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Conserved domains on  [gi|47680837|gb|AAT37401|]
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immunoglobulin mu heavy chain variable region, partial [Ginglymostoma cirratum]

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 ...
 3-116 9.65e-41

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 cd04981:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 118  Bit Score: 131.66  E-value: 9.65e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837   3 TLIQPEAETGHPGGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNY-APAIKDRFTASKDTGNNIFALE 81
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYyADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 47680837  82 MRSVKIDDTAIYYCATDIG---YGYTTYWGQGTMVTVT 116
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGgygYSYFDYWGQGTTVTVS 118
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 3-116 9.65e-41

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: 131.66  E-value: 9.65e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837   3 TLIQPEAETGHPGGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNY-APAIKDRFTASKDTGNNIFALE 81
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYyADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 47680837  82 MRSVKIDDTAIYYCATDIG---YGYTTYWGQGTMVTVT 116
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGgygYSYFDYWGQGTTVTVS 118
IGv smart00406
Immunoglobulin V-Type;
17-97 1.41e-26

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 94.37  E-value: 1.41e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837     17 SLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPAIKDRFTASKDTGNNIFALEMRSVKIDDTAIYYCA 96
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYCA 80


                   .
gi 47680837     97 T 97
Cdd:smart00406  81 V 81
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 5-116 1.33e-14

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: 64.79  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837     5 IQPEAETGHPGGSLSLTCKTSGF-NLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPaiKDRFTASKDTGNNIFALEMR 83
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGVK--KGRFSGRGDPSNGDGSLTIQ 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 47680837    84 SVKIDDTAIYYCAtdIGYGYTTYWGQGTMVTVT 116
Cdd:pfam07686  79 NLTLSDSGTYTCA--VIPSGEGVFGKGTRLTVL 109
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 3-116 9.65e-41

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: 131.66  E-value: 9.65e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837   3 TLIQPEAETGHPGGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNY-APAIKDRFTASKDTGNNIFALE 81
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYyADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 47680837  82 MRSVKIDDTAIYYCATDIG---YGYTTYWGQGTMVTVT 116
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGgygYSYFDYWGQGTTVTVS 118
IGv smart00406
Immunoglobulin V-Type;
17-97 1.41e-26

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 94.37  E-value: 1.41e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837     17 SLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPAIKDRFTASKDTGNNIFALEMRSVKIDDTAIYYCA 96
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYCA 80


                   .
gi 47680837     97 T 97
Cdd:smart00406  81 V 81
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 14-115 7.28e-22

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: 83.54  E-value: 7.28e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  14 PGGSLSLTCKTSGFNlGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYaPAIKDRFTASKDtGNNIFALEMRSVKIDDTAIY 93
Cdd:cd00099  12 EGESVTLSCEVSSSF-SSTYIYWYRQKPGQGPEFLIYLSSSKGKTK-GGVPGRFSGSRD-GTSSFSLTISNLQPEDSGTY 88

                        90       100
                ....*....|....*....|...
gi 47680837  94 YCATDIGYGYTT-YWGQGTMVTV 115
Cdd:cd00099  89 YCAVSESGGTDKlTFGSGTRLTV 111
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 14-115 3.87e-16

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: 68.85  E-value: 3.87e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  14 PGGSLSLTCKTsgfNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPAIKDRFTASKdTGNNIFALEMRSVKIDDTAIY 93
Cdd:cd05899  12 RGQSVTLRCSQ---KSGHDNMYWYRQDPGKGLQLLFYSYGGGLNEEGDLPGDRFSASR-PSLTRSSLTIKSAEPEDSAVY 87

                        90       100
                ....*....|....*....|...
gi 47680837  94 YCA-TDIGYGYTTYWGQGTMVTV 115
Cdd:cd05899  88 LCAsSLGGGADEAYFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 5-116 1.33e-14

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: 64.79  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837     5 IQPEAETGHPGGSLSLTCKTSGF-NLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPaiKDRFTASKDTGNNIFALEMR 83
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGVK--KGRFSGRGDPSNGDGSLTIQ 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 47680837    84 SVKIDDTAIYYCAtdIGYGYTTYWGQGTMVTVT 116
Cdd:pfam07686  79 NLTLSDSGTYTCA--VIPSGEGVFGKGTRLTVL 109
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 11-116 1.84e-14

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: 64.69  E-value: 1.84e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  11 TGHPGGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSNNYAPAI-KDRFTASKDTGNNIFALEMRSVKIDD 89
Cdd:cd04982   9 TREESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKtKNKFEARKDVGKSTSTLTITNLEKED 88

                        90       100       110
                ....*....|....*....|....*....|
gi 47680837  90 TAIYYCAT---DIGYgYTTYWGQGTMVTVT 116
Cdd:cd04982  89 SATYYCAYwesGSGY-YIKVFGSGTKLIVT 117
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 4-115 9.73e-14

