NCBI Conserved Domain Search

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: 165.97 E-value: 3.37e-50

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGapGFYFTHSILTVTEEEWNSG 409
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESD--GSFFVYSKLNVSTADWNSG 78

                        90       100
                ....*....|....*....|....*..
gi 85542908 410 ETYTCVVGHEALPHLVTERTVDKSTGK 436
Cdd:cd05768  79 DVFSCVVGHEALPLQFTQKSIDKSPGK 105

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: 135.66 E-value: 7.64e-39

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 225 TFTIPPSFADIFLSKSANLTCLVSNLATYETLNISWASQSGEPLETKIKIMESHPNGTFSAKGVASVCVEDWNNRKEFVC 304
Cdd:cd07696   3 VFLIPPSPKDLFLTKSAKVTCLVVDLTSIEEVNVTWSREDGNEVLASTTNPEKHYNATLSVVSTLTVCADDWDNGKTFKC 82

                        90
                ....*....|....*.
gi 85542908 305 TVTHRDLPSPQKKFIS 320
Cdd:cd07696  83 KVTHPDLPSPIVKSIQ 98

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: 123.98 E-value: 2.06e-34

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   4 FPNVFPLVSCESPLSDKnlVAMGCLARDFLPSTISFTWNYQNNTEVIqGIRTFPTLRTGGKYLATSQVLLSPKSILegSD 83
Cdd:cd21819   1 APTLFPLVSCGSSTSDP--VTVGCLATDFLPDSITFSWTDDNNSLTT-GVKTYPSVLTGGTYTASSQLQVPESEWK--SK 75

                        90       100
                ....*....|....*....|
gi 85542908  84 EYLVCKIHYGGKNRDLHVPI 103
Cdd:cd21819  76 ENFYCKVEHPGGNKEVPVPK 95

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: 112.49 E-value: 4.21e-30

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPRDGFSGPapRKSKLICEATNFTPKPITVSWLKDGKLVESGftTDPVTIENKGSTPQTYKVISTLTISEIDW 190
Cdd:cd16093   2 PTVSLHAPSREEFLGN--RTATFVCLATGFSPKTISFKWLRNGKEVTSS--TGAVVEEPKEDGKTLYSATSFLTITESEW 77

                        90       100
                ....*....|....*....|..
gi 85542908 191 LNLNVYTCRVDHRGLTFLKNVS 212
Cdd:cd16093  78 KSQTEFTCEFKHKGEIVEKNAS 99

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 106.18 E-value: 4.86e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   332 VYLLPPAREQLNlrESATVTCLVKGFSPADISVQWLQRGQLLPQEkYVTSAPMPEPGapGFYFTHSILTVTEEEWNSGET 411
Cdd:pfam07654   1 VYVFPPSPEELG--KPNTLTCLVTGFYPPDITVTWLKNGQEVTEG-VKTTPPSPNSD--WTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 85542908   412 YTCVVGHEAL 421
Cdd:pfam07654  76 YTCRVEHEGL 85

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 98.15 E-value: 3.23e-25

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85542908    347 SATVTCLVKGFSPADISVQWLQRGQLlPQEKYVTSAPMPEpgAPGFYFTHSILTVTEEEWNSGETYTCVVGHEALPH 423
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQE-VTEGVSTTDPLKN--SDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKE 74

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: 88.29 E-value: 2.41e-21

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 332 VYLLPPAREQlNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGApgfYFTHSILTVTEEEWNSGET 411
Cdd:cd00098   2 VTLLPPSPEE-KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNDGT---YSVTSSLTVPPSDWDEGAT 77

                        90
                ....*....|.
gi 85542908 412 YTCVVGHEALP 422
Cdd:cd00098  78 YTCVVTHESLK 88

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: 82.44 E-value: 2.85e-19

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGaPGFYFTHSILTVTEEEWNS 408
Cdd:cd16093   1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEEPKEDG-KTLYSATSFLTITESEWKS 79

                        90
                ....*....|...
gi 85542908 409 GETYTCVVGHEAL 421
Cdd:cd16093  80 QTEFTCEFKHKGE 92

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: 80.58 E-value: 1.20e-18

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 113 VNVFVPPRDGFSGpapRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGstpqTYKVISTLTISEIDWLN 192
Cdd:cd00098   2 VTLLPPSPEEKGG---GKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNDG----TYSVTSSLTVPPSDWDE 74

                        90
                ....*....|...
gi 85542908 193 LNVYTCRVDHRGL 205
Cdd:cd00098  75 GATYTCVVTHESL 87

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 76.91 E-value: 2.09e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   113 VNVFVPPRDGFSGPAprksKLICEATNFTPKPITVSWLKDGKLVESGF-TTDPvtIENKGStpqTYKVISTLTISEIDWL 191
Cdd:pfam07654   1 VYVFPPSPEELGKPN----TLTCLVTGFYPPDITVTWLKNGQEVTEGVkTTPP--SPNSDW---TYQLSSYLTVTPSDWE 71

                          90
                  ....*....|....
gi 85542908   192 NLNVYTCRVDHRGL 205
Cdd:pfam07654  72 SGDEYTCRVEHEGL 85

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: 74.93 E-value: 1.39e-16

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   5 PNVFPLVSCESpLSDKNLVAMGCLARDFLPSTISFTWNYQNNTEVIQGIRTFPT-LRTGGKYLATSQVLLSPKSILEGsd 83
Cdd:cd04985   2 PTVFPLQSATK-SQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVvLRSGGDYSCSSQLTVPLQEWNSG-- 78

                        90
                ....*....|...
gi 85542908  84 EYLVCKIHYGGKN 96
Cdd:cd04985  79 EVYKCQVQHSASN 91

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: 72.83 E-value: 8.23e-16

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPqEKYVTSAPMPEPGapGFYFTHSILTVTEEEWNSG 409
Cdd:cd05847   1 PTVQILHSSCASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVAT-LSAASTAPQKEEG--GTFSTTSKLNVTQEDWKSG 77

