIM domain of LIM and transglutaminase domains protein (Ltd-1); The LIM domain of LIM and ...
1342-1373 8.04e-03

The LIM domain of LIM and transglutaminase domains protein (Ltd-1); The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has putative function in muscle development. The mouse with ky mutant exhibits combined posterior and lateral curvature of the spine. The Ltd-1 gene in C. elegans is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell 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: 188827 [Multi-domain]  Cd Length: 55  Bit Score: 35.86  E-value: 8.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 568988041 1342 GLSYHLHCFKCVSCGCDLGGSS-----SGAEVRIRNH 1373
Cdd:cd09443    18 GTFYHKGCFKCRECGTRLSLKTftfvqGDGEVYCARH 54
PDZ1_syntenin-like cd06721
PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density ...
725-782 8.24e-03

PDZ domain 1 of syntenin-1, syntenin-2, and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of syntenin-1, syntenin-2, and related domains. Syntenins are implicated in various cellular processes such as trafficking, signaling, and cancer metastasis. They bind to signaling and adhesion molecules, such as syndecans, neurexins, ephrin B, and phospholipid PIP2. Through its tandem PDZ domains (PDZ1 and PDZ2), syntenin links syndecans to other cell surface receptors and kinases, such as E-cadherin and ephrin-B, establishing signaling crosstalk. During syndecan binding, syntenin PDZ2 serves as a high-affinity domain, and PDZ1, also necessary for binding, acts as a complementary, low-affinity domain; this is also the case for syntenin binding to proto-oncogene c-Src. The syntenin PDZ domain-PIP2 interaction controls Arf6-mediated syndecan recycling through endosomal compartments; both PDZ1 and PDZ2 interact with PIP2. Different binding partners and downstream regulators of syntenin1 PDZ domains, such as to proto-oncogene c-Src, mitogen-activated protein kinase (MAPK), and focal adhesion kinase (FAK), have been identified that promote the progression and invasion of a variety of cancers, such as melanoma, glioblastoma multiforme and breast cancer. 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 syntenin-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: 467204 [Multi-domain]  Cd Length: 79  Bit Score: 36.83  E-value: 8.24e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568988041  725 GIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVMANAqETGNLVMDVR 782
Cdd:cd06721    23 GVFVQLVQANSPAALAGLRFGDQILQINGENVAGWSSDKAHKVLKKA-SPERITLAVR 79
LIM2_LMO4 cd09387
The second LIM domain of LMO4 (LIM domain only protein 4); The second LIM domain of LMO4 (LIM ...
1323-1380 9.18e-03

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: 35.92  E-value: 9.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041 1323 CSYCNNILgKGAAMIIETLGLSYHLHCFKCVSCGCDLggsSSGAEVRIRNHQLYC-NDC 1380
Cdd:cd09387     1 CSACGQSI-PASELVMRAQGNVYHLKCFTCSTCHNQL---VPGDRFHYVNGSLFCeHDR 55
PDZ1_L-delphilin-like cd06743
PDZ domain 1 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 ...
715-773 9.29e-03

PDZ domain 1 of delphilin (L-delphilin isoform), and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. 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 delphilin-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: 467225 [Multi-domain]  Cd Length: 76  Bit Score: 36.49  E-value: 9.29e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 568988041  715 FGFTIKWDiSGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTkkwEEVMANAQE 773
Cdd:cd06743    11 FGFSIGGS-GPCYILSVEEGSSAHAAGLQPGDQILELDGQDVSSLSC---EAIIALARR 65
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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