NCBI Conserved Domain Search

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.

Pssm-ID: 409370 [Multi-domain] Cd Length: 118 Bit Score: 197.15 E-value: 8.61e-61

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  22 QLVESGGGLVKPGGSLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLYLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 41388180 102 MNSLRAEDTAVYYCARDLLIAVAGH---WGQGTLVTVS 136
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLGGYGYSYfdyWGQGTTVTVS 118

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: 174.83 E-value: 1.80e-52

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPqaPGRYFAHSILTVSEEEWNTG 545
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPES--DGSFFVYSKLNVSTADWNSG 78

                        90       100
                ....*....|....*....|....*..
gi 41388180 546 ETYTCVVAHEALPNRVTERTVDKSTGK 572
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: 162.62 E-value: 4.64e-48

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 359 IRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGERF 438
Cdd:cd07696   1 VSVFLIPPSPKDLFLTKSAKVTCLVVDLTSIEEVNVTWSREDGNEVLASTTNPEKHYNATLSVVSTLTVCADDWDNGKTF 80

                        90
                ....*....|....*...
gi 41388180 439 TCTVTHTDLPSPLKQTIS 456
Cdd:cd07696  81 KCKVTHPDLPSPIVKSIQ 98

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: 141.76 E-value: 2.57e-40

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRDGFFGNpRKSKLICQATGFSPRQIQVSWLREGKQVGSGvtTDQVQAEAKESGPTTYKVTSTLTIKESDW 326
Cdd:cd16093   1 PPTVSLHAPSREEFLGN-RTATFVCLATGFSPKTISFKWLRNGKEVTSS--TGAVVEEPKEDGKTLYSATSFLTITESEW 77

                        90       100
                ....*....|....*....|..
gi 41388180 327 LSQSMFTCRVDHRGLTFQQNAS 348
Cdd:cd16093  78 KSQTEFTCEFKHKGEIVEKNAS 99

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: 141.70 E-value: 2.67e-40

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 142 APTLFPLVSCENSPSDtsSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMqgTDE 221
Cdd:cd21819   1 APTLFPLVSCGSSTSD--PVTVGCLATDFLPDSITFSWTDDNNSLTTGVKTYPSVLTGGTYTASSQLQVPESEWK--SKE 76

                        90
                ....*....|....*...
gi 41388180 222 HVVCKVQHPNGNKEKNVP 239
Cdd:cd21819  77 NFYCKVEHPGGNKEVPVP 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: 118.46 E-value: 7.64e-32

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 142 APTLFPLVSCENSPSdTSSVAVGCLAQDFLPDSITFSWKYKNNSDIS-STRGFPSVLR-GGKYAATSQVLLPSKDVmqGT 219
Cdd:cd04985   1 APTVFPLQSATKSQS-NGPVALGCLISDYFPESITVSWQKNTNSITSgFTRTFPVVLRsGGDYSCSSQLTVPLQEW--NS 77

                        90       100
                ....*....|....*....|.
gi 41388180 220 DEHVVCKVQHP--NGNKEKNV 238
Cdd:cd04985  78 GEVYKCQVQHSasNSKQEKDV 98

Immunoglobulin V-Type;

Pssm-ID: 214650 Cd Length: 81 Bit Score: 116.33 E-value: 3.09e-31

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180     36 SLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYYAdSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSYYQE-SYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 41388180    116 AR 117
Cdd:smart00406  80 AV 81

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 108.11 E-value: 2.82e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   468 VYLLPPAREQLNlrESATITCLVTGFSPADVFVQWMQRGQPLsPEKYVTSAPMPepQAPGRYFAHSILTVSEEEWNTGET 547
Cdd:pfam07654   1 VYVFPPSPEELG--KPNTLTCLVTGFYPPDITVTWLKNGQEV-TEGVKTTPPSP--NSDWTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 41388180   548 YTCVVAHEAL 557
Cdd:pfam07654  76 YTCRVEHEGL 85

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 97.38 E-value: 1.13e-24

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41388180    483 SATITCLVTGFSPADVFVQWMQRGQPlSPEKYVTSAPMPepQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPN 559
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQE-VTEGVSTTDPLK--NSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKE 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: 92.91 E-value: 8.46e-23

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 468 VYLLPPAREQlNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmPEPQAPGRYFAHSILTVSEEEWNTGET 547
Cdd:cd00098   2 VTLLPPSPEE-KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSS---PVEPNDGTYSVTSSLTVPPSDWDEGAT 77

                        90
                ....*....|....*
gi 41388180 548 YTCVVAHEALPNRVT 562
Cdd:cd00098  78 YTCVVTHESLKSPLS 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: 89.06 E-value: 1.67e-21

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 249 KVSVFVPPRDGFFGNPRKskLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVqaeaKESGPTTYKVTSTLTIKESDWLS 328
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVT--LVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSP----VEPNDGTYSVTSSLTVPPSDWDE 74

                        90       100
                ....*....|....*....|
gi 41388180 329 QSMFTCRVDHRGLTFQQNAS 348
Cdd:cd00098  75 GATYTCVVTHESLKSPLSKT 94

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: 78.98 E-value: 6.90e-18

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 465 RPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPmPEPQAPGRYFAHSILTVSEEEWNT 544
Cdd:cd16093   1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEE-PKEDGKTLYSATSFLTITESEWKS 79

                        90
                ....*....|...
gi 41388180 545 GETYTCVVAHEAL 557
Cdd:cd16093  80 QTEFTCEFKHKGE 92

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E and, D strands in one sheet and A', G, F, C, C', and C" strands in the other.

Pssm-ID: 409355 [Multi-domain] Cd Length: 111 Bit Score: 79.30 E-value: 7.27e-18

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  30 LVKPGGSLRLSCAASGFtFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYyaDSVKGRFTISRDNAKnSLYLQMNSLRAED 109
Cdd:cd00099   9 SVQEGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFLIYLSSSKGKTK--GGVPGRFSGSRDGTS-SFSLTISNLQPED 84

                        90       100
                ....*....|....*....|....*..
gi 41388180 110 TAVYYCARDLLIAVAG-HWGQGTLVTV 135
Cdd:cd00099  85 SGTYYCAVSESGGTDKlTFGSGTRLTV 111

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: 75.62 E-value: 9.74e-17

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 143 PTLFPLVSCENSPSDtsSVAVGCLAQDFLPDSITFSWKYkNNSDIsSTRGFPSVL-RGGKYAATSQVLLPSKDVMQGtdE 221
Cdd:cd21818   2 PTVFPLSLCPSLSSD--PVVIGCLVQGFFPEPVNVTWNY-SGKGG-TARNFPAMLaSGGRYTQSSQLTLPADQCPEG--E 75

                        90
                ....*....|....*...
gi 41388180 222 HVVCKVQHPNGNKEKNVP 239
Cdd:cd21818  76 AYKCSVQHYSPSQDLNVP 93

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409514 Cd Length: 115 Bit Score: 75.68 E-value: 1.80e-16

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  20 EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVssissSSSYIYYADSVKGRFTISRDNAKNSLY 99
Cdd:cd16095   1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWL-----TSLDHISTKVSEDRITSSREDTNSQIF 75

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 41388180 100 LQMNSLRAEDTAVYYCAR--------DLLIavaghWGQGTLVTV 135
Cdd:cd16095  76 LQIKGLGLRDSGQYHCARrvgygddtDKLI-----FGPGTDVIV 114