                        90
                ....*....|..
gi 85542908 410 ETYTCVVGHEAL 421
Cdd:cd05847  78 KTYTCKVTHQGT 89

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 71.58 E-value: 1.19e-15

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85542908    133 LICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGstpqTYKVISTLTISEIDWLNLNVYTCRVDHRGLT 206
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDG----TYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73

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: 68.17 E-value: 4.61e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 110 NPNVNVFVPPRDGFSgpAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTienKGSTPQTYKVISTLTISEID 189
Cdd:cd05769   2 PPTVALFPPSEAEIR--NKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQA---LRENTSTYSLSSRLRVSATE 76

                        90
                ....*....|....*...
gi 85542908 190 WLNL-NVYTCRVDHRGLT 206
Cdd:cd05769  77 WFNPrNTFTCIVKFYGGT 94

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: 67.48 E-value: 5.89e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNlRESATVTCLVKGFSPADISVQWLQRGQLLpQEKYVTSAPMPEPGAPgfYFTHSILTVTEEEWNS 408
Cdd:cd07699   1 APSVTIFPPSSEELS-SGKATLVCLINKFYPGFATVTWKVDGSTV-SSGVTTSKTEQQSDNT--YSMSSYLTLSSSDWNK 76

                        90
                ....*....|...
gi 85542908 409 GETYTCVVGHEAL 421
Cdd:cd07699  77 HKVYTCEVTHEGL 89

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: 67.36 E-value: 6.67e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPRDGFSGPAprKSKLICEATNFTPKPITVSWLKDGKLVESG--FTTDPVTIENKgstpqTYKVISTLTISEI 188
Cdd:cd05768   1 PSVYLLPPPEEELSLNE--TVTLTCLVKGFYPEDIFVSWLQNGEPLPSAdyKTTAPVPESDG-----SFFVYSKLNVSTA 73

                        90
                ....*....|....*...
gi 85542908 189 DWLNLNVYTCRVDHRGLT 206
Cdd:cd05768  74 DWNSGDVFSCVVGHEALP 91

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: 66.33 E-value: 1.47e-13

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPRDGFSGpapRKSKLICEATNFTPKPITVSWLKDGKLVESG-FTTDPVTienkgSTPQTYKVISTLTISEID 189
Cdd:cd07699   2 PSVTIFPPSSEELSS---GKATLVCLINKFYPGFATVTWKVDGSTVSSGvTTSKTEQ-----QSDNTYSMSSYLTLSSSD 73

                        90
                ....*....|....*..
gi 85542908 190 WLNLNVYTCRVDHRGLT 206
Cdd:cd07699  74 WNKHKVYTCEVTHEGLS 90

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: 64.74 E-value: 4.98e-13

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPRDGFSGPAprKSKLICEATNFTPKPITVSWLKDGKLVE-SGFTTDPVTIENKgstpqTYKVISTLTISEID 189
Cdd:cd05847   1 PTVQILHSSCASTLTSE--TIQLLCLISGYTPSTIEVEWLVDGQVATlSAASTAPQKEEGG-----TFSTTSKLNVTQED 73

                        90       100
                ....*....|....*....|..
gi 85542908 190 WLNLNVYTCRVDHRGLTFLKNV 211
Cdd:cd05847  74 WKSGKTYTCKVTHQGTTFEAHT 95

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: 63.29 E-value: 1.50e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   5 PNVFPLVSCESPLSDKnlVAMGCLARDFLPSTISFTWNYQNnteviQGI--RTFP-TLRTGGKYLATSQVLLSPKSILEG 81
Cdd:cd21818   2 PTVFPLSLCPSLSSDP--VVIGCLVQGFFPEPVNVTWNYSG-----KGGtaRNFPaMLASGGRYTQSSQLTLPADQCPEG 74

                        90       100
                ....*....|....*....|.
gi 85542908  82 sdEYLVCKIHYGGKNRDLHVP 102
Cdd:cd21818  75 --EAYKCSVQHYSPSQDLNVP 93

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: 62.01 E-value: 4.24e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 229 PPSFADIFLSKSANLTCLVSNLATYETLNISWASQSGEplETKIKIMESHPNGTFSAKGVASVCVEDWNNRKEFVCTVTH 308
Cdd:cd04986   8 RPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGK--EAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTVTH 85

                        90
                ....*....|.
gi 85542908 309 RDLPSPQKKFI 319
Cdd:cd04986  86 PESKGTLTATI 96

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: 59.55 E-value: 3.23e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAreQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEkyvTSAPM-PEPGAPGFYFTHSILTVTEEewn 407
Cdd:cd21002   3 PPSVRVAPTT--PFNTREPVMLACHVWGFYPADVTITWLKNGDPVAPH---SSAPKtAQPNGDWTYQTQVTLAVTPS--- 74

                        90       100
                ....*....|....*....|
gi 85542908 408 SGETYTCVVGHEALPHLVTE 427
Cdd:cd21002  75 PGDTYTCSVQHASLPEPLLE 94

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: 59.26 E-value: 3.49e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 117 VPPRDGFSG---PAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGstpqTYKVISTLTISEIDWLNl 193
Cdd:cd21029   1 VKPRVRLSSrpsPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILPNHDG----TYQLRKTLDIAPGEGAG- 75

                        90
                ....*....|..
gi 85542908 194 nvYTCRVDHRGL 205
Cdd:cd21029  76 --YSCRVDHSSL 85

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: 56.96 E-value: 2.38e-10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPParEQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApMPEPGapgfyFTHSILTVTEEEWNS 408
Cdd:cd05766   3 QPSVKVSPT--KTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTEL-IPNGD-----WTFQILVMLETTPRR 74

                        90       100
                ....*....|....*....|
gi 85542908 409 GETYTCVVGHEALPHLVTER 428
Cdd:cd05766  75 GDVYTCQVEHSSLQSPLTVD 94

