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Conserved domains on  [gi|24158490|ref|NP_571724|]
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novel immune-type receptor 2b precursor [Danio rerio]

Protein Classification

immunoglobulin domain-containing protein( domain architecture ID 10058153)

immunoglobulin (Ig) domain-containing protein with one or more Ig domains, which adopt a fold comprised of a sandwich of two beta sheets; similar to Danio rerio Nitr2b (novel immune-type receptor 2b) that possesses features of both adaptive and innate immune receptors

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 29-129 3.12e-12

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: 62.35  E-value: 3.12e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKESRTSVV-WVKQRVGEKPLLIASAYQGlagKYENDFDKQNRFFIEKDEG-SFNLSIANTEISD 106
Cdd:cd00099   8 LSVQEGESVTLSCEVSSSFSSTYIyWYRQKPGQGPEFLIYLSSS---KGKTKGGVPGRFSGSRDGTsSFSLTISNLQPED 84

                        90       100
                ....*....|....*....|....*..
gi 24158490 107 TATYYCVAYV----YEFIFGNSTDLIV 129
Cdd:cd00099  85 SGTYYCAVSEsggtDKLTFGSGTRLTV 111
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 150-228 1.41e-03

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd04984:

Pssm-ID: 472250  Cd Length: 105  Bit Score: 37.44  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490 150 CSVISQSCAEEHkVYWFRQGSGESSPGVIYTQNSRSA----QCEKSSDLNsTAHKCIYSLPKTDEdpAIYYCAVAACGQI 225
Cdd:cd04984  20 CTGSSGNISGNY-VNWYQQKPGSAPRYLIYEDKHRPSgipdRFSGSKSGN-TASLTISGAQTEDE--ADYYCQVWDSNSY 95


                ...
gi 24158490 226 LFG 228
Cdd:cd04984  96 VFG 98
 
Name Accession Description Interval E-value
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 29-129 3.12e-12

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: 62.35  E-value: 3.12e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKESRTSVV-WVKQRVGEKPLLIASAYQGlagKYENDFDKQNRFFIEKDEG-SFNLSIANTEISD 106
Cdd:cd00099   8 LSVQEGESVTLSCEVSSSFSSTYIyWYRQKPGQGPEFLIYLSSS---KGKTKGGVPGRFSGSRDGTsSFSLTISNLQPED 84

                        90       100
                ....*....|....*....|....*..
gi 24158490 107 TATYYCVAYV----YEFIFGNSTDLIV 129
Cdd:cd00099  85 SGTYYCAVSEsggtDKLTFGSGTRLTV 111
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 25-129 4.42e-09

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: 53.23  E-value: 4.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490    25 QNHVMIVQAGVAVNLTCIFP---KESRTSVVWVKQRVGEKPLLIASAYQGLAGKYEndfdKQNRFFIEKD--EGSFNLSI 99
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSssmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGV----KKGRFSGRGDpsNGDGSLTI 77

                          90       100       110
                  ....*....|....*....|....*....|.
gi 24158490   100 ANTEISDTATYYC-VAYVYEFIFGNSTDLIV 129
Cdd:pfam07686  78 QNLTLSDSGTYTCaVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-129 8.06e-09

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: 51.74  E-value: 8.06e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490     28 VMIVQAGVAVNLTCIFPKESRTSVVWVKQrvGEKPLLiasayqglagkyendfdKQNRFFIEKDEGSFNLSIANTEISDT 107
Cdd:smart00410   3 SVTVKEGESVTLSCEASGSPPPEVTWYKQ--GGKLLA-----------------ESGRFSVSRSGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|..
gi 24158490    108 ATYYCVAYVYEFIFGNSTDLIV 129
Cdd:smart00410  64 GTYTCAATNSSGSASSGTTLTV 85
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 150-228 1.41e-03

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: 37.44  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490 150 CSVISQSCAEEHkVYWFRQGSGESSPGVIYTQNSRSA----QCEKSSDLNsTAHKCIYSLPKTDEdpAIYYCAVAACGQI 225
Cdd:cd04984  20 CTGSSGNISGNY-VNWYQQKPGSAPRYLIYEDKHRPSgipdRFSGSKSGN-TASLTISGAQTEDE--ADYYCQVWDSNSY 95


                ...
gi 24158490 226 LFG 228
Cdd:cd04984  96 VFG 98
 
Name Accession Description Interval E-value
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 29-129 3.12e-12

