C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   39 WTYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPK-SPYYYWIGIRKIGKMWTWVGTNKTLTkEAENWGAG 117
Cdd:cd03592   1 WTYHYSTEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFALKyNLGYYWIDGNDINNEGTWVDTDKKEL-EYKNWAPG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6755454  118 EPNNKKSkEDCVEIYIKrerDSGKWNDDACHKRKAALCYT 157
Cdd:cd03592  80 EPNNGRN-ENCLEIYIK---DNGKWNDEPCSKKKSAICYT 115

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6755454  259 CEPLEAPELGTMDCihPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPICQ 317
Cdd:cd00033   1 CPPPPVPENGTVTG--SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57

C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels); CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. P- E- and L-sels are cell adhesion receptors that mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. L- sel is expressed constitutively on most leukocytes. P-sel is stored in the Weibel-Palade bodies of endothelial cells and in the alpha granules of platlets. E- sels are present on endothelial cells. Following platelet and/or endothelial cell activation P- sel is rapidly translocated to the cell surface and E-sel expression is induced. The initial step in leukocyte migration involves interactions of selectins with fucosylated, sialylated, and sulfated carbohydrate moieties on target ligands displayed on glycoprotein scaffolds on endothelial cells and leucocytes. A major ligand of P- E- and L-sels is PSGL-1 (P-sel glycoprotein ligand). Interactions of E- and P- sels with tumor cells may promote extravasation of cancer cells. Regulation of L-sel and P-sel function includes proteolytic shedding of the most extracellular portion (containing the CTLD) from the cell surface. Increased levels of the soluble form of P-sel in the plasma have been found in a number of diseases including coronary disease and diabetes. E- and P- sel also play roles in the development of synovial inflammation in inflammatory arthritis. Platelet P-sel, but not endothelial P-sel, plays a role in the inflammatory response and neointimal formation after arterial injury. Selectins may also function as signal-transducing receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   39 WTYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPK-SPYYYWIGIRKIGKMWTWVGTNKTLTkEAENWGAG 117
Cdd:cd03592   1 WTYHYSTEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFALKyNLGYYWIDGNDINNEGTWVDTDKKEL-EYKNWAPG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6755454  118 EPNNKKSkEDCVEIYIKrerDSGKWNDDACHKRKAALCYT 157
Cdd:cd03592  80 EPNNGRN-ENCLEIYIK---DNGKWNDEPCSKKKSAICYT 115

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454      32 IHHGTHCwtYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPK--SPYYYWIGIRKIGKMWTWVGTNKTLTK 109
Cdd:smart00034   6 ISYGGKC--YKFSTEKKTWEDAQAFCQSLGGHLASIHSEAENDFVASLLKNsgSSDYYWIGLSDPDSNGSWQWSDGSGPV 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 6755454     110 EAENWGAGEPNNkkSKEDCVEIYikreRDSGKWNDDACHKRKAALC 155
Cdd:smart00034  84 SYSNWAPGEPNN--SSGDCVVLS----TSGGKWNDVSCTSKLPFVC 123

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6755454  259 CEPLEAPELGTMDCihPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPICQ 317
Cdd:cd00033   1 CPPPPVPENGTVTG--SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57

Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 6755454     197 CEPLEAPELGTMDCIHplGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPIC 254
Cdd:smart00032   1 CPPPPDIENGTVTSSS--GTYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56

Sushi repeat (SCR repeat);

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6755454    212 HPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPIC 254
Cdd:pfam00084  14 ATKNEYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56

EEV membrane glycoprotein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   196 QCEPLEapeLGTMDCIHPLGNFSFQSKCAFNCSEGRELLGTAETQCGASgNWSSPePICQvvqcEPLEAPELGtmDCIHP 275
Cdd:PHA02954 129 ECQPLQ---LEHGSCQPVKEKYSFGEHITINCDVGYEVIGASYISCTAN-SWNVI-PSCQ----QKCDIPSLS--NGLIS 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 6755454   276 LGNFSFQSKCAFNCSEGRELLGTAETQCgASGNWSSPEPICQETNRSFSKIKEG 329
Cdd:PHA02954 198 GSTFSIGGVIHLSCKSGFTLTGSPSSTC-IDGKWNPVLPICVRSNEEFDPVDDG 250

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 6755454    160 CQPGSCNGRGECVETINNHTCICDAGYYGPQ 190
Cdd:pfam00008   1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31

