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Conserved domains on  [gi|57999412|emb|CAH18705|]
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hypothetical protein [Homo sapiens]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-143 4.55e-59

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: 189.83  E-value: 4.55e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  22 QLVESGGGVVQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQHYADSVKGRATISRDNSNKTVSLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 57999412 102 LSGLSTEDTGVYYCARDFLPLSSWHTNYaldvWGQGTAVIVS 143
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGGYGYSYFDY----WGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 149-242 7.33e-52

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: 170.32  E-value: 7.33e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 149 GPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCN 228
Cdd:cd21817   1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWGSQTFTCN 80

                        90
                ....*....|....
gi 57999412 229 VDHKPSNTKVDKTV 242
Cdd:cd21817  81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 369-470 1.76e-48

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: 161.73  E-value: 1.76e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNV 445
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                        90       100
                ....*....|....*....|....*
gi 57999412 446 FSCSVMHEALHNHYTQKSLSLSPGK 470
Cdd:cd05768  81 FSCVVGHEALPLQFTQKSIDKSPGK 105
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 262-360 5.02e-37

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 cd07696:

Pssm-ID: 472250  Cd Length: 98  Bit Score: 131.03  E-value: 5.02e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDTLMiSRTPEVTCVVVDVShEDPEVQFNWYV-DGVEVHnAKTKPREEQFNSTFRVVSVLTVVHQDWLNGK 340
Cdd:cd07696   2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                        90       100
                ....*....|....*....|
gi 57999412 341 EYKCKVSNKGLPAPIEKTIS 360
Cdd:cd07696  79 TFKCKVTHPDLPSPIVKSIQ 98
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-143 4.55e-59

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: 189.83  E-value: 4.55e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  22 QLVESGGGVVQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQHYADSVKGRATISRDNSNKTVSLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 57999412 102 LSGLSTEDTGVYYCARDFLPLSSWHTNYaldvWGQGTAVIVS 143
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGGYGYSYFDY----WGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 149-242 7.33e-52

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: 170.32  E-value: 7.33e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 149 GPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCN 228
Cdd:cd21817   1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWGSQTFTCN 80

                        90
                ....*....|....
gi 57999412 229 VDHKPSNTKVDKTV 242
Cdd:cd21817  81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 369-470 1.76e-48

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: 161.73  E-value: 1.76e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNV 445
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                        90       100
                ....*....|....*....|....*
gi 57999412 446 FSCSVMHEALHNHYTQKSLSLSPGK 470
Cdd:cd05768  81 FSCVVGHEALPLQFTQKSIDKSPGK 105
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 262-360 5.02e-37

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and 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: 409493  Cd Length: 98  Bit Score: 131.03  E-value: 5.02e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDTLMiSRTPEVTCVVVDVShEDPEVQFNWYV-DGVEVHnAKTKPREEQFNSTFRVVSVLTVVHQDWLNGK 340
Cdd:cd07696   2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                        90       100
                ....*....|....*....|
gi 57999412 341 EYKCKVSNKGLPAPIEKTIS 360
Cdd:cd07696  79 TFKCKVTHPDLPSPIVKSIQ 98
C1-set pfam07654
Immunoglobulin C1-set domain;
371-455 3.27e-34

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 123.13  E-value: 3.27e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   371 VYTLPPSREEMtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 449
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 57999412   450 VMHEAL 455
Cdd:pfam07654  80 VEHEGL 85
IGv smart00406
Immunoglobulin V-Type;
36-117 1.13e-31

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 116.33  E-value: 1.13e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412     36 SVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQhYADSVKGRATISRDNSNKTVSLQLSGLSTEDTGVYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSY-YQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 57999412    116 AR 117
Cdd:smart00406  80 AV 81
IGc1 smart00407
Immunoglobulin C-Type;
385-458 5.31e-29

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 108.94  E-value: 5.31e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57999412    385 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 458
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
264-351 4.25e-19

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 81.53  E-value: 4.25e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   264 FLFPPKPNDTlmiSRTPEVTCVVVDVSHedPEVQFNWYVDGVEVHN-AKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEY 342
Cdd:pfam07654   2 YVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEY 76


                  ....*....
gi 57999412   343 KCKVSNKGL 351
Cdd:pfam07654  77 TCRVEHEGL 85
C1-set pfam07654
Immunoglobulin C1-set domain;
152-232 3.38e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.22  E-value: 3.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   152 VFPLAPCSRSTSEsTAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNF-GTQTYTCN 228
Cdd:pfam07654   1 VYVFPPSPEELGK-PNTLTCLVTGFYPPDITVTWlkNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWeSGDEYTCR 79


                  ....
gi 57999412   229 VDHK 232
Cdd:pfam07654  80 VEHE 83
IGc1 smart00407
Immunoglobulin C-Type;
166-231 1.39e-13

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 65.80  E-value: 1.39e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57999412    166 TAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGT-QTYTCNVDH 231
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWlrNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESgDVYTCQVTH 69
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 31-116 1.93e-09

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 55.16  E-value: 1.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412    31 VQPGKSVRLSCAASGFDFS-TYAMHWVRQSPGRRLEWVaVISYEGGKQHYADsvKGRATISRDNSNKTVSLQLSGLSTED 109
Cdd:pfam07686   8 VALGGSVTLPCTYSSSMSEaSTSVYWYRQPPGKGPTFL-IAYYSNGSEEGVK--KGRFSGRGDPSNGDGSLTIQNLTLSD 84


                  ....*..
gi 57999412   110 TGVYYCA 116
Cdd:pfam07686  85 SGTYTCA 91
IGc1 smart00407
Immunoglobulin C-Type;
282-354 3.08e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 3.08e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57999412    282 VTCVVVDVSHEDPEVQfnWYVDGVEVH-NAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAP 354
Cdd:smart00407   4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
PHA02865 PHA02865
MHC-like TNF binding protein; Provisional
 305-404 4.65e-03

MHC-like TNF binding protein; Provisional


Pssm-ID: 165199 [Multi-domain]  Cd Length: 338  Bit Score: 39.08  E-value: 4.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  305 VEVHN---AKTKPREEQF----NSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYTLPPS 377
Cdd:PHA02865 130 VEVAGgilARFDTKNKRFtkvtSKGFPKVGMLTVKSPFWKDVMKYLGSFVYLTCGLTANDYQKMAKGNIPKPVTPTVKVT 209

                         90       100
                 ....*....|....*....|....*..
gi 57999412  378 REEMTKNqVSLTCLVKGFYPSDIAVEW 404
Cdd:PHA02865 210 GEELGDN-TTLFCTFDSHYPSSVAAKW 235
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 45-59 6.36e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 38.50  E-value: 6.36e-03
                        10
                ....*....|....*
gi 57999412  45 GFDFSTYAMHWVRQS 59
Cdd:COG0568  80 GFRFSTYATWWIRQA 94
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-143 4.55e-59