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: 62.35  E-value: 3.12e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKESRTSVV-WVKQRVGEKPLLIASAYQGlagKYENDFDKQNRFFIEKDEG-SFNLSIANTEISD 106
Cdd:cd00099   8 LSVQEGESVTLSCEVSSSFSSTYIyWYRQKPGQGPEFLIYLSSS---KGKTKGGVPGRFSGSRDGTsSFSLTISNLQPED 84

                        90       100
                ....*....|....*....|....*..
gi 24158490 107 TATYYCVAYV----YEFIFGNSTDLIV 129
Cdd:cd00099  85 SGTYYCAVSEsggtDKLTFGSGTRLTV 111
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 30-129 8.81e-11

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: 58.06  E-value: 8.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  30 IVQAGVAVNLTCIfPKESRTSVVWVKQRVGEKPLLIASAYQGlaGKYENDFDKQNRFFIEKDEGS-FNLSIANTEISDTA 108
Cdd:cd05899   9 IKRRGQSVTLRCS-QKSGHDNMYWYRQDPGKGLQLLFYSYGG--GLNEEGDLPGDRFSASRPSLTrSSLTIKSAEPEDSA 85

                        90       100
                ....*....|....*....|....*
gi 24158490 109 TYYCVA----YVYEFIFGNSTDLIV 129
Cdd:cd05899  86 VYLCASslggGADEAYFGPGTRLTV 110
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 29-130 1.06e-10

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: 58.05  E-value: 1.06e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKESRTSVVWVKQRVGEKPLLIASAYqglaGKYENDFDKQNRFFIEKDEGSFNLSIANTEISDTA 108
Cdd:cd04983   8 LSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYIS----SDSGNKKKGRFSATLDKSRKSSSLHISAAQLSDSA 83

                        90       100
                ....*....|....*....|....*.
gi 24158490 109 TYYCVA----YVYEFIFGNSTDLIVN 130
Cdd:cd04983  84 VYFCALsesgGTGKLTFGKGTRLTVE 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 25-129 4.42e-09

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: 53.23  E-value: 4.42e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490    25 QNHVMIVQAGVAVNLTCIFP---KESRTSVVWVKQRVGEKPLLIASAYQGLAGKYEndfdKQNRFFIEKD--EGSFNLSI 99
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSssmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEGV----KKGRFSGRGDpsNGDGSLTI 77

                          90       100       110
                  ....*....|....*....|....*....|.
gi 24158490   100 ANTEISDTATYYC-VAYVYEFIFGNSTDLIV 129
Cdd:pfam07686  78 QNLTLSDSGTYTCaVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-129 8.06e-09

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: 51.74  E-value: 8.06e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490     28 VMIVQAGVAVNLTCIFPKESRTSVVWVKQrvGEKPLLiasayqglagkyendfdKQNRFFIEKDEGSFNLSIANTEISDT 107
Cdd:smart00410   3 SVTVKEGESVTLSCEASGSPPPEVTWYKQ--GGKLLA-----------------ESGRFSVSRSGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|..
gi 24158490    108 ATYYCVAYVYEFIFGNSTDLIV 129
Cdd:smart00410  64 GTYTCAATNSSGSASSGTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
37-112 1.06e-08

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 51.61  E-value: 1.06e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490     37 VNLTCIF--PKESRTSVVWVKQRVGeKPLLIASAYQGLAGKYENDFDKqNRFFIEKD--EGSFNLSIANTEISDTATYYC 112
Cdd:smart00406   2 VTLSCKFsgSTFSSYYVSWVRQPPG-KGLEWLGYIGSNGSSYYQESYK-GRFTISKDtsKNDVSLTISNLRVEDTGTYYC 79
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 37-129 2.40e-07

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: 48.51  E-value: 2.40e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  37 VNLTCIF--PKESRTSVVWVKQRVGEKPLLIASAYQGLAGKYENDFDKqNRFFIEKDEGSFN--LSIANTEISDTATYYC 112
Cdd:cd04982  16 VTISCKVsgIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTK-NKFEARKDVGKSTstLTITNLEKEDSATYYC 94

                        90       100
                ....*....|....*....|...
gi 24158490 113 vAY------VYEFIFGNSTDLIV 129
Cdd:cd04982  95 -AYwesgsgYYIKVFGSGTKLIV 116
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 25-129 1.38e-05

