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Conserved domains on  [gi|8980414|emb|CAB96917|]
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T-cell antigen receptor-alpha, partial [Homo sapiens]

Protein Classification

T-cell receptor alpha chain V region( domain architecture ID 10141821)

T-cell receptor alpha chain V (variable) region participates in the antigen recognition of an alpha-beta T cell antigen-specific receptor essential to the immune response; it is present on the cell surface of T lymphocytes to recognize peptide-major histocompatibility (pMH) complexes displayed by antigen presenting cells (APC), a prerequisite for efficient T cell adaptive immunity against pathogens

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 30-138 3.81e-56

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: 170.91  E-value: 3.81e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPG 109
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATLDKSRKSSSLHISAAQLS 80

                        90       100
                ....*....|....*....|....*....
gi 8980414  110 DSAVYFCAASAQSNTGKVIFGQGTTLQVK 138
Cdd:cd04983  81 DSAVYFCALSESGGTGKLTFGKGTRLTVE 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 ...
 30-138 3.81e-56

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: 170.91  E-value: 3.81e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPG 109
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATLDKSRKSSSLHISAAQLS 80

                        90       100
                ....*....|....*....|....*....
gi 8980414  110 DSAVYFCAASAQSNTGKVIFGQGTTLQVK 138
Cdd:cd04983  81 DSAVYFCALSESGGTGKLTFGKGTRLTVE 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 32-137 3.05e-17

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: 72.11  E-value: 3.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414     32 QNSPSLSVQEGRISILNCDYTNSM---FDYFLWYKKYPAEGPTFLISISSIKDKNE--DGRFTVFLNKSAKHLSLHIVPS 106
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMseaSTSVYWYRQPPGKGPTFLIAYYSNGSEEGvkKGRFSGRGDPSNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 8980414    107 QPGDSAVYFCAAsaqSNTGKVIFGQGTTLQV 137
Cdd:pfam07686  81 TLSDSGTYTCAV---IPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 34-137 3.58e-10

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: 52.89  E-value: 3.58e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414      34 SPSLSVQEGRISILNCDYTNSMFDYFLWYKkypaEGPTFLIsissikdknEDGRFTVFlnKSAKHLSLHIVPSQPGDSAV 113
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYK----QGGKLLA---------ESGRFSVS--RSGSTSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|....
gi 8980414     114 YFCAAsaqSNTGKVIFGqGTTLQV 137
Cdd:smart00410  66 YTCAA---TNSSGSASS-GTTLTV 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 ...
 30-138 3.81e-56

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: 170.91  E-value: 3.81e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPG 109
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATLDKSRKSSSLHISAAQLS 80

                        90       100
                ....*....|....*....|....*....
gi 8980414  110 DSAVYFCAASAQSNTGKVIFGQGTTLQVK 138
Cdd:cd04983  81 DSAVYFCALSESGGTGKLTFGKGTRLTVE 109
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 30-137 6.44e-33

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: 112.04  E-value: 6.44e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSM-FDYFLWYKKYPAEGPTFLISISSIKDKNEDG---RFTVFLNKSaKHLSLHIVP 105
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSSFsSTYIYWYRQKPGQGPEFLIYLSSSKGKTKGGvpgRFSGSRDGT-SSFSLTISN 79

                        90       100       110
                ....*....|....*....|....*....|..
gi 8980414  106 SQPGDSAVYFCAASAQSNTGKVIFGQGTTLQV 137
Cdd:cd00099  80 LQPEDSGTYYCAVSESGGTDKLTFGSGTRLTV 111
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 29-139 6.32e-28

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: 99.52  E-value: 6.32e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   29 QVKQNSPSLSVQEGRISILNCDYTNSMFDYFL-WYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQ 107
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNYYLfWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQKSISLTISALQ 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 8980414  108 PGDSAVYFCAASAQSNTGKVIFGQGTTLQVKP 139
Cdd:cd07706  81 LEDSAKYFCALSLPYDTDKLIFGKGTRLTVEP 112
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 30-137 1.55e-18

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: 75.40  E-value: 1.55e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSmFDYFLWYKKYPAEGPTFLISISSIKDKNEDG----RFTVfLNKSAKHLSLHIVP 105
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQKSG-HDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDlpgdRFSA-SRPSLTRSSLTIKS 78