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: 189.83  E-value: 4.55e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  22 QLVESGGGVVQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQHYADSVKGRATISRDNSNKTVSLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 57999412 102 LSGLSTEDTGVYYCARDFLPLSSWHTNYaldvWGQGTAVIVS 143
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGGYGYSYFDY----WGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 149-242 7.33e-52

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: 170.32  E-value: 7.33e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 149 GPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCN 228
Cdd:cd21817   1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWGSQTFTCN 80

                        90
                ....*....|....
gi 57999412 229 VDHKPSNTKVDKTV 242
Cdd:cd21817  81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 369-470 1.76e-48

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: 161.73  E-value: 1.76e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNV 445
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                        90       100
                ....*....|....*....|....*
gi 57999412 446 FSCSVMHEALHNHYTQKSLSLSPGK 470
Cdd:cd05768  81 FSCVVGHEALPLQFTQKSIDKSPGK 105
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 262-360 5.02e-37

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and 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: 409493  Cd Length: 98  Bit Score: 131.03  E-value: 5.02e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDTLMiSRTPEVTCVVVDVShEDPEVQFNWYV-DGVEVHnAKTKPREEQFNSTFRVVSVLTVVHQDWLNGK 340
Cdd:cd07696   2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                        90       100
                ....*....|....*....|
gi 57999412 341 EYKCKVSNKGLPAPIEKTIS 360
Cdd:cd07696  79 TFKCKVTHPDLPSPIVKSIQ 98
C1-set pfam07654
Immunoglobulin C1-set domain;
371-455 3.27e-34

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 123.13  E-value: 3.27e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   371 VYTLPPSREEMtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 449
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 57999412   450 VMHEAL 455
Cdd:pfam07654  80 VEHEGL 85
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 149-242 5.32e-34

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: 123.08  E-value: 5.32e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 149 GPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSW---NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGT-QT 224
Cdd:cd04985   1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqknTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSgEV 80

                        90
                ....*....|....*...
gi 57999412 225 YTCNVDHKPSNTKVDKTV 242
Cdd:cd04985  81 YKCQVQHSASNSKQEKDV 98
IGv smart00406
Immunoglobulin V-Type;
36-117 1.13e-31

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 116.33  E-value: 1.13e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412     36 SVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQhYADSVKGRATISRDNSNKTVSLQLSGLSTEDTGVYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSY-YQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 57999412    116 AR 117
Cdd:smart00406  80 AV 81
IGc1 smart00407
Immunoglobulin C-Type;
385-458 5.31e-29

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 108.94  E-value: 5.31e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57999412    385 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 458
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 30-142 4.67e-22

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: 90.86  E-value: 4.67e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  30 VVQPGKSVRLSCAASGFdFSTYAMHWVRQSPGRRLEWVavISYEGGKQHYADSVKGRATISRDnSNKTVSLQLSGLSTED 109
Cdd:cd00099   9 SVQEGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFL--IYLSSSKGKTKGGVPGRFSGSRD-GTSSFSLTISNLQPED 84

                        90       100       110
                ....*....|....*....|....*....|...
gi 57999412 110 TGVYYCArdflpLSSWHTNYALdVWGQGTAVIV 142
Cdd:cd00099  85 SGTYYCA-----VSESGGTDKL-TFGSGTRLTV 111
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 370-455 6.12e-20

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: 84.43  E-value: 6.12e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 370 QVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSC 448
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTsGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80


                ....*..
gi 57999412 449 SVMHEAL 455
Cdd:cd00098  81 VVTHESL 87
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 150-239 1.61e-19

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu 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 mu 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: 409624  Cd Length: 95  Bit Score: 83.15  E-value: 1.61e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAPCSRSTSeSTAALGCLVKDYFPEPVTVSWNSG--ALTSGVHTFPAVLqSSGLYSLSSVVTVPSSNFGTQTY-T 226
Cdd:cd21819   2 PTLFPLVSCGSSTS-DPVTVGCLATDFLPDSITFSWTDDnnSLTTGVKTYPSVL-TGGTYTASSQLQVPESEWKSKENfY 79

                        90
                ....*....|...
gi 57999412 227 CNVDHKPSNTKVD 239
Cdd:cd21819  80 CKVEHPGGNKEVP 92
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 150-242 1.66e-19

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha 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 alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, 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: 409623  Cd Length: 94  Bit Score: 82.94  E-value: 1.66e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAPCSRSTSESTAaLGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSN-FGTQTYTCN 228
Cdd:cd21818   2 PTVFPLSLCPSLSSDPVV-IGCLVQGFFPEPVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQcPEGEAYKCS 80

                        90
                ....*....|....
gi 57999412 229 VDHkpSNTKVDKTV 242
Cdd:cd21818  81 VQH--YSPSQDLNV 92
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 32-143 2.44e-19

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: 83.57  E-value: 2.44e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  32 QPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQHYADSVKGRATISRDNSNKTVSLQLSGLSTEDTG 111
Cdd:cd04982  11 EESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSA 90

                        90       100       110
                ....*....|....*....|....*....|....
gi 57999412 112 VYYCARdflplssW--HTNYALDVWGQGTAVIVS 143
Cdd:cd04982  91 TYYCAY-------WesGSGYYIKVFGSGTKLIVT 117
C1-set pfam07654
Immunoglobulin C1-set domain;
264-351 4.25e-19

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 81.53  E-value: 4.25e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   264 FLFPPKPNDTlmiSRTPEVTCVVVDVSHedPEVQFNWYVDGVEVHN-AKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEY 342
Cdd:pfam07654   2 YVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEY 76


                  ....*....
gi 57999412   343 KCKVSNKGL 351
Cdd:pfam07654  77 TCRVEHEGL 85
C1-set pfam07654
Immunoglobulin C1-set domain;
152-232 3.38e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.22  E-value: 3.38e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   152 VFPLAPCSRSTSEsTAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNF-GTQTYTCN 228
Cdd:pfam07654   1 VYVFPPSPEELGK-PNTLTCLVTGFYPPDITVTWlkNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWeSGDEYTCR 79


                  ....
gi 57999412   229 VDHK 232
Cdd:pfam07654  80 VEHE 83
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 20-142 7.51e-18

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 79.14  E-value: 7.51e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  20 QVQLVESGGGVVQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAVISYEggkqhYADSVKGRATISRDNSNKTVS 99
Cdd:cd16095   1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHI-----STKVSEDRITSSREDTNSQIF 75

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 57999412 100 LQLSGLSTEDTGVYYCARdflplsswHTNYALD----VWGQGTAVIV 142
Cdd:cd16095  76 LQIKGLGLRDSGQYHCAR--------RVGYGDDtdklIFGPGTDVIV 114
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 151-242 3.60e-17

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: 76.73  E-value: 3.60e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 151 SVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQ-TYTC 227
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWlkNGVPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGaTYTC 80

                        90
                ....*....|....*
gi 57999412 228 NVDHKPSNTKVDKTV 242
Cdd:cd00098  81 VVTHESLKSPLSKTW 95
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 368-455 4.59e-16

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. 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 determine the type of immunoglobulin: 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: 409496  Cd Length: 99  Bit Score: 73.64  E-value: 4.59e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 368 EPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVF 446
Cdd:cd07699   1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTvSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVY 80


