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Conserved domains on  [gi|2558070789|tpg|DBA11837|]
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TPA: IGKV2-12*01, partial [Lemur catta]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 22-120 3.34e-52

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 cd04980:

Pssm-ID: 472250  Cd Length: 106  Bit Score: 159.86  E-value: 3.34e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  22 TVMTQTPLSLSVTLGESASISCKASQSLlhtnGNTYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKIS 101
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90
                  ....*....|....*....
gi 2558070789 102 RVEAEDVGVYYCLQNLYIP 120
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFP 95
 
Name Accession Description Interval E-value
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 22-120 3.34e-52

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: 159.86  E-value: 3.34e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  22 TVMTQTPLSLSVTLGESASISCKASQSLlhtnGNTYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKIS 101
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90
                  ....*....|....*....
gi 2558070789 102 RVEAEDVGVYYCLQNLYIP 120
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFP 95
IGv smart00406
Immunoglobulin V-Type;
38-113 1.04e-20

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 79.35  E-value: 1.04e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789   38 SASISCKASQSllhTNGNTYLHWLLQKPGQPPRRLIYQVSNR----DSGVPDRFSGSG--SGTDFTLKISRVEAEDVGVY 111
Cdd:smart00406   1 SVTLSCKFSGS---TFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTY 77


                   ..
gi 2558070789  112 YC 113
Cdd:smart00406  78 YC 79
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 26-113 2.15e-18

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: 74.03  E-value: 2.15e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  26 QTPLSLSVTLGESASISCkaSQSLLHTNGNTYLHWLLQKPGQPPRRLIYQVSNRD--SGVPDRFSGSG--SGTDFTLKIS 101
Cdd:pfam07686   1 QTPREVTVALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIAYYSNGSeeGVKKGRFSGRGdpSNGDGSLTIQ 78

                          90
                  ....*....|..
gi 2558070789 102 RVEAEDVGVYYC 113
Cdd:pfam07686  79 NLTLSDSGTYTC 90
 
Name Accession Description Interval E-value
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 22-120 3.34e-52

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: 159.86  E-value: 3.34e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  22 TVMTQTPLSLSVTLGESASISCKASQSLlhtnGNTYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKIS 101
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90
                  ....*....|....*....
gi 2558070789 102 RVEAEDVGVYYCLQNLYIP 120
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFP 95
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 24-113 1.14e-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: 105.49  E-value: 1.14e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  24 MTQTPLSLSVTLGESASISCKASQSllhtNGNTYLHWLLQKPGQPPRRLIYQVSNRDS---GVPDRFSGSGSG-TDFTLK 99
Cdd:cd00099     1 VTQSPRSLSVQEGESVTLSCEVSSS----FSSTYIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLT 76

                          90
                  ....*....|....
gi 2558070789 100 ISRVEAEDVGVYYC 113
Cdd:cd00099    77 ISNLQPEDSGTYYC 90
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 23-114 1.55e-30

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: 104.85  E-value: 1.55e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  23 VMTQtPLSLSVTLGESASISCKASQSLLHTNgntYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKISR 102
Cdd:cd04984     1 VLTQ-PSSLSVSPGETVTITCTGSSGNISGN---YVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISG 76

                          90
                  ....*....|..
gi 2558070789 103 VEAEDVGVYYCL 114
Cdd:cd04984    77 AQTEDEADYYCQ 88
IGv smart00406
Immunoglobulin V-Type;
38-113 1.04e-20

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 79.35  E-value: 1.04e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789   38 SASISCKASQSllhTNGNTYLHWLLQKPGQPPRRLIYQVSNR----DSGVPDRFSGSG--SGTDFTLKISRVEAEDVGVY 111
Cdd:smart00406   1 SVTLSCKFSGS---TFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTY 77


                   ..
gi 2558070789  112 YC 113
Cdd:smart00406  78 YC 79
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 24-113 4.20e-20

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: 78.56  E-value: 4.20e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  24 MTQTPLSLSVTLGESASISCKASqslLHTNGNTYLHWLLQKPGQPPRRLIYQVSN----RDSG-VPDRFSG---SGSGTd 95
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVS---GIDFSTTYIHWYRQKPGQALERLLYVSSTsavrKDSGkTKNKFEArkdVGKST- 76