                        90       100       110
                ....*....|....*....|....*....|..
gi 8980414  106 SQPGDSAVYFCAASAQSNTGKVIFGQGTTLQV 137
Cdd:cd05899  79 AEPEDSAVYLCASSLGGGADEAYFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 32-137 3.05e-17

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: 72.11  E-value: 3.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414     32 QNSPSLSVQEGRISILNCDYTNSM---FDYFLWYKKYPAEGPTFLISISSIKDKNE--DGRFTVFLNKSAKHLSLHIVPS 106
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMseaSTSVYWYRQPPGKGPTFLIAYYSNGSEEGvkKGRFSGRGDPSNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 8980414    107 QPGDSAVYFCAAsaqSNTGKVIFGQGTTLQV 137
Cdd:pfam07686  81 TLSDSGTYTCAV---IPSGEGVFGKGTRLTV 108
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 30-137 6.96e-12

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: 58.14  E-value: 6.96e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   30 VKQNSPSLSVQEGRISILNCDYTNSMF--DYFLWYKKYPAEGPTFLISISSIKDKNED-----GRFTVFLNKSAKHLSLH 102
Cdd:cd04982   1 LEQPQLSITREESKSVTISCKVSGIDFstTYIHWYRQKPGQALERLLYVSSTSAVRKDsgktkNKFEARKDVGKSTSTLT 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 8980414  103 IVPSQPGDSAVYFCAA-SAQSNTGKVIFGQGTTLQV 137
Cdd:cd04982  81 ITNLEKEDSATYYCAYwESGSGYYIKVFGSGTKLIV 116
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 29-137 2.37e-11

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: 56.63  E-value: 2.37e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   29 QVKQNSPSLSVQEGRISILNCDYTNSMFDYFL-WYKKYPAEGPTFLISISSIKDKNEDGRFTVflNKSAKHLSLHIVPSQ 107
Cdd:cd04980   2 VMTQSPASLSVSPGERVTISCKASQSISSNYLaWYQQKPGQAPKLLIYYASTLHSGVPSRFSG--SGSGTDFTLTISSVE 79

                        90       100       110
                ....*....|....*....|....*....|
gi 8980414  108 PGDSAVYFCaasAQSNTGKVIFGQGTTLQV 137
Cdd:cd04980  80 PEDAAVYYC---QQGYTFPYTFGGGTKLEI 106
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 34-137 3.58e-10

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: 52.89  E-value: 3.58e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414      34 SPSLSVQEGRISILNCDYTNSMFDYFLWYKkypaEGPTFLIsissikdknEDGRFTVFlnKSAKHLSLHIVPSQPGDSAV 113
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYK----QGGKLLA---------ESGRFSVS--RSGSTSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|....
gi 8980414     114 YFCAAsaqSNTGKVIFGqGTTLQV 137
Cdd:smart00410  66 YTCAA---TNSSGSASS-GTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
47-117 3.39e-08

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 47.76  E-value: 3.39e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 8980414      47 LNCDYTNSMF--DYFLWYKKYPAEGPTFLISISSIKDKNED----GRFTVFLNKSAKHLSLHIVPSQPGDSAVYFCA 117
Cdd:smart00406   4 LSCKFSGSTFssYYVSWVRQPPGKGLEWLGYIGSNGSSYYQesykGRFTISKDTSKNDVSLTISNLRVEDTGTYYCA 80
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 34-137 7.55e-08

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: 47.46  E-value: 7.55e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   34 SPSLSVQEGRISILNCDYTNSMFD--YFLWYKKYPAEGPTFLISISSIKDKNEDGRFTVflNKSAKHLSLHIVPSQPGDS 111
Cdd:cd04984   5 PSSLSVSPGETVTITCTGSSGNISgnYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSG--SKSGNTASLTISGAQTEDE 82

                        90       100
                ....*....|....*....|....*.
gi 8980414  112 AVYFCAAsaqSNTGKVIFGQGTTLQV 137
Cdd:cd04984  83 ADYYCQV---WDSNSYVFGGGTKLTV 105
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 38-137 2.76e-06

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: 43.70  E-value: 2.76e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   38 SVQEGRISILNCD-----YTNSMFDYFLWYkkyPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPGDSA 112
Cdd:cd16095  11 SHPAGKTLSLKCQtsgfqFNTSQLSWYLWV---PGHAPLWLTSLDHISTKVSEDRITSSREDTNSQIFLQIKGLGLRDSG 87