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: 55.91 E-value: 6.61e-10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 331 AVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQlLPQEKyvTSAPMPEPGAPGFYFTHSILTVTEEEWNSGE 410
Cdd:cd16084   1 GVYLLTPAVQDLWLRDKATFTCFVVGSDLKDAHLTWEVAGK-VPTGG--VEEGLLERHSNGSQSQHSRLTLPRSLWNAGT 77

                        90
                ....*....|..
gi 85542908 411 TYTCVVGHEALP 422
Cdd:cd16084  78 SVTCTLNHPSLP 89

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: 54.65 E-value: 2.46e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 226 FTIPPSFADIFLSKSANLTCLVSNLATYEtLNISWaSQSGEPLE-TKIKIMES--HPNGTFSAKGVASVCVEDWNNRKEF 302
Cdd:cd05768   4 YLLPPPEEELSLNETVTLTCLVKGFYPED-IFVSW-LQNGEPLPsADYKTTAPvpESDGSFFVYSKLNVSTADWNSGDVF 81

                        90       100
                ....*....|....*....|
gi 85542908 303 VCTVTHRDLPSP-QKKFISK 321
Cdd:cd05768  82 SCVVGHEALPLQfTQKSIDK 101

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: 52.23 E-value: 9.97e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 347 SATVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTsapmPEPGAPGFYFTHSILTVTEEEWnsgETYTCVVGHEALPHLV 425
Cdd:cd07698  16 ESTLRCWALGFYPAEITLTWQRDGEDQTQDmELVE----TRPNGDGTFQKWAAVVVPSGEE---QRYTCHVQHEGLPEPL 88


                ...
gi 85542908 426 TER 428
Cdd:cd07698  89 TLR 91

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: 52.08 E-value: 1.28e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 227 TIPPSFADIFLSKSANLTCLVSNLAtYETLNISWaSQSGEPLETKIKIMES--HPNGTFSAKGVASVCVEDWNNRKEFVC 304
Cdd:cd00098   3 TLLPPSPEEKGGGKVTLVCLVSGFY-PKDITVTW-LKNGVPLTSGVSTSSPvePNDGTYSVTSSLTVPPSDWDEGATYTC 80

                        90
                ....*....|....*
gi 85542908 305 TVTHRDLPSPQKKFI 319
Cdd:cd00098  81 VVTHESLKSPLSKTW 95

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 51.87 E-value: 1.34e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908     7 VFPLVSCESPLSDKNLVAmgCLARDFLPSTISFTWnYQNNTEVIQGIRTF-PTLRTGGKYLATSQVLLSPKSILEGsDEY 85
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLT--CLVTGFYPPDITVTW-LKNGQEVTEGVKTTpPSPNSDWTYQLSSYLTVTPSDWESG-DEY 76


                  ....*....
gi 85542908    86 lVCKI-HYG 93
Cdd:pfam07654  77 -TCRVeHEG 84

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: 52.38 E-value: 1.78e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNLRESATVTCLVKGFSPADISVQWLQRGQllPQEKYVTSAPMPEPGAPGFYFTHSILTVTEEEW-N 407
Cdd:cd05769   2 PPTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGK--EVKDGVATDPQALRENTSTYSLSSRLRVSATEWfN 79

                        90
                ....*....|..
gi 85542908 408 SGETYTCVVGHE 419
Cdd:cd05769  80 PRNTFTCIVKFY 91

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: 51.05 E-value: 3.26e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPArEQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGapGFYFTHSILTVTEEEWNSG 409
Cdd:cd04985   2 PTVFPLQSA-TKSQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSG--GDYSCSSQLTVPLQEWNSG 78

                        90
                ....*....|.
gi 85542908 410 ETYTCVVGHEA 420
Cdd:cd04985  79 EVYKCQVQHSA 89

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: 50.84 E-value: 3.63e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPAREQLNLRESATVTCLVKGF-SPADISVQWLQRGQLLPQEKyvtsapMPEPGAPGFYFTHSILTVTEEEWNS 408
Cdd:cd04986   2 PRLSLQRPALEDLLLGSNASLTCTLSGLkDPEGATFTWEPSGGKEAIQG------PPERDSCGCYSVSSVLPGCAEPWNS 75

                        90
                ....*....|
gi 85542908 409 GETYTCVVGH 418
Cdd:cd04986  76 GDTFSCTVTH 85

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: 50.77 E-value: 4.15e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 85542908 133 LICEATNFTPKPITVSWLKDGKLVESGFTTDPVTienkGSTPQTYKVISTLTI--SEIDwlnlnVYTCRVDHRGL 205
Cdd:cd05767  21 LICFVDNFFPPVINVTWLRNGQPVTDGVSETVFL----PREDHSFRKFSYLPFtpSEGD-----IYDCRVEHWGL 86

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: 50.96 E-value: 4.62e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 346 ESATVTCLVKGFSPADISVQWLQRGqllPQEKYVTSAPM------PEPGAPGFYFTHSILTVTEEEWNSGETYTCVVGHE 419
Cdd:cd05771  15 LPQTLSCHIAGYYPLDVDVEWLREE---PGGSESQVSRDgvslssHRQSVDGTYSISSYLTLEPGTENRGATYTCRVTHV 91


                ...
gi 85542908 420 ALP 422
Cdd:cd05771  92 SLE 94

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: 50.40 E-value: 4.89e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85542908 349 TVTCLVKGFSPADISVQWLQRGQLLPQEkyvTSAPMPEPGAPGFYFTHSILTVTEEEwnsGETYTCVVGHEALP 422
Cdd:cd21029  19 QLSCHVTGFYPRPIEVTWLRDGQEQMDG---TQSGGILPNHDGTYQLRKTLDIAPGE---GAGYSCRVDHSSLK 86

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: 50.01 E-value: 7.98e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 124 SGPAPR-----KSKLICEATNFTPKPITVSWLKDGKLVESGFTtdpvTIENKGSTpQTYKVISTLTI--------SEIdw 190
Cdd:cd05772   8 SGPSGRatpgqTVSFTCKSHGFSPRDITLKWFKNGNELSALQT----TVFPEGDS-VSYSVSSTVQVvltkddvhSQL-- 80

