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Conserved domains on  [gi|2321188836|gb|UYP40541|]
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light chain variable region, partial [Macaca mulatta]

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 ...
 3-108 2.88e-50

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 cd04984:

Pssm-ID: 472250  Cd Length: 105  Bit Score: 154.16  E-value: 2.88e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   3 VLTQPPSVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGSKSGTSASLAITGLQTG 82
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*.
gi 2321188836  83 DEADYFCSTWDSSlrNLLFGGGTRLT 108
Cdd:cd04984    81 DEADYYCQVWDSN--SYVFGGGTKLT 104
 
Name Accession Description Interval E-value
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 3-108 2.88e-50

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). 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 seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 154.16  E-value: 2.88e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   3 VLTQPPSVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGSKSGTSASLAITGLQTG 82
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*.
gi 2321188836  83 DEADYFCSTWDSSlrNLLFGGGTRLT 108
Cdd:cd04984    81 DEADYYCQVWDSN--SYVFGGGTKLT 104
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 5-108 1.82e-19

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: 76.34  E-value: 1.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   5 TQPPSVSAAPGQKVTMSCSG-GSSNIGTSYVSWYQQVPGTAPKLLI--YQDNKRPSAVSDRFSGSK--SGTSASLAITGL 79
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYsSSMSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 2321188836  80 QTGDEADYFCSTWDSSLRNllFGGGTRLT 108
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGV--FGKGTRLT 107
IGv smart00406
Immunoglobulin V-Type;
18-91 3.65e-14

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 62.01  E-value: 3.65e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   18 VTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKR----PSAVSDRFSGSK--SGTSASLAITGLQTGDEADYFCST 91
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCAV 81
 
Name Accession Description Interval E-value
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 3-108 2.88e-50

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). 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 seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 154.16  E-value: 2.88e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   3 VLTQPPSVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGSKSGTSASLAITGLQTG 82
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*.
gi 2321188836  83 DEADYFCSTWDSSlrNLLFGGGTRLT 108
Cdd:cd04984    81 DEADYYCQVWDSN--SYVFGGGTKLT 104
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 4-108 2.45e-31

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. 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. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 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" strands in the other.


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 106.65  E-value: 2.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   4 LTQPP-SVSAAPGQKVTMSCSGgSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSA---VSDRFSGSKSG-TSASLAITG 78
Cdd:cd00099     1 VTQSPrSLSVQEGESVTLSCEV-SSSFSSTYIYWYRQKPGQGPEFLIYLSSSKGKTkggVPGRFSGSRDGtSSFSLTISN 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 2321188836  79 LQTGDEADYFCSTWDSSLRN-LLFGGGTRLT 108
Cdd:cd00099    80 LQPEDSGTYYCAVSESGGTDkLTFGSGTRLT 110
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 3-107 1.20e-30

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, 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. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). 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 seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 104.78  E-value: 1.20e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   3 VLTQPP-SVSAAPGQKVTMSCsGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGSKSGTSASLAITGLQT 81
Cdd:cd04980     2 VMTQSPaSLSVSPGERVTISC-KASQSISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                          90       100
                  ....*....|....*....|....*.
gi 2321188836  82 GDEADYFCSTWDSSLrnLLFGGGTRL 107
Cdd:cd04980    81 EDAAVYYCQQGYTFP--YTFGGGTKL 104
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 5-108 3.85e-22

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: 83.09  E-value: 3.85e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   5 TQPP-SVSAAPGQKVTMSCSggSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGS--KSGTSASLAITGLQT 81
Cdd:cd04983     2 TQSPqSLSVQEGENVTLNCN--YSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQL 79

                          90       100
                  ....*....|....*....|....*...
gi 2321188836  82 GDEADYFCSTWDSS-LRNLLFGGGTRLT 108
Cdd:cd04983    80 SDSAVYFCALSESGgTGKLTFGKGTRLT 107
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 4-108 1.51e-19