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 73.44 E-value: 4.84e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   250 VSVFvPPRDGFFGNPRKskLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQaeakESGPTTYKVTSTLTIKESDWLSQ 329
Cdd:pfam07654   1 VYVF-PPSPEELGKPNT--LTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPS----PNSDWTYQLSSYLTVTPSDWESG 73

                          90
                  ....*....|..
gi 41388180   330 SMFTCRVDHRGL 341
Cdd:pfam07654  74 DEYTCRVEHEGL 85

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: 73.91 E-value: 5.78e-16

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFVPPRDGFFGNPRKSkLICQATGFSPRQIQVSWLREGKQVGSG--VTTDQVQaeakeSGPTTYKVTSTLTIKESD 325
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVT-LTCLVKGFYPEDIFVSWLQNGEPLPSAdyKTTAPVP-----ESDGSFFVYSKLNVSTAD 74

                        90
                ....*....|....*....
gi 41388180 326 WLSQSMFTCRVDHRGLTFQ 344
Cdd:cd05768  75 WNSGDVFSCVVGHEALPLQ 93

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: 71.67 E-value: 2.28e-15

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFVPPRDGFFGNPrKSKLICQATGFSPRQIQVSWLREGKqvgSGVTTDQVQAEAKESGpTTYKVTSTLTIKESDWL 327
Cdd:cd05847   1 PTVQILHSSCASTLTSE-TIQLLCLISGYTPSTIEVEWLVDGQ---VATLSAASTAPQKEEG-GTFSTTSKLNVTQEDWK 75

                        90       100
                ....*....|....*....|
gi 41388180 328 SQSMFTCRVDHRGLTFQQNA 347
Cdd:cd05847  76 SGKTYTCKVTHQGTTFEAHT 95

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 70.42 E-value: 4.03e-15

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41388180    269 LICQATGFSPRQIQVSWLREGKQVGSGV-TTDQVQaeakeSGPTTYKVTSTLTIKESDWLSQSMFTCRVDHRGLT 342
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLRNGQEVTEGVsTTDPLK-----NSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73

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: 70.44 E-value: 9.33e-15

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 360 RVFAIPPSFASIFLTKSTKLTCLVTDLTTYDsVTISWTrQNGEAVKT---HTNISESHPNATFSAVGEASICEDDWNSGE 436
Cdd:cd05768   2 SVYLLPPPEEELSLNETVTLTCLVKGFYPED-IFVSWL-QNGEPLPSadyKTTAPVPESDGSFFVYSKLNVSTADWNSGD 79

                        90       100
                ....*....|....*....|....*
gi 41388180 437 RFTCTVTHTDLPSPLKQ-TISRPKG 460
Cdd:cd05768  80 VFSCVVGHEALPLQFTQkSIDKSPG 104

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: 69.71 E-value: 2.31e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFvPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVqaeAKESGPTTYKVTSTLTIKESDW 326
Cdd:cd05769   2 PPTVALF-PPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQ---ALRENTSTYSLSSRLRVSATEW 77

                        90       100
                ....*....|....*....|
gi 41388180 327 LS-QSMFTCRVDHRGLTFQQ 345
Cdd:cd05769  78 FNpRNTFTCIVKFYGGTDTD 97

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: 68.59 E-value: 3.10e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmPEPQAPGRYFAHSILTVSEEEWNTG 545
Cdd:cd05847   1 PTVQILHSSCASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVATLSAASTA---PQKEEGGTFSTTSKLNVTQEDWKSG 77

                        90
                ....*....|..
gi 41388180 546 ETYTCVVAHEAL 557
Cdd:cd05847  78 KTYTCKVTHQGT 89

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: 67.73 E-value: 5.16e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 254 VPPRDGFFGNPRKS----KLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKEsgptTYKVTSTLTIKESDwlsQ 329
Cdd:cd21029   1 VKPRVRLSSRPSPGdghlQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILPNHDG----TYQLRKTLDIAPGE---G 73

                        90
                ....*....|..
gi 41388180 330 SMFTCRVDHRGL 341
Cdd:cd21029  74 AGYSCRVDHSSL 85

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain the standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409371 Cd Length: 117 Bit Score: 68.16 E-value: 7.37e-14

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  33 PGGSLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAV 112
Cdd:cd04982  12 ESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSAT 91


                ....*
gi 41388180 113 YYCAR 117
Cdd:cd04982  92 YYCAY 96

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: 67.10 E-value: 1.05e-13

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRDGFFGNprKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTdqvqAEAKESGPTTYKVTSTLTIKESDW 326
Cdd:cd07699   1 APSVTIFPPSSEELSSG--KATLVCLINKFYPGFATVTWKVDGSTVSSGVTT----SKTEQQSDNTYSMSSYLTLSSSDW 74

                        90
                ....*....|....*.
gi 41388180 327 LSQSMFTCRVDHRGLT 342
Cdd:cd07699  75 NKHKVYTCEVTHEGLS 90

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: 63.63 E-value: 1.68e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 465 RPDVYLLPPAREQLNlRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyVTSAPmPEPQAPGRYFAHSILTVSEEEWNT 544
Cdd:cd07699   1 APSVTIFPPSSEELS-SGKATLVCLINKFYPGFATVTWKVDGSTVSSG--VTTSK-TEQQSDNTYSMSSYLTLSSSDWNK 76

                        90
                ....*....|...
gi 41388180 545 GETYTCVVAHEAL 557
Cdd:cd07699  77 HKVYTCEVTHEGL 89

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: 63.62 E-value: 1.70e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 142 APTLFPLVSCENSpSDTSSVAVGCLAQDFLPDSITFSWkyKNNSDISSTRGFPSVLR-GGKYAATSQVLLPSKDVMQGTd 220
Cdd:cd21817   1 APSVFPLAPCCKS-TNGSSVTLGCLVTGYFPEPVTVTW--NSGSLTSGVKTFPAVLQsSGLYTTSSQVTVPSSSWGSQT- 76

                        90
                ....*....|
gi 41388180 221 ehVVCKVQHP 230
Cdd:cd21817  77 --FTCNVEHK 84

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.

Pssm-ID: 214653 [Multi-domain] Cd Length: 85 Bit Score: 59.83 E-value: 2.72e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180     26 SGGGLVKPGGSLRLSCAASGFtfSTYSMNWVRQapgkGLEWVSSisssssyiyyadsvKGRFTISRDNakNSLYLQMNSL 105
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLLAE--------------SGRFSVSRSG--STSTLTISNV 58

                           90
                   ....*....|.
gi 41388180    106 RAEDTAVYYCA 116
Cdd:smart00410  59 TPEDSGTYTCA 69

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: 59.37 E-value: 5.92e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 468 VYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQplSPEKYVTSApMPEPQAPGRYFAHSILTVSEEEWNTGET 547
Cdd:cd16084   2 VYLLTPAVQDLWLRDKATFTCFVVGSDLKDAHLTWEVAGK--VPTGGVEEG-LLERHSNGSQSQHSRLTLPRSLWNAGTS 78

                        90
                ....*....|.
gi 41388180 548 YTCVVAHEALP 558
Cdd:cd16084  79 VTCTLNHPSLP 89

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: 59.17 E-value: 6.60e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 479 NLRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyvTSAPmPEPQAPG--RYFAHSILTVSEEewnTGETYTCVVAHEA 556
Cdd:cd21002  15 NTREPVMLACHVWGFYPADVTITWLKNGDPVAPH---SSAP-KTAQPNGdwTYQTQVTLAVTPS---PGDTYTCSVQHAS 87