                          90
                  ....*....|....*...
gi 2558070789  96 FTLKISRVEAEDVGVYYC 113
Cdd:cd04982    77 STLTITNLEKEDSATYYC 94
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 26-113 2.15e-18

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: 74.03  E-value: 2.15e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  26 QTPLSLSVTLGESASISCkaSQSLLHTNGNTYLHWLLQKPGQPPRRLIYQVSNRD--SGVPDRFSGSG--SGTDFTLKIS 101
Cdd:pfam07686   1 QTPREVTVALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIAYYSNGSeeGVKKGRFSGRGdpSNGDGSLTIQ 78

                          90
                  ....*....|..
gi 2558070789 102 RVEAEDVGVYYC 113
Cdd:pfam07686  79 NLTLSDSGTYTC 90
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 25-113 3.54e-15

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: 65.77  E-value: 3.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  25 TQTPLSLSVTLGESASISCKasqsllHTNGNTYLHWLLQKPGQPPRRLIYQVS---NRDSGVP-DRFSGSG-SGTDFTLK 99
Cdd:cd05899     2 TQSPRYLIKRRGQSVTLRCS------QKSGHDNMYWYRQDPGKGLQLLFYSYGgglNEEGDLPgDRFSASRpSLTRSSLT 75

                          90
                  ....*....|....
gi 2558070789 100 ISRVEAEDVGVYYC 113
Cdd:cd05899    76 IKSAEPEDSAVYLC 89
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 25-113 1.27e-14

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: 64.60  E-value: 1.27e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  25 TQTPLSLSVTLGESASISCKASqsllhTNGNTYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGS--GSGTDFTLKISR 102
Cdd:cd04983     2 TQSPQSLSVQEGENVTLNCNYS-----TSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISA 76

                          90
                  ....*....|.
gi 2558070789 103 VEAEDVGVYYC 113
Cdd:cd04983    77 AQLSDSAVYFC 87
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-113 1.39e-13

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: 61.37  E-value: 1.39e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789   28 PLSLSVTLGESASISCKASQsllhtNGNTYLHWLLQKPgqppRRLIYqvsnrdsgvPDRFSGSGSGTDFTLKISRVEAED 107
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASG-----SPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPED 62


                   ....*.
gi 2558070789  108 VGVYYC 113
Cdd:smart00410  63 SGTYTC 68
IgV_SIRP cd16097
Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The ...
 24-115 7.13e-07

Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three immunoglobulin superfamily domains, a single V-set, and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409516  Cd Length: 111  Bit Score: 44.47  E-value: 7.13e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  24 MTQTPLSLSVTLGESASISCKASqSLLHTNGntyLHWLlqKPGQPPRRLIYqvsNRDSGVPDRFSGSGSGT-----DFTL 98
Cdd:cd16097     2 VIQPEKSVSVAAGESATLHCTVT-SLIPVGP---IQWF--RGAGPGRELIY---NQKEGHFPRVTTVSDLTkrnnmDFSI 72

                          90
                  ....*....|....*..
gi 2558070789  99 KISRVEAEDVGVYYCLQ 115
Cdd:cd16097    73 RISNITPADAGTYYCVK 89
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 26-114 7.25e-07

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: 44.36  E-value: 7.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  26 QTPLSLSVTLGESASISCKASQSLLHTNgntyLHWLLQKPGQPPRR----LIYQVSNRDS----GV-PDRFS--GSGSGT 94
Cdd:cd07700     3 QTPGSLLVQTNQTVKMSCEAKTSPKNTR----IYWLRQRQAPSKDShfefLASWDPSKGIvygeGVdQEKLIilSDSDSS 78

                          90       100
                  ....*....|....*....|
gi 2558070789  95 DFTLKISRVEAEDVGVYYCL 114
Cdd:cd07700    79 RYILSLMSVKPEDSGTYFCM 98
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 36-113 1.23e-06

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: 43.84  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  36 GESASISCKASQSllhTNGNTYLHWLLQKPGQPPR--RLIYQV---SNRDSGVPDRFSGS--GSGTDFTLKISRVEAEDV 108
Cdd:cd04981    13 GQSLKLSCKASGF---TFTSYGMGWVRQAPGKGLEwiGLIYPGggdTYYADSFKGRFTITrdTSKSTAYLQLNSLTSEDT 89


