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Conserved domains on  [gi|6724178|gb|AAF26879|]
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T cell receptor V delta 6, partial [Rattus norvegicus]

Protein Classification

immunoglobulin domain-containing protein; fibroblast growth factor receptor 1( domain architecture ID 10309364)

immunoglobulin (Ig) domain-containing protein adopts a fold comprised of a sandwich of two beta sheets and may function in cell adhesion and pattern recognition; similar to Drosophila melanogaster DIP/Dpr cell recognition proteins, which are members of the Wirin family of IgSF proteins with neuronal wiring functions, and human IgLON proteins, a family of cell adhesion molecules| fibroblast growth factor receptor 1 (FGFR1) is a receptor tyrosine-protein kinase contains an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain that catalyzes the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates; it binds the ligands, FGF1 and FGF2, with high affinity and has also been reported to bind FGF4, FGF6, and FGF9

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 ...
 23-132 2.74e-46

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 cd07706:

Pssm-ID: 472250  Cd Length: 112  Bit Score: 150.75  E-value: 2.74e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   23 KVTQAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLILQPSFDsQNQRSGRYSVIFQQSLKSISLVISAS 102
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNYYLFWYKQLPSGEMTFLIRQDSSE-QNAKSGRYSVNFQKAQKSISLTISAL 79

                        90       100       110
                ....*....|....*....|....*....|...
gi 6724178  103 QPEDSGKYFCALWTRWHT---AFGQGTQVTVEP 132
Cdd:cd07706  80 QLEDSAKYFCALSLPYDTdklIFGKGTRLTVEP 112
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
 139-218 4.57e-45

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma 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. 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.


:

Pssm-ID: 409484  Cd Length: 80  Bit Score: 146.49  E-value: 4.57e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  139 KPSVFIMKNGTNVACLVKDFYPKDVNISLRSSKKIAEFDPAIAISPSGKYSAVKLGQYGDSNSVTCSVQHNSETVHSTDF 218
Cdd:cd07687   1 SPSVFVMKNGTNVACLVKNFYPKEVTISLSSSKKIIEFDPAIVISPNGKYSAVKLGKYGDSDSVTCSVQHSNKTVHSTDF 80
 
Name Accession Description Interval E-value
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 23-132 2.74e-46

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: 150.75  E-value: 2.74e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   23 KVTQAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLILQPSFDsQNQRSGRYSVIFQQSLKSISLVISAS 102
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNYYLFWYKQLPSGEMTFLIRQDSSE-QNAKSGRYSVNFQKAQKSISLTISAL 79

                        90       100       110
                ....*....|....*....|....*....|...
gi 6724178  103 QPEDSGKYFCALWTRWHT---AFGQGTQVTVEP 132
Cdd:cd07706  80 QLEDSAKYFCALSLPYDTdklIFGKGTRLTVEP 112
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
 139-218 4.57e-45

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma 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. 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.


Pssm-ID: 409484  Cd Length: 80  Bit Score: 146.49  E-value: 4.57e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  139 KPSVFIMKNGTNVACLVKDFYPKDVNISLRSSKKIAEFDPAIAISPSGKYSAVKLGQYGDSNSVTCSVQHNSETVHSTDF 218
Cdd:cd07687   1 SPSVFVMKNGTNVACLVKNFYPKEVTISLSSSKKIIEFDPAIVISPNGKYSAVKLGKYGDSDSVTCSVQHSNKTVHSTDF 80
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-130 2.58e-13

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: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178     34 QEGEEVTLECSYETSY--GTYYLFWYKQLLSGEMVFLILQPSFDSQ-NQRSGRYSVIFQQSLKSISLVISASQPEDSGKY 110
Cdd:pfam07686   9 ALGGSVTLPCTYSSSMseASTSVYWYRQPPGKGPTFLIAYYSNGSEeGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGTY 88

                          90       100
                  ....*....|....*....|
gi 6724178    111 FCALWTRWHTAFGQGTQVTV 130
Cdd:pfam07686  89 TCAVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 29-130 9.85e-12

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: 59.83  E-value: 9.85e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178      29 SSASRQEGEEVTLECSYeTSYGTYYLFWYKQllSGEMVFlilqpsfdsqnqRSGRYSVIFQQSlkSISLVISASQPEDSG 108
Cdd:smart00410   2 PSVTVKEGESVTLSCEA-SGSPPPEVTWYKQ--GGKLLA------------ESGRFSVSRSGS--TSTLTISNVTPEDSG 64

