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 1207184730   14 VYSEAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1207184730   94 GDLQDLSTRVTVKHQESSRRLKNVLITIYWLGRKAH 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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207184730  239 YRRSQVIAPKTTTQFNQFLPSRDKQSGYVPAPLRKKRAERNEDSRRSW-----ASPMFTEDDGTFTSPSPEMAGSDSS 311
Cdd:pfam15949    3 ARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQRLFQKVSDDLGS 80

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).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184730 1824 CSFCDTPLGkgAAMIIESLGLCYHLTCFKCSDCRSDLGGSqagaEVRIRNQQLYCNVCY 1882
Cdd:cd08368      1 CAGCGKPIE--GRELLRALGKKWHPECFKCAECGKPLGGD----SFYEKDGKPYCEKCY 53

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730 1396 EEERKRQEKwQKEQDRLLKEKyKKDQEKLDEEWKKAQQElnkenfkndEELNRHSLSTIRQPTvsweeQNASKLAQIEED 1475
Cdd:pfam15236   75 EEERRRQEE-QEEEERLRRER-EEEQKQFEEERRKQKEK---------EEAMTRKTQALLQAM-----QKAQELAQRLKQ 138

                   ....*....
gi 1207184730 1476 KKKRQEEMQ 1484
Cdd:pfam15236  139 EQRIRELAE 147

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 1207184730   14 VYSEAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1207184730   94 GDLQDLSTRVTVKHQESSRRLKNVLITIYWLGRKAH 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        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207184730  239 YRRSQVIAPKTTTQFNQFLPSRDKQSGYVPAPLRKKRAERNEDSRRSW-----ASPMFTEDDGTFTSPSPEMAGSDSS 311
Cdd:pfam15949    3 ARRTSSSEPKSSVPFNQFLPNKSNQSAYVPAPLRKKRAEKEEDIRRSWstrtqPSKVAYPPRQFVQRLFQKVSDDLGS 80

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 1207184730    17 EAQRWIEAVTKK--KFGNSNFRSSLENGLLLCDLINKIKPGII--KKLNRFSTPIAGLDNINLFLKACAKLGLKEaQLFH 92
Cdd:smart00033    2 TLLRWVNSLLAEydKPPVTNFSSDLKDGVALCALLNSLSPGLVdkKKVAASLSRFKKIENINLALSFAEKLGGKV-VLFE 80

                    ....*.
gi 1207184730    93 PGDLQD 98
Cdd:smart00033   81 PEDLVE 86

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207184730 1181 NSSRDFGFQ---HDWDSTGVRVKSVAPGSPAEF-GQVQAGDEILTVNGHRVADMSYSE 1234
Cdd:cd00136      7 DPGGGLGFSirgGKDGGGGIFVSRVEPGGPAARdGRLRVGDRILEVNGVSLEGLTHEE 64

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.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184730  1823 ICSFCDTPLGkGAAMIIESLGLCYHLTCFKCSDCRSDLGGSqagaEVRIRNQQLYCNVC 1881
Cdd:smart00132    1 KCAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPLSGD----TFFEKDGKLYCKDC 54

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730 1134 EEEEVERTqspvppVNRVSPLP---------KSTSPLnPPNE----VGYnemRISLNQKPNSSRDFGFQHDWDSTGVRVK 1200
Cdd:COG3975    430 TEDDVQAA------LEEVAGYDladffdryvYGTEDL-PLAEllapFGL---KLVYEDAPSLKPSLGLRVSADGGGLVVT 499

                           90       100
                   ....*....|....*....|....*..
gi 1207184730 1201 SVAPGSPAEFGQVQAGDEILTVNGHRV 1227
Cdd:COG3975    500 SVLWGSPAYKAGLSAGDELLAIDGLRV 526

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207184730 1824 CSFCDTPLGkgAAMIIESLGLCYHLTCFKCSDCRSDLGGSqagaEVRIRNQQLYCNVCYMRLK 1886
Cdd:pfam00412    1 CAGCNRPIY--DRELVRALGKVWHPECFRCAVCGKPLTTG----DFYEKDGKLYCKHDYYKLF 57

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207184730 1193 DSTGVRVKSVAPGSPAEFGQVQAGDEILTVNGHRVAdmSYSEWKNSMEEALQQGSLLMDIRRQG 1256
Cdd:TIGR02037  360 DVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVS--SVAELRKVLARAKKGGRVALLILRGG 421

Coiled-coil domain-containing protein 66; This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730 1396 EEERKRQEKwQKEQDRLLKEKyKKDQEKLDEEWKKAQQElnkenfkndEELNRHSLSTIRQPTvsweeQNASKLAQIEED 1475
Cdd:pfam15236   75 EEERRRQEE-QEEEERLRRER-EEEQKQFEEERRKQKEK---------EEAMTRKTQALLQAM-----QKAQELAQRLKQ 138