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable domain of the beta 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 includes the variable domain of the alpha chain of alpha/beta 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: 409480  Cd Length: 110  Bit Score: 76.55  E-value: 1.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   4 LTQPPS-VSAAPGQKVTMSCSggsSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSD----RFSGSK-SGTSASLAIT 77
Cdd:cd05899     1 VTQSPRyLIKRRGQSVTLRCS---QKSGHDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDlpgdRFSASRpSLTRSSLTIK 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2321188836  78 GLQTGDEADYFC-STWDSSLRNLLFGGGTRLT 108
Cdd:cd05899    78 SAEPEDSAVYLCaSSLGGGADEAYFGPGTRLT 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 5-108 1.82e-19

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: 76.34  E-value: 1.82e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   5 TQPPSVSAAPGQKVTMSCSG-GSSNIGTSYVSWYQQVPGTAPKLLI--YQDNKRPSAVSDRFSGSK--SGTSASLAITGL 79
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYsSSMSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 2321188836  80 QTGDEADYFCSTWDSSLRNllFGGGTRLT 108
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGV--FGKGTRLT 107
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 4-107 1.03e-17

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain the standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409371  Cd Length: 117  Bit Score: 72.01  E-value: 1.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   4 LTQPP-SVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIY-----QDNKRPSAVSDRFSGSK-SGTSAS-LA 75
Cdd:cd04982     1 LEQPQlSITREESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYvsstsAVRKDSGKTKNKFEARKdVGKSTStLT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2321188836  76 ITGLQTGDEADYFCSTWDSSLRNL--LFGGGTRL 107
Cdd:cd04982    81 ITNLEKEDSATYYCAYWESGSGYYikVFGSGTKL 114
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 8-108 3.00e-16

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 68.31  E-value: 3.00e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   8 PSVSAAPGQKVTMSCSGGSSNiGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGS--KSGTSASLAITGLQTGDEA 85
Cdd:cd07706     7 PDVSVQVGEEVTLNCRYETSW-TNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNfqKAQKSISLTISALQLEDSA 85

                          90       100
                  ....*....|....*....|....
gi 2321188836  86 DYFCSTWDS-SLRNLLFGGGTRLT 108
Cdd:cd07706    86 KYFCALSLPyDTDKLIFGKGTRLT 109
IGv smart00406
Immunoglobulin V-Type;
18-91 3.65e-14

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 62.01  E-value: 3.65e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   18 VTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKR----PSAVSDRFSGSK--SGTSASLAITGLQTGDEADYFCST 91
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCAV 81
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 7-95 2.94e-13

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: 59.83  E-value: 2.94e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836    7 PPSVSAAPGQKVTMSCSggSSNIGTSYVSWYQQvpgtAPKLLIYqdnkrpsavSDRFSGSKSGTSASLAITGLQTGDEAD 86
Cdd:smart00410   1 PPSVTVKEGESVTLSCE--ASGSPPPEVTWYKQ----GGKLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGT 65


                   ....*....
gi 2321188836   87 YFCSTWDSS 95
Cdd:smart00410  66 YTCAATNSS 74
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 9-108 5.38e-08

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409580  Cd Length: 114  Bit Score: 47.17  E-value: 5.38e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   9 SVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGS--KSGTSASLAITGLQTGDEAD 86
Cdd:cd20988     7 TVTVSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFIYREGGIYGPGFKDNFRGDidSSNNLAVLKILEASERDEGS 86

                          90       100
                  ....*....|....*....|....*.
gi 2321188836  87 YFCSTWDSSLRN----LLFGGGTRLT 108
Cdd:cd20988    87 YYCASDTPGGGReydpLIFGKGTYLT 112
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 15-90 1.21e-07

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 45.94  E-value: 1.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836  15 GQKVTMSCSggSSNIGTSYVSWYQQVPGTAPKL--LIY--QDNK---RPSAVSDRFSGSKSGTSASLAITGLQTGDEADY 87
Cdd:cd05720    13 GQKVELVCE--VLNSVPQGCSWLFQPRGSAPQPtfLLYlsSSNKtkwAEGLDSKRFSGSRSGSSYVLTLKDFRKEDEGYY 90


                  ...
gi 2321188836  88 FCS 90
Cdd:cd05720    91 FCS 93
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 15-108 5.75e-07

