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: 207.55 E-value: 1.29e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  22 QLVQSGAEVKKTGSSVKVSCKASGYTFTYRYLHWVRQAPGQALEWMGWITPFNGNTNYAQKFQDRVTITRDRSMNTAYME 101
Cdd:cd04981    1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 649152673 102 LSSLRSEDTAMYYCARGYSSSWDDAFDIWGQGTMVTVS 139
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: 169.05 E-value: 3.84e-50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPqaPGRYFAHSILTVSEEEWNTG 548
Cdd:cd05768    1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPES--DGSFFVYSKLNVSTADWNSG 78

                         90       100
                 ....*....|....*....|....*
gi 649152673 549 ETYTCVVAHEALPNRVTERTVDKST 573
Cdd:cd05768   79 DVFSCVVGHEALPLQFTQKSIDKSP 103

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: 161.08 E-value: 2.27e-47

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 362 IRVFAIPPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEASICEDDWNSGERF 441
Cdd:cd07696    1 VSVFLIPPSPKDLFLTKSAKVTCLVVDLTSIEEVNVTWSREDGNEVLASTTNPEKHYNATLSVVSTLTVCADDWDNGKTF 80

                         90
                 ....*....|....*...
gi 649152673 442 TCTVTHTDLPSPLKQTIS 459
Cdd:cd07696   81 KCKVTHPDLPSPIVKSIQ 98

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of mu chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

Pssm-ID: 409624 Cd Length: 95 Bit Score: 141.70 E-value: 3.42e-40

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 145 APTLFPLVSCENSPSDtsSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKYAATSQVLLPSKDVMqgTDE 224
Cdd:cd21819    1 APTLFPLVSCGSSTSD--PVTVGCLATDFLPDSITFSWTDDNNSLTTGVKTYPSVLTGGTYTASSQLQVPESEWK--SKE 76

                         90
                 ....*....|....*...
gi 649152673 225 HVVCKVQHPNGNKEKNVP 242
Cdd:cd21819   77 NFYCKVEHPGGNKEVPVP 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: 139.45 E-value: 2.73e-39

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRDGFFGNpRKSKLICQATGFSPRQIQVSWLREGKQVGSGvtTDQVQAEAKESGPTTYKVTSTLTIKESDW 329
Cdd:cd16093    1 PPTVSLHAPSREEFLGN-RTATFVCLATGFSPKTISFKWLRNGKEVTSS--TGAVVEEPKEDGKTLYSATSFLTITESEW 77

                         90       100
                 ....*....|....*....|..
gi 649152673 330 LSQSMFTCRVDHRGLTFQQNAS 351
Cdd:cd16093   78 KSQTEFTCEFKHKGEIVEKNAS 99

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: 118.85 E-value: 7.08e-32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 145 APTLFPLVSCENSPSdTSSVAVGCLAQDFLPDSITFSWKYKNNSDIS-STRGFPSVLR-GGKYAATSQVLLPSKDVmqGT 222
Cdd:cd04985    1 APTVFPLQSATKSQS-NGPVALGCLISDYFPESITVSWQKNTNSITSgFTRTFPVVLRsGGDYSCSSQLTVPLQEW--NS 77

                         90       100
                 ....*....|....*....|.
gi 649152673 223 DEHVVCKVQHP--NGNKEKNV 241
Cdd:cd04985   78 GEVYKCQVQHSasNSKQEKDV 98

Immunoglobulin V-Type;

Pssm-ID: 214650 Cd Length: 81 Bit Score: 110.16 E-value: 5.23e-29

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673    36 SVKVSCKASGYTFTYRYLHWVRQAPGQALEWMGWItPFNGNTNYAQKFQDRVTITRDRSMNTAYMELSSLRSEDTAMYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYI-GSNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 649152673   116 AR 117
Cdd:smart00406  80 AV 81

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 107.34 E-value: 5.48e-28

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  471 VYLLPPAREQLNlrESATITCLVTGFSPADVFVQWMQRGQPLsPEKYVTSAPMPepQAPGRYFAHSILTVSEEEWNTGET 550
Cdd:pfam07654   1 VYVFPPSPEELG--KPNTLTCLVTGFYPPDITVTWLKNGQEV-TEGVKTTPPSP--NSDWTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 649152673  551 YTCVVAHEAL 560
Cdd:pfam07654  76 YTCRVEHEGL 85

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 96.23 E-value: 3.33e-24

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 649152673   486 SATITCLVTGFSPADVFVQWMQRGQPlSPEKYVTSAPMPepQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEALPN 562
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQE-VTEGVSTTDPLK--NSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKE 74

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: 93.55 E-value: 9.52e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  23 LVQSGAEV-KKTGSSVKVSCKASGyTFTYRYLHWVRQAPGQALEWMGWITPfnGNTNYAQKFQDRVTITRDRSmNTAYME 101
Cdd:cd00099    1 VTQSPRSLsVQEGESVTLSCEVSS-SFSSTYIYWYRQKPGQGPEFLIYLSS--SKGKTKGGVPGRFSGSRDGT-SSFSLT 76

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 649152673 102 LSSLRSEDTAMYYCARGYSSSWDDAfdIWGQGTMVTV 138
Cdd:cd00099   77 ISNLQPEDSGTYYCAVSESGGTDKL--TFGSGTRLTV 111

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: 92.14 E-value: 1.68e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 471 VYLLPPAREQlNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmPEPQAPGRYFAHSILTVSEEEWNTGET 550
Cdd:cd00098    2 VTLLPPSPEE-KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSS---PVEPNDGTYSVTSSLTVPPSDWDEGAT 77

                         90
                 ....*....|....*
gi 649152673 551 YTCVVAHEALPNRVT 565
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: 88.67 E-value: 3.08e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 252 KVSVFVPPRDGFFGNPRKskLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVqaeaKESGPTTYKVTSTLTIKESDWLS 331
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVT--LVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSP----VEPNDGTYSVTSSLTVPPSDWDE 74

                         90       100
                 ....*....|....*....|
gi 649152673 332 QSMFTCRVDHRGLTFQQNAS 351
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: 77.82 E-value: 2.14e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 468 RPDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPmPEPQAPGRYFAHSILTVSEEEWNT 547
Cdd:cd16093    1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEE-PKEDGKTLYSATSFLTITESEWKS 79

                         90
                 ....*....|...
gi 649152673 548 GETYTCVVAHEAL 560
Cdd:cd16093   80 QTEFTCEFKHKGE 92

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: 76.00 E-value: 6.50e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 146 PTLFPLVSCENSPSDtsSVAVGCLAQDFLPDSITFSWKYkNNSDIsSTRGFPSVL-RGGKYAATSQVLLPSKDVMQGtdE 224
Cdd:cd21818    2 PTVFPLSLCPSLSSD--PVVIGCLVQGFFPEPVNVTWNY-SGKGG-TARNFPAMLaSGGRYTQSSQLTLPADQCPEG--E 75

                         90
                 ....*....|....*...
gi 649152673 225 HVVCKVQHPNGNKEKNVP 242
Cdd:cd21818   76 AYKCSVQHYSPSQDLNVP 93

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 72.67 E-value: 7.68e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  253 VSVFvPPRDGFFGNPRKskLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQaeakESGPTTYKVTSTLTIKESDWLSQ 332
Cdd:pfam07654   1 VYVF-PPSPEELGKPNT--LTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPS----PNSDWTYQLSSYLTVTPSDWESG 73