C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels); CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. P- E- and L-sels are cell adhesion receptors that mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. L- sel is expressed constitutively on most leukocytes. P-sel is stored in the Weibel-Palade bodies of endothelial cells and in the alpha granules of platlets. E- sels are present on endothelial cells. Following platelet and/or endothelial cell activation P- sel is rapidly translocated to the cell surface and E-sel expression is induced. The initial step in leukocyte migration involves interactions of selectins with fucosylated, sialylated, and sulfated carbohydrate moieties on target ligands displayed on glycoprotein scaffolds on endothelial cells and leucocytes. A major ligand of P- E- and L-sels is PSGL-1 (P-sel glycoprotein ligand). Interactions of E- and P- sels with tumor cells may promote extravasation of cancer cells. Regulation of L-sel and P-sel function includes proteolytic shedding of the most extracellular portion (containing the CTLD) from the cell surface. Increased levels of the soluble form of P-sel in the plasma have been found in a number of diseases including coronary disease and diabetes. E- and P- sel also play roles in the development of synovial inflammation in inflammatory arthritis. Platelet P-sel, but not endothelial P-sel, plays a role in the inflammatory response and neointimal formation after arterial injury. Selectins may also function as signal-transducing receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   39 WTYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPK-SPYYYWIGIRKIGKMWTWVGTNKTLTkEAENWGAG 117
Cdd:cd03592   1 WTYHYSTEKMTFNEAVKYCKSRGTDLVAIQNAEENALLNGFALKyNLGYYWIDGNDINNEGTWVDTDKKEL-EYKNWAPG 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 6755454  118 EPNNKKSkEDCVEIYIKrerDSGKWNDDACHKRKAALCYT 157
Cdd:cd03592  80 EPNNGRN-ENCLEIYIK---DNGKWNDEPCSKKKSAICYT 115

C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   39 WTYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPK-SPYYYWIGIRKIGKMWTWVGTNKTLTKEAENWGAG 117
Cdd:cd00037   1 SCYKFSTEKLTWEEAQEYCRSLGGHLASIHSEEENDFLASLLKKsSSSDVWIGLNDLSSEGTWKWSDGSPLVDYTNWAPG 80

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 6755454  118 EPNNKKSkEDCVEIYIkreRDSGKWNDDACHKRKAALCY 156
Cdd:cd00037  81 EPNPGGS-EDCVVLSS---SSDGKWNDVSCSSKLPFICE 115

C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR); CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   32 IHHGTHCwtYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPkSPYYYWIGIRKIGK--MWTWV-GTnkTLT 108
Cdd:cd03590   6 KSFQSSC--YFFSTEKKSWEESRQFCEDMGAHLVIINSQEEQEFISKILS-GNRSYWIGLSDEETegEWKWVdGT--PLN 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 6755454  109 KEAENWGAGEPNNKKS-KEDCVEIYIkrerDSGKWNDDACHKRKAALC 155
Cdd:cd03590  81 SSKTFWHPGEPNNWGGgGEDCAELVY----DSGGWNDVPCNLEYRWIC 124

C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; CLECT_1: C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   40 TYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPKSPYYYWIGIRKIGKMWTWVGTNKTltkEAENWGageP 119
Cdd:cd03602   2 TFYLVNESKTWSEAQQYCRENYTDLATVQNQEDNALLSNLSRVSNSAAWIGLYRDVDSWRWSDGSES---SFRNWN---T 75

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 6755454  120 NNKKSKEDCVEIYIkrerdSGKWNDDACHKRKAALCY 156
Cdd:cd03602  76 FQPFGQGDCATMYS-----SGRWYAALCSALKPFICY 107

Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system; SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6755454  197 CEPLEAPELGTMDCihPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPICQ 255
Cdd:cd00033   1 CPPPPVPENGTVTG--SKGSYSYGSTVTYSCNEGYTLVGSSTITCTENGGWSPPPPTCE 57

