NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|13540503|ref|NP_109616|]
View 

immunoglobulin superfamily member 6 precursor [Mus musculus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 35-142 4.54e-07

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 cd04983:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 109  Bit Score: 46.88  E-value: 4.54e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503  35 PGYLEVDYGsDAVTMECNFSTVGCPPVppksLWFRcgthQ-----PEALC---LDGCRNEADKFTVKETLDPDQVFLTVN 106
Cdd:cd04983   5 PQSLSVQEG-ENVTLNCNYSTSTFYYL----FWYR----QypgqgPQFLIyisSDSGNKKKGRFSATLDKSRKSSSLHIS 75

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 13540503 107 RLSPNDSAIYICgiAFPnELSPSAKHV-GKGTTLVVR 142
Cdd:cd04983  76 AAQLSDSAVYFC--ALS-ESGGTGKLTfGKGTRLTVE 109
 
Name Accession Description Interval E-value
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 35-142 4.54e-07

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 46.88  E-value: 4.54e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503  35 PGYLEVDYGsDAVTMECNFSTVGCPPVppksLWFRcgthQ-----PEALC---LDGCRNEADKFTVKETLDPDQVFLTVN 106
Cdd:cd04983   5 PQSLSVQEG-ENVTLNCNYSTSTFYYL----FWYR----QypgqgPQFLIyisSDSGNKKKGRFSATLDKSRKSSSLHIS 75

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 13540503 107 RLSPNDSAIYICgiAFPnELSPSAKHV-GKGTTLVVR 142
Cdd:cd04983  76 AAQLSDSAVYFC--ALS-ESGGTGKLTfGKGTRLTVE 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-142 6.60e-04

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 38.21  E-value: 6.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503    34 QPGYLEVDYGSDaVTMECNFSTVGCPPVPPKSlWFRCGTHQPEALCLDGCRNEA------DKFTVKETLDPDQVFLTVNR 107
Cdd:pfam07686   2 TPREVTVALGGS-VTLPCTYSSSMSEASTSVY-WYRQPPGKGPTFLIAYYSNGSeegvkkGRFSGRGDPSNGDGSLTIQN 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 13540503   108 LSPNDSAIYICGIAFPNELSPsakhvGKGTTLVVR 142
Cdd:pfam07686  80 LTLSDSGTYTCAVIPSGEGVF-----GKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 35-141 7.60e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 37.48  E-value: 7.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503     35 PGYLEVDYGSDaVTMECNFStvGCPPvpPKSLWFRcgtHQPEALCLDGcrneadKFTVKEtlDPDQVFLTVNRLSPNDSA 114
Cdd:smart00410   1 PPSVTVKEGES-VTLSCEAS--GSPP--PEVTWYK---QGGKLLAESG------RFSVSR--SGSTSTLTISNVTPEDSG 64

                           90       100
                   ....*....|....*....|....*..
gi 13540503    115 IYICgiafpnELSPSAKHVGKGTTLVV 141
Cdd:smart00410  65 TYTC------AATNSSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 35-142 4.54e-07

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 46.88  E-value: 4.54e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503  35 PGYLEVDYGsDAVTMECNFSTVGCPPVppksLWFRcgthQ-----PEALC---LDGCRNEADKFTVKETLDPDQVFLTVN 106
Cdd:cd04983   5 PQSLSVQEG-ENVTLNCNYSTSTFYYL----FWYR----QypgqgPQFLIyisSDSGNKKKGRFSATLDKSRKSSSLHIS 75

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 13540503 107 RLSPNDSAIYICgiAFPnELSPSAKHV-GKGTTLVVR 142
Cdd:cd04983  76 AAQLSDSAVYFC--ALS-ESGGTGKLTfGKGTRLTVE 109
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 87-141 6.37e-05

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 41.14  E-value: 6.37e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 13540503  87 ADKFTVKETLDPD----QVFLTVNRLSPNDSAIYICGIAFPNELSPSAKHVGKGTTLVV 141
Cdd:cd04981  59 ADSFKGRFTITRDtsksTAYLQLNSLTSEDTAVYYCARGLGGYGYSYFDYWGQGTTVTV 117
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-142 6.60e-04

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 38.21  E-value: 6.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503    34 QPGYLEVDYGSDaVTMECNFSTVGCPPVPPKSlWFRCGTHQPEALCLDGCRNEA------DKFTVKETLDPDQVFLTVNR 107
Cdd:pfam07686   2 TPREVTVALGGS-VTLPCTYSSSMSEASTSVY-WYRQPPGKGPTFLIAYYSNGSeegvkkGRFSGRGDPSNGDGSLTIQN 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 13540503   108 LSPNDSAIYICGIAFPNELSPsakhvGKGTTLVVR 142
Cdd:pfam07686  80 LTLSDSGTYTCAVIPSGEGVF-----GKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 35-141 7.60e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 37.48  E-value: 7.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13540503     35 PGYLEVDYGSDaVTMECNFStvGCPPvpPKSLWFRcgtHQPEALCLDGcrneadKFTVKEtlDPDQVFLTVNRLSPNDSA 114
Cdd:smart00410   1 PPSVTVKEGES-VTLSCEAS--GSPP--PEVTWYK---QGGKLLAESG------RFSVSR--SGSTSTLTISNVTPEDSG 64

                           90       100
                   ....*....|....*....|....*..
gi 13540503    115 IYICgiafpnELSPSAKHVGKGTTLVV 141
Cdd:smart00410  65 TYTC------AATNSSGSASSGTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
88-118 1.78e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 36.21  E-value: 1.78e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 13540503     88 DKFTVKETLDPDQVFLTVNRLSPNDSAIYIC 118
Cdd:smart00406  49 GRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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