                           90       100
                   ....*....|....*....|..
gi 6724178     109 KYFCALWTRWHTAFGqGTQVTV 130
Cdd:smart00410  65 TYTCAATNSSGSASS-GTTLTV 85
IGc1 smart00407
Immunoglobulin C-Type;
151-214 5.60e-04

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 37.68  E-value: 5.60e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6724178     151 VACLVKDFYPKDVNISLR-----SSKKIAEFDPaiAISPSGKYSA-----VKLGQYGDSNSVTCSVQHNSETVH 214
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLrngqeVTEGVSTTDP--LKNSDGTYFLssyltVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
151-210 5.64e-04

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 38.00  E-value: 5.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6724178    151 VACLVKDFYPKDVNIS-LRSSKKIAE----FDPaiaiSPSGKYS-------AVKLGQYGDSNSVTCSVQHNS 210
Cdd:pfam07654  17 LTCLVTGFYPPDITVTwLKNGQEVTEgvktTPP----SPNSDWTyqlssylTVTPSDWESGDEYTCRVEHEG 84
 
Name Accession Description Interval E-value
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 23-132 2.74e-46

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: 150.75  E-value: 2.74e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   23 KVTQAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLILQPSFDsQNQRSGRYSVIFQQSLKSISLVISAS 102
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNYYLFWYKQLPSGEMTFLIRQDSSE-QNAKSGRYSVNFQKAQKSISLTISAL 79

                        90       100       110
                ....*....|....*....|....*....|...
gi 6724178  103 QPEDSGKYFCALWTRWHT---AFGQGTQVTVEP 132
Cdd:cd07706  80 QLEDSAKYFCALSLPYDTdklIFGKGTRLTVEP 112
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
 139-218 4.57e-45

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma 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. 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.


Pssm-ID: 409484  Cd Length: 80  Bit Score: 146.49  E-value: 4.57e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  139 KPSVFIMKNGTNVACLVKDFYPKDVNISLRSSKKIAEFDPAIAISPSGKYSAVKLGQYGDSNSVTCSVQHNSETVHSTDF 218
Cdd:cd07687   1 SPSVFVMKNGTNVACLVKNFYPKEVTISLSSSKKIIEFDPAIVISPNGKYSAVKLGKYGDSDSVTCSVQHSNKTVHSTDF 80
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 24-131 4.38e-41

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: 137.40  E-value: 4.38e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYETSyGTYYLFWYKQLLSGEMVFLILQPSfDSQNQRSGRYSVIFQQSLKSISLVISASQ 103
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTS-TFYYLFWYRQYPGQGPQFLIYISS-DSGNKKKGRFSATLDKSRKSSSLHISAAQ 78

                        90       100       110
                ....*....|....*....|....*....|.
gi 6724178  104 PEDSGKYFCALWTRWHT---AFGQGTQVTVE 131
Cdd:cd04983  79 LSDSAVYFCALSESGGTgklTFGKGTRLTVE 109
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 24-130 7.48e-30

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: 108.58  E-value: 7.48e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLILQPSFDSQNQR--SGRYSVIFqQSLKSISLVISA 101
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKPGQGPEFLIYLSSSKGKTKGgvPGRFSGSR-DGTSSFSLTISN 79

                        90       100       110
                ....*....|....*....|....*....|..
gi 6724178  102 SQPEDSGKYFCALWTRWHTA---FGQGTQVTV 130
Cdd:cd00099  80 LQPEDSGTYYCAVSESGGTDkltFGSGTRLTV 111
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 24-130 6.88e-15

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: 68.64  E-value: 6.88e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAhSSASRQEGEEVTLECSYET-SYGTYYLFWYKQLLSGEMVFLIlqpsFDSQNQRSG---RYSviFQQSLKSISLVI 99
Cdd:cd04984   2 LTQP-SSLSVSPGETVTITCTGSSgNISGNYVNWYQQKPGSAPRYLI----YEDKHRPSGipdRFS--GSKSGNTASLTI 74

                        90       100       110
                ....*....|....*....|....*....|.
gi 6724178  100 SASQPEDSGKYFCALWTRWHTAFGQGTQVTV 130
Cdd:cd04984  75 SGAQTEDEADYYCQVWDSNSYVFGGGTKLTV 105
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 24-130 4.61e-14

