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Conserved domains on  [gi|1559988775|sp|A0A0B4J1U4|]
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RecName: Full=T cell receptor gamma variable 5; Flags: Precursor

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 ...
 22-118 2.00e-35

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 cd04982:

Pssm-ID: 472250  Cd Length: 117  Bit Score: 117.46  E-value: 2.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  22 LEGGTKSVTRPTRSSAEITCDLTVI--NAFYIHWYLHQEGKAPQRLLYYDvSNSKDVLESGLSPGKYYTHTPRR-WSWIL 98
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVSGIdfSTTYIHWYRQKPGQALERLLYVS-STSAVRKDSGKTKNKFEARKDVGkSTSTL 79

                          90       100
                  ....*....|....*....|
gi 1559988775  99 ILRNLIENDSGVYYCATWDR 118
Cdd:cd04982    80 TITNLEKEDSATYYCAYWES 99
 
Name Accession Description Interval E-value
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 22-118 2.00e-35

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: 117.46  E-value: 2.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  22 LEGGTKSVTRPTRSSAEITCDLTVI--NAFYIHWYLHQEGKAPQRLLYYDvSNSKDVLESGLSPGKYYTHTPRR-WSWIL 98
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVSGIdfSTTYIHWYRQKPGQALERLLYVS-STSAVRKDSGKTKNKFEARKDVGkSTSTL 79

                          90       100
                  ....*....|....*....|
gi 1559988775  99 ILRNLIENDSGVYYCATWDR 118
Cdd:cd04982    80 TITNLEKEDSATYYCAYWES 99
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 36-118 1.91e-07

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: 45.91  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  36 SAEITC---DLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLEsglsPGKYY-THTPRRWSWILILRNLIENDSGVY 111
Cdd:pfam07686  13 SVTLPCtysSSMSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGVK----KGRFSgRGDPSNGDGSLTIQNLTLSDSGTY 88


                  ....*..
gi 1559988775 112 YCATWDR 118
Cdd:pfam07686  89 TCAVIPS 95
IGv smart00406
Immunoglobulin V-Type;
36-115 2.75e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 36.98  E-value: 2.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775   36 SAEITCDLT--VINAFYIHWYLHQEGKAPqRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYC 113
Cdd:smart00406   1 SVTLSCKFSgsTFSSYYVSWVRQPPGKGL-EWLGYIGSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1559988775  114 AT 115
Cdd:smart00406  80 AV 81
 
Name Accession Description Interval E-value
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 22-118 2.00e-35

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: 117.46  E-value: 2.00e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  22 LEGGTKSVTRPTRSSAEITCDLTVI--NAFYIHWYLHQEGKAPQRLLYYDvSNSKDVLESGLSPGKYYTHTPRR-WSWIL 98
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVSGIdfSTTYIHWYRQKPGQALERLLYVS-STSAVRKDSGKTKNKFEARKDVGkSTSTL 79

                          90       100
                  ....*....|....*....|
gi 1559988775  99 ILRNLIENDSGVYYCATWDR 118
Cdd:cd04982    80 TITNLEKEDSATYYCAYWES 99
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 27-118 1.42e-19

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: 76.99  E-value: 1.42e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  27 KSVTRPTRSSAEITCDLTVINAF-YIHWYLHQEGKAPQRLLYYDVSNSKdvlESGLSPGKYYTHTPRRWSWILILRNLIE 105
Cdd:cd00099     6 RSLSVQEGESVTLSCEVSSSFSStYIYWYRQKPGQGPEFLIYLSSSKGK---TKGGVPGRFSGSRDGTSSFSLTISNLQP 82

                          90
                  ....*....|...
gi 1559988775 106 NDSGVYYCATWDR 118
Cdd:cd00099    83 EDSGTYYCAVSES 95
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 31-114 9.83e-10

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: 51.90  E-value: 9.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  31 RPTRSSAEITCDLTvINAFYIHWYLHQEGKAPQRLLYYDVSNSKDvlESGLSPGKYYTHTPRRWSWILILRNLIENDSGV 110
Cdd:cd05899    10 KRRGQSVTLRCSQK-SGHDNMYWYRQDPGKGLQLLFYSYGGGLNE--EGDLPGDRFSASRPSLTRSSLTIKSAEPEDSAV 86


                  ....
gi 1559988775 111 YYCA 114
Cdd:cd05899    87 YLCA 90
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 36-117 7.72e-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: 46.69  E-value: 7.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  36 SAEITCDLTVIN--AFYIHWYLHQEGKAPQRLLYYDVSNSKDVLE--SGLSPGKyythtprrwSWILILRNLIENDSGVY 111
Cdd:cd04984    15 TVTITCTGSSGNisGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDrfSGSKSGN---------TASLTISGAQTEDEADY 85


                  ....*.
gi 1559988775 112 YCATWD 117
Cdd:cd04984    86 YCQVWD 91
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 36-118 1.91e-07

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: 45.91  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  36 SAEITC---DLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLEsglsPGKYY-THTPRRWSWILILRNLIENDSGVY 111
Cdd:pfam07686  13 SVTLPCtysSSMSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGVK----KGRFSgRGDPSNGDGSLTIQNLTLSDSGTY 88


                  ....*..
gi 1559988775 112 YCATWDR 118
Cdd:pfam07686  89 TCAVIPS 95
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 28-114 1.16e-06

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: 43.80  E-value: 1.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  28 SVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYdVSNSKDVLESGLSpgkyYTHTPRRWSWILILRNLIEND 107
Cdd:cd04983     7 SLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYI-SSDSGNKKKGRFS----ATLDKSRKSSSLHISAAQLSD 81


                  ....*..
gi 1559988775 108 SGVYYCA 114
Cdd:cd04983    82 SAVYFCA 88
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 36-113 3.53e-06

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: 42.38  E-value: 3.53e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775  36 SAEITCDL-TVINAFYIHWYLHQEGKAPqRLLYYDVSNskdvLESGlspgkyythTPRRWS-------WILILRNLIEND 107
Cdd:cd04980    17 RVTISCKAsQSISSNYLAWYQQKPGQAP-KLLIYYAST----LHSG---------VPSRFSgsgsgtdFTLTISSVEPED 82


                  ....*.
gi 1559988775 108 SGVYYC 113
Cdd:cd04980    83 AAVYYC 88
IGv smart00406
Immunoglobulin V-Type;
36-115 2.75e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 36.98  E-value: 2.75e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775   36 SAEITCDLT--VINAFYIHWYLHQEGKAPqRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYC 113
Cdd:smart00406   1 SVTLSCKFSgsTFSSYYVSWVRQPPGKGL-EWLGYIGSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1559988775  114 AT 115
Cdd:smart00406  80 AV 81
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 27-117 5.93e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 35.94  E-value: 5.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1559988775   27 KSVTRPTRSSAEITCDLTVINAFYIHWYlHQEGKApqrllyydvsnskdvlesgLSPGKYYTHTPRRWSWILILRNLIEN 106
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGSPPPEVTWY-KQGGKL-------------------LAESGRFSVSRSGSTSTLTISNVTPE 61

                           90
                   ....*....|.
gi 1559988775  107 DSGVYYCATWD 117
Cdd:smart00410  62 DSGTYTCAATN 72
 
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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