                ....*....
gi 57999412 447 SCSVMHEAL 455
Cdd:cd07699  81 TCEVTHEGL 89
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 31-142 4.87e-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: 68.07  E-value: 4.87e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  31 VQPGKSVRLSCAASgfDFSTYAMHWVRQSPGRRLEWVAVISYEGGKQHyadsvKGRATISRDNSNKTVSLQLSGLSTEDT 110
Cdd:cd04983  10 VQEGENVTLNCNYS--TSTFYYLFWYRQYPGQGPQFLIYISSDSGNKK-----KGRFSATLDKSRKSSSLHISAAQLSDS 82

                        90       100       110
                ....*....|....*....|....*....|..
gi 57999412 111 GVYYCArdflpLSSWHTNYALdVWGQGTAVIV 142
Cdd:cd04983  83 AVYFCA-----LSESGGTGKL-TFGKGTRLTV 108
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 262-365 1.36e-13

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: 66.59  E-value: 1.36e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPkPNDTLMISRTPEVTCVVVDVSHEDPEVQfnWYVDGVEVHNAK---TKPREEQfNSTFRVVSVLTVVHQDWLN 338
Cdd:cd05768   2 SVYLLPP-PEEELSLNETVTLTCLVKGFYPEDIFVS--WLQNGEPLPSADyktTAPVPES-DGSFFVYSKLNVSTADWNS 77

                        90       100
                ....*....|....*....|....*...
gi 57999412 339 GKEYKCKVSNKGLPAP-IEKTISKTKGQ 365
Cdd:cd05768  78 GDVFSCVVGHEALPLQfTQKSIDKSPGK 105
IGc1 smart00407
Immunoglobulin C-Type;
166-231 1.39e-13

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 65.80  E-value: 1.39e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57999412    166 TAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGT-QTYTCNVDH 231
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWlrNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESgDVYTCQVTH 69
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 369-465 1.86e-13

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: 66.26  E-value: 1.86e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQ-VSLTCLVKGFYPSDIAVEWESNG---QPENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGN 444
Cdd:cd16093   2 PTVSLHAPSREEFLGNRtATFVCLATGFSPKTISFKWLRNGkevTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                        90       100
                ....*....|....*....|.
gi 57999412 445 VFSCSVMHEalhNHYTQKSLS 465
Cdd:cd16093  82 EFTCEFKHK---GEIVEKNAS 99
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 262-359 2.73e-13

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: 65.56  E-value: 2.73e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDTLmiSRTPEVTCVVVDVSHEDpeVQFNWYVDGVEVHNAKTKPRE-EQFNSTFRVVSVLTVVHQDWLNGK 340
Cdd:cd00098   1 TVTLLPPSPEEKG--GGKVTLVCLVSGFYPKD--ITVTWLKNGVPLTSGVSTSSPvEPNDGTYSVTSSLTVPPSDWDEGA 76

                        90
                ....*....|....*....
gi 57999412 341 EYKCKVSNKGLPAPIEKTI 359
Cdd:cd00098  77 TYTCVVTHESLKSPLSKTW 95
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 31-142 6.19e-12

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: 62.09  E-value: 6.19e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  31 VQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWVAvisyeGGKQHYADSVKGRatISRDNSNKTVSLQLSGLSTEDT 110
Cdd:cd04984  10 VSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLI-----YEDKHRPSGIPDR--FSGSKSGNTASLTISGAQTEDE 82

                        90       100       110
                ....*....|....*....|....*....|..
gi 57999412 111 GVYYCArdflplsSWHTNYAldVWGQGTAVIV 142
Cdd:cd04984  83 ADYYCQ-------VWDSNSY--VFGGGTKLTV 105
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 369-455 6.73e-12

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (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). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 61.66  E-value: 6.73e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPS-REEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVF 446
Cdd:cd05847   1 PTVQILHSScASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVaTLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTY 80


                ....*....
gi 57999412 447 SCSVMHEAL 455
Cdd:cd05847  81 TCKVTHQGT 89
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 150-244 6.93e-12

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. 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 determine the type of immunoglobulin: 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: 409496  Cd Length: 99  Bit Score: 61.70  E-value: 6.93e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGT-QTYT 226
Cdd:cd07699   2 PSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWkvDGSTVSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKhKVYT 81

                        90
                ....*....|....*...
gi 57999412 227 CNVDHKPSNTKVDKTVER 244
Cdd:cd07699  82 CEVTHEGLSSTITKSFNR 99
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 369-454 1.90e-11

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: 60.15  E-value: 1.90e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESnGQPENNYKATPPMLDSDGSFFLYSKLTVDKSRWqQGNVFSC 448
Cdd:cd21817   2 PSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNS-GSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSW-GSQTFTC 79


                ....*.
gi 57999412 449 SVMHEA 454
Cdd:cd21817  80 NVEHKP 85
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 367-456 3.09e-11

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. 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 beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 60.47  E-value: 3.09e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 367 REPQVYTLPPSREEMTKNQ-VSLTCLVKGFYPSDIAVEWESNGQPENNYKATPP--MLDSDGSFFLYSKLTVDKSRWQQ- 442
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRkATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPqaLRENTSTYSLSSRLRVSATEWFNp 80

                        90
                ....*....|....
gi 57999412 443 GNVFSCSVMHEALH 456
Cdd:cd05769  81 RNTFTCIVKFYGGT 94
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 369-454 5.36e-11

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: 59.14  E-value: 5.36e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVF 446
Cdd:cd04985   2 PTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqkNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVY 81


                ....*...
gi 57999412 447 SCSVMHEA 454
Cdd:cd04985  82 KCQVQHSA 89
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 150-245 7.12e-11

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: 58.89  E-value: 7.12e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAPCSRS-TSESTAALGCLVKDYFPEPVTVSWNSG---ALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNF-GTQT 224
Cdd:cd05768   1 PSVYLLPPPEEElSLNETVTLTCLVKGFYPEDIFVSWLQNgepLPSADYKTTAPVPESDGSFFVYSKLNVSTADWnSGDV 80

                        90       100
                ....*....|....*....|...
gi 57999412 225 YTCNVDHK--PSNTKVdKTVERK 245
Cdd:cd05768  81 FSCVVGHEalPLQFTQ-KSIDKS 102
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 26-142 2.24e-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: 56.74  E-value: 2.24e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412     26 SGGGVVQPGKSVRLSCAASGFdfSTYAMHWVRQSPgrrlEWVAVisyeggkqhyadsvKGRATISRDNSnkTVSLQLSGL 105
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQGG----KLLAE--------------SGRFSVSRSGS--TSTLTISNV 58

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 57999412    106 STEDTGVYYCARdflplsswhTNYALDVWGqGTAVIV 142
Cdd:smart00410  59 TPEDSGTYTCAA---------TNSSGSASS-GTTLTV 85
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 149-237 2.96e-10