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: 66.54  E-value: 4.61e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYETSYgtYYLFWYKQLLSGEMVFLIL---QPSFDSQNQRSGRYSVIfQQSLKSISLVIS 100
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQKSGH--DNMYWYRQDPGKGLQLLFYsygGGLNEEGDLPGDRFSAS-RPSLTRSSLTIK 77

                        90       100       110
                ....*....|....*....|....*....|...
gi 6724178  101 ASQPEDSGKYFCALWTRWHTA---FGQGTQVTV 130
Cdd:cd05899  78 SAEPEDSAVYLCASSLGGGADeayFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 34-130 2.58e-13

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: 2.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178     34 QEGEEVTLECSYETSY--GTYYLFWYKQLLSGEMVFLILQPSFDSQ-NQRSGRYSVIFQQSLKSISLVISASQPEDSGKY 110
Cdd:pfam07686   9 ALGGSVTLPCTYSSSMseASTSVYWYRQPPGKGPTFLIAYYSNGSEeGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGTY 88

                          90       100
                  ....*....|....*....|
gi 6724178    111 FCALWTRWHTAFGQGTQVTV 130
Cdd:pfam07686  89 TCAVIPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 29-130 9.85e-12

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: 59.83  E-value: 9.85e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178      29 SSASRQEGEEVTLECSYeTSYGTYYLFWYKQllSGEMVFlilqpsfdsqnqRSGRYSVIFQQSlkSISLVISASQPEDSG 108
Cdd:smart00410   2 PSVTVKEGESVTLSCEA-SGSPPPEVTWYKQ--GGKLLA------------ESGRFSVSRSGS--TSTLTISNVTPEDSG 64

                           90       100
                   ....*....|....*....|..
gi 6724178     109 KYFCALWTRWHTAFGqGTQVTV 130
Cdd:smart00410  65 TYTCAATNSSGSASS-GTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
39-113 5.24e-09

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 52.00  E-value: 5.24e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6724178      39 VTLECSYETS-YGTYYLFWYKQLLSGEMVFLILQPSFDS---QNQRSGRYSVIFQQSLKSISLVISASQPEDSGKYFCA 113
Cdd:smart00406   2 VTLSCKFSGStFSSYYVSWVRQPPGKGLEWLGYIGSNGSsyyQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYCA 80
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 24-130 8.83e-09

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: 52.37  E-value: 8.83e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYE-TSYGTYYLFWYKQLLSGEMVFLILQPSFDSQNQRSGRYSVIFQQSL----KSISLV 98
Cdd:cd04982   1 LEQPQLSITREESKSVTISCKVSgIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKdvgkSTSTLT 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 6724178   99 ISASQPEDSGKYFCALWTR----WHTAFGQGTQVTV 130
Cdd:cd04982  81 ITNLEKEDSATYYCAYWESgsgyYIKVFGSGTKLIV 116
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 28-131 3.12e-07

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: 47.94  E-value: 3.12e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   28 HSSASRQEGEEVTLECSYE-TSYGTYYLFWYKQLLSGEMVFL-----ILQPSFDSqNQRSGRYSVIFQQSLKsislvISA 101
Cdd:cd20988   5 HQTVTVSVGKPVTLKCSMKgEAISNYYINWYRKTQGNTMTFIyreggIYGPGFKD-NFRGDIDSSNNLAVLK-----ILE 78

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 6724178  102 SQPEDSGKYFCALWT------RWHTAFGQGTQVTVE 131
Cdd:cd20988  79 ASERDEGSYYCASDTpgggreYDPLIFGKGTYLTVE 114
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 24-130 8.74e-07

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: 46.61  E-value: 8.74e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLIlqpsFDSQNQRSG---RYSVifQQSLKSISLVIS 100
Cdd:cd04980   3 MTQSPASLSVSPGERVTISCKASQSISSNYLAWYQQKPGQAPKLLI----YYASTLHSGvpsRFSG--SGSGTDFTLTIS 76

                        90       100       110
                ....*....|....*....|....*....|
gi 6724178  101 ASQPEDSGKYFCALWTRWHTAFGQGTQVTV 130
Cdd:cd04980  77 SVEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 32-131 1.13e-05

Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their C-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620-residue extracellular region, a 23-residue transmembrane region, and a 103-residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions. This group also contains the Ig-like extracellular domains of other receptors such as NK cell receptor Nkp44 and myeloid receptors, among others.