                        90
                ....*....|....*.
gi 85542908 191 lnlnvyTCRVDHRGLT 206
Cdd:cd05772  81 ------TCEVAHVTLQ 90

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: 49.63 E-value: 8.91e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 135 CEATNFTPKPITVSWLKDGKLVESGFTTDPvTIENKGstpqTYKVISTLTISEIDWLNLNVYTCRVDHRG 204
Cdd:cd21819  22 CLATDFLPDSITFSWTDDNNSLTTGVKTYP-SVLTGG----TYTASSQLQVPESEWKSKENFYCKVEHPG 86

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: 49.75 E-value: 8.91e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 85542908   5 PNVFPLVSCESPLSDKNlVAMGCLARDFLPSTISFTWNYQNNTeviQGIRTFP-TLRTGGKYLATSQVLLSPKS 77
Cdd:cd21817   2 PSVFPLAPCCKSTNGSS-VTLGCLVTGYFPEPVTVTWNSGSLT---SGVKTFPaVLQSSGLYTTSSQVTVPSSS 71

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: 49.54 E-value: 1.09e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPRdgFSGPAPRKskLICEATNFTPKPITVSWLKDGKLVESGfTTDPVTIENKGStpQTYKVISTLTISEIDW 190
Cdd:cd21002   4 PSVRVAPTTP--FNTREPVM--LACHVWGFYPADVTITWLKNGDPVAPH-SSAPKTAQPNGD--WTYQTQVTLAVTPSPG 76

                        90
                ....*....|....*
gi 85542908 191 lnlNVYTCRVDHRGL 205
Cdd:cd21002  77 ---DTYTCSVQHASL 88

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: 48.22 E-value: 3.38e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   7 VFPLVSCESPLSDKNLVAMgCLARDFLPSTISFTWnYQNNTEVIQGIRTFPTLRTG-GKYLATSQVLLSPKSILEGSdEY 85
Cdd:cd00098   2 VTLLPPSPEEKGGGKVTLV-CLVSGFYPKDITVTW-LKNGVPLTSGVSTSSPVEPNdGTYSVTSSLTVPPSDWDEGA-TY 78

                        90
                ....*....|....
gi 85542908  86 lVCKIHYGGKNRDL 99
Cdd:cd00098  79 -TCVVTHESLKSPL 91

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: 47.22 E-value: 6.13e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85542908 130 KSKLICEATNFTPKPITVSWLKDGKlvESGFTTDPV-TIENKGSTPQTYkviSTLTISEIDWlnlNVYTCRVDHRGLT 206
Cdd:cd07698  16 ESTLRCWALGFYPAEITLTWQRDGE--DQTQDMELVeTRPNGDGTFQKW---AAVVVPSGEE---QRYTCHVQHEGLP 85

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: 47.06 E-value: 7.26e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNLrESATVTCLVKGFSPADISVQWlQRGQLlpqekyvTSAPMPEPGA---PGFYFTHSILTVTEEE 405
Cdd:cd21817   1 APSVFPLAPCCKSTNG-SSVTLGCLVTGYFPEPVTVTW-NSGSL-------TSGVKTFPAVlqsSGLYTTSSQVTVPSSS 71

                        90
                ....*....|....*
gi 85542908 406 WnSGETYTCVVGHEA 420
Cdd:cd21817  72 W-GSQTFTCNVEHKP 85

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: 45.79 E-value: 2.53e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVPPrdgfSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVtIENKGSTPQTYKVISTlTISEIDw 190
Cdd:cd05766   4 PSVKVSPTK----TGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTEL-IPNGDWTFQILVMLET-TPRRGD- 76

                        90
                ....*....|....*.
gi 85542908 191 lnlnVYTCRVDHRGLT 206
Cdd:cd05766  77 ----VYTCQVEHSSLQ 88

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: 45.52 E-value: 3.03e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFVP-PRDGFSGPAPrksKLICEATNFTPKP-ITVSWLKDGKLVESGFTTDPVTIENkgstpQTYKVISTLTISEI 188
Cdd:cd07696   1 VSVFLIPPsPKDLFLTKSA---KVTCLVVDLTSIEeVNVTWSREDGNEVLASTTNPEKHYN-----ATLSVVSTLTVCAD 72

                        90
                ....*....|....*..
gi 85542908 189 DWLNLNVYTCRVDHRGL 205
Cdd:cd07696  73 DWDNGKTFKCKVTHPDL 89

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: 45.38 E-value: 3.15e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 337 PAREQlNLRESATVTCLVKGFSPADISVQWLQRGQllPQEKYVTSAPMPEPGApgfyFTHSILTVTEEEWNSGETYTCVV 416
Cdd:cd21000  10 PAKTQ-PLQHHNLLVCSVNGFYPGSIEVRWFRNGQ--EEKAGVVSTGLIQNGD----WTFQTLVMLETVPRSGEVYTCQV 82

                        90
                ....*....|....*
gi 85542908 417 GHealPHLVTERTVD 431
Cdd:cd21000  83 EH---PSVTSPLTVE 94

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: 44.44 E-value: 7.22e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85542908   5 PNVFPLVS-CESPlSDKNLVAMGCLARDFLPSTISFTWNYQNNTeviQGIRTFPTLRTGGKYLATSQVLLSP 75
Cdd:cd16092   2 PDVFPIISgCRHP-KDNSPVVLACLITGYHPTSVTVTWYMGTQS---QPQRTFPEIQRRDSYYMTSSQLSTP 69

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily domains; The members here are composed of the third immunoglobulin constant domain (IgC) of delta 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. 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: 319343 Cd Length: 100 Bit Score: 44.07 E-value: 1.19e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85542908 352 CLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEPGAPGFYfTHSILTVTEEEWNSGETYTCVVGHE 419
Cdd:cd16094  21 CEVSGFSPPNILLMWLEDQREVNTSGFAPARPPPQPGSTTFW-AWSVLRVPAPPSPQPATYTCVVSHE 87