                          90
                  ....*....|..
gi 649152673  333 SMFTCRVDHRGL 344
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: 73.14 E-value: 9.26e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFVPPRDGFFGNPRKSkLICQATGFSPRQIQVSWLREGKQVGSG--VTTDQVQaeakeSGPTTYKVTSTLTIKESD 328
Cdd:cd05768    1 PSVYLLPPPEEELSLNETVT-LTCLVKGFYPEDIFVSWLQNGEPLPSAdyKTTAPVP-----ESDGSFFVYSKLNVSTAD 74

                         90
                 ....*....|....*....
gi 649152673 329 WLSQSMFTCRVDHRGLTFQ 347
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: 2.98e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFVPPRDGFFGNPrKSKLICQATGFSPRQIQVSWLREGKqvgSGVTTDQVQAEAKESGpTTYKVTSTLTIKESDWL 330
Cdd:cd05847    1 PTVQILHSSCASTLTSE-TIQLLCLISGYTPSTIEVEWLVDGQ---VATLSAASTAPQKEEG-GTFSTTSKLNVTQEDWK 75

                         90       100
                 ....*....|....*....|
gi 649152673 331 SQSMFTCRVDHRGLTFQQNA 350
Cdd:cd05847   76 SGKTYTCKVTHQGTTFEAHT 95

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 69.26 E-value: 9.35e-15

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 649152673   272 LICQATGFSPRQIQVSWLREGKQVGSGV-TTDQVQaeakeSGPTTYKVTSTLTIKESDWLSQSMFTCRVDHRGLT 345
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: 69.67 E-value: 1.54e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 363 RVFAIPPSFASIFLTKSTKLTCLVTDLTTYDsVTISWTrQNGEAVKT---HTNISESHPNATFSAVGEASICEDDWNSGE 439
Cdd:cd05768    2 SVYLLPPPEEELSLNETVTLTCLVKGFYPED-IFVSWL-QNGEPLPSadyKTTAPVPESDGSFFVYSKLNVSTADWNSGD 79

                         90       100
                 ....*....|....*....|....*
gi 649152673 440 RFTCTVTHTDLPSPLKQ-TISRPKG 463
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: 68.94 E-value: 3.88e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFvPPRDGFFGNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVqaeAKESGPTTYKVTSTLTIKESDW 329
Cdd:cd05769    2 PPTVALF-PPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVATDPQ---ALRENTSTYSLSSRLRVSATEW 77

                         90       100
                 ....*....|....*....|
gi 649152673 330 LS-QSMFTCRVDHRGLTFQQ 348
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: 68.21 E-value: 4.21e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmPEPQAPGRYFAHSILTVSEEEWNTG 548
Cdd:cd05847    1 PTVQILHSSCASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVATLSAASTA---PQKEEGGTFSTTSKLNVTQEDWKSG 77

                         90
                 ....*....|..
gi 649152673 549 ETYTCVVAHEAL 560
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: 5.49e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 257 VPPRDGFFGNPRKS----KLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKEsgptTYKVTSTLTIKESDwlsQ 332
Cdd:cd21029    1 VKPRVRLSSRPSPGdghlQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILPNHDG----TYQLRKTLDIAPGE---G 73

                         90
                 ....*....|..
gi 649152673 333 SMFTCRVDHRGL 344
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: 6.66e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  30 VKKTGSSVKVSCKASGYTFTYRYLHWVRQAPGQALEWMGWITPFNGNTNYAQKFQDRVTITRDRSMNTAYMELSSLRSED 109
Cdd:cd04982    9 TREESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKED 88

                         90       100       110
                 ....*....|....*....|....*....|
gi 649152673 110 TAMYYCARGYSSSWDDaFDIWGQGTMVTVS 139
Cdd:cd04982   89 SATYYCAYWESGSGYY-IKVFGSGTKLIVT 117

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.

Pssm-ID: 409496 Cd Length: 99 Bit Score: 66.33 E-value: 2.39e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRDGFFGNprKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTdqvqAEAKESGPTTYKVTSTLTIKESDW 329
Cdd:cd07699    1 APSVTIFPPSSEELSSG--KATLVCLINKFYPGFATVTWKVDGSTVSSGVTT----SKTEQQSDNTYSMSSYLTLSSSDW 74

                         90
                 ....*....|....*.
gi 649152673 330 LSQSMFTCRVDHRGLT 345
Cdd:cd07699   75 NKHKVYTCEVTHEGLS 90

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: 65.56 E-value: 5.16e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  23 LVQSGAEVKKTGSSVKVSCKASGYTFTYRYLHWVRQAPGQALewmgwITPFNGNTNYAQKFQDRVTITRDRsmNTAYMEL 102
Cdd:cd04984    2 LTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAP-----RYLIYEDKHRPSGIPDRFSGSKSG--NTASLTI 74

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 649152673 103 SSLRSEDTAMYYCARGYSSSWddafdIWGQGTMVTV 138
Cdd:cd04984   75 SGAQTEDEADYYCQVWDSNSY-----VFGGGTKLTV 105

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: 64.51 E-value: 1.35e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  22 QLVQSGAEVKKTGSSVKVSCKASGYTFTYRYLHWVRQAPGQALEWMGWItpfngNTNYAQKFQDRVTITRDRSMNTAYME 101
Cdd:cd16095    3 QLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSL-----DHISTKVSEDRITSSREDTNSQIFLQ 77

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 649152673 102 LSSLRSEDTAMYYCAR--GYSSSWDDAfdIWGQGTMVTV 138
Cdd:cd16095   78 IKGLGLRDSGQYHCARrvGYGDDTDKL--IFGPGTDVIV 114

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: 63.24 E-value: 2.14e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 145 APTLFPLVSCENSpSDTSSVAVGCLAQDFLPDSITFSWkyKNNSDISSTRGFPSVLR-GGKYAATSQVLLPSKDVMQGTd 223
Cdd:cd21817    1 APSVFPLAPCCKS-TNGSSVTLGCLVTGYFPEPVTVTW--NSGSLTSGVKTFPAVLQsSGLYTTSSQVTVPSSSWGSQT- 76

                         90
                 ....*....|
gi 649152673 224 ehVVCKVQHP 233
Cdd:cd21817   77 --FTCNVEHK 84

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: 62.86 E-value: 3.87e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 468 RPDVYLLPPAREQLNlRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyVTSAPmPEPQAPGRYFAHSILTVSEEEWNT 547
Cdd:cd07699    1 APSVTIFPPSSEELS-SGKATLVCLINKFYPGFATVTWKVDGSTVSSG--VTTSK-TEQQSDNTYSMSSYLTLSSSDWNK 76

                         90
                 ....*....|...
gi 649152673 548 GETYTCVVAHEAL 560
Cdd:cd07699   77 HKVYTCEVTHEGL 89

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: 61.53 E-value: 1.32e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  30 VKKTGSSVKVSC-KASGYTFTYrylhWVRQAPGQALEWMgwITPFNGNTNYAQKF-QDRVTITRdRSMNTAYMELSSLRS 107
Cdd:cd05899    9 IKRRGQSVTLRCsQKSGHDNMY----WYRQDPGKGLQLL--FYSYGGGLNEEGDLpGDRFSASR-PSLTRSSLTIKSAEP 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 649152673 108 EDTAMYYCARGYSSSWDDAFdiWGQGTMVTV 138
Cdd:cd05899   82 EDSAVYLCASSLGGGADEAY--FGPGTRLTV 110

