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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907102160   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277     81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907102160  242 MSYRRISAIEPKSALPFNRFLPNKSKQPSYVPAPLRKKRPDKHEDNRRSW-----ASPVYTETDGTFS 304
Cdd:pfam15949    1 MLARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQ 68

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907102160   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277     81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907102160  242 MSYRRISAIEPKSALPFNRFLPNKSKQPSYVPAPLRKKRPDKHEDNRRSW-----ASPVYTETDGTFS 304
Cdd:pfam15949    1 MLARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQ 68

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   20 RWVEAVTEKNFET---TDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQ-IGLKEAQLfhpgD 95
Cdd:pfam00307    9 RWINSHLAEYGPGvrvTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKLENINLALDVAEKkLGVPKVLI----E 84

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907102160   96 LQDLsnrvtvkqeeTDRRLKNVLITLYWLGRKAQS 130
Cdd:pfam00307   85 PEDL----------VEGDNKSVLTYLASLFRRFQA 109

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907102160 1109 TPGNKPVFGFTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSykdTKKWEEVMANAQETGNLVMDVRRYGK 1187
Cdd:COG3975    478 APSLKPSLGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVT---ADNLDDALAAYKPGDPIELLVFRRDE 553

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1907102160 1116 FGFTIK----WDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFS 1158
Cdd:pfam00595   12 LGFSLKggsdQGDPGIFVSEVLPGGAAEAGGLKVGDRILSINGQDVE 58

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]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1085 RGSPLREVSRSLDQFSDmrvsiNQTPGNKPVFGFT-------------IKWDISGIFVASVEQGSPAEFSQLQVDDEILA 1151
Cdd:TIGR02037  314 RKGKEKTITVTLGASPE-----EQASSSNPFLGLTvanlspeirkelrLKGDVKGVVVTKVVSGSPAARAGLQPGDVILS 388

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1907102160 1152 INNTkfSYKDTKKWEEVMANAQETGNLVMDVRR 1184
Cdd:TIGR02037  389 VNQQ--PVSSVAELRKVLARAKKGGRVALLILR 419

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907102160   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQ 129
Cdd:cd21277     81 GDLQDLSTRVTVKQEETDRRLKNVLITLYWLGRKAQ 116

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   14 AFAEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHP 93
Cdd:cd21278      1 AFTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDP 80

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1907102160   94 GDLQDLSNRVTVKQEETDRRLKNVLITLYWLGRKAQS 130
Cdd:cd21278     81 GDLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANS 117

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).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   16 AEAQRWVEAVTEKNF--ETTDFRASLENGVLLCDLINKLKPGVVKKINRLS-TPIAGLDNINVFLRACEQIGLKEAQLFH 92
Cdd:cd00014      2 EELLKWINEVLGEELpvSITDLFESLRDGVLLCKLINKLSPGSIPKINKKPkSPFKKRENINLFLNACKKLGLPELDLFE 81

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1907102160   93 PGDLQDlsnrvtvkqeetDRRLKNVLITLYWLGR 126
Cdd:cd00014     82 PEDLYE------------KGNLKKVLGTLWALAL 103

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   16 AEAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21210      3 QEAREWIEEVLGEKLAQGDLLDALKDGVVLCKLANRILPADIRKYKESKMPFVQMENISAFLNAARKLGVPENDLFQTVD 82

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1907102160   96 LQDlsnrvtvkqeetDRRLKNVLITLYWLGR 126
Cdd:cd21210     83 LFE------------RKNPAQVLQCLHALSR 101

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   16 AEAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21211      6 AELRTWIEGVTGLSI-GPNFQKGLKDGIILCELINKLQPGSVKKINESMQNWHQLENIGNFIKAIVSYGMKPHDIFEAND 84

                           90
                   ....*....|.
gi 1907102160   96 LQDLSNRVTVK 106
Cdd:cd21211     85 LFENGNMTQVQ 95

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   16 AEAQRWVEAVTEKNFeTTDFRASLENGVLLCDLINKLKPGVVKKINRLSTPIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:cd21282      6 EELRVWIEGVTGRRI-GDNFMDGLKDGVILCELINKLQPGSVRKINESTQNWHKLENIGNFIKAIMHYGVKPHDIFEAND 84

                           90
                   ....*....|.
gi 1907102160   96 LQDLSNRVTVK 106
Cdd:cd21282     85 LFENTNHTQVQ 95