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: 43.67 E-value: 1.38e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85542908 350 VTCLVKGFSPADISVQWLQRGQLLPQEKYvtsapmPE-PGAPGFYFTHSILTVTEEEWNSGEtYTCVVGHEA 420
Cdd:cd16092  22 LACLITGYHPTSVTVTWYMGTQSQPQRTF------PEiQRRDSYYMTSSQLSTPLQQWRQGE-YKCVVQHTA 86

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: 43.22 E-value: 2.13e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 109 MNPNVNVFvPPRdgfSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVtIENKGSTPQTYKVISTLTISEi 188
Cdd:cd20998   5 VEPTVTVY-PTK---TQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGL-VRNGDWTFQTLVMLETVPQSG- 78

                        90
                ....*....|....*...
gi 85542908 189 dwlnlNVYTCRVDHRGLT 206
Cdd:cd20998  79 -----EVYTCQVEHPSLT 91

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: 42.85 E-value: 2.55e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 348 ATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFYFTHSILTVTEEEwnsGETYTCVVGHEALPHLVTE 427
Cdd:cd21024  20 ATLRCWALGFYPAEITLTWQQDGEGHTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPVTL 93


                .
gi 85542908 428 R 428
Cdd:cd21024  94 R 94

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: 2.88e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 336 PPAREQLNLRESATVT--CLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEEWNsgetY 412
Cdd:cd21015   5 PEAHVTLHPRPEGDVTlrCWALGFYPADITLTWQLNGEDLTQDmELVETRP---AGDGTFQKWASVVVPLGKEQN----Y 77

                        90
                ....*....|....*.
gi 85542908 413 TCVVGHEALPHLVTER 428
Cdd:cd21015  78 TCRVEHEGLPKPLSQR 93

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: 42.42 E-value: 3.67e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 327 KHPPAVYLLPPAREQlnlrESATVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEE 405
Cdd:cd21013   2 SDPPKAHVTHHPRSE----GYVTLRCWALGFYPADITLTWQLNGEELTQDmEFVETRP---AGDGTFQKWASVVVPLGKE 74

                        90       100
                ....*....|....*....|...
gi 85542908 406 WNsgetYTCVVGHEALPHLVTER 428
Cdd:cd21013  75 QK----YTCHVEHEGLPEPLTLR 93

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: 42.45 E-value: 3.86e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQlnlrESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFY--FTHSILTVTEEEW 406
Cdd:cd21820   5 PPKAHVTHHPRSE----DEVTLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWAAVVVPLGKEQY 77

                        90       100
                ....*....|....*....|..
gi 85542908 407 nsgetYTCVVGHEALPHLVTER 428
Cdd:cd21820  78 -----YTCHVYHEGLPEPLTLR 94

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: 42.29 E-value: 4.02e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPpaREQLNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApMPEPGapGFYFTHSILTVTEEEwns 408
Cdd:cd05767   2 PPEVTVFP--KSPVELGEPNTLICFVDNFFPPVINVTWLRNGQPVTDGVSETVF-LPRED--HSFRKFSYLPFTPSE--- 73

                        90
                ....*....|....
gi 85542908 409 GETYTCVVGHEALP 422
Cdd:cd05767  74 GDIYDCRVEHWGLE 87

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: 41.91 E-value: 5.54e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFvPPRdgfSGPAPRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVtIENKGSTPQTYKVISTLTISEidw 190
Cdd:cd21000   4 PKVTVY-PAK---TQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGL-IQNGDWTFQTLVMLETVPRSG--- 75

                        90
                ....*....|....*.
gi 85542908 191 lnlNVYTCRVDHRGLT 206
Cdd:cd21000  76 ---EVYTCQVEHPSVT 88

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: 41.69 E-value: 5.80e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85542908 349 TVTCLVKGFSPADISVQWLQRGQLLPQEKYvtSAPMPEPGAPGFYFTHSILTVTEeewnsGETYTCVVGHEAL 421
Cdd:cd05770  20 VLNCYVSGFHPPDIEIRLLKNGVKIEDVEQ--SDLSFSKDWTFYLLKYTEFTPTK-----GDEYACRVRHNTL 85

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: 41.27 E-value: 1.04e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 226 FTIPPSFADIFLSKSANLTCLVSNlATYETLNISWASQSGEPLE-TKIKIMESHPNGTFSAKGVASVCVEDWNNRKEFVC 304
Cdd:cd16084   3 YLLTPAVQDLWLRDKATFTCFVVG-SDLKDAHLTWEVAGKVPTGgVEEGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTC 81

                        90
                ....*....|..
gi 85542908 305 TVTHRDLPsPQK 316
Cdd:cd16084  82 TLNHPSLP-PQR 92

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: 41.27 E-value: 1.09e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 349 TVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEEWNsgetYTCVVGHEALPHLVTE 427
Cdd:cd21018  21 TLRCWALGFYPADITLTWQLNGEELTQDmELVETRP---AGDGTFQKWASVVVPLGKEQN----YTCRVYHEGLPEPLTL 93


                .
gi 85542908 428 R 428
Cdd:cd21018  94 R 94

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: 40.94 E-value: 1.18e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 131 SKLICEATNFTPKPITVSWLKDgklvESGFTTDPVTIENKG-STPQ-----TYKVISTLTISEIDWLNLNVYTCRVDHRG 204
Cdd:cd05771  17 QTLSCHIAGYYPLDVDVEWLRE----EPGGSESQVSRDGVSlSSHRqsvdgTYSISSYLTLEPGTENRGATYTCRVTHVS 92


                .
gi 85542908 205 L 205
Cdd:cd05771  93 L 93

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: 40.48 E-value: 1.57e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPAREQLNlrESATVTCLVKGFSPADISVQWLQRGQllPQEKYVTSAPMPEPGApgfyFTHSILTVTEEEWNSG 409
Cdd:cd21001   4 PTVTISPSRTEALN--HHNLLVCSVTDFYPGQIKVRWFRNDQ--EETAGVVSTPLIRNGD----WTFQILVMLEMTPQRG 75