                   ....*....
gi 1207184730 1476 KKKRQEEMQ 1484
Cdd:pfam15236  139 EQRIRELAE 147

DNA topoisomerase 2-like protein; Provisional

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730  809 NSTMELRLEELQKMRNrlKESEDKWQDDLSRWKskrrsvnsdivKKKEEREQIEQITSVGTRKSKTfKEMQDERESRGQS 888
Cdd:PTZ00108  1108 NAELEKKEKELEKLKN--TTPKDMWLEDLDKFE-----------EALEEQEEVEEKEIAKEQRLKS-KTKGKASKLRKPK 1173

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730  889 nLRDSFNSIVDDVFEDPVPRSRTLPPRSYTIDTPYTATDKPfvpsipsLREKEPVAGTLASDQTDLSTKPARASPDIPDK 968
Cdd:PTZ00108  1174 -LKKKEKKKKKSSADKSKKASVVGNSKRVDSDEKRKLDDKP-------DNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKS 1245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730  969 INNSNQMSQTTTQSLLDDPVPAFSNSSTsliKPASATKPTSSTKPNISEFISNTKPAESSSDAIsslyKPNSMDTKPSGL 1048
Cdd:PTZ00108  1246 KKNNSSKSSEDNDEFSSDDLSKEGKPKN---APKRVSAVQYSPPPPSKRPDGESNGGSKPSSPT----KKKVKKRLEGSL 1318

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 1207184730 1049 DQVSASLPKIYQRSDSARLTSVVMPRPfGTQSNRIASLPRAFTMDDSV 1096
Cdd:PTZ00108  1319 AALKKKKKSEKKTARKKKSKTRVKQAS-ASQSSRLLRRPRKKKSDSSS 1365

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 1207184730   14 VYSEAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHP 93
Cdd:cd21277      1 AFSEAQRWIEAVTGKNFGNKDFRSALENGVLLCDLINKIKPGIIKKINRLSTPIAGLDNINVFLKACEKLGLKEAQLFHP 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1207184730   94 GDLQDLSTRVTVKHQESSRRLKNVLITIYWLGRKAH 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 1207184730   15 YSEAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHPG 94
Cdd:cd21278      2 FTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDPG 81

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1207184730   95 DLQDLSTRVTVKHQESSRRLKNVLITIYWLGRKAHA 130
Cdd:cd21278     82 DLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANS 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 1207184730   16 SEAQRWIEAVTKKKFGNS--NFRSSLENGLLLCDLINKIKPGIIKKLNRFS-TPIAGLDNINLFLKACAKLGLKEAQLFH 92
Cdd:cd00014      2 EELLKWINEVLGEELPVSitDLFESLRDGVLLCKLINKLSPGSIPKINKKPkSPFKKRENINLFLNACKKLGLPELDLFE 81

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1207184730   93 PGDLQDlstrvtvkhqesSRRLKNVLITIYWLGR 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 1207184730   17 EAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHPGDL 96
Cdd:cd21210      4 EAREWIEEVLGEKLAQGDLLDALKDGVVLCKLANRILPADIRKYKESKMPFVQMENISAFLNAARKLGVPENDLFQTVDL 83

                           90       100       110
                   ....*....|....*....|....*....|
gi 1207184730   97 QDlstrvtvkhqesSRRLKNVLITIYWLGR 126
Cdd:cd21210     84 FE------------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 1207184730   16 SEAQRWIEAVTKKKFGNsNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHPGD 95
Cdd:cd21211      6 AELRTWIEGVTGLSIGP-NFQKGLKDGIILCELINKLQPGSVKKINESMQNWHQLENIGNFIKAIVSYGMKPHDIFEAND 84

                   .
gi 1207184730   96 L 96
Cdd:cd21211     85 L 85

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 1207184730   17 EAQRWIEAVTKKKFGNsNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACAKLGLKEAQLFHPGDL 96
Cdd:cd21282      7 ELRVWIEGVTGRRIGD-NFMDGLKDGVILCELINKLQPGSVRKINESTQNWHKLENIGNFIKAIMHYGVKPHDIFEANDL 85

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207184730   20 RWIEAVTKKKFGN---SNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTPIAGLDNINLFLKACA-KLGLKE 87
Cdd:pfam00307    9 RWINSHLAEYGPGvrvTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKLENINLALDVAEkKLGVPK 80

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 1207184730   36 RSSLENGLLLCDLINKIKPGIIKKLnrFSTPIAG---LDNINLFLKACAKLGLKEAQLFHPGDL 96
Cdd:cd21202     31 SESLKNGVVLCRLVNRLKPGTVEKI--YDEPTTEeecLYNFESFLKACQELGILAEEIFDPNDL 92

