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Conserved domains on  [gi|4757946|ref|NP_004224|]
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CD83 antigen isoform a precursor [Homo sapiens]

Protein Classification

immunoglobulin domain-containing family protein (domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
21-127 6.68e-06

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member pfam07686:

Pssm-ID: 416386  Cd Length: 109  Bit Score: 43.60  E-value: 6.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     21 PEVKVACSEDVDLPCT-APWDPQVPYTVSWVklleggeeRMETPQEDHLRGQHYHQKGQNGSFDA-------PNERPYSL 92
Cdd:pfam07686   4 RSVTVALGGSVTLPCTySSSMSEASTSVYWY--------RQPPGKGPTFLIAYYSNGSEEGKKKGrfslrgdPSNSDGSL 75
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 4757946     93 KIRNTTSCNSGTYRCTLqDPDGQRNLSGKVILRVT 127
Cdd:pfam07686  76 TIQNLTLSDSGTYTCAV-IPSGEGVFGKGTRLTVL 109
 
Name Accession Description Interval E-value
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
21-127 6.68e-06

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 400157  Cd Length: 109  Bit Score: 43.60  E-value: 6.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     21 PEVKVACSEDVDLPCT-APWDPQVPYTVSWVklleggeeRMETPQEDHLRGQHYHQKGQNGSFDA-------PNERPYSL 92
Cdd:pfam07686   4 RSVTVALGGSVTLPCTySSSMSEASTSVYWY--------RQPPGKGPTFLIAYYSNGSEEGKKKGrfslrgdPSNSDGSL 75
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 4757946     93 KIRNTTSCNSGTYRCTLqDPDGQRNLSGKVILRVT 127
Cdd:pfam07686  76 TIQNLTLSDSGTYTCAV-IPSGEGVFGKGTRLTVL 109
IG smart00409
Immunoglobulin;
21-126 4.56e-04

Immunoglobulin;


Pssm-ID: 214652  Cd Length: 85  Bit Score: 37.87  E-value: 4.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946      21 PEVKVACSEDVDLPCTAPwdPQVPYTVSWVKlleggeermeTPQEDHLRGQHYHQKGQNGSFdapnerpySLKIRNTTSC 100
Cdd:smart00409   2 PSVTVKEGESVTLSCEAS--GSPPPEVTWYK----------QGGKLLAESGRFSVSRSGSTS--------TLTISNVTPE 61
                           90       100
                   ....*....|....*....|....*.
gi 4757946     101 NSGTYRCTLQDPDGQrnLSGKVILRV 126
Cdd:smart00409  62 DSGTYTCAATNSSGS--ASSGTTLTV 85
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
20-129 5.88e-04

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), 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. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 38.08  E-value: 5.88e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946   20 TPEVKV--ACSEDVDLPCTAPWDPQVP----YTVSWVKLleggeERMETPQEDHLRGQHYHQKgQNGSFD------APNE 87
Cdd:cd05877   2 TVQAKVfsHRGGNVTLPCRYHYEPELSaprkIRVKWTKL-----EVDYAKEEDVLVAIGTRHK-SYGSYQgrvflrRADD 75
                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 4757946   88 RPYSLKIRNTTSCNSGTYRCTLQdpDGQRNLSGKVILRVTGC 129
Cdd:cd05877  76 LDASLVITDLRLEDYGRYRCEVI--DGLEDESVVVALRLRGV 115
 
Name Accession Description Interval E-value
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
21-127 6.68e-06

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 400157  Cd Length: 109  Bit Score: 43.60  E-value: 6.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     21 PEVKVACSEDVDLPCT-APWDPQVPYTVSWVklleggeeRMETPQEDHLRGQHYHQKGQNGSFDA-------PNERPYSL 92
Cdd:pfam07686   4 RSVTVALGGSVTLPCTySSSMSEASTSVYWY--------RQPPGKGPTFLIAYYSNGSEEGKKKGrfslrgdPSNSDGSL 75
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 4757946     93 KIRNTTSCNSGTYRCTLqDPDGQRNLSGKVILRVT 127
Cdd:pfam07686  76 TIQNLTLSDSGTYTCAV-IPSGEGVFGKGTRLTVL 109
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
18-119 7.56e-05

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 39.87  E-value: 7.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     18 PATPEVKVACSEDVDLPCTA-PWDPQVpyTVSWVKllEGGEermetpqedhLRGQHYHQKGQNGSFDApnerpySLKIRN 96
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSAsTGSPGP--DVTWSK--EGGT----------LIESLKVKHDNGRTTQS------SLLISN 60
                          90       100
                  ....*....|....*....|...
gi 4757946     97 TTSCNSGTYRCTLQDPDGQRNLS 119
Cdd:pfam00047  61 VTKEDAGTYTCVVNNPGGSATLS 83
IG smart00409
Immunoglobulin;
21-126 4.56e-04

Immunoglobulin;


Pssm-ID: 214652  Cd Length: 85  Bit Score: 37.87  E-value: 4.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946      21 PEVKVACSEDVDLPCTAPwdPQVPYTVSWVKlleggeermeTPQEDHLRGQHYHQKGQNGSFdapnerpySLKIRNTTSC 100
Cdd:smart00409   2 PSVTVKEGESVTLSCEAS--GSPPPEVTWYK----------QGGKLLAESGRFSVSRSGSTS--------TLTISNVTPE 61
                           90       100
                   ....*....|....*....|....*.
gi 4757946     101 NSGTYRCTLQDPDGQrnLSGKVILRV 126
Cdd:smart00409  62 DSGTYTCAATNSSGS--ASSGTTLTV 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
21-126 4.56e-04