                ..
gi 41388180 557 LP 558
Cdd:cd21002  88 LP 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: 58.93 E-value: 7.62e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 365 PPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEasICEDDWNSGERFTCTVTH 444
Cdd:cd04986   8 RPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLP--GCAEPWNSGDTFSCTVTH 85

                        90
                ....*....|.
gi 41388180 445 TDLPSPLKQTI 455
Cdd:cd04986  86 PESKGTLTATI 96

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: 58.78 E-value: 7.99e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPR-DGffgnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESD 325
Cdd:cd07698   2 PPKVHVTHHPRsDG------ESTLRCWALGFYPAEITLTWQRDGED----QTQDMELVETRPNGDGTFQKWAAVVVPSGE 71

                        90
                ....*....|....*..
gi 41388180 326 WLSqsmFTCRVDHRGLT 342
Cdd:cd07698  72 EQR---YTCHVQHEGLP 85

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: 58.63 E-value: 1.03e-10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 360 RVFAIPPSfASIFLTKSTKLTCLVTDLTtYDSVTISWTRQNGEAVKTHTNISESHPNA-TFSAVGEASICEDDWNSGERF 438
Cdd:cd00098   1 TVTLLPPS-PEEKGGGKVTLVCLVSGFY-PKDITVTWLKNGVPLTSGVSTSSPVEPNDgTYSVTSSLTVPPSDWDEGATY 78

                        90
                ....*....|....*..
gi 41388180 439 TCTVTHTDLPSPLKQTI 455
Cdd:cd00098  79 TCVVTHESLKSPLSKTW 95

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: 57.08 E-value: 3.21e-10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 144 TLFPLVSCEnSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISS-TRGFPSVLRGGKYAATSQVLLPSKDVMQGTdeH 222
Cdd:cd00098   1 TVTLLPPSP-EEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGvSTSSPVEPNDGTYSVTSSLTVPPSDWDEGA--T 77

                        90
                ....*....|..
gi 41388180 223 VVCKVQHPNGNK 234
Cdd:cd00098  78 YTCVVTHESLKS 89

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: 55.79 E-value: 9.44e-10

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 465 RPDVYLlppAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyvTSAPMPEPQAPGRYFAHSILTVSEEEwnt 544
Cdd:cd21029   2 KPRVRL---SSRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDG---TQSGGILPNHDGTYQLRKTLDIAPGE--- 72

                        90       100
                ....*....|....*....|
gi 41388180 545 GETYTCVVAHEALPNRVTER 564
Cdd:cd21029  73 GAGYSCRVDHSSLKQDLIVY 92

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409373 Cd Length: 105 Bit Score: 55.55 E-value: 1.33e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  31 VKPGGSLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVSSISSSSSyiyyaDSVKGRFTISRDNakNSLYLQMNSLRAEDT 110
Cdd:cd04984  10 VSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRP-----SGIPDRFSGSKSG--NTASLTISGAQTEDE 82

                        90       100
                ....*....|....*....|....*..
gi 41388180 111 AVYYCArdllIAVAGHW--GQGTLVTV 135
Cdd:cd04984  83 ADYYCQ----VWDSNSYvfGGGTKLTV 105

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409372 [Multi-domain] Cd Length: 109 Bit Score: 54.20 E-value: 4.31e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  34 GGSLRLSCAASgfTFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYyadsvKGRFTISRDNAKNSLYLQMNSLRAEDTAVY 113
Cdd:cd04983  13 GENVTLNCNYS--TSTFYYLFWYRQYPGQGPQFLIYISSDSGNKK-----KGRFSATLDKSRKSSSLHISAAQLSDSAVY 85

                        90       100
                ....*....|....*....|....*.
gi 41388180 114 YCArdlLIAVAGHW----GQGTLVTV 135
Cdd:cd04983  86 FCA---LSESGGTGkltfGKGTRLTV 108

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409480 Cd Length: 110 Bit Score: 54.21 E-value: 5.32e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  30 LVKPGGSLRLSCAAsgfTFSTYSMNWVRQAPGKGLEWVSSISSSSSYIYyaDSVKG-RFTISRDNAKNSLyLQMNSLRAE 108
Cdd:cd05899   9 IKRRGQSVTLRCSQ---KSGHDNMYWYRQDPGKGLQLLFYSYGGGLNEE--GDLPGdRFSASRPSLTRSS-LTIKSAEPE 82

                        90       100
                ....*....|....*....|....*...
gi 41388180 109 DTAVYYCARDLLIAVAG-HWGQGTLVTV 135
Cdd:cd05899  83 DSAVYLCASSLGGGADEaYFGPGTRLTV 110

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: 53.54 E-value: 6.24e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 465 RPDVYLLPPAREQLNLRESATITCLVTGF-SPADVFVQWmqrgQPLSPEKYVTSAPmpEPQAPGRYFAHSILTVSEEEWN 543
Cdd:cd04986   1 QPRLSLQRPALEDLLLGSNASLTCTLSGLkDPEGATFTW----EPSGGKEAIQGPP--ERDSCGCYSVSSVLPGCAEPWN 74

                        90
                ....*....|....*....
gi 41388180 544 TGETYTCVVAHEALPNRVT 562
Cdd:cd04986  75 SGDTFSCTVTHPESKGTLT 93

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: 53.49 E-value: 6.77e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKVTSTL--TIKES 324
Cdd:cd05766   3 QPSVKVS-PTKTGPLEHP--NLLVCSVTGFYPAEIEVKWFRNGQEETAGV----VSTELIPNGDWTFQILVMLetTPRRG 75

                        90
                ....*....|....*...
gi 41388180 325 DwlsqsMFTCRVDHRGLT 342
Cdd:cd05766  76 D-----VYTCQVEHSSLQ 88

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: 52.98 E-value: 9.98e-09

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPArEQLNLRESATITCLVTGFSPADVFVQWmQRGQPLSPEKYVTSAPmPEPQAPGRYFAHSILTVSEEEWNTG 545
Cdd:cd04985   2 PTVFPLQSA-TKSQSNGPVALGCLISDYFPESITVSW-QKNTNSITSGFTRTFP-VVLRSGGDYSCSSQLTVPLQEWNSG 78

                        90
                ....*....|.
gi 41388180 546 ETYTCVVAHEA 556
Cdd:cd04985  79 EVYKCQVQHSA 89

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: 1.50e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 41388180 483 SATITCLVTGFSPADVFVQWMQRGQPLS-PEKYVTsapmPEPQAPGRYFAHSILTVSEEEWntgETYTCVVAHEALP 558
Cdd:cd07698  16 ESTLRCWALGFYPAEITLTWQRDGEDQTqDMELVE----TRPNGDGTFQKWAAVVVPSGEE---QRYTCHVQHEGLP 85

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

Pssm-ID: 462230 Cd Length: 109 Bit Score: 52.46 E-value: 1.85e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180    30 LVKPGGSLRLSCAASGFTFS-TYSMNWVRQAPGKGLEWVSSISSSSSYIYyadSVKGRFTISRDNAKNSLYLQMNSLRAE 108
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEaSTSVYWYRQPPGKGPTFLIAYYSNGSEEG---VKKGRFSGRGDPSNGDGSLTIQNLTLS 83