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: 60.75 E-value: 2.68e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  34 GSSVKVSCKASgyTFTYRYLHWVRQAPGQALEWMgwitpFNGNTNYAQKFQDRVTITRDRSMNTAYMELSSLRSEDTAMY 113
Cdd:cd04983   13 GENVTLNCNYS--TSTFYYLFWYRQYPGQGPQFL-----IYISSDSGNKKKGRFSATLDKSRKSSSLHISAAQLSDSAVY 85

                         90       100
                 ....*....|....*....|....*
gi 649152673 114 YCARGYSSSWDDAfdIWGQGTMVTV 138
Cdd:cd04983   86 FCALSESGGTGKL--TFGKGTRLTV 108

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: 59.76 E-value: 4.71e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 471 VYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQplSPEKYVTSApMPEPQAPGRYFAHSILTVSEEEWNTGET 550
Cdd:cd16084    2 VYLLTPAVQDLWLRDKATFTCFVVGSDLKDAHLTWEVAGK--VPTGGVEEG-LLERHSNGSQSQHSRLTLPRSLWNAGTS 78

                         90
                 ....*....|.
gi 649152673 551 YTCVVAHEALP 561
Cdd:cd16084   79 VTCTLNHPSLP 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: 59.32 E-value: 6.12e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 368 PPSFASIFLTKSTKLTCLVTDLTTYDSVTISWTRQNGEAVKTHTNISESHPNATFSAVGEasICEDDWNSGERFTCTVTH 447
Cdd:cd04986    8 RPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLP--GCAEPWNSGDTFSCTVTH 85

                         90
                 ....*....|.
gi 649152673 448 TDLPSPLKQTI 458
Cdd:cd04986   86 PESKGTLTATI 96

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.

Pssm-ID: 409593 Cd Length: 97 Bit Score: 58.78 E-value: 8.54e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 482 NLRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyvTSAPmPEPQAPG--RYFAHSILTVSEEewnTGETYTCVVAHEA 559
Cdd:cd21002   15 NTREPVMLACHVWGFYPADVTITWLKNGDPVAPH---SSAP-KTAQPNGdwTYQTQVTLAVTPS---PGDTYTCSVQHAS 87


                 ..
gi 649152673 560 LP 561
Cdd:cd21002   88 LP 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: 58.40 E-value: 9.66e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPR-DGffgnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESD 328
Cdd:cd07698    2 PPKVHVTHHPRsDG------ESTLRCWALGFYPAEITLTWQRDGED----QTQDMELVETRPNGDGTFQKWAAVVVPSGE 71

                         90
                 ....*....|....*..
gi 649152673 329 WLSqsmFTCRVDHRGLT 345
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: 57.85 E-value: 1.66e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 363 RVFAIPPSfASIFLTKSTKLTCLVTDLTtYDSVTISWTRQNGEAVKTHTNISESHPNA-TFSAVGEASICEDDWNSGERF 441
Cdd:cd00098    1 TVTLLPPS-PEEKGGGKVTLVCLVSGFY-PKDITVTWLKNGVPLTSGVSTSSPVEPNDgTYSVTSSLTVPPSDWDEGATY 78

                         90
                 ....*....|....*..
gi 649152673 442 TCTVTHTDLPSPLKQTI 458
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: 56.70 E-value: 5.05e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 147 TLFPLVSCEnSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISS-TRGFPSVLRGGKYAATSQVLLPSKDVMQGTdeH 225
Cdd:cd00098    1 TVTLLPPSP-EEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGvSTSSPVEPNDGTYSVTSSLTVPPSDWDEGA--T 77

                         90
                 ....*....|..
gi 649152673 226 VVCKVQHPNGNK 237
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: 1.02e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 468 RPDVYLlppAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEkyvTSAPMPEPQAPGRYFAHSILTVSEEEwnt 547
Cdd:cd21029    2 KPRVRL---SSRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDG---TQSGGILPNHDGTYQLRKTLDIAPGE--- 72

                         90       100
                 ....*....|....*....|
gi 649152673 548 GETYTCVVAHEALPNRVTER 567
Cdd:cd21029   73 GAGYSCRVDHSSLKQDLIVY 92

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: 53.92 E-value: 4.96e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 468 RPDVYLLPPAREQLNLRESATITCLVTGF-SPADVFVQWmqrgQPLSPEKYVTSAPmpEPQAPGRYFAHSILTVSEEEWN 546
Cdd:cd04986    1 QPRLSLQRPALEDLLLGSNASLTCTLSGLkDPEGATFTW----EPSGGKEAIQGPP--ERDSCGCYSVSSVLPGCAEPWN 74

                         90
                 ....*....|....*....
gi 649152673 547 TGETYTCVVAHEALPNRVT 565
Cdd:cd04986   75 SGDTFSCTVTHPESKGTLT 93

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: 9.18e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPArEQLNLRESATITCLVTGFSPADVFVQWmQRGQPLSPEKYVTSAPmPEPQAPGRYFAHSILTVSEEEWNTG 548
Cdd:cd04985    2 PTVFPLQSA-TKSQSNGPVALGCLISDYFPESITVSW-QKNTNSITSGFTRTFP-VVLRSGGDYSCSSQLTVPLQEWNSG 78

                         90
                 ....*....|.
gi 649152673 549 ETYTCVVAHEA 559
Cdd:cd04985   79 EVYKCQVQHSA 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: 53.11 E-value: 9.46e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKVTSTL--TIKES 327
Cdd:cd05766    3 QPSVKVS-PTKTGPLEHP--NLLVCSVTGFYPAEIEVKWFRNGQEETAGV----VSTELIPNGDWTFQILVMLetTPRRG 75

                         90
                 ....*....|....*...
gi 649152673 328 DwlsqsMFTCRVDHRGLT 345
Cdd:cd05766   76 D-----VYTCQVEHSSLQ 88

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: 1.78e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 649152673 486 SATITCLVTGFSPADVFVQWMQRGQPLS-PEKYVTsapmPEPQAPGRYFAHSILTVSEEEWntgETYTCVVAHEALP 561
Cdd:cd07698   16 ESTLRCWALGFYPAEITLTWQRDGEDQTqDMELVE----TRPNGDGTFQKWAAVVVPSGEE---QRYTCHVQHEGLP 85

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: 51.08 E-value: 3.92e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRdgffGNPRKS-KLICQATGFSPRQIQVSWLREGKQVGSGvttDQVQAEAKESGPTTYKVTSTLTIKESD 328
Cdd:cd21002    3 PPSVRVAPTTP----FNTREPvMLACHVWGFYPADVTITWLKNGDPVAPH---SSAPKTAQPNGDWTYQTQVTLAVTPSP 75

                         90
                 ....*....|....*.
gi 649152673 329 WlsqSMFTCRVDHRGL 344
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: 4.49e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 485 ESATITCLVTGFSPADVFVQWMQR-----GQPLSPEKYVTSAPmpEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEA 559
Cdd:cd05771   15 LPQTLSCHIAGYYPLDVDVEWLREepggsESQVSRDGVSLSSH--RQSVDGTYSISSYLTLEPGTENRGATYTCRVTHVS 92


