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Conserved domains on  [gi|1220359003|gb|ASN79571|]
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immunoglobulin light chain variable region, partial [Bos taurus]

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 9.11e-49

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: 151.46  E-value: 9.11e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGSRSGNTATLTISSLQAE 100
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*..
gi 1220359003 101 DEADYFCASPEdsSSNAVFGSGTTLTV 127
Cdd:cd04984    81 DEADYYCQVWD--SNSYVFGGGTKLTV 105
 
Name Accession Description Interval E-value
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 21-127 9.11e-49

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: 151.46  E-value: 9.11e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGSRSGNTATLTISSLQAE 100
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*..
gi 1220359003 101 DEADYFCASPEdsSSNAVFGSGTTLTV 127
Cdd:cd04984    81 DEADYYCQVWD--SNSYVFGGGTKLTV 105
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 23-128 4.50e-21

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: 81.35  E-value: 4.50e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  23 TQPSSVSGSLGQRVSITCSGSSSNV-GNGYVSWYQLIPGSAPRTLI--YGDTSRASGVPDRFS--GSRSGNTATLTISSL 97
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSgrGDPSNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1220359003  98 QAEDEADYFCASPEDSSSnaVFGSGTTLTVL 128
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEG--VFGKGTRLTVL 109
IGv smart00406
Immunoglobulin V-Type;
36-108 1.60e-17

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 71.26  E-value: 1.60e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1220359003   36 VSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSR----ASGVPDRFSGSR--SGNTATLTISSLQAEDEADYFCA 108
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCA 80
 
Name Accession Description Interval E-value
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 21-127 9.11e-49

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: 151.46  E-value: 9.11e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGSRSGNTATLTISSLQAE 100
Cdd:cd04984     1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                          90       100
                  ....*....|....*....|....*..
gi 1220359003 101 DEADYFCASPEdsSSNAVFGSGTTLTV 127
Cdd:cd04984    81 DEADYYCQVWD--SNSYVFGGGTKLTV 105
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 21-127 2.15e-32

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: 109.79  E-value: 2.15e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQ-PSSVSGSLGQRVSITCsGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGSRSGNTATLTISSLQA 99
Cdd:cd04980     2 VMTQsPASLSVSPGERVTISC-KASQSISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                          90       100
                  ....*....|....*....|....*...
gi 1220359003 100 EDEADYFCASpeDSSSNAVFGSGTTLTV 127
Cdd:cd04980    81 EDAAVYYCQQ--GYTFPYTFGGGTKLEI 106
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 22-127 4.78e-30

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: 103.95  E-value: 4.78e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  22 LTQ-PSSVSGSLGQRVSITCSGSSSNvGNGYVSWYQLIPGSAPRTLIYGDTSRAS---GVPDRFSGSRSG-NTATLTISS 96
Cdd:cd00099     1 VTQsPRSLSVQEGESVTLSCEVSSSF-SSTYIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLTISN 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1220359003  97 LQAEDEADYFCASPEDSSSN-AVFGSGTTLTV 127
Cdd:cd00099    80 LQPEDSGTYYCAVSESGGTDkLTFGSGTRLTV 111
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 23-128 4.50e-21

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: 81.35  E-value: 4.50e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  23 TQPSSVSGSLGQRVSITCSGSSSNV-GNGYVSWYQLIPGSAPRTLI--YGDTSRASGVPDRFS--GSRSGNTATLTISSL 97
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSgrGDPSNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1220359003  98 QAEDEADYFCASPEDSSSnaVFGSGTTLTVL 128
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEG--VFGKGTRLTVL 109
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 22-127 8.97e-18

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: 73.17  E-value: 8.97e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  22 LTQPS-SVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIY----GDTSRASG-VPDRFSGSRSGN--TATLT 93
Cdd:cd04982     1 LEQPQlSITREESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYvsstSAVRKDSGkTKNKFEARKDVGksTSTLT 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1220359003  94 ISSLQAEDEADYFCASPEDSSSN--AVFGSGTTLTV 127
Cdd:cd04982    81 ITNLEKEDSATYYCAYWESGSGYyiKVFGSGTKLIV 116
IGv smart00406
Immunoglobulin V-Type;
36-108 1.60e-17

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 71.26  E-value: 1.60e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1220359003   36 VSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSR----ASGVPDRFSGSR--SGNTATLTISSLQAEDEADYFCA 108
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCA 80
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 22-127 1.79e-17