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta 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 delta 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: 319341  Cd Length: 96  Bit Score: 57.16  E-value: 2.96e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 149 GPSVFPL-APCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTC 227
Cdd:cd16092   1 APDVFPIiSGCRHPKDNSPVVLACLITGYHPTSVTVTWYMGTQSQPQRTFPEIQRRDSYYMTSSQLSTPLQQWRQGEYKC 80

                        90
                ....*....|
gi 57999412 228 NVDHKPSNTK 237
Cdd:cd16092  81 VVQHTASKSK 90
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 30-116 3.14e-10

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: 57.29  E-value: 3.14e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  30 VVQPGKSVRLSCAAsgfDFSTYAMHWVRQSPGRRLEWVaVISYEGGKQHYADSVKGRATISRdNSNKTVSLQLSGLSTED 109
Cdd:cd05899   9 IKRRGQSVTLRCSQ---KSGHDNMYWYRQDPGKGLQLL-FYSYGGGLNEEGDLPGDRFSASR-PSLTRSSLTIKSAEPED 83


                ....*..
gi 57999412 110 TGVYYCA 116
Cdd:cd05899  84 SAVYLCA 90
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
 381-453 5.38e-10

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). 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 that 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, but with much less affinity.


Pssm-ID: 409507  Cd Length: 96  Bit Score: 56.28  E-value: 5.38e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57999412 381 MTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHE 453
Cdd:cd16085  13 MVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTCQVEHD 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 31-116 1.93e-09

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 55.16  E-value: 1.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412    31 VQPGKSVRLSCAASGFDFS-TYAMHWVRQSPGRRLEWVaVISYEGGKQHYADsvKGRATISRDNSNKTVSLQLSGLSTED 109
Cdd:pfam07686   8 VALGGSVTLPCTYSSSMSEaSTSVYWYRQPPGKGPTFL-IAYYSNGSEEGVK--KGRFSGRGDPSNGDGSLTIQNLTLSD 84


                  ....*..
gi 57999412   110 TGVYYCA 116
Cdd:pfam07686  85 SGTYTCA 91
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 377-455 4.48e-09

Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Cluster of Differentiation (CD) 1. CD1 family of transmembrane glycoproteins, are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. They mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes (CD1a, CD1b, CD1c, CD1d, and CD1e) organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. CD1a localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. C1-set Ig domains 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: 409620  Cd Length: 93  Bit Score: 53.48  E-value: 4.48e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 377 SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKATPPML-DSDGSFFLYSKLTVDKsrwQQGNVFSCSVMHEAL 455
Cdd:cd21029   9 SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILpNHDGTYQLRKTLDIAP---GEGAGYSCRVDHSSL 85
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 262-351 6.87e-09

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (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). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 53.18  E-value: 6.87e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDTLMiSRTPEVTCVVVdvSHEDPEVQFNWYVDGVEVHN--AKTKPREEQfNSTFRVVSVLTVVHQDWLNG 339
Cdd:cd05847   2 TVQILHSSCASTLT-SETIQLLCLIS--GYTPSTIEVEWLVDGQVATLsaASTAPQKEE-GGTFSTTSKLNVTQEDWKSG 77

                        90
                ....*....|..
gi 57999412 340 KEYKCKVSNKGL 351
Cdd:cd05847  78 KTYTCKVTHQGT 89
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
 370-455 8.00e-09

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.


Pssm-ID: 409427  Cd Length: 94  Bit Score: 52.87  E-value: 8.00e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 370 QVYTLPPSrEEMTKNQvsLTCLVKGFYPSDIAVEWESNGQPENNYKATPPMLDSDGSFFL--YSKLTVDKsrwqqGNVFS 447
Cdd:cd05770   6 QVYSRFPA-ENGKPNV--LNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYLlkYTEFTPTK-----GDEYA 77


                ....*...
gi 57999412 448 CSVMHEAL 455
Cdd:cd05770  78 CRVRHNTL 85
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 369-455 2.20e-08

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 51.73  E-value: 2.20e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVyTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPE-----NNYKATPPMLDSDGSFFLYSKLTVDKSRWQ 441
Cdd:cd05771   1 PRV-RLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWlrEEPGGSEsqvsrDGVSLSSHRQSVDGTYSISSYLTLEPGTEN 79

                        90
                ....*....|....
gi 57999412 442 QGNVFSCSVMHEAL 455
Cdd:cd05771  80 RGATYTCRVTHVSL 93
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 369-452 3.02e-08

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha 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 alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, 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: 409623  Cd Length: 94  Bit Score: 51.35  E-value: 3.02e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVY--TLPPSReemTKNQVSLTCLVKGFYPSDIAVEWESNGQpENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVF 446
Cdd:cd21818   2 PTVFplSLCPSL---SSDPVVIGCLVQGFFPEPVNVTWNYSGK-GGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAY 77


                ....*.
gi 57999412 447 SCSVMH 452
Cdd:cd21818  78 KCSVQH 83
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 368-455 3.31e-08

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; 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 human histocompatibility antigen (HLA) DQ and mouse I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. Human HLA-DR, -DQ, and -DP are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. 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, and 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: 409592  Cd Length: 97  Bit Score: 51.26  E-value: 3.31e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 368 EPQVyTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKATPPMLDSDGSFFLYSKLTVDKsrwQQGNVF 446
Cdd:cd21001   3 EPTV-TISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETaGVVSTPLIRNGDWTFQILVMLEMTP---QRGDVY 78


                ....*....
gi 57999412 447 SCSVMHEAL 455
Cdd:cd21001  79 TCHVEHPSL 87
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 150-243 5.43e-08

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: 50.47  E-value: 5.43e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAPcSRS--TSESTAALGCLVKDYFPEPVTVSW--NSGALTS--GVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQ 223
Cdd:cd16093   2 PTVSLHAP-SREefLGNRTATFVCLATGFSPKTISFKWlrNGKEVTSstGAVVEEPKEDGKTLYSATSFLTITESEWKSQ 80

                        90       100
                ....*....|....*....|.
gi 57999412 224 T-YTCNVDHKpsNTKVDKTVE 243
Cdd:cd16093  81 TeFTCEFKHK--GEIVEKNAS 99
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 375-460 6.06e-08

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 50.31  E-value: 6.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 375 PPS----REEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPEnnykaTPPML------DSDGSFFLYSKLTVDKSRWQqgn 444
Cdd:cd07698   2 PPKvhvtHHPRSDGESTLRCWALGFYPAEITLTWQRDGEDQ-----TQDMElvetrpNGDGTFQKWAAVVVPSGEEQ--- 73

                        90
                ....*....|....*.
gi 57999412 445 VFSCSVMHEALHNHYT 460
Cdd:cd07698  74 RYTCHVQHEGLPEPLT 89
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 369-455 6.68e-08

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. 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 also 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: 409424  Cd Length: 95  Bit Score: 50.00  E-value: 6.68e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEMTKNQVsLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRwqqGNVFS 447
Cdd:cd05767   3 PEVTVFPKSPVELGEPNT-LICFVDNFFPPVINVTWLRNGQPvTDGVSETVFLPREDHSFRKFSYLPFTPSE---GDIYD 78