                 ....*..
gi 649152673 560 LPNRVTE 566
Cdd:cd05771   93 LEEPLSV 99

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: 50.99 E-value: 5.72e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 145 APTLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSdiSSTRGFPSVLRGGKYAAT-SQVLLPSKDVMQGTD 223
Cdd:cd16092    1 APDVFPIISGCRHPKDNSPVVLACLITGYHPTSVTVTWYMGTQS--QPQRTFPEIQRRDSYYMTsSQLSTPLQQWRQGEY 78

                         90
                 ....*....|....*...
gi 649152673 224 EhvvCKVQHPNGNKEKNV 241
Cdd:cd16092   79 K---CVVQHTASKSKKEI 93

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: 50.84 E-value: 9.19e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSpeKYVTSAPMPEPQAPGRYFAHSILTVSEEEW-NT 547
Cdd:cd05769    3 PTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVK--DGVATDPQALRENTSTYSLSSRLRVSATEWfNP 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 649152673 548 GETYTCVVAHEalpNRVTERTVDKSTEGEVS 578
Cdd:cd05769   81 RNTFTCIVKFY---GGTDTDTWTQGIAGPVT 108

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: 49.64 E-value: 1.37e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPParEQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApMPEPQapgryFAHSILTVSEEEWNTG 548
Cdd:cd05766    4 PSVKVSPT--KTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTEL-IPNGD-----WTFQILVMLETTPRRG 75

                         90
                 ....*....|....*....
gi 649152673 549 ETYTCVVAHEALPNRVTER 567
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: 2.35e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLRE-GKQVGSGVTTDQVQ-AEAKESGPTTYKVTSTLTIKESD 328
Cdd:cd05771    1 PRVRLS-PKNLVKPDLP--QTLSCHIAGYYPLDVDVEWLREePGGSESQVSRDGVSlSSHRQSVDGTYSISSYLTLEPGT 77

                         90
                 ....*....|....*.
gi 649152673 329 WLSQSMFTCRVDHRGL 344
Cdd:cd05771   78 ENRGATYTCRVTHVSL 93

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 48.02 E-value: 3.52e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  364 VFAIPPSFASifLTKSTKLTCLVTDLttY-DSVTISWTRqNGEAVKTHTNISESHPNA--TFSAVGEASICEDDWNSGER 440
Cdd:pfam07654   1 VYVFPPSPEE--LGKPNTLTCLVTGF--YpPDITVTWLK-NGQEVTEGVKTTPPSPNSdwTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 649152673  441 FTCTVTHTDL 450
Cdd:pfam07654  76 YTCRVEHEGL 85

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of epsilon and gamma chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

Pssm-ID: 409622 Cd Length: 94 Bit Score: 48.21 E-value: 3.76e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPAREQLNLrESATITCLVTGFSPADVFVQWmqrgqplSPEKyVTSAPMPEP---QAPGRYFAHSILTVSEEEW 545
Cdd:cd21817    2 PSVFPLAPCCKSTNG-SSVTLGCLVTGYFPEPVTVTW-------NSGS-LTSGVKTFPavlQSSGLYTTSSQVTVPSSSW 72

                         90       100
                 ....*....|....*....|..
gi 649152673 546 NTgETYTCVVAHEALPNRVTER 567
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: 3.83e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 489 ITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSAPMPEPQAPgRYFAHSILTVSEEEWNTGETYTCVVAHE 558
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: 48.47 E-value: 4.80e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 649152673 272 LICQATGFSPRQIQVSWLREGKQVGSGVTTdqVQAEAKESgptTYKVTSTLTIKESDWLSQSMFTCRVDHRGLT 345
Cdd:cd05772   22 FTCKSHGFSPRDITLKWFKNGNELSALQTT--VFPEGDSV---SYSVSSTVQVVLTKDDVHSQLTCEVAHVTLQ 90

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: 48.16 E-value: 6.17e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  22 QLVQSGAEVK-KTGSSVKVSCKASGyTFTYRYLHWVRQAPGQALEWMgwitpFNGNTNYAQKFQDRVTITRDRSMNTayM 100
Cdd:cd04980    2 VMTQSPASLSvSPGERVTISCKASQ-SISSNYLAWYQQKPGQAPKLL-----IYYASTLHSGVPSRFSGSGSGTDFT--L 73

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 649152673 101 ELSSLRSEDTAMYYCARGYSSSWddafdIWGQGTMVTV 138
Cdd:cd04980   74 TISSVEPEDAAVYYCQQGYTFPY-----TFGGGTKLEI 106

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: 47.84 E-value: 6.24e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 364 VFAIPPSFASIFLTKSTkLTCLVTDLTTYDsVTISW-----TRQNGeaVKTHTNISEshPNATFSAVGEASICEDDWNSG 438
Cdd:cd07699    4 VTIFPPSSEELSSGKAT-LVCLINKFYPGF-ATVTWkvdgsTVSSG--VTTSKTEQQ--SDNTYSMSSYLTLSSSDWNKH 77

                         90       100
                 ....*....|....*....|..
gi 649152673 439 ERFTCTVTHTDLPSPLKQTISR 460
Cdd:cd07699   78 KVYTCEVTHEGLSSTITKSFNR 99

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: 47.11 E-value: 7.98e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673    30 VKKTGSSVKVSCKASGytFTYRYLHWVRQAPgqalEWMGwitpfngntnyaqkFQDRVTITRDRsmNTAYMELSSLRSED 109
Cdd:smart00410   5 TVKEGESVTLSCEASG--SPPPEVTWYKQGG----KLLA--------------ESGRFSVSRSG--STSTLTISNVTPED 62

                           90       100
                   ....*....|....*....|....*....
gi 649152673   110 TAMYYCARgysssWDDAFDIWGqGTMVTV 138
Cdd:smart00410  63 SGTYTCAA-----TNSSGSASS-GTTLTV 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: 47.45 E-value: 1.01e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673   33 TGSSVKVSCKASGY-TFTYRYLHWVRQAPGQALEWMgwITPFNGNTNYaQKFQDRVTITRDRSMNTAYMELSSLRSEDTA 111
Cdd:pfam07686  10 LGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFL--IAYYSNGSEE-GVKKGRFSGRGDPSNGDGSLTIQNLTLSDSG 86

                          90       100
                  ....*....|....*....|....*..
gi 649152673  112 MYYCARGYSSSWddafdIWGQGTMVTV 138
Cdd:pfam07686  87 TYTCAVIPSGEG-----VFGKGTRLTV 108

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: 45.87 E-value: 2.81e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 364 VFAIPPSFASIFLTKSTKLTCLVTDLTTyDSVTISWTRQNGEA-VKTHTNISESHPNATFSAVGEASICEDDWNSGERFT 442
Cdd:cd05847    3 VQILHSSCASTLTSETIQLLCLISGYTP-STIEVEWLVDGQVAtLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTYT 81


                 ....*
gi 649152673 443 CTVTH 447
Cdd:cd05847   82 CKVTH 86

Immunoglobulin C1-set domain;

Pssm-ID: 462221 Cd Length: 85 Bit Score: 44.93 E-value: 5.12e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  147 TLFPLVSCENSpsdtSSVAVGCLAQDFLPDSITFSWkYKNNSDISS-TRGFPSVLRG-GKYAATSQVLLPSKDVMQGtdE 224
Cdd:pfam07654   2 YVFPPSPEELG----KPNTLTCLVTGFYPPDITVTW-LKNGQEVTEgVKTTPPSPNSdWTYQLSSYLTVTPSDWESG--D 74