                          90       100
                  ....*....|....*....|....*..
gi 41388180   109 DTAVYYCArdLLIAVAGHWGQGTLVTV 135
Cdd:pfam07686  84 DSGTYTCA--VIPSGEGVFGKGTRLTV 108

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: 51.76 E-value: 2.53e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 142 APTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSdiSSTRGFPSVLRGGKYAAT-SQVLLPSKDVMQGTD 220
Cdd:cd16092   1 APDVFPIISGCRHPKDNSPVVLACLITGYHPTSVTVTWYMGTQS--QPQRTFPEIQRRDSYYMTsSQLSTPLQQWRQGEY 78

                        90
                ....*....|....*...
gi 41388180 221 EhvvCKVQHPNGNKEKNV 238
Cdd:cd16092  79 K---CVVQHTASKSKKEI 93

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: 51.46 E-value: 3.15e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRdgffGNPRKS-KLICQATGFSPRQIQVSWLREGKQVGSGvttDQVQAEAKESGPTTYKVTSTLTIKESD 325
Cdd:cd21002   3 PPSVRVAPTTP----FNTREPvMLACHVWGFYPADVTITWLKNGDPVAPH---SSAPKTAQPNGDWTYQTQVTLAVTPSP 75

                        90
                ....*....|....*.
gi 41388180 326 WlsqSMFTCRVDHRGL 341
Cdd:cd21002  76 G---DTYTCSVQHASL 88

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

Pssm-ID: 409428 Cd Length: 100 Bit Score: 51.34 E-value: 4.34e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 482 ESATITCLVTGFSPADVFVQWMQR-----GQPLSPEKYVTSAPmpEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEA 556
Cdd:cd05771  15 LPQTLSCHIAGYYPLDVDVEWLREepggsESQVSRDGVSLSSH--RQSVDGTYSISSYLTLEPGTENRGATYTCRVTHVS 92


                ....*..
gi 41388180 557 LPNRVTE 563
Cdd:cd05771  93 LEEPLSV 99

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: 51.61 E-value: 4.73e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSpeKYVTSAPMPEPQAPGRYFAHSILTVSEEEW-NT 544
Cdd:cd05769   3 PTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVK--DGVATDPQALRENTSTYSLSSRLRVSATEWfNP 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 41388180 545 GETYTCVVAHEalpNRVTERTVDKSTGKPTLYNVS 579
Cdd:cd05769  81 RNTFTCIVKFY---GGTDTDTWTQGIAGPVTCGVS 112

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: 50.02 E-value: 1.06e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPParEQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApMPEPQapgryFAHSILTVSEEEWNTG 545
Cdd:cd05766   4 PSVKVSPT--KTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTEL-IPNGD-----WTFQILVMLETTPRRG 75

                        90
                ....*....|....*....
gi 41388180 546 ETYTCVVAHEALPNRVTER 564
Cdd:cd05766  76 DVYTCQVEHSSLQSPLTVD 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: 49.03 E-value: 2.27e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLRE-GKQVGSGVTTDQVQ-AEAKESGPTTYKVTSTLTIKESD 325
Cdd:cd05771   1 PRVRLS-PKNLVKPDLP--QTLSCHIAGYYPLDVDVEWLREePGGSESQVSRDGVSlSSHRQSVDGTYSISSYLTLEPGT 77

                        90
                ....*....|....*.
gi 41388180 326 WLSQSMFTCRVDHRGL 341
Cdd:cd05771  78 ENRGATYTCRVTHVSL 93

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 48.79 E-value: 2.35e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   361 VFAIPPSFASifLTKSTKLTCLVTDLttY-DSVTISWTRqNGEAVKTHTNISESHPNA--TFSAVGEASICEDDWNSGER 437
Cdd:pfam07654   1 VYVFPPSPEE--LGKPNTLTCLVTGF--YpPDITVTWLK-NGQEVTEGVKTTPPSPNSdwTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 41388180   438 FTCTVTHTDL 447
Cdd:pfam07654  76 YTCRVEHEGL 85

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: 48.99 E-value: 2.94e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 361 VFAIPPSFASIFLTKSTkLTCLVTDLTTYDsVTISW-----TRQNGeaVKTHTNISEshPNATFSAVGEASICEDDWNSG 435
Cdd:cd07699   4 VTIFPPSSEELSSGKAT-LVCLINKFYPGF-ATVTWkvdgsTVSSG--VTTSKTEQQ--SDNTYSMSSYLTLSSSDWNKH 77

                        90       100
                ....*....|....*....|..
gi 41388180 436 ERFTCTVTHTDLPSPLKQTISR 457
Cdd:cd07699  78 KVYTCEVTHEGLSSTITKSFNR 99

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: 48.60 E-value: 3.21e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPAREQLNLrESATITCLVTGFSPADVFVQWmqrgqplSPEKyVTSAPMPEP---QAPGRYFAHSILTVSEEEW 542
Cdd:cd21817   2 PSVFPLAPCCKSTNG-SSVTLGCLVTGYFPEPVTVTW-------NSGS-LTSGVKTFPavlQSSGLYTTSSQVTVPSSSW 72

                        90       100
                ....*....|....*....|..
gi 41388180 543 NTgETYTCVVAHEALPNRVTER 564
Cdd:cd21817  73 GS-QTFTCNVEHKPSSTKVDKK 93

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: 48.69 E-value: 3.30e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 486 ITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPgRYFAHSILTVSEEEWNTGETYTCVVAHE 555
Cdd:cd16094  19 LLCEVSGFSPPNILLMWLEDQREVNTSGFAPARPPPQPGST-TFWAWSVLRVPAPPSPQPATYTCVVSHE 87

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: 48.09 E-value: 5.16e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41388180 269 LICQATGFSPRQIQVSWLREGKQVGSGVTTdqVQAEAKESgptTYKVTSTLTIKESDWLSQSMFTCRVDHRGLT 342
Cdd:cd05772  22 FTCKSHGFSPRDITLKWFKNGNELSALQTT--VFPEGDSV---SYSVSSTVQVVLTKDDVHSQLTCEVAHVTLQ 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: 46.25 E-value: 2.32e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 361 VFAIPPSFASIFLTKSTKLTCLVTDLTTyDSVTISWTRQNGEA-VKTHTNISESHPNATFSAVGEASICEDDWNSGERFT 439
Cdd:cd05847   3 VQILHSSCASTLTSETIQLLCLISGYTP-STIEVEWLVDGQVAtLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTYT 81


                ....*
gi 41388180 440 CTVTH 444
Cdd:cd05847  82 CKVTH 86

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: 45.91 E-value: 3.16e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFVP-PRDGFFgnpRKS-KLICQATGF-SPRQIQVSWLREGkqvGSGVTTDQVQAEAKESGptTYKVTSTLTIKES 324
Cdd:cd07696   1 VSVFLIPPsPKDLFL---TKSaKVTCLVVDLtSIEEVNVTWSRED---GNEVLASTTNPEKHYNA--TLSVVSTLTVCAD 72

                        90
                ....*....|....*..
gi 41388180 325 DWLSQSMFTCRVDHRGL 341
Cdd:cd07696  73 DWDNGKTFKCKVTHPDL 89

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 45.32 E-value: 3.66e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   144 TLFPLVSCENSpsdtSSVAVGCLAQDFLPDSITFSWkYKNNSDISS-TRGFPSVLRG-GKYAATSQVLLPSKDVMQGtdE 221
Cdd:pfam07654   2 YVFPPSPEELG----KPNTLTCLVTGFYPPDITVTW-LKNGQEVTEgVKTTPPSPNSdWTYQLSSYLTVTPSDWESG--D 74