                ....*...
gi 57999412 448 CSVMHEAL 455
Cdd:cd05767  79 CRVEHWGL 86
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 262-361 1.08e-07

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. 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 determine the type of immunoglobulin: 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: 409496  Cd Length: 99  Bit Score: 49.76  E-value: 1.08e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 262 SAFLFPPKPNDtlMISRTPEVTCVVVDVSHEDpeVQFNWYVDGVEVHNA-KTKPREEQFNSTFRVVSVLTVVHQDWLNGK 340
Cdd:cd07699   3 SVTIFPPSSEE--LSSGKATLVCLINKFYPGF--ATVTWKVDGSTVSSGvTTSKTEQQSDNTYSMSSYLTLSSSDWNKHK 78

                        90       100
                ....*....|....*....|.
gi 57999412 341 EYKCKVSNKGLPAPIEKTISK 361
Cdd:cd07699  79 VYTCEVTHEGLSSTITKSFNR 99
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 31-142 2.74e-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: 49.09  E-value: 2.74e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  31 VQPGKSVRLSCAASGFDFSTYAMHWVRQSPGRRLEWvavISYEGGKqhYADSVKGRATISRDNSNKTVSLQLSGLSTEDT 110
Cdd:cd20988  10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTF---IYREGGI--YGPGFKDNFRGDIDSSNNLAVLKILEASERDE 84

                        90       100       110
                ....*....|....*....|....*....|..
gi 57999412 111 GVYYCARDFLPLSswhTNYALDVWGQGTAVIV 142
Cdd:cd20988  85 GSYYCASDTPGGG---REYDPLIFGKGTYLTV 113
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 148-240 3.64e-07

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. 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 beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 48.53  E-value: 3.64e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 148 KGPSVFPLAPCSRSTSEST-AALGCLVKDYFPEPVTVSW--NSGALTSGVHTFPAVLQSSG-LYSLSSVVTVPS------ 217
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRkATLVCLATGFYPDHVSLSWkvNGKEVKDGVATDPQALRENTsTYSLSSRLRVSAtewfnp 80

                        90       100
                ....*....|....*....|...
gi 57999412 218 SNfgtqTYTCNVDHKPsNTKVDK 240
Cdd:cd05769  81 RN----TFTCIVKFYG-GTDTDT 98
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 369-454 4.91e-07

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu 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 mu 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: 409624  Cd Length: 95  Bit Score: 47.71  E-value: 4.91e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSrEEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLdSDGSFFLYSKLTVDKSRWQQGNVFS 447
Cdd:cd21819   2 PTLFPLVSC-GSSTSDPVTVGCLATDFLPDSITFSWTDDNNSLtTGVKTYPSVL-TGGTYTASSQLQVPESEWKSKENFY 79


                ....*..
gi 57999412 448 CSVMHEA 454
Cdd:cd21819  80 CKVEHPG 86
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 368-455 5.62e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; 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) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. 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: 409594  Cd Length: 96  Bit Score: 47.44  E-value: 5.62e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 368 EPQVYtLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKATPPMLDSDGSFFLYSKLTVDKsrwQQGNVF 446
Cdd:cd21003   3 QPKVN-VSPSKKGPLQHHNLLVCHVTDFYPGNIQVRWFLNGQEETaGVVSTNLIHNGDWTFQILVMLEMTP---QQGDVY 78


                ....*....
gi 57999412 447 SCSVMHEAL 455
Cdd:cd21003  79 TCQVEHPSL 87
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 368-455 7.72e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; 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) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). 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: 409591  Cd Length: 96  Bit Score: 47.30  E-value: 7.72e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 368 EPQVyTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKATPPMLDSDGSFFLYSKL-TVDKSrwqqGNV 445
Cdd:cd21000   3 EPKV-TVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKaGVVSTGLIQNGDWTFQTLVMLeTVPRS----GEV 77

                        90
                ....*....|
gi 57999412 446 FSCSVMHEAL 455
Cdd:cd21000  78 YTCQVEHPSV 87
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 382-455 8.88e-07

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: 47.23  E-value: 8.88e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57999412 382 TKNQVSLTCLVKGFYPSDIAVEWESNGQP----ENNYKATPPMldSDGSFFLYSKLTVDKSrwqQGNVFSCSVMHEAL 455
Cdd:cd21002  16 TREPVMLACHVWGFYPADVTITWLKNGDPvaphSSAPKTAQPN--GDWTYQTQVTLAVTPS---PGDTYTCSVQHASL 88
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 367-455 9.64e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. 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 also 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 has 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: 409423  Cd Length: 96  Bit Score: 46.94  E-value: 9.64e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 367 REPQVyTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKA-TPPMLDSDGSFFLYSKLTVDKSRwqqGNV 445
Cdd:cd05766   2 VQPSV-KVSPTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVsTELIPNGDWTFQILVMLETTPRR---GDV 77

                        90
                ....*....|
gi 57999412 446 FSCSVMHEAL 455
Cdd:cd05766  78 YTCQVEHSSL 87
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 150-231 1.18e-06

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (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). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 46.64  E-value: 1.18e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSVFPLAP-CSRSTSESTAALGCLVKDYFPEPVTVSW---NSGALTSGVHTFPAVlQSSGLYSLSSVVTVPSSNFGTQ-T 224
Cdd:cd05847   1 PTVQILHSsCASTLTSETIQLLCLISGYTPSTIEVEWlvdGQVATLSAASTAPQK-EEGGTFSTTSKLNVTQEDWKSGkT 79


                ....*..
gi 57999412 225 YTCNVDH 231
Cdd:cd05847  80 YTCKVTH 86
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 21-138 1.30e-06

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: 47.00  E-value: 1.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  21 VQLVESGGGV-VQPGKSVRLSCAASGfDFSTYAMHWVRQSPGrrlEWVAVISYEGGKQHyaDSVKGRatISRDNSNKTVS 99
Cdd:cd04980   1 IVMTQSPASLsVSPGERVTISCKASQ-SISSNYLAWYQQKPG---QAPKLLIYYASTLH--SGVPSR--FSGSGSGTDFT 72

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 57999412 100 LQLSGLSTEDTGVYYCardflpLSSWHTNYAldvWGQGT 138
Cdd:cd04980  73 LTISSVEPEDAAVYYC------QQGYTFPYT---FGGGT 102
IgC1_CH2_IgD cd16084
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; ...
 371-455 3.21e-06

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin constant domain (IgC) in delta heavy chains. The IgC family includes 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, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409506  Cd Length: 97  Bit Score: 45.51  E-value: 3.21e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 371 VYTLPPSREEM-TKNQVSLTCLVKGFYPSDIAVEWESNGQ-PENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSC 448
Cdd:cd16084   2 VYLLTPAVQDLwLRDKATFTCFVVGSDLKDAHLTWEVAGKvPTGGVEEGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTC 81


                ....*..
gi 57999412 449 SVMHEAL 455
Cdd:cd16084  82 TLNHPSL 88
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 31-116 4.94e-06