Pssm-ID: 409381  Cd Length: 100  Bit Score: 43.16  E-value: 1.13e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   32 SRQEGEEVTLECSYETSYGTYYLFWYKQLLSGemvfliLQPSFDSQN-QRSGRYSVIFQQSLKSISLVISASQPEDSGKY 110
Cdd:cd05716   8 TGVEGGSVTIQCPYPPKYASSRKYWCKWGSEG------CQTLVSSEGvVPGGRISLTDDPDNGVFTVTLNQLRKEDAGWY 81

                        90       100
                ....*....|....*....|.
gi 6724178  111 FCALWTRWHtaFGQGTQVTVE 131
Cdd:cd05716  82 WCGVGDDGD--RGLTVQVKLV 100
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-113 2.89e-05

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


Pssm-ID: 409509  Cd Length: 112  Bit Score: 42.49  E-value: 2.89e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   34 QEGEEVTLECSYETSYGTYYLFWYKQLLSGEMVFLILQPSFDSQNQRSGRYSVIFQQSLKSISLVISASQPEDSGKYFCA 113
Cdd:cd16088  12 TEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRARRNDSGTYLCG 91
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 23-112 8.23e-05

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 40.24  E-value: 8.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178     23 KVTQAHSSASRQEGEEVTLECSYeTSYGTYYLFWYKqllsgemvflilqpsfDSQNQRSGRYSVIFQQSLKSiSLVISAS 102
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCEA-TGSPPPTITWYK----------------NGEPISSGSTRSRSLSGSNS-TLTISNV 64

                          90
                  ....*....|
gi 6724178    103 QPEDSGKYFC 112
Cdd:pfam13927  65 TRSDAGTYTC 74
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 36-130 2.53e-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: 2.53e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   36 GEEVTLEC--SYETsYGTYYLFWYKQLLSG--EMVFLILQPSFDSQNQRS--GRYSVIFQQSLKSISLVISASQPEDSGK 109
Cdd:cd04981  13 GQSLKLSCkaSGFT-FTSYGMGWVRQAPGKglEWIGLIYPGGGDTYYADSfkGRFTITRDTSKSTAYLQLNSLTSEDTAV 91

                        90       100
                ....*....|....*....|....*.
gi 6724178  110 YFCALWTRW--HTAF---GQGTQVTV 130
Cdd:cd04981  92 YYCARGLGGygYSYFdywGQGTTVTV 117
IGc1 smart00407
Immunoglobulin C-Type;
151-214 5.60e-04

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 37.68  E-value: 5.60e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6724178     151 VACLVKDFYPKDVNISLR-----SSKKIAEFDPaiAISPSGKYSA-----VKLGQYGDSNSVTCSVQHNSETVH 214
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLrngqeVTEGVSTTDP--LKNSDGTYFLssyltVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
151-210 5.64e-04

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 38.00  E-value: 5.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6724178    151 VACLVKDFYPKDVNIS-LRSSKKIAE----FDPaiaiSPSGKYS-------AVKLGQYGDSNSVTCSVQHNS 210
Cdd:pfam07654  17 LTCLVTGFYPPDITVTwLKNGQEVTEgvktTPP----SPNSDWTyqlssylTVTPSDWESGDEYTCRVEHEG 84
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 26-130 8.22e-04

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: 38.20  E-value: 8.22e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   26 QAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQLLSgemvflilqPSFDS-----------------QNQRSGRYSVIF 88
Cdd:cd07700   3 QTPGSLLVQTNQTVKMSCEAKTSPKNTRIYWLRQRQA---------PSKDShfeflaswdpskgivygEGVDQEKLIILS 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 6724178   89 QQSLKSISLVISASQPEDSGKYFCALWTRWHTAFGQGTQVTV 130
Cdd:cd07700  74 DSDSSRYILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKLSV 115
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 140-216 9.67e-04

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc 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.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 37.70  E-value: 9.67e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  140 PSVFIM--------KNGT-NVACLVKDFYPKDVNIS-LRSSKKIAEFD---PAIAISPSGKYSA-----VKLGQYGDSNS 201
Cdd:cd05768   1 PSVYLLpppeeelsLNETvTLTCLVKGFYPEDIFVSwLQNGEPLPSADyktTAPVPESDGSFFVysklnVSTADWNSGDV 80