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.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160    17 EAQRWVEAVTEKNFE--TTDFRASLENGVLLCDLINKLKPGVV--KKINRLSTPIAGLDNINVFLRACEQIGLKEaQLFH 92
Cdd:smart00033    2 TLLRWVNSLLAEYDKppVTNFSSDLKDGVALCALLNSLSPGLVdkKKVAASLSRFKKIENINLALSFAEKLGGKV-VLFE 80

                    ....*.
gi 1907102160    93 PGDLQD 98
Cdd:smart00033   81 PEDLVE 86

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907102160   34 DFRASLENGVLLCDLINKLKPGVVKKINRLSTP----IAGLDNINVFLRAC-EQIGLKEAQLFHPGDLQDLSN 101
Cdd:cd21201     31 DLAQALRDGVLLCQLLNRLSPGSVDDREINLRPqmsqFLCLKNIRTFLQACrTVFGLRSADLFEPEDLYDVTN 103

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907102160   36 RASLENGVLLCDLINKLKPGVVKKInrLSTPIAG---LDNINVFLRACEQIGLKEAQLFHPGDL 96
Cdd:cd21202     31 SESLKNGVVLCRLVNRLKPGTVEKI--YDEPTTEeecLYNFESFLKACQELGILAEEIFDPNDL 92

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   20 RWVEAVTEKNFETTDFRASLENGVLLCDLINKL--------------KPGVVKKI----NRLSTPIAGLDNINVFLRACE 81
Cdd:cd21204     13 EWLNDLLGDDLTPDNFLDELRNGVVLCQLAQKIqeaaekareagkknGPPPSYKLkcneNAKPGSFFARDNVANFLRWCR 92

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1907102160   82 QIGLKEAQLFHPGDLqdlsnrVTVKQEetdrrlKNVLITLYWLGRKAQS 130
Cdd:cd21204     93 KLGVDEVLLFESEDL------VLHKNP------RQVLLCLLELARIAAR 129

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907102160   34 DFRASLENGVLLCDLINKLKPGVVKKI--------NRLSTPIAGLDNINVFLRACEQIGLKeaqLFHPGDLQ 97
Cdd:cd21203     25 EFRLCLRDGVVLCKLLNKLQPGAVPKVvespddpdGAAGSAFQYFENVRNFLVAIEEMGLP---TFEASDLE 93

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907102160 1109 TPGNKPVFGFTIKWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSykdTKKWEEVMANAQETGNLVMDVRRYGK 1187
Cdd:COG3975    478 APSLKPSLGLRVSADGGGLVVTSVLWGSPAYKAGLSAGDELLAIDGLRVT---ADNLDDALAAYKPGDPIELLVFRRDE 553

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   17 EAQRWVEAVTEKNFETTDFRASLENGVLLCDLINKLKPGVVKKINRLST-PIAGLDNINVFLRACEQIGLKEAQLFHPGD 95
Cdd:COG5261     48 EAKIWIEEVIEEALPELCFEDSLRNGVFLAKLTQRFNPDLTTVIFPADKlQFRHTDNINAFLDLIEHVGLPESFHFELQD 127

                           90
                   ....*....|
gi 1907102160   96 LQDLSNRVTV 105
Cdd:COG5261    128 LYEKKNIPKV 137

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907102160   36 RASLENGVLLCDLINKLKPGVVKKI-NRLSTPIAGLDNINVFLRACEQIGLkeaQLFHPGDL 96
Cdd:cd21265     32 KSSLKDGVVLCKLIERLLPGSVEKYcLEPKTEADCIGNIKEFLKGCAALKV---ETFEPDDL 90

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   25 VTEKNFETTDFRASLENGVLLCDLINKLKPGVV--KKIN---RLSTPIAgLDNINVFLRAC-EQIGLKEAQLFHPGDLQD 98
Cdd:cd21262     22 VTWDSAQVCDLAQALRDGVLLCQLLNNLLPHAVnlREINlrpQMSQFLC-LKNIRTFLSTCcEKFGLRKSELFEAFDLFD 100

                   .
gi 1907102160   99 L 99
Cdd:cd21262    101 V 101

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160   17 EAQRWVEAVTEKNFET-TDFRASLENGVLLCDLINKLKPGVV--KKI---NRLSTPIAGL-----DNINVFLRACEQIGL 85
Cdd:cd21276     12 EAKRWMEACLKEELPPpTELEESLRNGVYLAKLGHCFAPRVVplKKIydlEQMRYQATGLhfrhtDNINHWRNAMMHIGL 91