                  ....*....
gi 649152673  225 HVVCKVQHP 233
Cdd:pfam07654  75 EYTCRVEHE 83

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: 45.14 E-value: 5.70e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFVP-PRDGFFgnpRKS-KLICQATGF-SPRQIQVSWLREGkqvGSGVTTDQVQAEAKESGptTYKVTSTLTIKES 327
Cdd:cd07696    1 VSVFLIPPsPKDLFL---TKSaKVTCLVVDLtSIEEVNVTWSRED---GNEVLASTTNPEKHYNA--TLSVVSTLTVCAD 72

                         90
                 ....*....|....*..
gi 649152673 328 DWLSQSMFTCRVDHRGL 344
Cdd:cd07696   73 DWDNGKTFKCKVTHPDL 89

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

Pssm-ID: 409497 Cd Length: 116 Bit Score: 45.52 E-value: 5.94e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  32 KTGSSVKVSCKASGYTFTYRyLHWVR--QAPG--QALEWMGWITPfNGNTNYAQKF-QDRVTITRDRSMNTAYMELSSLR 106
Cdd:cd07700   11 QTNQTVKMSCEAKTSPKNTR-IYWLRqrQAPSkdSHFEFLASWDP-SKGIVYGEGVdQEKLIILSDSDSSRYILSLMSVK 88

                         90       100       110
                 ....*....|....*....|....*....|..
gi 649152673 107 SEDTAMYYCARGYSSSWddafdIWGQGTMVTV 138
Cdd:cd07700   89 PEDSGTYFCMTVGSPEL-----IFGTGTKLSV 115

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: 44.61 E-value: 9.73e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFvpprdgffgnPRKSK-------LICQATGFSPRQIQVSWLREGKQVGSG-VTTDQVQaeakeSGPTTYKvtsTL 322
Cdd:cd21000    4 PKVTVY----------PAKTQplqhhnlLVCSVNGFYPGSIEVRWFRNGQEEKAGvVSTGLIQ-----NGDWTFQ---TL 65

                         90       100
                 ....*....|....*....|...
gi 649152673 323 TIKESDWLSQSMFTCRVDHRGLT 345
Cdd:cd21000   66 VMLETVPRSGEVYTCQVEHPSVT 88

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

Pssm-ID: 409503 Cd Length: 112 Bit Score: 44.82 E-value: 1.04e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  19 SQMQLVQSGAEvkktGSSVKVSCKASgYTFTYRYLHWVRQAPGQALEWMgwitpFNGNTNYAQKFQDRVTITRDRSMNTA 98
Cdd:cd07706    3 TQAQPDVSVQV----GEEVTLNCRYE-TSWTNYYLFWYKQLPSGEMTFL-----IRQDSSEQNAKSGRYSVNFQKAQKSI 72

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 649152673  99 YMELSSLRSEDTAMYYCArgYSSSWDDAFDIWGQGTMVTV 138
Cdd:cd07706   73 SLTISALQLEDSAKYFCA--LSLPYDTDKLIFGKGTRLTV 110

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: 43.86 E-value: 1.31e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPL--SPEKYvtsapmPEPQAPGRYFAHSILTVSEEEWNTGETYTCVVAHEA 559
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: 1.62e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 274 CQATGFSPRQIQVSWLREGKQvgSGVTTDQVQAEAKESgptTYKVTSTLTIKESDWLSQSMFTCRVDHRG 343
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: 43.83 E-value: 1.63e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTtdqvqaeakesgPTTYKVTSTLTIKESDW 329
Cdd:cd05767    2 PPEVTVF-PKSPVELGEP--NTLICFVDNFFPPVINVTWLRNGQPVTDGVS------------ETVFLPREDHSFRKFSY 66

                         90       100
                 ....*....|....*....|
gi 649152673 330 LS-----QSMFTCRVDHRGL 344
Cdd:cd05767   67 LPftpseGDIYDCRVEHWGL 86

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 43.07 E-value: 1.71e-05

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 649152673   382 LTCLVTDLttY-DSVTISWTRqNGEAVKTHTNISESHPNA--TFSAVGEASICEDDWNSGERFTCTVTHTDLPSP 453
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: 42.68 E-value: 3.40e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPpaREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntG 548
Cdd:cd05767    3 PEVTVFP--KSPVELGEPNTLICFVDNFFPPVINVTWLRNGQPVTDGVSETVF---LPREDHSFRKFSYLPFTPSE---G 74

                         90
                 ....*....|...
gi 649152673 549 ETYTCVVAHEALP 561
Cdd:cd05767   75 DIYDCRVEHWGLE 87

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: 3.74e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 649152673 272 LICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKvtsTLTIKESDWLSQSMFTCRVDHRGLT 345
Cdd:cd20998   25 LVCSVSDFYPGNIEVRWFRNGKEEKTGI----VSTGLVRNGDWTFQ---TLVMLETVPQSGEVYTCQVEHPSLT 91

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: 42.44 E-value: 4.33e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 475 PPAREQLNLRESATIT--CLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgET 550
Cdd:cd21015    5 PEAHVTLHPRPEGDVTlrCWALGFYPADITLTWQLNGEDLTQDMELVET---RPAGDGTFqkWASVVVPLGKE-----QN 76

                         90
                 ....*....|....*..
gi 649152673 551 YTCVVAHEALPNRVTER 567
Cdd:cd21015   77 YTCRVEHEGLPKPLSQR 93

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

Pssm-ID: 409625 Cd Length: 98 Bit Score: 42.45 E-value: 5.06e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 485 ESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEWntgetYTCVVAHEALPN 562
Cdd:cd21820   18 DEVTLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWAAVVVPLGKEQY-----YTCHVYHEGLPE 89


                 ....*
gi 649152673 563 RVTER 567
Cdd:cd21820   90 PLTLR 94

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: 42.41 E-value: 5.63e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 272 LICQATGFSPRQIQVSWLREGKQVGSGvttdqvqaeakesgpttykVTSTLTIKESDWLSQSM------------FTCRV 339
Cdd:cd21001   22 LVCSVTDFYPGQIKVRWFRNDQEETAG-------------------VVSTPLIRNGDWTFQILvmlemtpqrgdvYTCHV 82


                 ....*
gi 649152673 340 DHRGL 344
Cdd:cd21001   83 EHPSL 87

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: 42.11 E-value: 7.97e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 329
Cdd:cd21023    5 PPKAHVAHHPI-----SDHEATLRCWALGFYPAEITLTWQRDGEE----QTQDTELVETRPAGDGTFQKWAAVVVPPGE- 74

                         90
                 ....*....|....*
gi 649152673 330 lsQSMFTCRVDHRGL 344
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: 41.70 E-value: 8.35e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 258 PPRDGFFGNP---RKSKLICQATGFSPRQIQVSWlregKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDwlsQSM 334
Cdd:cd21024    5 PPKTHVTHHPisdHEATLRCWALGFYPAEITLTW----QQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGE---EQR 77

                         90
                 ....*....|
gi 649152673 335 FTCRVDHRGL 344
Cdd:cd21024   78 YTCHVQHEGL 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: 41.70 E-value: 9.57e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntGETYTCVVAHEALPNRVTE 566
Cdd:cd21024   20 ATLRCWALGFYPAEITLTWQQDGEGHTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPVTL 93