                  ....*....
gi 41388180   222 HVVCKVQHP 230
Cdd:pfam07654  75 EYTCRVEHE 83

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: 44.99 E-value: 6.96e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFvpprdgffgnPRKSK-------LICQATGFSPRQIQVSWLREGKQVGSG-VTTDQVQaeakeSGPTTYKvtsTL 319
Cdd:cd21000   4 PKVTVY----------PAKTQplqhhnlLVCSVNGFYPGSIEVRWFRNGQEEKAGvVSTGLIQ-----NGDWTFQ---TL 65

                        90       100
                ....*....|....*....|...
gi 41388180 320 TIKESDWLSQSMFTCRVDHRGLT 342
Cdd:cd21000  66 VMLETVPRSGEVYTCQVEHPSVT 88

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 43.84 E-value: 8.92e-06

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 41388180    379 LTCLVTDLttY-DSVTISWTRqNGEAVKTHTNISESHPNA--TFSAVGEASICEDDWNSGERFTCTVTHTDLPSP 450
Cdd:smart00407   4 LVCLVSGF--YpPDITVTWLR-NGQEVTEGVSTTDPLKNSdgTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75

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: 44.22 E-value: 1.07e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTtdqvqaeakesgPTTYKVTSTLTIKESDW 326
Cdd:cd05767   2 PPEVTVF-PKSPVELGEP--NTLICFVDNFFPPVINVTWLRNGQPVTDGVS------------ETVFLPREDHSFRKFSY 66

                        90       100
                ....*....|....*....|
gi 41388180 327 LS-----QSMFTCRVDHRGL 341
Cdd:cd05767  67 LPftpseGDIYDCRVEHWGL 86

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: 44.24 E-value: 1.23e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPL--SPEKYvtsapmPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEA 556
Cdd:cd21819  19 TVGCLATDFLPDSITFSWTDDNNSLttGVKTY------PSVLTGGTYTASSQLQVPESEWKSKENFYCKVEHPG 86

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: 43.95 E-value: 1.27e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 271 CQATGFSPRQIQVSWLREGKQvgSGVTTDQVQAEAKESgptTYKVTSTLTIKESDWLSQSMFTCRVDHRG 340
Cdd:cd16085  22 CQVEKFYPQRLQLTWLENGNV--SRTETPSTLTVNKDG---TYNWTSWLLVNVSAHREDVVLTCQVEHDG 86

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: 43.06 E-value: 2.45e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPpaREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntG 545
Cdd:cd05767   3 PEVTVFP--KSPVELGEPNTLICFVDNFFPPVINVTWLRNGQPVTDGVSETVF---LPREDHSFRKFSYLPFTPSE---G 74

                        90
                ....*....|...
gi 41388180 546 ETYTCVVAHEALP 558
Cdd:cd05767  75 DIYDCRVEHWGLE 87

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: 3.35e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 472 PPAREQLNLRESATIT--CLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgET 547
Cdd:cd21015   5 PEAHVTLHPRPEGDVTlrCWALGFYPADITLTWQLNGEDLTQDMELVET---RPAGDGTFqkWASVVVPLGKE-----QN 76

                        90
                ....*....|....*..
gi 41388180 548 YTCVVAHEALPNRVTER 564
Cdd:cd21015  77 YTCRVEHEGLPKPLSQR 93

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: 42.84 E-value: 3.58e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41388180 269 LICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKvtsTLTIKESDWLSQSMFTCRVDHRGLT 342
Cdd:cd20998  25 LVCSVSDFYPGNIEVRWFRNGKEEKTGI----VSTGLVRNGDWTFQ---TLVMLETVPQSGEVYTCQVEHPSLT 91

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: 42.79 E-value: 4.03e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 269 LICQATGFSPRQIQVSWLREGKQVGSGvttdqvqaeakesgpttykVTSTLTIKESDWLSQSM------------FTCRV 336
Cdd:cd21001  22 LVCSVTDFYPGQIKVRWFRNDQEETAG-------------------VVSTPLIRNGDWTFQILvmlemtpqrgdvYTCHV 82


                ....*
gi 41388180 337 DHRGL 341
Cdd:cd21001  83 EHPSL 87

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: 4.85e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 482 ESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEWntgetYTCVVAHEALPN 559
Cdd:cd21820  18 DEVTLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWAAVVVPLGKEQY-----YTCHVYHEGLPE 89


                ....*
gi 41388180 560 RVTER 564
Cdd:cd21820  90 PLTLR 94

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: 42.49 E-value: 5.07e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 326
Cdd:cd21023   5 PPKAHVAHHPI-----SDHEATLRCWALGFYPAEITLTWQRDGEE----QTQDTELVETRPAGDGTFQKWAAVVVPPGE- 74

                        90
                ....*....|....*
gi 41388180 327 lsQSMFTCRVDHRGL 341
Cdd:cd21023  75 --EQRYTCHVQHEGL 87

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: 42.47 E-value: 5.36e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 255 PPRDGFFGNP---RKSKLICQATGFSPRQIQVSWlregKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDwlsQSM 331
Cdd:cd21024   5 PPKTHVTHHPisdHEATLRCWALGFYPAEITLTW----QQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGE---EQR 77

                        90
                ....*....|
gi 41388180 332 FTCRVDHRGL 341
Cdd:cd21024  78 YTCHVQHEGL 87

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.

Pssm-ID: 409369 Cd Length: 106 Bit Score: 42.38 E-value: 5.82e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  21 VQLVESGGGL-VKPGGSLRLSCAASGFTFSTYsMNWVRQAPGKglewvSSISSSSSYIYYADSVKGRFTISrdNAKNSLY 99
Cdd:cd04980   1 IVMTQSPASLsVSPGERVTISCKASQSISSNY-LAWYQQKPGQ-----APKLLIYYASTLHSGVPSRFSGS--GSGTDFT 72

                        90
                ....*....|....*.
gi 41388180 100 LQMNSLRAEDTAVYYC 115
Cdd:cd04980  73 LTISSVEPEDAAVYYC 88

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: 42.13 E-value: 5.96e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQrGQPLSPEKyvtsaPMPEPQAPGRYF-AHSILTVSEEEWNT 544
Cdd:cd16092   2 PDVFPIISGCRHPKDNSPVVLACLITGYHPTSVTVTWYM-GTQSQPQR-----TFPEIQRRDSYYmTSSQLSTPLQQWRQ 75

                        90
                ....*....|..
gi 41388180 545 GEtYTCVVAHEA 556
Cdd:cd16092  76 GE-YKCVVQHTA 86

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: 42.08 E-value: 6.33e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntGETYTCVVAHEALPNRVTE 563
Cdd:cd21024  20 ATLRCWALGFYPAEITLTWQQDGEGHTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPVTL 93


                .
gi 41388180 564 R 564
Cdd:cd21024  94 R 94

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: 41.80 E-value: 7.03e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   471 LPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmpepqaPGRYFAHSILTVSEEEWNTGeTYTC 550
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIESLKVKHD--------NGRTTQSSLLISNVTKEDAG-TYTC 71