                        90
                ....*....|....*
gi 6724178  202 VTCSVQHNSETVHST 216
Cdd:cd05768  81 FSCVVGHEALPLQFT 95
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 140-210 9.99e-04

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. 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 strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 37.44  E-value: 9.99e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  140 PSVFIMKNGTN-VACLVKDFYPKDVNIS-LRSSKKIAEFD--PAIAISPSGKYSA-----VKLGQYGDSNSVTCSVQHNS 210
Cdd:cd00098   7 PSPEEKGGGKVtLVCLVSGFYPKDITVTwLKNGVPLTSGVstSSPVEPNDGTYSVtssltVPPSDWDEGATYTCVVTHES 86
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 135-213 1.62e-03

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc 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.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 36.99  E-value: 1.62e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  135 QPPAKPSVFIMKNGTnVACLVKDFYPKDVNIS-LRSSKKIAEFDPAIAISP----SGKYSA-----VKLGQYGDSNSVTC 204
Cdd:cd16093   7 HAPSREEFLGNRTAT-FVCLATGFSPKTISFKwLRNGKEVTSSTGAVVEEPkedgKTLYSAtsfltITESEWKSQTEFTC 85


                ....*....
gi 6724178  205 SVQHNSETV 213
Cdd:cd16093  86 EFKHKGEIV 94
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 26-119 1.81e-03

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 36.79  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178     26 QAHSSASRQEGEEVTLECSYETSYGTYYLFWYKQllsgemvflilqpsfDSQNQRSGRYSVIFQQSlKSISLVISASQPE 105
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPGPDVTWSKE---------------GGTLIESLKVKHDNGRT-TQSSLLISNVTKE 64

                          90
                  ....*....|....
gi 6724178    106 DSGKYFCALWTRWH 119
Cdd:pfam00047  65 DAGTYTCVVNNPGG 78
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 24-126 1.87e-03

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 37.04  E-value: 1.87e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178   24 VTQAHSSASRQEGEEVTLECSYETSYGTYY--LFWYKQLLSGEMVFLILQPSF--DSQNQRSGRYS-VIFQQSLKSISLV 98
Cdd:cd05718   2 RVQVPTEVTGFLGGSVTLPCSLTSPGTTKItqVTWMKIGAGSSQNVAVFHPQYgpSVPNPYAERVEfLAARLGLRNATLR 81

                        90       100
                ....*....|....*....|....*...
gi 6724178   99 ISASQPEDSGKYFCALWTrwhtaFGQGT 126
Cdd:cd05718  82 IRNLRVEDEGNYICEFAT-----FPQGN 104
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 140-210 4.14e-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: 4.14e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  140 PSVFIMKNGTN--------VACLVKDFYPKDVNIS----LRSSKKIAEFDPAIAISPSGKYSA-----VKLGQYGDSNSV 202
Cdd:cd04985   2 PTVFPLQSATKsqsngpvaLGCLISDYFPESITVSwqknTNSITSGFTRTFPVVLRSGGDYSCssqltVPLQEWNSGEVY 81


                ....*...
gi 6724178  203 TCSVQHNS 210
Cdd:cd04985  82 KCQVQHSA 89
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 152-210 4.87e-03

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409593  Cd Length: 97  Bit Score: 35.67  E-value: 4.87e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6724178  152 ACLVKDFYPKDVNIS-LRSSKKIAEFDPA-IAISPSGKYS-------AVKLgQYGDsnSVTCSVQHNS 210
Cdd:cd21002  23 ACHVWGFYPADVTITwLKNGDPVAPHSSApKTAQPNGDWTyqtqvtlAVTP-SPGD--TYTCSVQHAS 87
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 139-208 6.76e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of epsilon and gamma chains. It belongs to a family 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: 409622  Cd Length: 94  Bit Score: 35.12  E-value: 6.76e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6724178  139 KPSVFIM------KNGTNVA--CLVKDFYPKDVNISLRS---SKKIAEFdPAIaISPSGKYSAVKL----GQYGDSNSVT 203
Cdd:cd21817   1 APSVFPLapccksTNGSSVTlgCLVTGYFPEPVTVTWNSgslTSGVKTF-PAV-LQSSGLYTTSSQvtvpSSSWGSQTFT 78


                ....*
gi 6724178  204 CSVQH 208
Cdd:cd21817  79 CNVEH 83
 
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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