                        90       100
                ....*....|....*....|....*..
gi 8980414  113 VYFCAASAQS--NTGKVIFGQGTTLQV 137
Cdd:cd16095  88 QYHCARRVGYgdDTDKLIFGPGTDVIV 114
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-118 3.37e-06

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


Pssm-ID: 409509  Cd Length: 112  Bit Score: 43.26  E-value: 3.37e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   34 SPS-LSVQEGRISILNCDYTN-SMFDYFLWYKKYPAEGPTFLISISsiKDKNE---DGRFTVFLNKSAKHLSLHIVPSQP 108
Cdd:cd16088   5 SPAlLVVTEGANATFTCSFSNtSESFVLNWYRLSPSNQTDKLAAFP--EDRSQpgqDWRFRVTQLPNGRDFHMSVVRARR 82

                        90
                ....*....|
gi 8980414  109 GDSAVYFCAA 118
Cdd:cd16088  83 NDSGTYLCGA 92
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 32-137 4.88e-06

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: 42.82  E-value: 4.88e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   32 QNSPSLSVQEGRISILNCD---YTNSMFDYflWYKKypAEGPT------FLISISSIK-----DKNEDGRFTVFLNKSAK 97
Cdd:cd07700   3 QTPGSLLVQTNQTVKMSCEaktSPKNTRIY--WLRQ--RQAPSkdshfeFLASWDPSKgivygEGVDQEKLIILSDSDSS 78

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 8980414   98 HLSLHIVPSQPGDSAVYFCAASAQSNtgkVIFGQGTTLQV 137
Cdd:cd07700  79 RYILSLMSVKPEDSGTYFCMTVGSPE---LIFGTGTKLSV 115
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 29-137 5.62e-06

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: 42.68  E-value: 5.62e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   29 QVKQNSPSLsVQEGRISILNCD---YTNSMFdYFLWYKKYPAEGPTFLISISSIKDK---NED--GRFTVFLNKSAKHLS 100
Cdd:cd04981   1 QLQESGPGL-VKPGQSLKLSCKasgFTFTSY-GMGWVRQAPGKGLEWIGLIYPGGGDtyyADSfkGRFTITRDTSKSTAY 78

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 8980414  101 LHIVPSQPGDSAVYFCAAS--AQSNTGKVIFGQGTTLQV 137
Cdd:cd04981  79 LQLNSLTSEDTAVYYCARGlgGYGYSYFDYWGQGTTVTV 117
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 36-138 2.47e-03

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: 35.61  E-value: 2.47e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   36 SLSVQEGRISILNCDYT-NSMFDYFL-WYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPGDSAV 113
Cdd:cd20988   7 TVTVSVGKPVTLKCSMKgEAISNYYInWYRKTQGNTMTFIYREGGIYGPGFKDNFRGDIDSSNNLAVLKILEASERDEGS 86

                        90       100
                ....*....|....*....|....*...
gi 8980414  114 YFCAAS---AQSNTGKVIFGQGTTLQVK 138
Cdd:cd20988  87 YYCASDtpgGGREYDPLIFGKGTYLTVE 114
IgV_CD33 cd05712
Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic ...
 36-115 3.06e-03

Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic acid-binding Ig-like lectins); The members here are composed of the immunoglobulin (Ig) domain at the N-terminus of Cluster of Differentiation (CD) 33 and related Siglecs (sialic acid-binding Ig-like lectins). Siglec refers to a structurally related protein family that specifically recognizes sialic acid in oligosaccharide chains of glycoproteins and glycolipids. Siglecs are type I transmembrane proteins, organized as an extracellular module composed of Ig-like domains, an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains, followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG, the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11.


Pssm-ID: 409377  Cd Length: 119  Bit Score: 35.44  E-value: 3.06e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 8980414   36 SLSVQEGRISILNC------DYTNSMFDYFLWYKKYP---AEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPS 106
Cdd:cd05712   8 SVTVQEGLCVLIPCsfsypaDYWVSNPVHGYWYRGGPypkYRPPVATNNRTREVHESTQGRFRLLGDPGKKNCSLSISDA 87


                ....*....
gi 8980414  107 QPGDSAVYF 115
Cdd:cd05712  88 RPEDSGKYF 96
 
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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