                  ....
gi 41388180   551 VVAH 554
Cdd:pfam00047  72 VVNN 75

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: 41.72 E-value: 7.92e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 326
Cdd:cd21026   5 PPKTHVTHHPI-----SDHEATLRCWALGFYPAEITLTWQRDGED----QTQDTELVETRPAGDRTFQKWAAVVVPSGE- 74

                        90
                ....*....|....*
gi 41388180 327 lsQSMFTCRVDHRGL 341
Cdd:cd21026  75 --EQRYTCHVQHEGL 87

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409503 Cd Length: 112 Bit Score: 42.12 E-value: 8.02e-05

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  48 FSTYSMNWVRQAPGKGLEWVSSISSSSSyiyyaDSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCA------RDLLI 121
Cdd:cd07706  27 WTNYYLFWYKQLPSGEMTFLIRQDSSEQ-----NAKSGRYSVNFQKAQKSISLTISALQLEDSAKYFCAlslpydTDKLI 101

                        90
                ....*....|....
gi 41388180 122 avaghWGQGTLVTV 135
Cdd:cd07706 102 -----FGKGTRLTV 110

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: 41.65 E-value: 1.02e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgETYTCVVAHEALPNRVT 562
Cdd:cd21018  21 TLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWASVVVPLGKE-----QNYTCRVYHEGLPEPLT 92


                ..
gi 41388180 563 ER 564
Cdd:cd21018  93 LR 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: 41.67 E-value: 1.04e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRdgffgnPRKS-KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESd 325
Cdd:cd21015   4 PPEAHVTLHPR------PEGDvTLRCWALGFYPADITLTWQLNGED----LTQDMELVETRPAGDGTFQKWASVVVPLG- 72

                        90
                ....*....|....*.
gi 41388180 326 wlSQSMFTCRVDHRGL 341
Cdd:cd21015  73 --KEQNYTCRVEHEGL 86

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: 41.31 E-value: 1.20e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPEKYvtSAPMPEPQAPGRYFAHSILTVSEeewntGETYTCVVAHEAL 557
Cdd:cd05770  20 VLNCYVSGFHPPDIEIRLLKNGVKIEDVEQ--SDLSFSKDWTFYLLKYTEFTPTK-----GDEYACRVRHNTL 85

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: 40.89 E-value: 1.50e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 458 PKGVALHRPDVYllppareqlnlrESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSIL 535
Cdd:cd21014   5 PKAHVTHHPRSY------------GAVTLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWASVVV 69

                        90       100
                ....*....|....*....|....*....
gi 41388180 536 TVSEEewntgETYTCVVAHEALPNRVTER 564
Cdd:cd21014  70 PLGKE-----QNYTCHVNHEGLPEPLTLR 93

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409580 Cd Length: 114 Bit Score: 41.39 E-value: 1.56e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  31 VKPGGSLRLSCAASGFTFSTYSMNWVRQAPGKGLEWVssissSSSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDT 110
Cdd:cd20988  10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFI-----YREGGIYGPGFKDNFRGDIDSSNNLAVLKILEASERDE 84

                        90       100
                ....*....|....*....|....*....
gi 41388180 111 AVYYCARD--LLIAVAGH--WGQGTLVTV 135
Cdd:cd20988  85 GSYYCASDtpGGGREYDPliFGKGTYLTV 113

immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of neonatal Fc receptor (FcRn). FcRn performs two distinct functions: the transport of maternal immunoglobulin G (IgG) to pre- or neonatal mammals which provides passive immunity and protection of IgG from normal serum protein catabolism. FcRn is related to class I MHC proteins, but lacks a functional peptide binding groove. 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: 409602 Cd Length: 93 Bit Score: 40.87 E-value: 1.81e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 262 GNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGvttdqvQAEAKESGPTTYKVTSTLTIKESDwlsQSMFTCRVDHRGL 341
Cdd:cd21011  15 GSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGSG------EGDFGPNGDGSFHAWSSLTVKSGD---EHHYRCVVQHAGL 85


                .
gi 41388180 342 T 342
Cdd:cd21011  86 A 86

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: 40.49 E-value: 2.54e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPE-KYVTSAPMPEpqAPGRYFAHSILTVSEEewntgETYTCVVAHEALPNRVTE 563
Cdd:cd21013  20 TLRCWALGFYPADITLTWQLNGEELTQDmEFVETRPAGD--GTFQKWASVVVPLGKE-----QKYTCHVEHEGLPEPLTL 92


                .
gi 41388180 564 R 564
Cdd:cd21013  93 R 93

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: 40.13 E-value: 2.68e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 246 LPPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKVTSTL--TIKE 323
Cdd:cd21003   2 VQPKVNVS-PSKKGPLQHH--NLLVCHVTDFYPGNIQVRWFLNGQEETAGV----VSTNLIHNGDWTFQILVMLemTPQQ 74

                        90
                ....*....|....*...
gi 41388180 324 SDwlsqsMFTCRVDHRGL 341
Cdd:cd21003  75 GD-----VYTCQVEHPSL 87

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 39.60 E-value: 2.76e-04

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41388180    160 SVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL-RGGKYAATSQVLLPSKDVMQGtdEHVVCKVQHPN 231
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKnSDGTYFLSSYLTVPASTWESG--DVYTCQVTHEG 71

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: 40.27 E-value: 3.06e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 269 LICQATGFSPRQIQVSWlreGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLSQSMFTCRVDH 338
Cdd:cd04985  21 LGCLISDYFPESITVSW---QKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVYKCQVQH 87

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; 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 MIC-A and MIC-B. MIC-A and MIC-B are homologs that serve as stress-inducible antigens on epithelial and epithelially derived cells. Both serve as ligands for the widely expressed activating immunoreceptor NKG2D, a C-type lectin-like activating immunoreceptor. MIC-B is very similar in structure to MIC-A and likely interacts with NKG2D in an analogous manner. The interdomain flexibility observed in the MIC-A structures, a feature unique to MIC proteins among MHC class I proteins and homologs, is also displayed by MIC-B, with an interdomain relationship intermediate between the two examples of MIC-A structures. Mapping sequence variations onto the structures of MIC-A and MIC-B reveals patterns completely distinct from those displayed by classical MHC class I proteins, with a number of substitutions falling on positions likely to affect interactions with NKG2D, but with other positions lying distant from the NKG2D binding sites or buried within the core of the proteins. 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: 409608 Cd Length: 95 Bit Score: 40.20 E-value: 3.39e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 144 TLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKyaATSQVLLPSKdVMQGTDEHV 223
Cdd:cd21017   2 TVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGN--GTYQTWVATR-ICQGEEQRF 78

                        90
                ....*....|....*.
gi 41388180 224 VCKVQHPNGNKEKNVP 239
Cdd:cd21017  79 TCYMEHSGNHSTHPVP 94

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.