                        90
                ....*....|..
gi 85542908 410 ETYTCVVGHEAL 421
Cdd:cd21001  76 DVYTCHVEHPSL 87

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: 40.50 E-value: 1.72e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 347 SATVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEEWNsgetYTCVVGHEALPHLV 425
Cdd:cd21014  18 AVTLRCWALGFYPADITLTWQLNGEELTQDmELVETRP---AGDGTFQKWASVVVPLGKEQN----YTCHVNHEGLPEPL 90


                ...
gi 85542908 426 TER 428
Cdd:cd21014  91 TLR 93

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: 40.09 E-value: 2.74e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85542908 133 LICEATNFTPKPITVSWLKDGKLVESGFTTDPVtIENKGstpQTYKVISTLtisEIDWLNLNVYTCRVDHRGL 205
Cdd:cd21001  22 LVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPL-IRNGD---WTFQILVML---EMTPQRGDVYTCHVEHPSL 87

Class II major histocompatibility complex (MHC) alpha 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 immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DR. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DR 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-DRA1 and HLA-DRB1, that are adjacent to each other on chromosome band 6p21.31. Susceptibility to multiple sclerosis and rheumatoid arthritis are associated with the human histocompatibility leukocyte antigen HLA-DR2 and HLA-DR4, respectively. 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: 409598 Cd Length: 95 Bit Score: 39.65 E-value: 3.24e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85542908 133 LICEATNFTPKPITVSWLKDGKLVESGfTTDPVTIENKGSTPQTYKVISTLTISEidwlnlNVYTCRVDHRGL 205
Cdd:cd21007  21 LICFIDKFTPPVVNVTWLRNGKPVTTG-VSETVFLPREDHLFRKFHYLPFLPSTE------DVYDCRVEHWGL 86

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: 39.70 E-value: 3.44e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 349 TVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEEwnsgETYTCVVGHEALPHLVTE 427
Cdd:cd21016  21 TLRCWALGFYPADITLTWQKDGEELTQDmEFVETRP---AGDGTFQKWAAVVVPLGKE----QSYTCHVYHEGLPEPLTL 93


                .
gi 85542908 428 R 428
Cdd:cd21016  94 R 94

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: 39.35 E-value: 3.57e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85542908 135 CEATNFTPKPITVSWlKDGKLVeSGFTTDPVTIENKGstpqTYKVISTLTISEiDWLNLNVYTCRVDH 202
Cdd:cd21817  23 CLVTGYFPEPVTVTW-NSGSLT-SGVKTFPAVLQSSG----LYTTSSQVTVPS-SSWGSQTFTCNVEH 83

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: 39.41 E-value: 4.23e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85542908 348 ATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFYFTHSILTVTEEEwnsGETYTCVVGHEALPH 423
Cdd:cd21023  20 ATLRCWALGFYPAEITLTWQRDGEEQTQDTELVET---RPAGDGTFQKWAAVVVPPGE---EQRYTCHVQHEGLPQ 89

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; 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) B and similar proteins. 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-B 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. Human leukocyte antigen (HLA) B*3501 (B35) is a common human allele involved in mediating protective immunity against HIV. 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: 409617 Cd Length: 97 Bit Score: 39.41 E-value: 4.47e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 348 ATVTCLVKGFSPADISVQWLQRGQLLPQE-KYVTSAPmpePGAPGFYFTHSILTVTEEEwnsgETYTCVVGHEALPHLVT 426
Cdd:cd21026  20 ATLRCWALGFYPAEITLTWQRDGEDQTQDtELVETRP---AGDRTFQKWAAVVVPSGEE----QRYTCHVQHEGLPKPLT 92


                ..
gi 85542908 427 ER 428
Cdd:cd21026  93 LR 94

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 38.77 E-value: 5.29e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   226 FTIPPSFADifLSKSANLTCLVSNLatY-ETLNISWaSQSGEPLETKIK----IMEShpNGTFSAKGVASVCVEDWNNRK 300
Cdd:pfam07654   2 YVFPPSPEE--LGKPNTLTCLVTGF--YpPDITVTW-LKNGQEVTEGVKttppSPNS--DWTYQLSSYLTVTPSDWESGD 74

                          90
                  ....*....|.
gi 85542908   301 EFVCTVTHRDL 311
Cdd:pfam07654  75 EYTCRVEHEGL 85

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: 39.02 E-value: 5.51e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 348 ATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFYFTHSILTVTEEEwnsGETYTCVVGHEALPHLVTE 427
Cdd:cd21025  20 ATLRCWALGFYPAEITLTWQWDGEDQTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPLTL 93


                .
gi 85542908 428 R 428
Cdd:cd21025  94 R 94

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: 39.00 E-value: 5.53e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 111 PNVNVFV--PPRDGfsgpapRKSKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTieNKGSTPQTYKVIStLTISEI 188
Cdd:cd05770   3 PKVQVYSrfPAENG------KPNVLNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSF--SKDWTFYLLKYTE-FTPTKG 73

                        90
                ....*....|....*..
gi 85542908 189 DwlnlnVYTCRVDHRGL 205
Cdd:cd05770  74 D-----EYACRVRHNTL 85

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: 38.94 E-value: 6.10e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 346 ESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFY--FTHSILTVTEEEWnsgetYTCVVGHEALPH 423
Cdd:cd21019  17 DKVTLRCWALGFYPADITLTWQLNGEELIQDMELVET---RPAGDGTFqkWASVVVPLGKEQY-----YTCHVYHQGLPE 88


                ....*
gi 85542908 424 LVTER 428
Cdd:cd21019  89 PLTLR 93

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: 38.97 E-value: 6.26e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNLresaTVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFYFTHSILTVTeeeWNS 408
Cdd:cd21020   5 PPKAHVTHHRRPEGDV----TLRCWALGFYPADITLTWQLNGEELTQEMELVET---RPAGDGTFQKWASVVVP---LGK 74

