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Conserved domains on  [gi|2322547357|gb|UYS90897|]
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TRAV2.1, partial [Tiliqua rugosa]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DUF1968 super family cl48051
Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell ...
40-110 2.70e-09

Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.


The actual alignment was detected with superfamily member pfam09291:

Pssm-ID: 462744  Cd Length: 80  Bit Score: 51.26  E-value: 2.70e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2322547357  40 PSVYELESTnKSHPLSACLFTDyFPGNINVS-ATGSNLVGIESSVVVVE--DQASYGAVLWQNaNENLQCVANY 110
Cdd:pfam09291   1 PAVYQLRSP-KSSNTSVCLFTD-FDSQVNVSqSEESTVIKTDSTVLDMKsmDSKSNGALAWSN-NTDFGCQDTF 71
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
1-31 2.23e-05

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 cd04983:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 109  Bit Score: 41.49  E-value: 2.23e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2322547357   1 EMANAGVYYCAAEGASEWGKIIFGSGSKLEV 31
Cdd:cd04983    78 QLSDSAVYFCALSESGGTGKLTFGKGTRLTV 108
 
Name Accession Description Interval E-value
DUF1968 pfam09291
Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell ...
40-110 2.70e-09

Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.


Pssm-ID: 462744  Cd Length: 80  Bit Score: 51.26  E-value: 2.70e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2322547357  40 PSVYELESTnKSHPLSACLFTDyFPGNINVS-ATGSNLVGIESSVVVVE--DQASYGAVLWQNaNENLQCVANY 110
Cdd:pfam09291   1 PAVYQLRSP-KSSNTSVCLFTD-FDSQVNVSqSEESTVIKTDSTVLDMKsmDSKSNGALAWSN-NTDFGCQDTF 71
IgC_TCR_alpha cd07688
Immunoglobulin (Ig) constant domain the alpha chain of alpha/beta T-cell antigen receptors ...
39-100 2.80e-09

Immunoglobulin (Ig) constant domain the alpha chain of alpha/beta T-cell antigen receptors (TCRs); The members here are composed of the constant 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 includes the variable domain of the alpha chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409485  Cd Length: 83  Bit Score: 51.41  E-value: 2.80e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2322547357  39 EPSVYELEStNKSHPLSACLFTDyFPGNINVSAT-GSNLVGIESSVVV---VEDQASYGAVLWQNA 100
Cdd:cd07688     1 EPAVYQLKD-PRSSDISVCLFTD-FDSQTNVTKSmDSETVFITNKTVLdmkSMDSKSNGAVAWSNQ 64
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
1-31 2.23e-05

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: 41.49  E-value: 2.23e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2322547357   1 EMANAGVYYCAAEGASEWGKIIFGSGSKLEV 31
Cdd:cd04983    78 QLSDSAVYFCALSESGGTGKLTFGKGTRLTV 108
 
Name Accession Description Interval E-value
DUF1968 pfam09291
Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell ...
40-110 2.70e-09

Domain of unknown function (DUF1968); Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.


Pssm-ID: 462744  Cd Length: 80  Bit Score: 51.26  E-value: 2.70e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2322547357  40 PSVYELESTnKSHPLSACLFTDyFPGNINVS-ATGSNLVGIESSVVVVE--DQASYGAVLWQNaNENLQCVANY 110
Cdd:pfam09291   1 PAVYQLRSP-KSSNTSVCLFTD-FDSQVNVSqSEESTVIKTDSTVLDMKsmDSKSNGALAWSN-NTDFGCQDTF 71
IgC_TCR_alpha cd07688
Immunoglobulin (Ig) constant domain the alpha chain of alpha/beta T-cell antigen receptors ...
39-100 2.80e-09

Immunoglobulin (Ig) constant domain the alpha chain of alpha/beta T-cell antigen receptors (TCRs); The members here are composed of the constant 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 includes the variable domain of the alpha chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409485  Cd Length: 83  Bit Score: 51.41  E-value: 2.80e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2322547357  39 EPSVYELEStNKSHPLSACLFTDyFPGNINVSAT-GSNLVGIESSVVV---VEDQASYGAVLWQNA 100
Cdd:cd07688     1 EPAVYQLKD-PRSSDISVCLFTD-FDSQTNVTKSmDSETVFITNKTVLdmkSMDSKSNGAVAWSNQ 64
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
1-31 2.23e-05

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: 41.49  E-value: 2.23e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2322547357   1 EMANAGVYYCAAEGASEWGKIIFGSGSKLEV 31
Cdd:cd04983    78 QLSDSAVYFCALSESGGTGKLTFGKGTRLTV 108
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
5-31 8.52e-05

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: 40.01  E-value: 8.52e-05
                          10        20
                  ....*....|....*....|....*..
gi 2322547357   5 AGVYYCAAEGASEWGKIIFGSGSKLEV 31
Cdd:cd00099    85 SGTYYCAVSESGGTDKLTFGSGTRLTV 111
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
40-84 1.98e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. 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 is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409374  Cd Length: 98  Bit Score: 36.03  E-value: 1.98e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2322547357  40 PSVYELESTNKSHPLS----ACLFTDYFPGNINVSATGSNLVGIESSVV 84
Cdd:cd04985     2 PTVFPLQSATKSQSNGpvalGCLISDYFPESITVSWQKNTNSITSGFTR 50
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
5-31 8.66e-03

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: 34.65  E-value: 8.66e-03
                          10        20
                  ....*....|....*....|....*...
gi 2322547357   5 AGVYYCAA-EGASEWGKIIFGSGSKLEV 31
Cdd:cd04982    89 SATYYCAYwESGSGYYIKVFGSGTKLIV 116
 
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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