C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina; CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CEL-1 CTLD binds three calcium ions and has a high specificity for N-acteylgalactosamine (GalNAc). CEL-1 exhibits strong cytotoxicity which is inhibited by GalNAc. This protein may play a role as a toxin defending against predation. Echinoidin is found in the coelomic fluid of the sea urchin and is specific for GalBeta1-3GalNAc. Echinoidin has a cell adhesive activity towards human cancer cells which is not mediated through the CTLD. Both CEL-1 and Echinoidin are multimeric proteins comprised of multiple dimers linked by disulfide bonds.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   27 CCDFLIHHGTHCWTYHYSEKPmnWENARKFCkQNYT------DLVAIQNKRE----IEYLENTLPKSPYY-YWIGI--RK 93
Cdd:cd03589   1 CPTFWTAFGGYCYRFFGDRLT--WEEAELRC-RSFSipgliaHLVSIHSQEEndfvYDLFESSRGPDTPYgLWIGLhdRT 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6755454   94 IGKMWTWV-GTNKTLTKeaenWGAGEPNNKKSKEDCVEIYiKRERDSGKWNDDACHKRKAALC 155
Cdd:cd03589  78 SEGPFEWTdGSPVDFTK----WAGGQPDNYGGNEDCVQMW-RRGDAGQSWNDMPCDAVFPYIC 135

Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 6755454     197 CEPLEAPELGTMDCIHplGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPIC 254
Cdd:smart00032   1 CPPPPDIENGTVTSSS--GTYSYGDTVTYSCDPGYTLIGSSTITCLENGTWSPPPPTC 56

A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; CLECT_VCBS: A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Bacterial CTLDs within this group are functionally uncharacterized. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   40 TYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPKSPyYYWIGIRKIGKMWTWV---GTNKTLTkeaeNWGA 116
Cdd:cd03603   2 FYKFVDGGMTWEAAQTLAESLGGHLVTINSAEENDWLLSNFGGYG-ASWIGASDAATEGTWKwsdGEESTYT----NWGS 76

                        90       100       110
                ....*....|....*....|....*....|.
gi 6755454  117 GEP-NNKKSKEDCVEIYIKRErDSGKWNDDA 146
Cdd:cd03603  77 GEPhNNGGGNEDYAAINHFPG-ISGKWNDLA 106

C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins; CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   37 HCwtYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENtlpKSPYYYWIGI--RKIGKMWTWVGTNKTLTkeaENW 114
Cdd:cd03588  11 HC--YRHFPDRETWEDAERRCREQQGHLSSIVTPEEQEFVNN---NAQDYQWIGLndRTIEGDFRWSDGHPLQF---ENW 82

                        90       100       110
                ....*....|....*....|....*....|....*
gi 6755454  115 GAGEPNNK-KSKEDCVeIYIKRERdsGKWNDDACH 148
Cdd:cd03588  83 RPNQPDNFfATGEDCV-VMIWHEE--GEWNDVPCN 114

EEV host range protein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   233 LLGTAETQCGASGNWSSPEPICQVVQCEpLEAPELGTMDCIHPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSP 312
Cdd:PHA02639 123 LVGNEKITCIQDKSWKPDPPICKMINCR-FPALQNGYINGIPSNKKFYYKTRVGFSCKSGFDLVGEKYSTCNINATWFPS 201

                 ....
gi 6755454   313 EPIC 316
Cdd:PHA02639 202 IPTC 205

C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   34 HGTHCwtYHYSEKPMNWENARKFCKQNYTDLVAIQNKREIEYLENTLPksPYYYWIGIR--KIGKMWTWV 101
Cdd:cd03593   8 YGNKC--YYFSMEKKTWNESKEACSSKNSSLLKIDDEEELEFLQSQIG--SSSYWIGLSreKSEKPWKWI 73

Sushi repeat (SCR repeat);

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 6755454    274 HPLGNFSFQSKCAFNCSEGRELLGTAETQCGASGNWSSPEPIC 316
Cdd:pfam00084  14 ATKNEYNYGASVSYECDPGYRLVGSPTITCQEDGTWSPPFPEC 56

EEV membrane glycoprotein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755454   196 QCEPLEapeLGTMDCIHPLGNFSFQSKCAFNCSEGRELLGTAETQCGASgNWSSPePICQvvqcEPLEAPELGtmDCIHP 275
Cdd:PHA02954 129 ECQPLQ---LEHGSCQPVKEKYSFGEHITINCDVGYEVIGASYISCTAN-SWNVI-PSCQ----QKCDIPSLS--NGLIS 197

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 6755454   276 LGNFSFQSKCAFNCSEGRELLGTAETQCgASGNWSSPEPICQETNRSFSKIKEG 329
Cdd:PHA02954 198 GSTFSIGGVIHLSCKSGFTLTGSPSSTC-IDGKWNPVLPICVRSNEEFDPVDDG 250

EGF-like domain; There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 6755454    160 CQPGSCNGRGECVETINNHTCICDAGYYGPQ 190
Cdd:pfam00008   1 CAPNPCSNGGTCVDTPGGYTCICPEGYTGKR 31