                 .
gi 649152673 567 R 567
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: 41.41 E-value: 1.02e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  474 LPPAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSapmpepqaPGRYFAHSILTVSEEEWNTGeTYTC 553
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIESLKVKHD--------NGRTTQSSLLISNVTKEDAG-TYTC 71


                  ....
gi 649152673  554 VVAH 557
Cdd:pfam00047  72 VVNN 75

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: 1.07e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgETYTCVVAHEALPNRVT 565
Cdd:cd21018   21 TLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWASVVVPLGKE-----QNYTCRVYHEGLPEPLT 92


                 ..
gi 649152673 566 ER 567
Cdd:cd21018   93 LR 94

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of delta chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

Pssm-ID: 319341 Cd Length: 96 Bit Score: 41.36 E-value: 1.27e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLPPAREQLNLRESATITCLVTGFSPADVFVQWMQrGQPLSPEKyvtsaPMPEPQAPGRYF-AHSILTVSEEEWNT 547
Cdd:cd16092    2 PDVFPIISGCRHPKDNSPVVLACLITGYHPTSVTVTWYM-GTQSQPQR-----TFPEIQRRDSYYmTSSQLSTPLQQWRQ 75

                         90
                 ....*....|..
gi 649152673 548 GEtYTCVVAHEA 559
Cdd:cd16092   76 GE-YKCVVQHTA 86

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: 41.29 E-value: 1.34e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRdgffgnPRKS-KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESd 328
Cdd:cd21015    4 PPEAHVTLHPR------PEGDvTLRCWALGFYPADITLTWQLNGED----LTQDMELVETRPAGDGTFQKWASVVVPLG- 72

                         90
                 ....*....|....*.
gi 649152673 329 wlSQSMFTCRVDHRGL 344
Cdd:cd21015   73 --KEQNYTCRVEHEGL 86

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: 1.41e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 265 GNPRKSKLICQATGFSPRQIQVSWLREGKQVGSGvttdqvQAEAKESGPTTYKVTSTLTIKESDwlsQSMFTCRVDHRGL 344
Cdd:cd21011   15 GSPGFSVLTCSAFSFYPPELQLRFLRNGLAAGSG------EGDFGPNGDGSFHAWSSLTVKSGD---EHHYRCVVQHAGL 85


                 .
gi 649152673 345 T 345
Cdd:cd21011   86 A 86

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: 41.34 E-value: 1.43e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 329
Cdd:cd21026    5 PPKTHVTHHPI-----SDHEATLRCWALGFYPAEITLTWQRDGED----QTQDTELVETRPAGDRTFQKWAAVVVPSGE- 74

                         90
                 ....*....|....*
gi 649152673 330 lsQSMFTCRVDHRGL 344
Cdd:cd21026   75 --EQRYTCHVQHEGL 87

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

Pssm-ID: 409605 Cd Length: 94 Bit Score: 40.89 E-value: 1.85e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 461 PKGVALHRPDVYllppareqlnlrESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSIL 538
Cdd:cd21014    5 PKAHVTHHPRSY------------GAVTLRCWALGFYPADITLTWQLNGEELTQDMELVET---RPAGDGTFqkWASVVV 69

                         90       100
                 ....*....|....*....|....*....
gi 649152673 539 TVSEEewntgETYTCVVAHEALPNRVTER 567
Cdd:cd21014   70 PLGKE-----QNYTCHVNHEGLPEPLTLR 93

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: 40.54 E-value: 2.22e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPEKYvtSAPMPEPQAPGRYFAHSILTVSEeewntGETYTCVVAHEAL 560
Cdd:cd05770   20 VLNCYVSGFHPPDIEIRLLKNGVKIEDVEQ--SDLSFSKDWTFYLLKYTEFTPTK-----GDEYACRVRHNTL 85

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.

Pssm-ID: 409374 Cd Length: 98 Bit Score: 40.27 E-value: 2.99e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 272 LICQATGFSPRQIQVSWlreGKQVGSGVTTDQVQAEAKESGPTTYKVTSTLTIKESDWLSQSMFTCRVDH 341
Cdd:cd04985   21 LGCLISDYFPESITVSW---QKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVYKCQVQH 87

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: 3.06e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 249 LPPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVttdqVQAEAKESGPTTYKVTSTL--TIKE 326
Cdd:cd21003    2 VQPKVNVS-PSKKGPLQHH--NLLVCHVTDFYPGNIQVRWFLNGQEETAGV----VSTNLIHNGDWTFQILVMLemTPQQ 74

                         90
                 ....*....|....*...
gi 649152673 327 SDwlsqsMFTCRVDHRGL 344
Cdd:cd21003   75 GD-----VYTCQVEHPSL 87

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: 40.10 E-value: 3.73e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPE-KYVTSAPMPEpqAPGRYFAHSILTVSEEewntgETYTCVVAHEALPNRVTE 566
Cdd:cd21013   20 TLRCWALGFYPADITLTWQLNGEELTQDmEFVETRPAGD--GTFQKWASVVVPLGKE-----QKYTCHVEHEGLPEPLTL 92


                 .
gi 649152673 567 R 567
Cdd:cd21013   93 R 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: 40.23 E-value: 3.90e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  34 GSSVKVSCKASGYTFTYRYLHWVRQAPGQALEWMgwitpFNGNTNYAQKFQDRVTITRDRSMNTAYMELSSLRSEDTAMY 113
Cdd:cd20988   13 GKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFI-----YREGGIYGPGFKDNFRGDIDSSNNLAVLKILEASERDEGSY 87

                         90       100
                 ....*....|....*....|....*..
gi 649152673 114 YCArGYSSSWDDAFD--IWGQGTMVTV 138
Cdd:cd20988   88 YCA-SDTPGGGREYDplIFGKGTYLTV 113

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: 39.81 E-value: 4.43e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 147 TLFPLVSCENSPSDTSSVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVLRGGKyaATSQVLLPSKdVMQGTDEHV 226
Cdd:cd21017    2 TVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGN--GTYQTWVATR-ICQGEEQRF 78

                         90
                 ....*....|....*.
gi 649152673 227 VCKVQHPNGNKEKNVP 242
Cdd:cd21017   79 TCYMEHSGNHSTHPVP 94

Immunoglobulin C-Type;

Pssm-ID: 214651 Cd Length: 75 Bit Score: 39.22 E-value: 4.48e-04

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 649152673   163 SVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL-RGGKYAATSQVLLPSKDVMQGtdEHVVCKVQHPN 234
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKnSDGTYFLSSYLTVPASTWESG--DVYTCQVTHEG 71

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: 5.19e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 485 ESATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEWntgetYTCVVAHEALPN 562
Cdd:cd21019   17 DKVTLRCWALGFYPADITLTWQLNGEELIQDMELVET---RPAGDGTFqkWASVVVPLGKEQY-----YTCHVYHQGLPE 88


                 ....*
gi 649152673 563 RVTER 567
Cdd:cd21019   89 PLTLR 93

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: 39.36 E-value: 6.86e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRDGFfgnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESDw 329
Cdd:cd21022    4 PPKTHVTHHPVFDY-----EATLRCWALGFYPAEIILTWQRDGED----QTQDVELVETRPAGDGTFQKWAAVVVPSGE- 73