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: 45.52  E-value: 4.94e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  31 VQPGKSVRLSCAASGFDFSTyAMHWVRQ----SPGRRLEWVAVISYEGGKQHYADSVKGRATISRDNSNKTVSLQLSGLS 106
Cdd:cd07700  10 VQTNQTVKMSCEAKTSPKNT-RIYWLRQrqapSKDSHFEFLASWDPSKGIVYGEGVDQEKLIILSDSDSSRYILSLMSVK 88

                        90
                ....*....|
gi 57999412 107 TEDTGVYYCA 116
Cdd:cd07700  89 PEDSGTYFCM 98
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 382-455 5.91e-06

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409609  Cd Length: 95  Bit Score: 44.73  E-value: 5.91e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 57999412 382 TKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21018  16 SKGEVTLRCWALGFYPADITLTWQLNGEElTQDMELVETRPAGDGTFQKWASVVVPLGKEQN---YTCRVYHEGL 87
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 366-460 7.00e-06

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; 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) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. 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: 409590  Cd Length: 99  Bit Score: 44.76  E-value: 7.00e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 366 PR--EPQVyTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN-YKATPPMLDSDGSFflySKLTVDKSRWQQ 442
Cdd:cd20998   2 PRrvEPTV-TVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTgIVSTGLVRNGDWTF---QTLVMLETVPQS 77

                        90
                ....*....|....*...
gi 57999412 443 GNVFSCSVMHEALHNHYT 460
Cdd:cd20998  78 GEVYTCQVEHPSLTDPVT 95
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 20-142 1.57e-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: 44.05  E-value: 1.57e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  20 QVQLVESgggvVQPGKSVRLSCAASGFDfSTYAMHWVRQSPgrRLEWVAVISyegGKQHYADSVKGRATISRDNSNKTVS 99
Cdd:cd07706   4 QAQPDVS----VQVGEEVTLNCRYETSW-TNYYLFWYKQLP--SGEMTFLIR---QDSSEQNAKSGRYSVNFQKAQKSIS 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 57999412 100 LQLSGLSTEDTGVYYCA-RDFLPLSSWhtnyaldVWGQGTAVIV 142
Cdd:cd07706  74 LTISALQLEDSAKYFCAlSLPYDTDKL-------IFGKGTRLTV 110
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
 363-455 1.70e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the C1-set of Ig superfamily (IgSF) domains; The non-classical mouse MHC class I (MHC-I) molecule Qa-1b is a non-polymorphic MHC molecule with an important function in innate immunity. It binds and presents signal peptides of classical MHC-I molecules at the cell surface and, as such, act as an indirect sensor for the normal expression of MHC-I molecules. This signal peptide dominantly accommodated in the groove of Qa-1b is called Qdm, for Qa-1 determinant modifier, and its amino acid sequence AMAPRTLLL is highly conserved among mammalian species. The Qdm/Qa-1b complex serves as a ligand for the germ-line encoded heterodimeric CD94/NKG2A receptors expressed on natural killer (NK) cells and activated CD8+ T cells and transduces inhibitory signals to these lymphocytes. Thus, upon binding, Qa-1b signals NK cells not to engage in cell lysis. The molecular basis of Qa-1b function is unclear.


Pssm-ID: 409625  Cd Length: 98  Bit Score: 43.60  E-value: 1.70e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 363 KGQPREPQVYTLPPSREEMTknqvsLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQ 441
Cdd:cd21820   2 RSDPPKAHVTHHPRSEDEVT-----LRCWALGFYPADITLTWQLNGEElTQDMELVETRPAGDGTFQKWAAVVVPLGKEQ 76

                        90
                ....*....|....
gi 57999412 442 qgnVFSCSVMHEAL 455
Cdd:cd21820  77 ---YYTCHVYHEGL 87
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
 382-455 1.98e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins. Qa-1 presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vbeta8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409604  Cd Length: 97  Bit Score: 43.19  E-value: 1.98e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57999412 382 TKNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKATPPMldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21013  15 SEGYVTLRCWALGFYPADITLTWQLNGEEltqDMEFVETRPA--GDGTFQKWASVVVPLGKEQK---YTCHVEHEGL 86
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 378-454 2.19e-05

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta 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 delta 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: 319341  Cd Length: 96  Bit Score: 43.29  E-value: 2.19e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 57999412 378 REEMTKNQVSLTCLVKGFYPSDIAVEWE--SNGQPENNYkatPPMLDSDGSFFLYSKLTVDKSRWQQGNvFSCSVMHEA 454
Cdd:cd16092  12 RHPKDNSPVVLACLITGYHPTSVTVTWYmgTQSQPQRTF---PEIQRRDSYYMTSSQLSTPLQQWRQGE-YKCVVQHTA 86
IgC1_MHC_Ia_RT1-Aa cd21015
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the ...
 373-462 2.94e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa. While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, RT1-Aa and RT1-A1c, which are associated with TAP-A and TAP-B. The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409606  Cd Length: 95  Bit Score: 42.83  E-value: 2.94e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 373 TLPPSREemtkNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVM 451
Cdd:cd21015  10 TLHPRPE----GDVTLRCWALGFYPADITLTWQLNGEDlTQDMELVETRPAGDGTFQKWASVVVPLGKEQN---YTCRVE 82

                        90
                ....*....|.
gi 57999412 452 HEALHNHYTQK 462
Cdd:cd21015  83 HEGLPKPLSQR 93
IGc1 smart00407
Immunoglobulin C-Type;
282-354 3.08e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 3.08e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 57999412    282 VTCVVVDVSHEDPEVQfnWYVDGVEVH-NAKTKPREEQFNSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAP 354
Cdd:smart00407   4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
 375-455 3.12e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC 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, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409607  Cd Length: 97  Bit Score: 42.78  E-value: 3.12e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 375 PP----SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKATPPMldSDGSFFLYSKLTVDKSRWQQgnvFS 447
Cdd:cd21016   5 PPkahvTRHPRPEGDVTLRCWALGFYPADITLTWQKDGEEltqDMEFVETRPA--GDGTFQKWAAVVVPLGKEQS---YT 79


                ....*...
gi 57999412 448 CSVMHEAL 455
Cdd:cd21016  80 CHVYHEGL 87
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
 369-455 3.52e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409610  Cd Length: 94  Bit Score: 42.40  E-value: 3.52e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 369 PQVYTLPPSREEmtkNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKATPPMldSDGSFFLYSKLTVDKSRWQqgnV 445
Cdd:cd21019   5 PKAHVTHHSRPE---DKVTLRCWALGFYPADITLTWQLNGEEliqDMELVETRPA--GDGTFQKWASVVVPLGKEQ---Y 76

                        90
                ....*....|
gi 57999412 446 FSCSVMHEAL 455
Cdd:cd21019  77 YTCHVYHQGL 86
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 264-360 5.23e-05