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653  Cd Length: 85  Bit Score: 37.87  E-value: 4.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946      21 PEVKVACSEDVDLPCTAPwdPQVPYTVSWVKlleggeermeTPQEDHLRGQHYHQKGQNGSFdapnerpySLKIRNTTSC 100
Cdd:smart00410   2 PSVTVKEGESVTLSCEAS--GSPPPEVTWYK----------QGGKLLAESGRFSVSRSGSTS--------TLTISNVTPE 61
                           90       100
                   ....*....|....*....|....*.
gi 4757946     101 NSGTYRCTLQDPDGQrnLSGKVILRV 126
Cdd:smart00410  62 DSGTYTCAATNSSGS--ASSGTTLTV 85
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
20-129 5.88e-04

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), 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. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 38.08  E-value: 5.88e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946   20 TPEVKV--ACSEDVDLPCTAPWDPQVP----YTVSWVKLleggeERMETPQEDHLRGQHYHQKgQNGSFD------APNE 87
Cdd:cd05877   2 TVQAKVfsHRGGNVTLPCRYHYEPELSaprkIRVKWTKL-----EVDYAKEEDVLVAIGTRHK-SYGSYQgrvflrRADD 75
                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 4757946   88 RPYSLKIRNTTSCNSGTYRCTLQdpDGQRNLSGKVILRVTGC 129
Cdd:cd05877  76 LDASLVITDLRLEDYGRYRCEVI--DGLEDESVVVALRLRGV 115
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
31-114 5.89e-04

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409353  Cd Length: 70  Bit Score: 36.92  E-value: 5.89e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946   31 VDLPCTAPWDPqvPYTVSWVKlleggeERMETPQEDHLRGQHYHQKGqngsfdapnerpySLKIRNTTSCNSGTYRCTLQ 110
Cdd:cd00096   1 VTLTCSASGNP--PPTITWYK------NGKPLPPSSRDSRRSELGNG-------------TLTISNVTLEDSGTYTCVAS 59

                ....
gi 4757946  111 DPDG 114
Cdd:cd00096  60 NSAG 63
Ig_CSPGs_LP_like cd05714
Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage ...
20-107 1.29e-03

Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. There is considerable evidence that HA-binding CSPGs are involved in developmental processes in the central nervous system. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409379  Cd Length: 123  Bit Score: 37.19  E-value: 1.29e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946   20 TPEVKVACSEDVDLPCTAPWDPQVPYT------VSWVKLLEGGEERMETPQEDHLRGQHYHQK---GQNGSFDAPNERP- 89
Cdd:cd05714   4 SAKVFSHLGGNVTLPCKFYRDPTAFGSgihkirIKWTKLTSDSGYLKEVDVLVAMGNVVYHKKtygGRVSVPLKPGSDSd 83
                        90
                ....*....|....*...
gi 4757946   90 YSLKIRNTTSCNSGTYRC 107
Cdd:cd05714  84 ASLVITDLTASDYGLYRC 101
IgV_1_JAM1-like cd20946
First Ig-like domain of Junctional adhesion molecule-1 (JAM1)and similar domains; a member of ...
15-118 2.19e-03

First Ig-like domain of Junctional adhesion molecule-1 (JAM1)and similar domains; a member of the V-set of IgSF domains; The members here are composed of the first Ig-like domain of Junctional Adhesion Molecule-1 (JAM1)and similar domains. JAM1 is an immunoglobulin superfamily (IgSF) protein with two Ig-like domains in its extracellular region; it plays a role in the formation of endothelial and epithelial tight junction and acts as a receptor for mammalian reovirus sigma-1. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of JAM1 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C" in the other.


Pssm-ID: 409538  Cd Length: 102  Bit Score: 36.36  E-value: 2.19e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946   15 SLAPATPEVKVACSEDVDLPCTAPwDPQVPYTVSWVKLleggeermetpQEDHLRGQHYHQKGQnGSFDAPNE-RPYSLK 93
Cdd:cd20946   1 TVPSSQQVVTVVENQEVILSCKTP-KKTSSPRVEWKKL-----------QRDVTFVVFQNNKIQ-GDYKGRAEiLGTNIT 67
                        90       100
                ....*....|....*....|....*
gi 4757946   94 IRNTTSCNSGTYRCTLQDPDGQRNL 118
Cdd:cd20946  68 IKNVTRSDSGKYRCEVSARSDGQNL 92
I-set pfam07679
Immunoglobulin I-set domain;
23-115 2.37e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151  Cd Length: 90  Bit Score: 35.70  E-value: 2.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     23 VKVACSEDVDLPCTAPWDPQvPyTVSWVKlleGGEErmeTPQEDHLRgqhYHQKGQNgsfdapnerpYSLKIRNTTSCNS 102
Cdd:pfam07679  10 VEVQEGESARFTCTVTGTPD-P-EVSWFK---DGQP---LRSSDRFK---VTYEGGT----------YTLTISNVQPDDS 68
                          90
                  ....*....|...
gi 4757946    103 GTYRCTLQDPDGQ 115
Cdd:pfam07679  69 GKYTCVATNSAGE 81
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
29-108 5.58e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 404760  Cd Length: 79  Bit Score: 34.42  E-value: 5.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4757946     29 EDVDLPCTAPWDPQVpyTVSWVKlleGGEERMETPQEDHLRGQHYHQkgqngsfdapnerpySLKIRNTTSCNSGTYRCT 108
Cdd:pfam13927  17 ESVTLTCEATGGPPP--TITWYK---NGEEILSGSTSDRISLSGSNS---------------TLTISNVTRSDSGTYTCV 76
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.19
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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