                        90       100
                ....*....|....*....|
gi 85542908 409 GETYTCVVGHEALPHLVTER 428
Cdd:cd21020  75 EQKYTCHVEHEGLPEPLTLR 94

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: 38.59 E-value: 8.38e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 226 FTIPPSFADIfLSKSANLTCLVSNLATYEtLNISWAS-----QSGEPLETKIKimesHPNGTFSAKGVASVCVEDWNNRK 300
Cdd:cd07699   5 TIFPPSSEEL-SSGKATLVCLINKFYPGF-ATVTWKVdgstvSSGVTTSKTEQ----QSDNTYSMSSYLTLSSSDWNKHK 78

                        90       100
                ....*....|....*....|.
gi 85542908 301 EFVCTVTHRDLPSPQKKFISK 321
Cdd:cd07699  79 VYTCEVTHEGLSSTITKSFNR 99

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: 38.60 E-value: 1.03e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 330 PAVYLLPPAREQLnlRESATVTCLVKGFSPADISVQWLQRGQllPQEKYVTSAPMPEPGApgfyFTHSILTVTEEEWNSG 409
Cdd:cd20998   7 PTVTVYPTKTQPL--EHHNLLVCSVSDFYPGNIEVRWFRNGK--EEKTGIVSTGLVRNGD----WTFQTLVMLETVPQSG 78

                        90
                ....*....|....*..
gi 85542908 410 ETYTCVVGHEALPHLVT 426
Cdd:cd20998  79 EVYTCQVEHPSLTDPVT 95

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 37.68 E-value: 1.05e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908    240 SANLTCLVSNLatY-ETLNISWASQsGEPLETKIK----IMEShpNGTFSAKGVASVCVEDWNNRKEFVCTVTHRDLPSP 314
Cdd:smart00407   1 KATLVCLVSGF--YpPDITVTWLRN-GQEVTEGVSttdpLKNS--DGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75

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: 38.17 E-value: 1.09e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQLNLresaTVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSApmpEPGAPGFYFTHSILTVTEEEwns 408
Cdd:cd21012   5 PPKTHVTHHPRPEGYV----TLRCWALGFYPAHITLTWQLNGEELIQDTELVET---RPAGDGTFQKWAAVVVPSGE--- 74

                        90       100
                ....*....|....*....|
gi 85542908 409 GETYTCVVGHEALPHLVTER 428
Cdd:cd21012  75 EQKYTCHVYHEGLPEPLTLR 94

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: 38.34 E-value: 1.11e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 118 PPRDGFSGPAprksKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGStpqTYKVISTLTISEIDWLNLNVYT 197
Cdd:cd04985  10 ATKSQSNGPV----ALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSGG---DYSCSSQLTVPLQEWNSGEVYK 82


                ....*
gi 85542908 198 CRVDH 202
Cdd:cd04985  83 CQVQH 87

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: 38.08 E-value: 1.30e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREqlNLRESATVTCLVKGFSPADISVQWLQRGQLLpqekyvTSAPMPEPGA--PGFYFTHSILTVTEEEW 406
Cdd:cd21819   1 APTLFPLVSCGS--STSDPVTVGCLATDFLPDSITFSWTDDNNSL------TTGVKTYPSVltGGTYTASSQLQVPESEW 72

                        90
                ....*....|....
gi 85542908 407 NSGETYTCVVGHEA 420
Cdd:cd21819  73 KSKENFYCKVEHPG 86

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; 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 alpha chain of histocompatibility antigen (HLA) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which 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. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. 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 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: 409599 Cd Length: 95 Bit Score: 38.00 E-value: 1.42e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85542908 133 LICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGStpqtYKVISTLTISEIDwlnLNVYTCRVDHRGL 205
Cdd:cd21008  21 LICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKSDHS----FLKISYLTFLPSA---DDIYDCKVEHWGL 86

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: 38.07 E-value: 1.49e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 336 PPAREQLNlrESATVTCLVKGFSPADISVQWLQRGQLLP-QEKYVTsapmPEPGAPGfYFTHSILTVTEEEWNSGETYTC 414
Cdd:cd05772  10 PSGRATPG--QTVSFTCKSHGFSPRDITLKWFKNGNELSaLQTTVF----PEGDSVS-YSVSSTVQVVLTKDDVHSQLTC 82


                ....*..
gi 85542908 415 VVGHEAL 421
Cdd:cd05772  83 EVAHVTL 89

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 36.91 E-value: 1.85e-03

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908     27 CLARDFLPSTISFTWNyQNNTEVIQGIRTFPTLRTG-GKYLATSqVLLSPKSILEGSDEY 85
Cdd:smart00407   6 CLVSGFYPPDITVTWL-RNGQEVTEGVSTTDPLKNSdGTYFLSS-YLTVPASTWESGDVY 63

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: 37.46 E-value: 2.12e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85542908 130 KSKLICEATNFTPKPITVSWLKDGKlvesGFTTDPVTIENKGSTPQTYKVISTLTISEIDWlnlNVYTCRVDHRGL 205
Cdd:cd21024  19 EATLRCWALGFYPAEITLTWQQDGE----GHTQDTELVETRPAGDGTFQKWAAVVVPSGEE---QRYTCHVQHEGL 87

Immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG). ZAG is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta-2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions. IgC_MHC_I_alpha3; 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: 409601 Cd Length: 93 Bit Score: 37.30 E-value: 2.37e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 127 APRKSK-LICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENkgSTPQTYKVIstltisEIDWLNLNVYTCRVDHRGL 205
Cdd:cd21010  14 APGKNRtLKCLAYDFYPRGISLHWTRAGKVQESESGGDVLPSGN--GTYQSWVVV------EVPPQDRAPYSCHVEHSSL 85