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: 42.00  E-value: 5.23e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 264 FLFPPkPNDTLMISRTPEVTCVVVDVSHEDpeVQFNWYVDGVEVHNAKTKPREEQFNS---TFRVVSVLTVVHQDWLNGK 340
Cdd:cd16093   5 SLHAP-SREEFLGNRTATFVCLATGFSPKT--ISFKWLRNGKEVTSSTGAVVEEPKEDgktLYSATSFLTITESEWKSQT 81

                        90       100
                ....*....|....*....|
gi 57999412 341 EYKCKVSNKGlpAPIEKTIS 360
Cdd:cd16093  82 EFTCEFKHKG--EIVEKNAS 99
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
 373-455 1.06e-04

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd. Mouse MHC is composed of 11 subclasses. It includes the classical MHC class I (MHC-Ia) that comprises H-2D, H-2K and H-2L subclasses, the non-classical MHC class I (MHCIb) that comprises H-2Q, H-2M and H-2T subclasses, the classical MHC class II (MHC-IIa) that includes H-2A(I-A) and H-2E(I-E) subclasses, and the non-classical MHC class II (MHC-IIb) comprises H-2M and H-2O. H-2K, H-2D, and H-2L are 80 to 90% homologous at the amino acid level yet appear to be involved in different recognition reactions and are differentially expressed on lymphoid cells. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409611  Cd Length: 95  Bit Score: 41.28  E-value: 1.06e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 373 TLPP----SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKATPPMldSDGSFFLYSKLTVDKSRWQQgnv 445
Cdd:cd21020   3 TDPPkahvTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEEltqEMELVETRPA--GDGTFQKWASVVVPLGKEQK--- 77

                        90
                ....*....|
gi 57999412 446 FSCSVMHEAL 455
Cdd:cd21020  78 YTCHVEHEGL 87
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 155-232 1.74e-04

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 40.56  E-value: 1.74e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 155 LAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA--VLQSS------GLYSLSSVVTVPSSNFGT-QTY 225
Cdd:cd05771   5 LSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLREEPGGSESQVSRdgVSLSShrqsvdGTYSISSYLTLEPGTENRgATY 84


                ....*..
gi 57999412 226 TCNVDHK 232
Cdd:cd05771  85 TCRVTHV 91
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 375-455 1.79e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409614  Cd Length: 98  Bit Score: 40.57  E-value: 1.79e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 375 PP----SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN---YKATPPMldSDGSFFLYSKLTVDKSRWQQgnvFS 447
Cdd:cd21023   5 PPkahvAHHPISDHEATLRCWALGFYPAEITLTWQRDGEEQTQdteLVETRPA--GDGTFQKWAAVVVPPGEEQR---YT 79


                ....*...
gi 57999412 448 CSVMHEAL 455
Cdd:cd21023  80 CHVQHEGL 87
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
 386-455 2.55e-04

H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the major histocompatibility complex (MHC) H-2 class I histocompatibility complex TLA (thymus leukemia antigen). The murine MHC class I histocompatibility TLA (Thymus leukemia antigen), which is encoded in the T region by T3 and T18 genes, is expressed mainly by intestinal epithelial cells and thymocytes. The murine TLAs are class I, beta-2-microglobulin-associated glycoproteins. The TLA function is not defined by antigen presentation, but rather by its relatively high affinity binding to CD8-alpha-alpha compared with CD8-alpha-beta. The existence of a human homolog for murine TLA remains unresolved. This group is a member of the C1-set Ig domains, which 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: 409603  Cd Length: 95  Bit Score: 40.10  E-value: 2.55e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57999412 386 VSLTCLVKGFYPSDIAVEWESNGQP---ENNYKATPPMldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21012  20 VTLRCWALGFYPAHITLTWQLNGEEliqDTELVETRPA--GDGTFQKWAAVVVPSGEEQK---YTCHVYHEGL 87
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
 386-455 2.77e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of QA-2. Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409605  Cd Length: 94  Bit Score: 40.12  E-value: 2.77e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 57999412 386 VSLTCLVKGFYPSDIAVEWESNGQP-ENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21014  19 VTLRCWALGFYPADITLTWQLNGEElTQDMELVETRPAGDGTFQKWASVVVPLGKEQN---YTCHVNHEGL 86
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
 373-456 2.98e-04

CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.


Pssm-ID: 400489  Cd Length: 89  Bit Score: 39.71  E-value: 2.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412   373 TLPPSREEMTKNQVSLTCLVKGFYPsDIAVEWESNGQPENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH 452
Cdd:pfam08205   4 EPPASLLEGEGPEVVATCSSAGGKP-APRITWYLDGKPLEAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSY 82


                  ....
gi 57999412   453 EALH 456
Cdd:pfam08205  83 GALR 86
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 150-231 3.44e-04

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: 39.52  E-value: 3.44e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 150 PSV--FPLAPcsRSTSESTAaLGCLVKDYFPEPVTVSW-NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYT 226
Cdd:cd21002   4 PSVrvAPTTP--FNTREPVM-LACHVWGFYPADVTITWlKNGDPVAPHSSAPKTAQPNGDWTYQTQVTLAVTPSPGDTYT 80


                ....*
gi 57999412 227 CNVDH 231
Cdd:cd21002  81 CSVQH 85
IgI_2_Necl-1 cd07705
Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set ...
 364-457 4.00e-04

Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1; also known as cell adhesion molecule3 (CADM3)). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one 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 and Necl-2 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. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 409502  Cd Length: 103  Bit Score: 39.57  E-value: 4.00e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 364 GQPREPQVYTLPPSREEmtKNQVSLTCLVKGFYPSdIAVEWESNGQpenNYKATPPMLDSDG---SFFLYSKLTVDKSRW 440
Cdd:cd07705   2 GIPQKPQITGYESAFKE--KDKAKLRCTSSGSKPA-ANIKWRKGDQ---ELEGAPTSVQEDGngkTFTVSSSVEFQVTRE 75

                        90
                ....*....|....*..
gi 57999412 441 QQGNVFSCSVMHEALHN 457
Cdd:cd07705  76 DDGAEITCSVGHESLHD 92
IgV_CAR_like cd20960
Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and ...
 55-115 5.20e-04

Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins; The members here are composed of the Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. CAR, which is encoded by human CXADR gene, is a cell adhesion molecule of the Immunoglobulin (Ig) superfamily. The CAR acts as a type I membrane receptor for group B1-B6 coxsackie viruses and subgroup C adenoviruses. For instance, adenovirus interacts with the coxsackievirus and adenovirus receptor to enter epithelial airway cells. The CAR is also shown to be involved in physiological processes such as neuronal and heart development, epithelial tight junction integrity, and tumor suppression. The CAR is a component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. The CAR is also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. The CAR is composed of one V-set and one C2-set Ig module, a single transmembrane helix, and an intracellular domain. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C" in the other