                         90
                 ....*....|....*
gi 649152673 330 lsQSMFTCRVDHRGL 344
Cdd:cd21022   74 --EQRYTCHVQHEGL 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: 7.02e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 649152673 384 CLVTDLTTyDSVTISWTRQNgeavKTHTNISESHP----NATFSAVGEASICEDDWNSGERFTCTVTH 447
Cdd:cd21819   22 CLATDFLP-DSITFSWTDDN----NSLTTGVKTYPsvltGGTYTASSQLQVPESEWKSKENFYCKVEH 84

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: 7.54e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 475 PPAREQLNlrESATITCLVTGFSPADVFVQWMQRGQPLSPEKyVTSAPMPEPQApgrYFAHSILTVSEEEWNTGETYTCV 554
Cdd:cd05772   10 PSGRATPG--QTVSFTCKSHGFSPRDITLKWFKNGNELSALQ-TTVFPEGDSVS---YSVSSTVQVVLTKDDVHSQLTCE 83


                 ....*.
gi 649152673 555 VAHEAL 560
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: 38.96 E-value: 8.49e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 364 VFAIPPSFASIFLTKSTKLTCLVTDLTTYDSvTISWtrQNGEAVKT---HTNISESHPNATFSAVGEASICEDDWNSGER 440
Cdd:cd16084    2 VYLLTPAVQDLWLRDKATFTCFVVGSDLKDA-HLTW--EVAGKVPTggvEEGLLERHSNGSQSQHSRLTLPRSLWNAGTS 78

                         90
                 ....*....|.
gi 649152673 441 FTCTVTHTDLP 451
Cdd:cd16084   79 VTCTLNHPSLP 89

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: 38.93 E-value: 8.59e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPE-KYVTSAPMPEpqAPGRYFAHSILTVSEEewntgETYTCVVAHEALPNRVTE 566
Cdd:cd21016   21 TLRCWALGFYPADITLTWQKDGEELTQDmEFVETRPAGD--GTFQKWAAVVVPLGKE-----QSYTCHVYHEGLPEPLTL 93


                 .
gi 649152673 567 R 567
Cdd:cd21016   94 R 94

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.

Pssm-ID: 409599 Cd Length: 95 Bit Score: 38.77 E-value: 9.32e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESgpttYKVTSTLTIKESDwl 330
Cdd:cd21008    3 PEVTVF-PKSPVTLGQP--NTLICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKSDHS----FLKISYLTFLPSA-- 73

                         90
                 ....*....|....
gi 649152673 331 sQSMFTCRVDHRGL 344
Cdd:cd21008   74 -DDIYDCKVEHWGL 86

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: 38.59 E-value: 9.88e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEwntgeTYTCVVAHEALPNRVT 565
Cdd:cd21020   21 TLRCWALGFYPADITLTWQLNGEELTQEMELVET---RPAGDGTFqkWASVVVPLGKEQ-----KYTCHVEHEGLPEPLT 92


                 ..
gi 649152673 566 ER 567
Cdd:cd21020   93 LR 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: 38.63 E-value: 1.19e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 374 IFLTKSTKLTCLVTDLTTYDsVTISWTRQ---NGEAVKTHTNISES----HPNATFSAVGEASICEDDWNSGERFTCTVT 446
Cdd:cd05771   11 VKPDLPQTLSCHIAGYYPLD-VDVEWLREepgGSESQVSRDGVSLSshrqSVDGTYSISSYLTLEPGTENRGATYTCRVT 89


                 ....*...
gi 649152673 447 HTDLPSPL 454
Cdd:cd05771   90 HVSLEEPL 97

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: 1.36e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 374 IFLTKS------TKLTCLVTDLTTYDsVTISWtRQNGEAVKTHTNISESHPNA--TFSAVgeaSICEDDWNSGERFTCTV 445
Cdd:cd05766    8 VSPTKTgplehpNLLVCSVTGFYPAE-IEVKW-FRNGQEETAGVVSTELIPNGdwTFQIL---VMLETTPRRGDVYTCQV 82


                 ....*....
gi 649152673 446 THTDLPSPL 454
Cdd:cd05766   83 EHSSLQSPL 91

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: 38.26 E-value: 1.37e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVFVQWMQRGQPLSPE-KYVTSAPmpepqAPGRYFAH--SILTVSEEEwntgETYTCVVAHEALPNR 563
Cdd:cd21026   20 ATLRCWALGFYPAEITLTWQRDGEDQTQDtELVETRP-----AGDRTFQKwaAVVVPSGEE----QRYTCHVQHEGLPKP 90


                 ....
gi 649152673 564 VTER 567
Cdd:cd21026   91 LTLR 94

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

Pssm-ID: 400489 Cd Length: 89 Bit Score: 38.17 E-value: 1.43e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  256 FVPPRDGFFGNPRKSK-LICQATGFSPrQIQVSWLREGKQVGSGVTTDQVQAEakesgPTTYKVTSTLTIKESDWLSQSM 334
Cdd:pfam08205   2 TIEPPASLLEGEGPEVvATCSSAGGKP-APRITWYLDGKPLEAAETSSEQDPE-----SGLVTVTSELKLVPSRSDHGQS 75

                          90
                  ....*....|....
gi 649152673  335 FTCRVDHRGLTFQQ 348
Cdd:pfam08205  76 LTCQVSYGALRGSI 89

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: 1.55e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdw 329
Cdd:cd21820    5 PPKAHVTHHPR-----SEDEVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWAAVVVPLG-- 73

                         90
                 ....*....|....*
gi 649152673 330 lSQSMFTCRVDHRGL 344
Cdd:cd21820   74 -KEQYYTCHVYHEGL 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: 1.60e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 649152673 274 CQATGFSPRQIQVSWlregkqvGSGVTTDQVQA-EAKESGPTTYKVTSTLTIKESDWLSQsMFTCRVDH 341
Cdd:cd21817   23 CLVTGYFPEPVTVTW-------NSGSLTSGVKTfPAVLQSSGLYTTSSQVTVPSSSWGSQ-TFTCNVEH 83

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: 38.25 E-value: 1.63e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 649152673 485 ESATITCLVTGFSPADVFVQWMQRGQPlspekyVTSAPMPEPQAPG-RYFAHSILTVSEEEWNTGETYTCVVAH 557
Cdd:cd21818   16 DPVVIGCLVQGFFPEPVNVTWNYSGKG------GTARNFPAMLASGgRYTQSSQLTLPADQCPEGEAYKCSVQH 83

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: 38.16 E-value: 1.63e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 258 PPRDGFFGNPRKS---KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSM 334
Cdd:cd21016    5 PPKAHVTRHPRPEgdvTLRCWALGFYPADITLTWQKDGEE----LTQDMEFVETRPAGDGTFQKWAAVVVPLG---KEQS 77

                         90
                 ....*....|
gi 649152673 335 FTCRVDHRGL 344
Cdd:cd21016   78 YTCHVYHEGL 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: 37.80 E-value: 2.02e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSVFVPPRDgfFGnprKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdw 329
Cdd:cd21014    4 PPKAHVTHHPRS--YG---AVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWASVVVPLG-- 72

                         90
                 ....*....|....*
gi 649152673 330 lSQSMFTCRVDHRGL 344
Cdd:cd21014   73 -KEQNYTCHVNHEGL 86

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: 37.49 E-value: 3.08e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEewntgETYTCVVAHEALPNRV 564
Cdd:cd21023   20 ATLRCWALGFYPAEITLTWQRDGEEQTQDTELVET---RPAGDGTFqkWAAVVVPPGEE-----QRYTCHVQHEGLPQPL 91