                  ....*
gi 2558070789 109 GVYYC 113
Cdd:cd04981    90 AVYYC 94
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 25-113 3.27e-05

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: 40.20  E-value: 3.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  25 TQTPLSLSVTLGESASISCKASQSllhtNGNTYLHWLLQKPGQPPRRLIYQVSNRDSGVPDRFSGSGSGTD--FTLKISR 102
Cdd:cd07706     3 TQAQPDVSVQVGEEVTLNCRYETS----WTNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksISLTISA 78

                          90
                  ....*....|.
gi 2558070789 103 VEAEDVGVYYC 113
Cdd:cd07706    79 LQLEDSAKYFC 89
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 23-113 5.65e-05

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 38.70  E-value: 5.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  23 VMTQTPLSLSVTLGESASISCKASqsllhtngntylhwllqkpGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKISR 102
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCEAT-------------------GSPPPTITWYKNGEPISSGSTRSRSLSGSNSTLTISN 63

                          90
                  ....*....|.
gi 2558070789 103 VEAEDVGVYYC 113
Cdd:pfam13927  64 VTRSDAGTYTC 74
I-set pfam07679
Immunoglobulin I-set domain;
23-113 5.75e-05

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 38.78  E-value: 5.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  23 VMTQTPLSLSVTLGESASISCKASqsllhtnGNTYLH--WLlqKPGQPPRrliyqvsnrdsgVPDRFSGSGSGTDFTLKI 100
Cdd:pfam07679   2 KFTQKPKDVEVQEGESARFTCTVT-------GTPDPEvsWF--KDGQPLR------------SSDRFKVTYEGGTYTLTI 60

                          90
                  ....*....|...
gi 2558070789 101 SRVEAEDVGVYYC 113
Cdd:pfam07679  61 SNVQPDDSGKYTC 73
IgV_CD79b_beta cd16096
Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are ...
 51-115 1.45e-04

Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are composed of the immunoglobulin variable domain (IgV) of the Cluster of Differentiation (CD) 79B (also known as CD79b molecule, immunoglobulin-associated beta (Ig-beta), and B29). The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. Members of the IgV family 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409515  Cd Length: 96  Bit Score: 38.01  E-value: 1.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2558070789  51 HTNGNTYLHWLLQKPGQPPRRLIYQvsnrdsgvPDRFSGSGSGTDFTLKISRVEAEDVGVYYCLQ 115
Cdd:cd16096    21 YTNYSGVMTWFRKKGNQRPQELFPE--------DGRISQTQNGSVYTLTIQNIQYEDNGIYFCQQ 77
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 28-113 3.76e-04

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. 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. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 37.08  E-value: 3.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  28 PLSLSVTLGESASISCKASQSLlhTNGNTylhWLLQKPGQP--PRRLIYQVSNRDSGVPD-----RFSGSGSGTDFTLKI 100
Cdd:cd05720     5 PRKRDAQLGQKVELVCEVLNSV--PQGCS---WLFQPRGSApqPTFLLYLSSSNKTKWAEgldskRFSGSRSGSSYVLTL 79

                          90
                  ....*....|...
gi 2558070789 101 SRVEAEDVGVYYC 113
Cdd:cd05720    80 KDFRKEDEGYYFC 92
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 25-113 3.98e-04

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: 37.10  E-value: 3.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2558070789  25 TQTPLSLSVTLGESASISCkasqSLLHTNGNTYLHWLLQKPG--------------QPPRRLIYQVSNrdsgVPDrfsgs 90
Cdd:cd16088     3 TFSPALLVVTEGANATFTC----SFSNTSESFVLNWYRLSPSnqtdklaafpedrsQPGQDWRFRVTQ----LPN----- 69

                          90       100
                  ....*....|....*....|...
gi 2558070789  91 gsGTDFTLKISRVEAEDVGVYYC 113
Cdd:cd16088    70 --GRDFHMSVVRARRNDSGTYLC 90
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 65-113 6.08e-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: 33.07  E-value: 6.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2558070789  65 PGQPPRRLIYQVSNRDSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYC 113
Cdd:cd00096     8 SGNPPPTITWYKNGKPLPPSSRDSRRSELGNGTLTISNVTLEDSGTYTC 56
 
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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