Pssm-ID: 409613 Cd Length: 94 Bit Score: 39.74 E-value: 4.24e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRDGFfgnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 326
Cdd:cd21022   4 PPKTHVTHHPVFDY-----EATLRCWALGFYPAEIILTWQRDGED----QTQDVELVETRPAGDGTFQKWAAVVVPSGE- 73

                        90
                ....*....|....*
gi 41388180 327 lsQSMFTCRVDHRGL 341
Cdd:cd21022  74 --EQRYTCHVQHEGL 86

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: 39.71 E-value: 4.98e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 482 ESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEWntgetYTCVVAHEALPN 559
Cdd:cd21019  17 DKVTLRCWALGFYPADITLTWQLNGEELIQDMELVET---RPAGDGTFqkWASVVVPLGKEQY-----YTCHVYHQGLPE 88


                ....*
gi 41388180 560 RVTER 564
Cdd:cd21019  89 PLTLR 93

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: 39.16 E-value: 6.34e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESgpttYKVTSTLTIKESDwl 327
Cdd:cd21008   3 PEVTVF-PKSPVTLGQP--NTLICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKSDHS----FLKISYLTFLPSA-- 73

                        90
                ....*....|....
gi 41388180 328 sQSMFTCRVDHRGL 341
Cdd:cd21008  74 -DDIYDCKVEHWGL 86

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: 39.23 E-value: 6.47e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 41388180 381 CLVTDLTTyDSVTISWTRQNgeavKTHTNISESHP----NATFSAVGEASICEDDWNSGERFTCTVTH 444
Cdd:cd21819  22 CLATDFLP-DSITFSWTDDN----NSLTTGVKTYPsvltGGTYTASSQLQVPESEWKSKENFYCKVEH 84

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: 39.31 E-value: 6.90e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgETYTCVVAHEALPNRVT 562
Cdd:cd21016  21 TLRCWALGFYPADITLTWQKDGEELTQDMEFVET---RPAGDGTFqkWAAVVVPLGKE-----QSYTCHVYHEGLPEPLT 92


                ..
gi 41388180 563 ER 564
Cdd:cd21016  93 LR 94

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: 6.92e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEwntgeTYTCVVAHEALPNRVT 562
Cdd:cd21020  21 TLRCWALGFYPADITLTWQLNGEELTQEMELVET---RPAGDGTFqkWASVVVPLGKEQ-----KYTCHVEHEGLPEPLT 92


                ..
gi 41388180 563 ER 564
Cdd:cd21020  93 LR 94

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: 39.03 E-value: 7.68e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVFVQWMQRGQPLSPE-KYVTSAPmpepqAPGRYFAH--SILTVSEEEwntgETYTCVVAHEALPNR 560
Cdd:cd21026  20 ATLRCWALGFYPAEITLTWQRDGEDQTQDtELVETRP-----AGDRTFQKwaAVVVPSGEE----QRYTCHVQHEGLPKP 90


                ....
gi 41388180 561 VTER 564
Cdd:cd21026  91 LTLR 94

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: 39.23 E-value: 7.72e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 472 PPAREQLNlrESATITCLVTGFSPADVFVQWMQRGQPLSPEKyVTSAPMPEPQApgrYFAHSILTVSEEEWNTGETYTCV 551
Cdd:cd05772  10 PSGRATPG--QTVSFTCKSHGFSPRDITLKWFKNGNELSALQ-TTVFPEGDSVS---YSVSSTVQVVLTKDDVHSQLTCE 83


                ....*.
gi 41388180 552 VAHEAL 557
Cdd:cd05772  84 VAHVTL 89

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: 38.57 E-value: 9.98e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 361 VFAIPPSFASIFLTKSTKLTCLVTDLTTYDSvTISWtrQNGEAVKT---HTNISESHPNATFSAVGEASICEDDWNSGER 437
Cdd:cd16084   2 VYLLTPAVQDLWLRDKATFTCFVVGSDLKDA-HLTW--EVAGKVPTggvEEGLLERHSNGSQSQHSRLTLPRSLWNAGTS 78

                        90
                ....*....|.
gi 41388180 438 FTCTVTHTDLP 448
Cdd:cd16084  79 VTCTLNHPSLP 89

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: 38.47 E-value: 1.01e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 371 IFLTKS------TKLTCLVTDLTTYDsVTISWtRQNGEAVKTHTNISESHPNA--TFSAVgeaSICEDDWNSGERFTCTV 442
Cdd:cd05766   8 VSPTKTgplehpNLLVCSVTGFYPAE-IEVKW-FRNGQEETAGVVSTELIPNGdwTFQIL---VMLETTPRRGDVYTCQV 82


                ....*....
gi 41388180 443 THTDLPSPL 451
Cdd:cd05766  83 EHSSLQSPL 91

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: 38.63 E-value: 1.14e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 371 IFLTKSTKLTCLVTDLTTYDsVTISWTRQ---NGEAVKTHTNISES----HPNATFSAVGEASICEDDWNSGERFTCTVT 443
Cdd:cd05771  11 VKPDLPQTLSCHIAGYYPLD-VDVEWLREepgGSESQVSRDGVSLSshrqSVDGTYSISSYLTLEPGTENRGATYTCRVT 89


                ....*...
gi 41388180 444 HTDLPSPL 451
Cdd:cd05771  90 HVSLEEPL 97

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: 38.54 E-value: 1.29e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 255 PPRDGFFGNPRKS---KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSM 331
Cdd:cd21016   5 PPKAHVTRHPRPEgdvTLRCWALGFYPADITLTWQKDGEE----LTQDMEFVETRPAGDGTFQKWAAVVVPLG---KEQS 77

                        90
                ....*....|
gi 41388180 332 FTCRVDHRGL 341
Cdd:cd21016  78 YTCHVYHEGL 87

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: 38.20 E-value: 1.35e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41388180 271 CQATGFSPRQIQVSWlregkqvGSGVTTDQVQA-EAKESGPTTYKVTSTLTIKESDWLSQsMFTCRVDH 338
Cdd:cd21817  23 CLVTGYFPEPVTVTW-------NSGSLTSGVKTfPAVLQSSGLYTTSSQVTVPSSSWGSQ-TFTCNVEH 83

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: 38.23 E-value: 1.47e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 246 LPPKVSVFV--PPRDGffgnpRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQvqaeAKESGPTTYKVTST-LTIK 322
Cdd:cd05770   1 STPKVQVYSrfPAENG-----KPNVLNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDL----SFSKDWTFYLLKYTeFTPT 71

                        90
                ....*....|....*....
gi 41388180 323 ESDwlsqsMFTCRVDHRGL 341
Cdd:cd05770  72 KGD-----EYACRVRHNTL 85

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: 38.21 E-value: 1.48e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdw 326
Cdd:cd21820   5 PPKAHVTHHPR-----SEDEVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWAAVVVPLG-- 73

                        90
                ....*....|....*
gi 41388180 327 lSQSMFTCRVDHRGL 341
Cdd:cd21820  74 -KEQYYTCHVYHEGL 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: 38.19 E-value: 1.56e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSVFVPPRDgfFGnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdw 326
Cdd:cd21014   4 PPKAHVTHHPRS--YG---AVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWASVVVPLG-- 72

                        90
                ....*....|....*
gi 41388180 327 lSQSMFTCRVDHRGL 341
Cdd:cd21014  73 -KEQNYTCHVNHEGL 86

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

Pssm-ID: 400489 Cd Length: 89 Bit Score: 37.78 E-value: 1.70e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   253 FVPPRDGFFGNPRKSK-LICQATGFSPrQIQVSWLREGKQVGSGVTTDQVQAEakesgPTTYKVTSTLTIKESDWLSQSM 331
Cdd:pfam08205   2 TIEPPASLLEGEGPEVvATCSSAGGKP-APRITWYLDGKPLEAAETSSEQDPE-----SGLVTVTSELKLVPSRSDHGQS 75

                          90
                  ....*....|....
gi 41388180   332 FTCRVDHRGLTFQQ 345
Cdd:pfam08205  76 LTCQVSYGALRGSI 89

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: 37.86 E-value: 1.83e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntGETYTCVVAHEALPNRVTE 563
Cdd:cd21025  20 ATLRCWALGFYPAEITLTWQWDGEDQTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPLTL 93


                .
gi 41388180 564 R 564
Cdd:cd21025  94 R 94

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: 37.87 E-value: 1.85e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgETYTCVVAHEALPNRV 561
Cdd:cd21023  20 ATLRCWALGFYPAEITLTWQRDGEEQTQDTELVET---RPAGDGTFqkWAAVVVPPGEE-----QRYTCHVQHEGLPQPL 91


                ...
gi 41388180 562 TER 564
Cdd:cd21023  92 ILR 94

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: 37.87 E-value: 2.03e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41388180 482 ESATITCLVTGFSPADVFVQWMQRGQPlspekyVTSAPMPEPQAPG-RYFAHSILTVSEEEWNTGETYTCVVAH 554
Cdd:cd21818  16 DPVVIGCLVQGFFPEPVNVTWNYSGKG------GTARNFPAMLASGgRYTQSSQLTLPADQCPEGEAYKCSVQH 83

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.