                           90
                   ....*....|....*...
gi 1907102160   86 keAQLFHP--GDLQDLSN 101
Cdd:cd21276     92 --PSIFHPetTDIYDKKN 107

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1103 RVSINQTPGnKPvFGFTIK----WD-ISGIFVASVEQGSPAEFSQ-LQVDDEILAINNTKFSYKDTkkwEEVMANAQETG 1176
Cdd:cd06718      2 RVELIKPPG-KP-LGFYIRdgngVErVPGIFISRLVLGSLADSTGlLAVGDEILEVNGVEVTGKSL---DDVTDMMVAPT 76

                   ....*...
gi 1907102160 1177 NLVMDVRR 1184
Cdd:cd06718     77 RLIITVKP 84

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1116 FGFTIKWDiSGIFVASVEQGSPAEFSQLQVDDEILAINNtkfsyKDTK--KWEEVMANAQETGNLVMDVR 1183
Cdd:cd06712     13 FGFTLRGD-SPVQVASVDPGSCAAEAGLKEGDYIVSVGG-----VDCKwsKHSEVVKLLKSAGEEGLELQ 76

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907102160   34 DFRASLENGVLLCDLINKLKPGVV--KKIN---RLSTPIAgLDNINVFLRAC-EQIGLKEAQLFHPGDLQDLSN 101
Cdd:cd21263     31 DLAQALRDGVLLCQLLHNLSPGSIdlKDINfrpQMSQFLC-LKNIRTFLKVChDKFGLRNSELFDPFDLFDVRD 103

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.

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1104 VSINQTPGNKpvFGFTIKWDIS---GIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVManaqeTGN--L 1178
Cdd:cd10833      4 VTVEKSPDGS--LGFSVRGGSEhglGIFVSKVEEGSAAERAGLCVGDKITEVNGVSLENITMSSAVKVL-----TGSnrL 76

                   ....*...
gi 1907102160 1179 VMDVRRYG 1186
Cdd:cd10833     77 RMVVRRMG 84

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907102160 1105 SINQTPGNKPvfgftikwdisGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKkwEEVMA 1170
Cdd:cd06738     18 SISSGPTQKP-----------GIFISNVKPGSLAEEVGLEVGDQIVEVNGTSFTNVDHK--EAVMA 70

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]

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                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1085 RGSPLREVSRSLDQFSDmrvsiNQTPGNKPVFGFT-------------IKWDISGIFVASVEQGSPAEFSQLQVDDEILA 1151
Cdd:TIGR02037  314 RKGKEKTITVTLGASPE-----EQASSSNPFLGLTvanlspeirkelrLKGDVKGVVVTKVVSGSPAARAGLQPGDVILS 388

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1907102160 1152 INNTkfSYKDTKKWEEVMANAQETGNLVMDVRR 1184
Cdd:TIGR02037  389 VNQQ--PVSSVAELRKVLARAKKGGRVALLILR 419

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1103 RVSINQTPGNKPVfGFTI---KWDISGIFVASVEQGSPAEFSQLQVDDEILAINNTKFSYKDTKKWEEVMANAQEtgnLV 1179
Cdd:cd06752      1 RTVVLKRPPGEQL-GFNIrggKASGLGIFISKVIPDSDAHRLGLKEGDQILSVNGVDFEDIEHSEAVKVLKTARE---IQ 76

                   ....*.
gi 1907102160 1180 MDVRRY 1185
Cdd:cd06752     77 MRVRYF 82

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907102160 1129 VASVEQGSPAEFSQLQVDDEILAINNTKFSYkdtkkWEEVMANAQETGN--LVMDVRRYGK 1187
Cdd:COG0750    132 VGEVVPGSPAAKAGLQPGDRIVAINGQPVTS-----WDDLVDIIRASPGkpLTLTVERDGE 187

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907102160 1125 SGIFVASVEQGSPAEfSQLQVDDEILAINNTKFSYKDTKKWEEVMANAQETGNLVmdVRR 1184
Cdd:cd06764     38 CSIFVTKVDKGSIAD-GRLRVNDCLLRINDVDLTNKDKKQAIQAVLNGGGVINMV--VRR 94