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Conserved domains on  [gi|672066230|ref|XP_008765618|]
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programmed cell death protein 1 isoform X2 [Rattus norvegicus]

Protein Classification

IgV_PD1 domain-containing protein( domain architecture ID 11610716)

IgV_PD1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 1.33e-72

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: 218.14  E-value: 1.33e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  34 PLTFSPTWLTVSEGANATFTCSFSNWSEDLKLNWYRLSPSNQTEKQAAFCNGYSQPVRDARFQIVQLPNGHDFHMNILDA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 672066230 114 RRNDSGIYLCGAISLPPKAQIKESPGAELVVT 145
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 1.33e-72

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: 218.14  E-value: 1.33e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  34 PLTFSPTWLTVSEGANATFTCSFSNWSEDLKLNWYRLSPSNQTEKQAAFCNGYSQPVRDARFQIVQLPNGHDFHMNILDA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 672066230 114 RRNDSGIYLCGAISLPPKAQIKESPGAELVVT 145
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-145 9.95e-21

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: 84.82  E-value: 9.95e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230   38 SPTWLTVSEGANATFTCSFSNW--SEDLKLNWYRLSPSNQ-TEKQAAFCNGYSQPVRDARFQIVQLPNGHDFHMNILDAR 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQPPGKGpTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 672066230  115 RNDSGIYLCGAIslpPKAQIKESPGAELVVT 145
Cdd:pfam07686  82 LSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 39-144 5.39e-10

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: 54.82  E-value: 5.39e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230    39 PTWLTVSEGANATFTCSFSNwSEDLKLNWYRlspsnqtekqaafcNGYSQPVRDARFQIVQlpNGHDFHMNILDARRNDS 118
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASG-SPPPEVTWYK--------------QGGKLLAESGRFSVSR--SGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 672066230   119 GIYLCGAISlppkAQIKESPGAELVV 144
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 1.33e-72

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: 218.14  E-value: 1.33e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  34 PLTFSPTWLTVSEGANATFTCSFSNWSEDLKLNWYRLSPSNQTEKQAAFCNGYSQPVRDARFQIVQLPNGHDFHMNILDA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 672066230 114 RRNDSGIYLCGAISLPPKAQIKESPGAELVVT 145
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-145 9.95e-21

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: 84.82  E-value: 9.95e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230   38 SPTWLTVSEGANATFTCSFSNW--SEDLKLNWYRLSPSNQ-TEKQAAFCNGYSQPVRDARFQIVQLPNGHDFHMNILDAR 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQPPGKGpTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 672066230  115 RNDSGIYLCGAIslpPKAQIKESPGAELVVT 145
Cdd:pfam07686  82 LSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 35-144 1.60e-11

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: 60.04  E-value: 1.60e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  35 LTFSPTWLTVSEGANATFTCSFSNWSEDLKLNWYRLSPsNQTEKQAAFCNGYSQPVRD---ARFQIVqLPNGHDFHMNIL 111
Cdd:cd00099    1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKP-GQGPEFLIYLSSSKGKTKGgvpGRFSGS-RDGTSSFSLTIS 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 672066230 112 DARRNDSGIYLCGAISLPPKAQIKESPGAELVV 144
Cdd:cd00099   79 NLQPEDSGTYYCAVSESGGTDKLTFGSGTRLTV 111
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 39-144 5.39e-10

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: 54.82  E-value: 5.39e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230    39 PTWLTVSEGANATFTCSFSNwSEDLKLNWYRlspsnqtekqaafcNGYSQPVRDARFQIVQlpNGHDFHMNILDARRNDS 118
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASG-SPPPEVTWYK--------------QGGKLLAESGRFSVSR--SGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 672066230   119 GIYLCGAISlppkAQIKESPGAELVV 144
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
49-123 7.08e-08

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 48.92  E-value: 7.08e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230    49 NATFTCSFSNWS-EDLKLNWYRLSPSNQTE----KQAAFCNGYSQPVRDaRFQIVQLPNGHDFHMNILDARRNDSGIYLC 123
Cdd:smart00406   1 SVTLSCKFSGSTfSSYYVSWVRQPPGKGLEwlgyIGSNGSSYYQESYKG-RFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
IgV_1_Necl_like cd05717
First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the ...
 42-131 7.63e-08

First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2), and similar proteins. At least five nectin-like molecules have been identified (Necl-1 to Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Necl-3 accumulates in central and peripheral nervous system tissue and has been shown to selectively interact with oligodendrocytes. This group also contains Class-I MHC-restricted T-cell-associated molecule (CRTAM), whose expression pattern is consistent with its expression in Class-I MHC-restricted T-cells.


Pssm-ID: 409382  Cd Length: 94  Bit Score: 49.44  E-value: 7.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  42 LTVSEGANATFTCSFSNwSEDLKLNWyrLSPSNQTekqaAFCNGYsQPVRDARFQIVQLpNGHDFHMNILDARRNDSGIY 121
Cdd:cd05717    6 VTVVEGETLTLKCQVSL-RDDSSLQW--LNPNGQT----IYFNDK-RALRDSRYQLLNH-SASELSISVSNVTLSDEGVY 76

                         90
                 ....*....|
gi 672066230 122 LCGAISLPPK 131
Cdd:cd05717   77 TCLHYTDPVS 86
IgV_1_Necl-3 cd07701
First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the ...
 42-131 2.09e-05

First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-3, Necl-3 (also known as cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-3 accumulates in central and peripheral nervous system tissue, and has been shown to selectively interact with oligodendrocytes.