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 44.47  E-value: 5.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836  15 GQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLLIYQDNKRPSAVSDRFSGSKSGTSA--SLAITGLQTGDEADYFCST- 91
Cdd:cd16095    15 GKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVSEDRITSSREDTNSqiFLQIKGLGLRDSGQYHCARr 94

                          90
                  ....*....|....*....
gi 2321188836  92 --WDSSLRNLLFGGGTRLT 108
Cdd:cd16095    95 vgYGDDTDKLIFGPGTDVI 113
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 4-108 2.75e-04

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409497  Cd Length: 116  Bit Score: 37.43  E-value: 2.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   4 LTQPP-SVSAAPGQKVTMSCSGGSSNIGTSyVSWYQQVPGTAPK-----LLIYQDNKRP------SAVSDRFSGSKSGTS 71
Cdd:cd07700     1 LLQTPgSLLVQTNQTVKMSCEAKTSPKNTR-IYWLRQRQAPSKDshfefLASWDPSKGIvygegvDQEKLIILSDSDSSR 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2321188836  72 ASLAITGLQTGDEADYFCSTWDSSlrNLLFGGGTRLT 108
Cdd:cd07700    80 YILSLMSVKPEDSGTYFCMTVGSP--ELIFGTGTKLS 114
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 4-89 6.71e-04

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: 36.13  E-value: 6.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   4 LTQPPSVSAAPGQKVTMSCSGGSSNIGTSYVSWYQQVPGTAPKLL--IYQDNKRP---SAVSDRFSGS--KSGTSASLAI 76
Cdd:cd04981     2 LQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIglIYPGGGDTyyaDSFKGRFTITrdTSKSTAYLQL 81

                          90
                  ....*....|...
gi 2321188836  77 TGLQTGDEADYFC 89
Cdd:cd04981    82 NSLTSEDTAVYYC 94
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 7-90 7.08e-04

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 36.27  E-value: 7.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   7 PPSVSAAPGQKVTMSCSGGSSNIGT-SYVSWYQQVPGTAPKLLIYQDNKRPS---AVSDRFSG---SKSGTSASLAITGL 79
Cdd:cd05718     6 PTEVTGFLGGSVTLPCSLTSPGTTKiTQVTWMKIGAGSSQNVAVFHPQYGPSvpnPYAERVEFlaaRLGLRNATLRIRNL 85

                          90
                  ....*....|.
gi 2321188836  80 QTGDEADYFCS 90
Cdd:cd05718    86 RVEDEGNYICE 96
IgV_1_Nectin-2_NecL-5_like_CD112_CD155 cd20989
First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar ...
 7-89 3.41e-03

First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'.


Pssm-ID: 409581  Cd Length: 112  Bit Score: 34.48  E-value: 3.41e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   7 PPSVSAAPGQKVTMSCSGGSSNIGT--SYVSWyqQVPGTAPKLLIYQDNKRPS-AVSDR--FSGSKSGT---SASLAITG 78
Cdd:cd20989     6 PPEVRGFLGGSVTLPCHLLPPNMVThvSQVTW--QRHDEHGSVAVFHPKQGPSfPESERlsFVAARLGAelrNASLAMFG 83

                          90
                  ....*....|.
gi 2321188836  79 LQTGDEADYFC 89
Cdd:cd20989    84 LRVEDEGNYTC 94
I-set pfam07679
Immunoglobulin I-set domain;
3-89 8.02e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 33.00  E-value: 8.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2321188836   3 VLTQPPSVSAAPGQKVTMSCSGgssnIGTS--YVSWYQqvpgtapklliyqdNKRPSAVSDRFSGSKSGTSASLAITGLQ 80
Cdd:pfam07679   3 FTQKPKDVEVQEGESARFTCTV----TGTPdpEVSWFK--------------DGQPLRSSDRFKVTYEGGTYTLTISNVQ 64


                  ....*....
gi 2321188836  81 TGDEADYFC 89
Cdd:pfam07679  65 PDDSGKYTC 73
 
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.
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