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: 43.22  E-value: 1.38e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  25 QNHVMIVQAGVAVNLTCIFPKESRTS--VVWVKQRVGEKPLLIASayqglagkyendFDKQ------NRFFIEKDEGSFN 96
Cdd:cd04984   4 QPSSLSVSPGETVTITCTGSSGNISGnyVNWYQQKPGSAPRYLIY------------EDKHrpsgipDRFSGSKSGNTAS 71

                        90       100       110
                ....*....|....*....|....*....|....
gi 24158490  97 LSIANTEISDTATYYC-VAYVYEFIFGNSTDLIV 129
Cdd:cd04984  72 LTISGAQTEDEADYYCqVWDSNSYVFGGGTKLTV 105
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 29-127 1.34e-04

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: 40.45  E-value: 1.34e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKE-SRTSVVWVKQRVGEKP-LLIASAYQGLAGKyendfdkQNRFfiekdEGS-----FNLSIAN 101
Cdd:cd04980  10 LSVSPGERVTISCKASQSiSSNYLAWYQQKPGQAPkLLIYYASTLHSGV-------PSRF-----SGSgsgtdFTLTISS 77

                        90       100
                ....*....|....*....|....*..
gi 24158490 102 TEISDTATYYCVAY-VYEFIFGNSTDL 127
Cdd:cd04980  78 VEPEDAAVYYCQQGyTFPYTFGGGTKL 104
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 29-112 3.79e-04

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: 39.60  E-value: 3.79e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTCIFPKESRTS--VVWVKQRVGEKPLLIASAYQGLAGKYENDfDKQNRFFIEKDEGS--FNLSIANTEI 104
Cdd:cd04981   8 GLVKPGQSLKLSCKASGFTFTSygMGWVRQAPGKGLEWIGLIYPGGGDTYYAD-SFKGRFTITRDTSKstAYLQLNSLTS 86


                ....*...
gi 24158490 105 SDTATYYC 112
Cdd:cd04981  87 EDTAVYYC 94
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 31-129 4.91e-04

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: 39.04  E-value: 4.91e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  31 VQAGVAVNLTCIFpkESRTS---VVWVKQR-VGEKPLLI--ASAYQG-LAGKYENDFDKQNRffiekdegSFNLSIANTE 103
Cdd:cd07706  11 VQVGEEVTLNCRY--ETSWTnyyLFWYKQLpSGEMTFLIrqDSSEQNaKSGRYSVNFQKAQK--------SISLTISALQ 80

                        90       100       110
                ....*....|....*....|....*....|
gi 24158490 104 ISDTATYYCVAYVY----EFIFGNSTDLIV 129
Cdd:cd07706  81 LEDSAKYFCALSLPydtdKLIFGKGTRLTV 110
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 150-228 1.41e-03

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: 37.44  E-value: 1.41e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490 150 CSVISQSCAEEHkVYWFRQGSGESSPGVIYTQNSRSA----QCEKSSDLNsTAHKCIYSLPKTDEdpAIYYCAVAACGQI 225
Cdd:cd04984  20 CTGSSGNISGNY-VNWYQQKPGSAPRYLIYEDKHRPSgipdRFSGSKSGN-TASLTISGAQTEDE--ADYYCQVWDSNSY 95


                ...
gi 24158490 226 LFG 228
Cdd:cd04984  96 VFG 98
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 29-129 4.06e-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: 36.66  E-value: 4.06e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24158490  29 MIVQAGVAVNLTC---IFPKEsrTSVVWVKQRVGEKP-----LLIASAYQGLAGKYENDFDKQNRFFIEKDEGSFNLSIA 100
Cdd:cd07700   8 LLVQTNQTVKMSCeakTSPKN--TRIYWLRQRQAPSKdshfeFLASWDPSKGIVYGEGVDQEKLIILSDSDSSRYILSLM 85

                        90       100       110
                ....*....|....*....|....*....|
gi 24158490 101 NTEISDTATYYCVAY-VYEFIFGNSTDLIV 129
Cdd:cd07700  86 SVKPEDSGTYFCMTVgSPELIFGTGTKLSV 115
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 37-114 8.87e-03

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.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 34.61  E-value: 8.87e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24158490  37 VNLTCIFPKESRTSVVWVKQrvgekplliasayqglagkyENDFDKQNRFFIEKDEGSFNLSIANTEISDTATYYCVA 114
Cdd:cd00096   1 VTLTCSASGNPPPTITWYKN--------------------GKPLPPSSRDSRRSELGNGTLTISNVTLEDSGTYTCVA 58
 
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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