Pssm-ID: 409498  Cd Length: 96  Bit Score: 42.38  E-value: 2.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  42 LTVSEGANATFTCSFSNwSEDLKLNWyrlspSNQTEKQAAFcnGYSQPVRDARFQIVQlPNGHDFHMNILDARRNDSGIY 121
Cdd:cd07701    7 VTVVEGGTANLTCRVDQ-NDNTSLQW-----SNPAQQTLYF--DDKKALRDNRIELVR-ASWHELSISISDVSLSDEGQY 77

                         90
                 ....*....|
gi 672066230 122 LCGAISLPPK 131
Cdd:cd07701   78 TCSLFTMPVK 87
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 38-123 1.41e-04

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: 40.33  E-value: 1.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  38 SPTWLTVSEGANATFTCSFSNWSEDlKLNWYRLSPSNQTE---KQAAFcngySQPVRDARFQIVQLPNGHDFHMNILDAR 114
Cdd:cd04983    4 SPQSLSVQEGENVTLNCNYSTSTFY-YLFWYRQYPGQGPQfliYISSD----SGNKKKGRFSATLDKSRKSSSLHISAAQ 78


                 ....*....
gi 672066230 115 RNDSGIYLC 123
Cdd:cd04983   79 LSDSAVYFC 87
IgV_1_Necl-2 cd05881
First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2; member of the ...
 42-131 1.78e-04

First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-2, Necl-2 (also known as cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A, Tslc1, sgIGSF, and RA175). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma.


Pssm-ID: 409465  Cd Length: 94  Bit Score: 39.60  E-value: 1.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  42 LTVSEGANATFTCSFSNwSEDLKLNWyrLSPSNQTEKQAAFcngysQPVRDARFQIVQLPNgHDFHMNILDARRNDSGIY 121
Cdd:cd05881    6 VTVVEGEVATISCRVKN-SDDSVIQL--LNPNRQTIYFRDF-----RPLKDSRFQLVNFSS-SELRVSLTNVSISDEGRY 76

                         90
                 ....*....|
gi 672066230 122 LCGAISLPPK 131
Cdd:cd05881   77 FCQLYTDPPQ 86
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 35-123 3.50e-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: 39.30  E-value: 3.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  35 LTFSPTWLTVSEGANATFTCSFSNWSEDLKLNWYRLSPsNQTEKQAAFCNGYSQPVRDARFQivQLPNGHDFHMNILDAR 114
Cdd:cd04980    3 MTQSPASLSVSPGERVTISCKASQSISSNYLAWYQQKP-GQAPKLLIYYASTLHSGVPSRFS--GSGSGTDFTLTISSVE 79


                 ....*....
gi 672066230 115 RNDSGIYLC 123
Cdd:cd04980   80 PEDAAVYYC 88
I-set pfam07679
Immunoglobulin I-set domain;
42-125 1.30e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 37.24  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230   42 LTVSEGANATFTCSFSNWsEDLKLNWYRlspsnqtekqaafcNGysQPVR-DARFQIVQLPNGHDFHmnILDARRNDSGI 120
Cdd:pfam07679  10 VEVQEGESARFTCTVTGT-PDPEVSWFK--------------DG--QPLRsSDRFKVTYEGGTYTLT--ISNVQPDDSGK 70


                  ....*
gi 672066230  121 YLCGA 125
Cdd:pfam07679  71 YTCVA 75
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 38-130 2.62e-03

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: 36.88  E-value: 2.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230  38 SPTWLTVSEGANATFTCSFSNWSEdlKLNWYRLSPSNQTEKQAAFCNG---YSQPVRDARFQiVQLPNGHDFHMNILDAR 114
Cdd:cd05899    4 SPRYLIKRRGQSVTLRCSQKSGHD--NMYWYRQDPGKGLQLLFYSYGGglnEEGDLPGDRFS-ASRPSLTRSSLTIKSAE 80

                         90
                 ....*....|....*.
gi 672066230 115 RNDSGIYLCgAISLPP 130
Cdd:cd05899   81 PEDSAVYLC-ASSLGG 95
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 35-125 8.49e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 34.46  E-value: 8.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672066230   35 LTFSPTWLTVSEGANATFTCSFSNWSEDlKLNWYRlspsnqtekqaafcNGYSQPVRDARFQIVQLPNGHdfhMNILDAR 114
Cdd:pfam13927   4 ITVSPSSVTVREGETVTLTCEATGSPPP-TITWYK--------------NGEPISSGSTRSRSLSGSNST---LTISNVT 65

                          90
                  ....*....|.
gi 672066230  115 RNDSGIYLCGA 125
Cdd:pfam13927  66 RSDAGTYTCVA 76
 
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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