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.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207184730   17 EAQRWIEAVTKK-KFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFSTpiaGL-----DNINLFLKACAKLGLKEaqL 90
Cdd:cd21206     12 EAKQWIEACLNEeLPPTTEFEEELRNGVVLAKLANKFAPKLVPLKKIYDV---GLqfrhtDNINHFLRALKKIGLPK--I 86

                   ....*....
gi 1207184730   91 FHPgDLQDL 99
Cdd:cd21206     87 FHF-ETTDL 94

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1207184730 1181 NSSRDFGFQ---HDWDSTGVRVKSVAPGSPAEF-GQVQAGDEILTVNGHRVADMSYSE 1234
Cdd:cd00136      7 DPGGGLGFSirgGKDGGGGIFVSRVEPGGPAARdGRLRVGDRILEVNGVSLEGLTHEE 64

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184730   32 NSNFRSSLENGLLLCDLINKIKPGII--KKLNRFS--TPIAGLDNINLFLKACAKLGLK 86
Cdd:cd21217     30 GDDLFEALRDGVLLCKLINKIVPGTIdeRKLNKKKpkNIFEATENLNLALNAAKKIGCK 88

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.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1207184730  1823 ICSFCDTPLGkGAAMIIESLGLCYHLTCFKCSDCRSDLGGSqagaEVRIRNQQLYCNVC 1881
Cdd:smart00132    1 KCAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPLSGD----TFFEKDGKLYCKDC 54

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

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1207184730 1186 FGFQHDWDSTGVRVKSVAPGSPAEFGQVQAGDEILTVNGHRVADMSYSE 1234
Cdd:COG0793     62 LGAELGEEDGKVVVVSVIPGSPAEKAGIKPGDIILAIDGKSVAGLTLDD 110

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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207184730 1173 RISLNQKPnsSRDFGFQ----HDWD-STGVRVKSVAPGSPAEF-GQVQAGDEILTVNGHRVADMS 1231
Cdd:cd06718      2 RVELIKPP--GKPLGFYirdgNGVErVPGIFISRLVLGSLADStGLLAVGDEILEVNGVEVTGKS 64

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 1207184730   36 RSSLENGLLLCDLINKIKPGIIKKL-NRFSTPIAGLDNINLFLKACAKLGLkeaQLFHPGDL 96
Cdd:cd21265     32 KSSLKDGVVLCKLIERLLPGSVEKYcLEPKTEADCIGNIKEFLKGCAALKV---ETFEPDDL 90

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1207184730 1197 VRVKSVAPGSPA-EFGQVQAGDEILTVNGHRVADMSYSEWKNSMEEALQQGSLLM 1250
Cdd:cd06695     33 VRIKKLFPGQPAaESGLIQEGDVILAVNGEPLKGLSYQEVLSLLRGAPPEVTLLL 87

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207184730 1824 CSFCDTPLGkgAAMIIESLGLCYHLTCFKCSDCRSDLGGSqagaEVRIRNQQLYCNVCYMRLK 1886
Cdd:pfam00412    1 CAGCNRPIY--DRELVRALGKVWHPECFRCAVCGKPLTTG----DFYEKDGKLYCKHDYYKLF 57

circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains; PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. 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 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 HtrA-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.

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207184730 1194 STGVRVKSVAPGSPAEFGQVQAGDEILTVNGHRVadmsysewKNSME--EALQQG-SLLMDIRR 1254
Cdd:cd06785     30 SSGVYVHKVIPGSPAQRAGLKDGDVIISINGKPV--------KSSSDvyEAVKSGsSLLVVVRR 85

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];

                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1207184730 1194 STGVRVKSVAPGSPAEfGQVQAGDEILTVNGHRVAD 1229
Cdd:COG3480    137 TEGVYVASVLEGSPAD-GVLQPGDVITAVDGKPVTT 171

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1207184730 1186 FGF--QHDWDSTGVRVKSVAPGSPAEFGQVQAGDEILTVNGHRVADMSYSE 1234
Cdd:cd06768     12 YGFnlHAEKGRPGHFIREVDPGSPAERAGLKDGDRLVEVNGENVEGESHEQ 62

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 1207184730   10 DYETVYSEAQRWIEAVTKKKFGNSNFRSSLENGLLLCDLINKIKPGIIKKLNRFST-PIAGLDNINLFLKACAKLGLKEa 88
Cdd:COG5261     41 EYLCRVSEAKIWIEEVIEEALPELCFEDSLRNGVFLAKLTQRFNPDLTTVIFPADKlQFRHTDNINAFLDLIEHVGLPE- 119

                           90
                   ....*....|.
gi 1207184730   89 qLFHpGDLQDL 99
Cdd:COG5261    120 -SFH-FELQDL 128

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]