Pssm-ID: 409552  Cd Length: 114  Bit Score: 39.74  E-value: 5.20e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57999412  55 WVRQSPGRRLEWV---------AVISYEGGK--QHYADSVKGRATISRDNSNKTVSLQLSGLSTEDTGVYYC 115
Cdd:cd20960  27 GLEDQGTLDIEWLllpsdkvekVVITYSGDRvyNHYYPALKGRVAFTSNDLSGDASLNISNLKLSDTGTYQC 98
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 375-455 5.39e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E. HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. Like other MHC class I molecules, HLA-E is a heterodimer consisting of an a heavy chain and light chain beta-2-microglobulin. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409615  Cd Length: 95  Bit Score: 39.00  E-value: 5.39e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 375 PP----SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQ---PENNYKATPPMldSDGSFFLYSKLTVDKSRWQqgnVFS 447
Cdd:cd21024   5 PPkthvTHHPISDHEATLRCWALGFYPAEITLTWQQDGEghtQDTELVETRPA--GDGTFQKWAAVVVPSGEEQ---RYT 79


                ....*...
gi 57999412 448 CSVMHEAL 455
Cdd:cd21024  80 CHVQHEGL 87
IgC1_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig ...
 374-457 5.80e-04

T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) constant (C) 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 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: 409494  Cd Length: 98  Bit Score: 39.17  E-value: 5.80e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 374 LPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNG------QPENNykatpPMLDSDgSFFLYSKLTVDKSrwQQGNVFS 447
Cdd:cd07697   8 LPSIAETEKQKAGTYLCLLENFFPDVIKIHWREKKsdtileSQEGN-----TEKTKD-TYMKFSWLTVPKK--SLGKEHR 79

                        90
                ....*....|
gi 57999412 448 CSVMHEALHN 457
Cdd:cd07697  80 CIYKHENNKN 89
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 385-455 1.06e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. 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: 409613  Cd Length: 94  Bit Score: 38.20  E-value: 1.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57999412 385 QVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21022  18 EATLRCWALGFYPAEIILTWQRDGEDQtQDVELVETRPAGDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 86
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
 381-455 1.08e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC 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, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409616  Cd Length: 96  Bit Score: 38.25  E-value: 1.08e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 57999412 381 MTKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21025  15 VSDHEATLRCWALGFYPAEITLTWQWDGEDQtQDTELVETRPAGDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 87
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 377-455 1.25e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-A gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. HLA-A2 is associated with spontaneous abortions, HIV, and Hodgkin lymphoma. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409618  Cd Length: 95  Bit Score: 38.28  E-value: 1.25e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 377 SREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKATPPMLDSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 455
Cdd:cd21027  11 THHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQtQDTELVETRPAGDGTFQKWAAVVVPSGQEQR---YTCHVQHEGL 87
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 375-457 1.72e-03

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). 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 contain either ITIMs or transmembrane regions that 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, but with much less affinity.


Pssm-ID: 409429  Cd Length: 102  Bit Score: 37.69  E-value: 1.72e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 375 PPSREEMTKnQVSLTCLVKGFYPSDIAVEWESNGqpeNNYKATPPMLDSDGSFFLYS-------KLTVDKSRWQqgnvFS 447
Cdd:cd05772  10 PSGRATPGQ-TVSFTCKSHGFSPRDITLKWFKNG---NELSALQTTVFPEGDSVSYSvsstvqvVLTKDDVHSQ----LT 81

                        90
                ....*....|
gi 57999412 448 CSVMHEALHN 457
Cdd:cd05772  82 CEVAHVTLQA 91
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 81-118 4.23e-03

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: 36.61  E-value: 4.23e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 57999412  81 DSVKGRATISRDNSNKTVSLQLSGLSTEDTGVYYCARD 118
Cdd:cd05716  49 VVPGGRISLTDDPDNGVFTVTLNQLRKEDAGWYWCGVG 86
PHA02865 PHA02865
MHC-like TNF binding protein; Provisional
 305-404 4.65e-03

MHC-like TNF binding protein; Provisional


Pssm-ID: 165199 [Multi-domain]  Cd Length: 338  Bit Score: 39.08  E-value: 4.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412  305 VEVHN---AKTKPREEQF----NSTFRVVSVLTVVHQDWLNGKEYKCKVSNKGLPAPIEKTISKTKGQPREPQVYTLPPS 377
Cdd:PHA02865 130 VEVAGgilARFDTKNKRFtkvtSKGFPKVGMLTVKSPFWKDVMKYLGSFVYLTCGLTANDYQKMAKGNIPKPVTPTVKVT 209

                         90       100
                 ....*....|....*....|....*..
gi 57999412  378 REEMTKNqVSLTCLVKGFYPSDIAVEW 404
Cdd:PHA02865 210 GEELGDN-TTLFCTFDSHYPSSVAAKW 235
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 30-115 4.66e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.00  E-value: 4.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412    30 VVQPGKSVRLSCAASGFDFSTYamHWvrqspgrrlewvavisYEGGKQhyadsVKGRATISRDNSNKTVSLQLSGLSTED 109
Cdd:pfam13927  12 TVREGETVTLTCEATGSPPPTI--TW----------------YKNGEP-----ISSGSTRSRSLSGSNSTLTISNVTRSD 68


                  ....*.
gi 57999412   110 TGVYYC 115
Cdd:pfam13927  69 AGTYTC 74
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 368-452 5.03e-03

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha 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. 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: 409375  Cd Length: 96  Bit Score: 36.20  E-value: 5.03e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 368 EPQVYTLPPSREEMTKN-QVSLTCLVKGFYPSDIAV-EWESNGqpENNYKATPPMLDSDGSFFLYSKLTVDKSRWQQGNV 445
Cdd:cd04986   1 QPRLSLQRPALEDLLLGsNASLTCTLSGLKDPEGATfTWEPSG--GKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDT 78


                ....*..
gi 57999412 446 FSCSVMH 452
Cdd:cd04986  79 FSCTVTH 85
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 45-59 6.36e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 38.50  E-value: 6.36e-03
                        10
                ....*....|....*
gi 57999412  45 GFDFSTYAMHWVRQS 59
Cdd:COG0568  80 GFRFSTYATWWIRQA 94
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 169-243 6.42e-03

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. 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 also 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: 409424  Cd Length: 95  Bit Score: 36.13  E-value: 6.42e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57999412 169 LGCLVKDYFPEPVTVSW--NSGALTSGV-HTFPAVLQSSGLYSLSSVVTVPSSnfgTQTYTCNVDHKPSNTKVDKTVE 243
Cdd:cd05767  21 LICFVDNFFPPVINVTWlrNGQPVTDGVsETVFLPREDHSFRKFSYLPFTPSE---GDIYDCRVEHWGLEEPLLKHWE 95
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 265-381 7.88e-03

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. 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 beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 36.20  E-value: 7.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57999412 265 LFPPKPNDtlmISRTPEVTCVVVDVSHEDPEVQFNWYVDGVEVH-NAKTKP---REEqfNSTFRVVSVLTVVHQDWLN-G 339
Cdd:cd05769   7 LFPPSEAE---IRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKdGVATDPqalREN--TSTYSLSSRLRVSATEWFNpR 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 57999412 340 KEYKCKVSNKGLpapiEKTISKTKGQPREPqvyTLPPSREEM 381
Cdd:cd05769  82 NTFTCIVKFYGG----TDTDTWTQGIAGPV---TCGVSAEEL 116
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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