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: 62.48  E-value: 9.73e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837   4 LIQPEAETGHPGGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIVYYYSSSSnnyaPAIKDRFTASKDtgNNIFALEMR 83
Cdd:cd04984   2 LTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRP----SGIPDRFSGSKS--GNTASLTIS 75

                        90       100       110
                ....*....|....*....|....*....|..
gi 47680837  84 SVKIDDTAIYYCAtdIGYGYTTYWGQGTMVTV 115
Cdd:cd04984  76 GAQTEDEADYYCQ--VWDSNSYVFGGGTKLTV 105
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 13-115 2.14e-12

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: 59.11  E-value: 2.14e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  13 HPGG-SLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIvyyySSSSNNYAPAIKDRFTASKDTGNNIFALEMRSVKIDDTA 91
Cdd:cd16095  12 HPAGkTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWL----TSLDHISTKVSEDRITSSREDTNSQIFLQIKGLGLRDSG 87

                        90       100
                ....*....|....*....|....*..
gi 47680837  92 IYYCATDIGYGYTT---YWGQGTMVTV 115
Cdd:cd16095  88 QYHCARRVGYGDDTdklIFGPGTDVIV 114
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 15-116 8.17e-12

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: 57.67  E-value: 8.17e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  15 GGSLSLTC--KTSGFNlgssSMYWIRQVPGQGLEWIVYYYSSSSnnyaPAIKDRFTASKDTGNNIFALEMRSVKIDDTAI 92
Cdd:cd04983  13 GENVTLNCnySTSTFY----YLFWYRQYPGQGPQFLIYISSDSG----NKKKGRFSATLDKSRKSSSLHISAAQLSDSAV 84

                        90       100
                ....*....|....*....|....*
gi 47680837  93 YYCATDIGYG-YTTYWGQGTMVTVT 116
Cdd:cd04983  85 YFCALSESGGtGKLTFGKGTRLTVE 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 7-115 2.40e-11

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: 55.97  E-value: 2.40e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837      7 PEAETGHPGGSLSLTCKTSGFnlGSSSMYWIRQvpgqGLEWIvyyyssssnnyapAIKDRFTASKDtgNNIFALEMRSVK 86
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLL-------------AESGRFSVSRS--GSTSTLTISNVT 59

                           90       100
                   ....*....|....*....|....*....
gi 47680837     87 IDDTAIYYCATDIGYGYTTywgQGTMVTV 115
Cdd:smart00410  60 PEDSGTYTCAATNSSGSAS---SGTTLTV 85
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 15-115 1.14e-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: 49.48  E-value: 1.14e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  15 GGSLSLTCKTSGFNLGSSSMYWIRQVPGQGLEWIvyyySSSSNNYAPAIKDRFTASKDTGNNIFALEMRSVKIDDTAIYY 94
Cdd:cd20988  13 GKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFI----YREGGIYGPGFKDNFRGDIDSSNNLAVLKILEASERDEGSYY 88

                        90       100
                ....*....|....*....|....*
gi 47680837  95 CATDIGYGYTTY----WGQGTMVTV 115
Cdd:cd20988  89 CASDTPGGGREYdpliFGKGTYLTV 113
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 14-115 9.56e-08

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: 47.00  E-value: 9.56e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837  14 PGGSLSLTCKTSGfNLGSSSMYWIRQVPGQGLEWIVYYYSSSsnnyAPAIKDRFTAS-KDTGnniFALEMRSVKIDDTAI 92
Cdd:cd04980  14 PGERVTISCKASQ-SISSNYLAWYQQKPGQAPKLLIYYASTL----HSGVPSRFSGSgSGTD---FTLTISSVEPEDAAV 85

                        90       100
                ....*....|....*....|....*
gi 47680837  93 YYCATdigyGYTTYW--GQGTMVTV 115
Cdd:cd04980  86 YYCQQ----GYTFPYtfGGGTKLEI 106
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 4-115 3.01e-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: 35.12  E-value: 3.01e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47680837   4 LIQ-PEAETGHPGGSLSLTCKTSGFnLGSSSMYWIRQVPG----QGLEWIVYYYSSSSNNYAPAIK-DRFTASKDTGNNI 77
Cdd:cd07700   1 LLQtPGSLLVQTNQTVKMSCEAKTS-PKNTRIYWLRQRQApskdSHFEFLASWDPSKGIVYGEGVDqEKLIILSDSDSSR 79

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 47680837  78 FALEMRSVKIDDTAIYYCATdIGYGYTTYwGQGTMVTV 115
Cdd:cd07700  80 YILSLMSVKPEDSGTYFCMT-VGSPELIF-GTGTKLSV 115
 
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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