Pssm-ID: 409613 Cd Length: 94 Bit Score: 37.43 E-value: 2.45e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEwntgeTYTCVVAHEALPNRV 561
Cdd:cd21022  19 ATLRCWALGFYPAEIILTWQRDGEDQTQDVELVET---RPAGDGTFqkWAAVVVPSGEEQ-----RYTCHVQHEGLPEPL 90


                ...
gi 41388180 562 TER 564
Cdd:cd21022  91 MLR 93

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

Pssm-ID: 409497 Cd Length: 116 Bit Score: 38.20 E-value: 2.53e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180  30 LVKPGGSLRLSCAASGFTFST--YSMNWvRQAPGKG--LEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLYLQMNSL 105
Cdd:cd07700   9 LVQTNQTVKMSCEAKTSPKNTriYWLRQ-RQAPSKDshFEFLASWDPSKGIVYGEGVDQEKLIILSDSDSSRYILSLMSV 87

                        90
                ....*....|.
gi 41388180 106 RAEDTAVYYCA 116
Cdd:cd07700  88 KPEDSGTYFCM 98

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: 37.41 E-value: 2.91e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 255 PPRDGFFGNPRKS---KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSM 331
Cdd:cd21013   4 PPKAHVTHHPRSEgyvTLRCWALGFYPADITLTWQLNGEE----LTQDMEFVETRPAGDGTFQKWASVVVPLG---KEQK 76

                        90
                ....*....|
gi 41388180 332 FTCRVDHRGL 341
Cdd:cd21013  77 YTCHVEHEGL 86

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: 37.41 E-value: 3.06e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwl 327
Cdd:cd21018   6 PKAHVTHHPR-----SKGEVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWASVVVPLG--- 73

                        90
                ....*....|....
gi 41388180 328 SQSMFTCRVDHRGL 341
Cdd:cd21018  74 KEQNYTCRVYHEGL 87

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: 37.40 E-value: 3.14e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 485 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEwntgeTYTCVVAHEALPNRVT 562
Cdd:cd21012  21 TLRCWALGFYPAHITLTWQLNGEELIQDTELVET---RPAGDGTFqkWAAVVVPSGEEQ-----KYTCHVYHEGLPEPLT 92


                ..
gi 41388180 563 ER 564
Cdd:cd21012  93 LR 94

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-A; 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) 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 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 a 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: 409597 Cd Length: 95 Bit Score: 37.36 E-value: 3.20e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 248 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESgpttYKVTSTLTIKESDwl 327
Cdd:cd21006   3 PQATVF-PKSPVLLGQP--NTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHS----FHKLSYLTFIPSD-- 73

                        90
                ....*....|....
gi 41388180 328 sQSMFTCRVDHRGL 341
Cdd:cd21006  74 -DDIYDCKVEHWGL 86

HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. 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: 409595 Cd Length: 95 Bit Score: 37.10 E-value: 3.49e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 41388180 246 LPPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVT 297
Cdd:cd21004   1 VPPRVTVL-PKSRVELGQP--NILICIVDNIFPPVINITWLRNGQTVTEGVA 49

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: 37.05 E-value: 4.42e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41388180 269 LICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSMFTCRVDHRGL 341
Cdd:cd21020  22 LRCWALGFYPADITLTWQLNGEE----LTQEMELVETRPAGDGTFQKWASVVVPLG---KEQKYTCHVEHEGL 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: 36.53 E-value: 4.65e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 247 PPKVSV--FVPPRdgffgnpRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQaeakeSGPTTYKVTSTLTIKES 324
Cdd:cd21010   4 PPSVSVtsHVAPG-------KNRTLKCLAYDFYPRGISLHWTRAGKVQESESGGDVLP-----SGNGTYQSWVVVEVPPQ 71

                        90
                ....*....|....*...
gi 41388180 325 DwlsQSMFTCRVDHRGLT 342
Cdd:cd21010  72 D---RAPYSCHVEHSSLA 86

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: 37.36 E-value: 4.97e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 359 IRVFaiPPSFASIFLTKSTKLTCLVTDLttY-DSVTISWtRQNGEAVKT--HTNISESHPNA-TFSAVGEASICEDDW-N 433
Cdd:cd05769   5 VALF--PPSEAEIRNKRKATLVCLATGF--YpDHVSLSW-KVNGKEVKDgvATDPQALRENTsTYSLSSRLRVSATEWfN 79

                        90       100
                ....*....|....*....|....*...
gi 41388180 434 SGERFTCTVTHTDLPSPLKQTISRPKGV 461
Cdd:cd05769  80 PRNTFTCIVKFYGGTDTDTWTQGIAGPV 107

Class II major histocompatibility complex (MHC) alpha 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 immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-E. 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: 409596 Cd Length: 95 Bit Score: 36.57 E-value: 5.02e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 466 PDVYLLppAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSpEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWntg 545
Cdd:cd21005   3 PEVTVL--SRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVT-EGVSETVFLPRDDHLFRKFHYLTFLPSTDDF--- 76

                        90
                ....*....|..
gi 41388180 546 etYTCVVAHEAL 557
Cdd:cd21005  77 --YDCEVDHWGL 86

Immunoglobulin domain; This family contains immunoglobulin-like domains.

Pssm-ID: 464046 [Multi-domain] Cd Length: 78 Bit Score: 36.00 E-value: 5.27e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180   471 LPPAREQLNLRESATITCLVTGFSPADvfVQWMQRGQPLSPEKYvtsapmpepQAPGRYFAHSILTVSEEEWNTGETYTC 550
Cdd:pfam13927   6 VSPSSVTVREGETVTLTCEATGSPPPT--ITWYKNGEPISSGST---------RSRSLSGSNSTLTISNVTRSDAGTYTC 74


                  ..
gi 41388180   551 VV 552
Cdd:pfam13927  75 VA 76

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: 5.75e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41388180 484 ATITCLVTGFSPADVfVQWMQRGQPLSPEKYVTSApMPEPQapgRYFAHSILTVSEEEWNTGETYTCVVAHEALPN-RVT 562
Cdd:cd05759  18 YNLTCRARGAKPAAE-IIWFRDGEQLEGAVYSKEL-LKDGK---RETTVSTLLITPSDLDTGRTFTCRARNEAIPNgKET 92


                ....*
gi 41388180 563 ERTVD 567
Cdd:cd05759  93 SITLD 97