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: 71.93  E-value: 1.79e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  22 LTQ-PSSVSGSLGQRVSITCSGSSsnvGNGYVSWYQLIPGSAPRTLIY---GDTSRASGVP-DRFSGSRSGNT-ATLTIS 95
Cdd:cd05899     1 VTQsPRYLIKRRGQSVTLRCSQKS---GHDNMYWYRQDPGKGLQLLFYsygGGLNEEGDLPgDRFSASRPSLTrSSLTIK 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1220359003  96 SLQAEDEADYFCASPEDSSSN-AVFGSGTTLTV 127
Cdd:cd05899    78 SAEPEDSAVYLCASSLGGGADeAYFGPGTRLTV 110
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 23-127 9.00e-17

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: 70.38  E-value: 9.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  23 TQ-PSSVSGSLGQRVSITCSGSSSnvGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGS--RSGNTATLTISSLQA 99
Cdd:cd04983     2 TQsPQSLSVQEGENVTLNCNYSTS--TFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQL 79

                          90       100
                  ....*....|....*....|....*....
gi 1220359003 100 EDEADYFCASPEDSSSNA-VFGSGTTLTV 127
Cdd:cd04983    80 SDSAVYFCALSESGGTGKlTFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 25-127 2.07e-15

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: 65.99  E-value: 2.07e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003   25 PSSVSGSLGQRVSITCSGSSSnvGNGYVSWYQlipgSAPRTLIYgdtsrasgvPDRFSGSRSGNTATLTISSLQAEDEAD 104
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYK----QGGKLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|...
gi 1220359003  105 YFCASpedSSSNAVFGSGTTLTV 127
Cdd:smart00410  66 YTCAA---TNSSGSASSGTTLTV 85
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-127 1.21e-11

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: 57.32  E-value: 1.21e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  22 LTQPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSAPR--TLIY---GDTSRASGVPDRFSGSR--SGNTATLTI 94
Cdd:cd04981     2 LQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEwiGLIYpggGDTYYADSFKGRFTITRdtSKSTAYLQL 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1220359003  95 SSLQAEDEADYFCAS---PEDSSSNAVFGSGTTLTV 127
Cdd:cd04981    82 NSLTSEDTAVYYCARglgGYGYSYFDYWGQGTTVTV 117
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 23-127 1.45e-11

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: 56.76  E-value: 1.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  23 TQPSS-VSGSLGQRVSITCSGSSSNvGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGS--RSGNTATLTISSLQA 99
Cdd:cd07706     3 TQAQPdVSVQVGEEVTLNCRYETSW-TNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNfqKAQKSISLTISALQL 81

                          90       100       110
                  ....*....|....*....|....*....|
gi 1220359003 100 EDEADYFCA--SPEDsSSNAVFGSGTTLTV 127
Cdd:cd07706    82 EDSAKYFCAlsLPYD-TDKLIFGKGTRLTV 110
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 24-127 1.20e-10

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: 54.49  E-value: 1.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  24 QPSSVSGSLGQRVSITCSGSSSNVGNGYVSWYQLIPGSApRTLIYGDTSR-ASGVPDRFSGS--RSGNTATLTISSLQAE 100
Cdd:cd20988     4 EHQTVTVSVGKPVTLKCSMKGEAISNYYINWYRKTQGNT-MTFIYREGGIyGPGFKDNFRGDidSSNNLAVLKILEASER 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1220359003 101 DEADYFCASP----EDSSSNAVFGSGTTLTV 127
Cdd:cd20988    83 DEGSYYCASDtpggGREYDPLIFGKGTYLTV 113
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 32-107 5.67e-09

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: 50.18  E-value: 5.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  32 LGQRVSITCSGSSSnVGNGyVSWYQLIPGSA--PRTLIYGDTSRASGVPD-----RFSGSRSGNTATLTISSLQAEDEAD 104
Cdd:cd05720    12 LGQKVELVCEVLNS-VPQG-CSWLFQPRGSApqPTFLLYLSSSNKTKWAEgldskRFSGSRSGSSYVLTLKDFRKEDEGY 89


                  ...
gi 1220359003 105 YFC 107
Cdd:cd05720    90 YFC 92
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 33-127 9.37e-09

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: 49.87  E-value: 9.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  33 GQRVSITCSGSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVPDRFSGSRSGNTA--TLTISSLQAEDEADYFCA-- 108
Cdd:cd16095    15 GKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVSEDRITSSREDTNSqiFLQIKGLGLRDSGQYHCArr 94

                          90       100
                  ....*....|....*....|
gi 1220359003 109 -SPEDSSSNAVFGSGTTLTV 127
Cdd:cd16095    95 vGYGDDTDKLIFGPGTDVIV 114
IgV_CD79b_beta cd16096
Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are ...
 33-127 1.49e-06

Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are composed of the immunoglobulin variable domain (IgV) of the Cluster of Differentiation (CD) 79B (also known as CD79b molecule, immunoglobulin-associated beta (Ig-beta), and B29). The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. Members of the IgV family 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409515  Cd Length: 96  Bit Score: 43.40  E-value: 1.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  33 GQRVSITCSGSSSnvgnGYVSWYQLIPGSAPRTLIYGDtsrasgvpDRFSGSRSGNTATLTISSLQAEDEADYFCASPED 112
Cdd:cd16096    13 SSMVKFHCYTNYS----GVMTWFRKKGNQRPQELFPED--------GRISQTQNGSVYTLTIQNIQYEDNGIYFCQQKCN 80

                          90
                  ....*....|....*.
gi 1220359003 113 SSSNAVF-GSGTTLTV 127
Cdd:cd16096    81 STEPDVTdGCGTELLV 96
IgV_1_Nectin-1_like cd05886
First immunoglobulin variable (IgV) domain of nectin-1, and similar domains; The members here ...
 27-107 4.00e-05

First immunoglobulin variable (IgV) domain of nectin-1, and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1 (PVRL1) or cluster of differentiation (CD) 111). Nectin-1 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). 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. In addition nectins heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls), nectin-1 for example, has been shown to trans-interact with Necl-1. Nectins also interact with various other proteins, including the actin filament (F-actin)-binding protein, afadin. Mutation in the human nectin-1 gene is associated with cleft lip/palate ectodermal dysplasia syndrome (CLPED1). Nectin-1 is a major receptor for herpes simplex virus through interaction with the viral envelope glycoprotein D.


Pssm-ID: 409469  Cd Length: 113  Bit Score: 39.95  E-value: 4.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  27 SVSGSLGQRVSITCS--GSSSNVGNGYVSWYQLIPGSAPRTLIYGDTSRASGVP---DRFSGSR-SGNTATLTISSLQAE 100
Cdd:cd05886     8 SMSGFIGTDVVLHCSfaNPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLPpyrERVTFLNpSFTDGTIRLSRLELE 87


                  ....*..
gi 1220359003 101 DEADYFC 107
Cdd:cd05886    88 DEGVYIC 94
I-set pfam07679
Immunoglobulin I-set domain;
21-107 6.69e-05

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 38.78  E-value: 6.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQPSSVSGSLGQRVSITC--SGSSSNVgngyVSWYqlipgsaprtliYGDTSRASGvpDRFSGSRSGNTATLTISSLQ 98
Cdd:pfam07679   3 FTQKPKDVEVQEGESARFTCtvTGTPDPE----VSWF------------KDGQPLRSS--DRFKVTYEGGTYTLTISNVQ 64


                  ....*....
gi 1220359003  99 AEDEADYFC 107
Cdd:pfam07679  65 PDDSGKYTC 73
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 21-107 1.23e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 37.93  E-value: 1.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  21 VLTQPSSVSGSLGQRVSITCSGSSSNVGNgyVSWYQlipgsaprtliygDTSRASGVPDRfSGSRSGNTATLTISSLQAE 100
Cdd:pfam13927   4 ITVSPSSVTVREGETVTLTCEATGSPPPT--ITWYK-------------NGEPISSGSTR-SRSLSGSNSTLTISNVTRS 67


                  ....*..
gi 1220359003 101 DEADYFC 107
Cdd:pfam13927  68 DAGTYTC 74
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 82-127 2.35e-03

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: 35.50  E-value: 2.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1220359003  82 SGSRSGNTATLTISSLQAEDEADYFCASPedSSSNAVFGSGTTLTV 127
Cdd:cd07700    72 LSDSDSSRYILSLMSVKPEDSGTYFCMTV--GSPELIFGTGTKLSV 115
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 25-107 3.47e-03

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: 34.73  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1220359003  25 PSSVSGSLGQRVSITCS-GSSSNVGNGYVSWYQliPGSAPRTLI------YGDTSRASgVPDRFSGSRS---GNTATLTI 94
Cdd:cd05718     6 PTEVTGFLGGSVTLPCSlTSPGTTKITQVTWMK--IGAGSSQNVavfhpqYGPSVPNP-YAERVEFLAArlgLRNATLRI 82

                          90
                  ....*....|...
gi 1220359003  95 SSLQAEDEADYFC 107
Cdd:cd05718    83 RNLRVEDEGNYIC 95
 
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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