                .
gi 85542908 206 T 206
Cdd:cd21010  86 A 86

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

Pssm-ID: 395002 Cd Length: 86 Bit Score: 36.79 E-value: 2.46e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908   335 LPPAREQLNLRESATVTCLVKGFSPaDISVQWLQRGQLLPQekyvtsaPMPEPGAPGFYFTHSILTVTEEEWNSGeTYTC 414
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSP-GPDVTWSKEGGTLIE-------SLKVKHDNGRTTQSSLLISNVTKEDAG-TYTC 71


                  ....
gi 85542908   415 VVGH 418
Cdd:pfam00047  72 VVNN 75

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H; 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 H (HLA-H). HLA-H (also known as hereditary hemochromatosis protein; HFE) is a major histocompatibility complex (MHC) class I-like protein that is mutated in Hereditary Hemochromatosis. HFE is a protein of 343 amino acids that includes a signal peptide, an extracellular transferrin receptor-binding region (a1 and a2), an immunoglobulin-like domain (a3), a transmembrane region, and a short cytoplasmic tail. HFE binds beta-2-microglobulin to form a heterodimer expressed at the cell surface. It binds transferrin receptor (TFRC) in its extracellular alpha1-alpha2 domain. HFE plays an important part in the regulation of hepcidin expression in response to iron overload and the liver is important in the pathophysiology of HFE-associated hemochromatosis. Nine HFE splicing variants have been reported with transcripts lacking exon 2 or exon 3, or exons 2-3, 2-4, or 2-5. Diverse mutations involving HFE introns and exons discovered in persons with hemochromatosis or their family members cause or probably cause high iron phenotypes. 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: 409612 Cd Length: 94 Bit Score: 36.68 E-value: 3.87e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 85542908 131 SKLICEATNFTPKPITVSWLKDGKLVESGFTTDPVTIENKGSTPQTYKVISTLTISEidwlnlNVYTCRVDHRGL 205
Cdd:cd21021  18 TTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEE------QRYTCQVEHPGL 86

Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and Drosophila RST (irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development.

Pssm-ID: 409416 Cd Length: 98 Bit Score: 36.66 E-value: 3.88e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 85542908 351 TCLVKGFSPADiSVQWLQRGqlLPQEKYVTSAPMPEPGAPGFyfTHSILTVTEEEWNSGETYTCVVGHEALP 422
Cdd:cd05759  21 TCRARGAKPAA-EIIWFRDG--EQLEGAVYSKELLKDGKRET--TVSTLLITPSDLDTGRTFTCRARNEAIP 87

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: 36.47 E-value: 4.45e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 329 PPAVYLLPPAREQlNLRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYvTSAPMPEPGApgfYFTHSILTVTEEewNS 408
Cdd:cd07697   2 PKPTIFLPSIAET-EKQKAGTYLCLLENFFPDVIKIHWREKKSDTILESQ-EGNTEKTKDT---YMKFSWLTVPKK--SL 74

                        90
                ....*....|.
gi 85542908 409 GETYTCVVGHE 419
Cdd:cd07697  75 GKEHRCIYKHE 85

Immunoglobulin I-set domain;

Pssm-ID: 400151 [Multi-domain] Cd Length: 90 Bit Score: 36.08 E-value: 4.92e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85542908   135 CEATNfTPKPiTVSWLKDGKLVESGfttDPVTIENKGSTpqtykviSTLTISEIDWLNLNVYTCRV 200
Cdd:pfam07679  22 CTVTG-TPDP-EVSWFKDGQPLRSS---DRFKVTYEGGT-------YTLTISNVQPDDSGKYTCVA 75

Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and Drosophila RST (irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development.

Pssm-ID: 409416 Cd Length: 98 Bit Score: 36.27 E-value: 5.95e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85542908 133 LICEATNFTPKPiTVSWLKDGKLVESGFTTDPVTIENKGSTpqtykVISTLTISEIDWLNLNVYTCRV 200
Cdd:cd05759  20 LTCRARGAKPAA-EIIWFRDGEQLEGAVYSKELLKDGKRET-----TVSTLLITPSDLDTGRTFTCRA 81

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: 35.86 E-value: 6.42e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85542908 324 EVHKHPPAVyllppareqlnlRESATVTCLVKGFSPADISVQWLQRGQLLPQEKYVTSAPMPEpgapGFYFTHSILTVTE 403
Cdd:cd16085   6 EVTQQPTMV------------WNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKD----GTYNWTSWLLVNV 69

                        90       100
                ....*....|....*....|....*..
gi 85542908 404 EEWNSGETYTCVVGHEALPHLVTERTV 430
Cdd:cd16085  70 SAHREDVVLTCQVEHDGQPAVTKNHTL 96

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: 35.94 E-value: 7.00e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85542908 346 ESATVTCLVKGFSPADISVQWLQRGQLLPQEKYvtsAPMPEPGapGFYFTHSILTVTEEEWNSGETYTCVVGH 418
Cdd:cd21818  16 DPVVIGCLVQGFFPEPVNVTWNYSGKGGTARNF---PAMLASG--GRYTQSSQLTLPADQCPEGEAYKCSVQH 83

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

Pssm-ID: 409353 [Multi-domain] Cd Length: 70 Bit Score: 35.38 E-value: 7.31e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85542908 133 LICEATNFtPKPiTVSWLKDGKLVESGFTTDPVTIENKGstpqtykvisTLTISEIDWLNLNVYTCRV 200
Cdd:cd00096   3 LTCSASGN-PPP-TITWYKNGKPLPPSSRDSRRSELGNG----------TLTISNVTLEDSGTYTCVA 58

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: 35.89 E-value: 7.51e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 85542908 351 TCLVKGFSPADISVQWLQRGQllPQEKYVTSAPMPEPGApgfyFTHSILTVTEEEWNSGETYTCVVGHEALPHLVT 426
Cdd:cd21003  23 VCHVTDFYPGNIQVRWFLNGQ--EETAGVVSTNLIHNGD----WTFQILVMLEMTPQQGDVYTCQVEHPSLDSPVT 92