                 ...
gi 649152673 565 TER 567
Cdd:cd21023   92 ILR 94

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: 3.19e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFVPPRdgffgNPRKSKLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwl 330
Cdd:cd21018    6 PKAHVTHHPR-----SKGEVTLRCWALGFYPADITLTWQLNGEE----LTQDMELVETRPAGDGTFQKWASVVVPLG--- 73

                         90
                 ....*....|....
gi 649152673 331 SQSMFTCRVDHRGL 344
Cdd:cd21018   74 KEQNYTCRVYHEGL 87

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: 37.48 E-value: 3.21e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntGETYTCVVAHEALPNRVTE 566
Cdd:cd21025   20 ATLRCWALGFYPAEITLTWQWDGEDQTQDTELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPLTL 93


                 .
gi 649152673 567 R 567
Cdd:cd21025   94 R 94

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

Pssm-ID: 409427 Cd Length: 94 Bit Score: 37.07 E-value: 3.35e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 249 LPPKVSVFV--PPRDGffgnpRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQvqaeAKESGPTTYKVTST-LTIK 325
Cdd:cd05770    1 STPKVQVYSrfPAENG-----KPNVLNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDL----SFSKDWTFYLLKYTeFTPT 71

                         90
                 ....*....|....*....
gi 649152673 326 ESDwlsqsMFTCRVDHRGL 344
Cdd:cd05770   72 KGD-----EYACRVRHNTL 85

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: 3.64e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 649152673 249 LPPKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVT 300
Cdd:cd21004    1 VPPRVTVL-PKSRVELGQP--NILICIVDNIFPPVINITWLRNGQTVTEGVA 49

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: 37.05 E-value: 3.82e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRYFAHSILTVSEEEwntGETYTCVVAHEALPNRVTE 566
Cdd:cd21022   19 ATLRCWALGFYPAEIILTWQRDGEDQTQDVELVET---RPAGDGTFQKWAAVVVPSGE---EQRYTCHVQHEGLPEPLML 92


                 .
gi 649152673 567 R 567
Cdd:cd21022   93 R 93

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: 37.02 E-value: 4.22e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 488 TITCLVTGFSPADVFVQWMQRGQPLSPEKYVTSApmpEPQAPGRY--FAHSILTVSEEEwntgeTYTCVVAHEALPNRVT 565
Cdd:cd21012   21 TLRCWALGFYPAHITLTWQLNGEELIQDTELVET---RPAGDGTFqkWAAVVVPSGEEQ-----KYTCHVYHEGLPEPLT 92


                 ..
gi 649152673 566 ER 567
Cdd:cd21012   93 LR 94

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: 37.02 E-value: 4.27e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 258 PPRDGFFGNPRKS---KLICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSM 334
Cdd:cd21013    4 PPKAHVTHHPRSEgyvTLRCWALGFYPADITLTWQLNGEE----LTQDMEFVETRPAGDGTFQKWASVVVPLG---KEQK 76

                         90
                 ....*....|
gi 649152673 335 FTCRVDHRGL 344
Cdd:cd21013   77 YTCHVEHEGL 86

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

Pssm-ID: 409416 Cd Length: 98 Bit Score: 37.05 E-value: 4.35e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 487 ATITCLVTGFSPADVfVQWMQRGQPLSPEKYVTSApMPEPQapgRYFAHSILTVSEEEWNTGETYTCVVAHEALPN-RVT 565
Cdd:cd05759   18 YNLTCRARGAKPAAE-IIWFRDGEQLEGAVYSKEL-LKDGK---RETTVSTLLITPSDLDTGRTFTCRARNEAIPNgKET 92


                 ....*
gi 649152673 566 ERTVD 570
Cdd:cd05759   93 SITLD 97

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: 36.92 E-value: 4.36e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 250 PPKVSV--FVPPRdgffgnpRKSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVqaeakESGPTTYKVTSTLTIKES 327
Cdd:cd21010    4 PPSVSVtsHVAPG-------KNRTLKCLAYDFYPRGISLHWTRAGKVQESESGGDVL-----PSGNGTYQSWVVVEVPPQ 71

                         90
                 ....*....|....*...
gi 649152673 328 DwlsQSMFTCRVDHRGLT 345
Cdd:cd21010   72 D---RAPYSCHVEHSSLA 86

Immunoglobulin domain; This family contains immunoglobulin-like domains.

Pssm-ID: 464046 [Multi-domain] Cd Length: 78 Bit Score: 36.39 E-value: 5.13e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673  474 LPPAREQLNLRESATITCLVTGFSPADvfVQWMQRGQPLSPEKYvtsapmpepQAPGRYFAHSILTVSEEEWNTGETYTC 553
Cdd:pfam13927   6 VSPSSVTVREGETVTLTCEATGSPPPT--ITWYKNGEPISSGST---------RSRSLSGSNSTLTISNVTRSDAGTYTC 74


                  ..
gi 649152673  554 VV 555
Cdd:pfam13927  75 VA 76

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: 36.59 E-value: 5.99e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 251 PKVSVFvPPRDGFFGNPrkSKLICQATGFSPRQIQVSWLREGKQVGSGVTTDQVQAEAKESgpttYKVTSTLTIKESDwl 330
Cdd:cd21006    3 PQATVF-PKSPVLLGQP--NTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHS----FHKLSYLTFIPSD-- 73

                         90
                 ....*....|....
gi 649152673 331 sQSMFTCRVDHRGL 344
Cdd:cd21006   74 -DDIYDCKVEHWGL 86

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: 36.66 E-value: 6.12e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 649152673 272 LICQATGFSPRQIQVSWLREGKQvgsgVTTDQVQAEAKESGPTTYKVTSTLTIKESdwlSQSMFTCRVDHRGL 344
Cdd:cd21020   22 LRCWALGFYPADITLTWQLNGEE----LTQEMELVETRPAGDGTFQKWASVVVPLG---KEQKYTCHVEHEGL 87

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: 6.49e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 469 PDVYLLppAREQLNLRESATITCLVTGFSPADVFVQWMQRGQPLSpEKYVTSAPMPEPQAPGRYFAHSILTVSEEEWntg 548
Cdd:cd21005    3 PEVTVL--SRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVT-EGVSETVFLPRDDHLFRKFHYLTFLPSTDDF--- 76

                         90
                 ....*....|..
gi 649152673 549 etYTCVVAHEAL 560
Cdd:cd21005   77 --YDCEVDHWGL 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: 36.59 E-value: 8.26e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 649152673 362 IRVFaiPPSFASIFLTKSTKLTCLVTDLttY-DSVTISWtRQNGEAVKT--HTNISESHPNA-TFSAVGEASICEDDW-N 436
Cdd:cd05769    5 VALF--PPSEAEIRNKRKATLVCLATGF--YpDHVSLSW-KVNGKEVKDgvATDPQALRENTsTYSLSSRLRVSATEWfN 79

                         90       100
                 ....*....|....*....|....*...
gi 649152673 437 SGERFTCTVTHTDLPSPLKQTISRPKGV 464
Cdd:cd05769   80 PRNTFTCIVKFYGGTDTDTWTQGIAGPV 107