NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|418206463|gb|AFX62604|]
View 

anti-Langerin 4C7 immunoglobulin heavy chain [synthetic construct]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 39-150 3.12e-55

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: 180.20  E-value: 3.12e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  39 AELVRPGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDTGYNQKFKGKAILTADKSSRTAYMELRSLTS 118
Cdd:cd04981    7 PGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQLNSLTS 86

                         90       100       110
                 ....*....|....*....|....*....|..
gi 418206463 119 EDSAVYYCTIPFYYSNYSPFAYWGQGTLVTVS 150
Cdd:cd04981   87 EDTAVYYCARGLGGYGYSYFDYWGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 156-248 1.27e-52

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


:

Pssm-ID: 409622  Cd Length: 94  Bit Score: 172.63  E-value: 1.27e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQ-SGLYTLSSSVTVTSNTWPSQTITCN 234
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQsSGLYTTSSQVTVPSSSWGSQTFTCN 80

                         90
                 ....*....|....
gi 418206463 235 VAHPASSTKVDKKI 248
Cdd:cd21817   81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 383-484 3.48e-43

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: 148.25  E-value: 3.48e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMTKKE-FSLTCMITGFLPAEIAVDWTSNGRT--EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSL 459
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                         90       100
                 ....*....|....*....|....*
gi 418206463 460 FACSVVHEGLHNHLTTKTISRSLGK 484
Cdd:cd05768   81 FSCVVGHEALPLQFTQKSIDKSPGK 105
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 275-374 9.56e-29

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


The actual alignment was detected with superfamily member cd07696:

Pssm-ID: 472250  Cd Length: 98  Bit Score: 109.08  E-value: 9.56e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDVLMiSLSPMVTCVVVDVSEDDpDVQISWFV-NNVEVHTAQTQThREDYNSTLRVVSALPIQHQDWMSG 353
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLTSIE-EVNVTWSReDGNEVLASTTNP-EKHYNATLSVVSTLTVCADDWDNG 77

                         90       100
                 ....*....|....*....|.
gi 418206463 354 KEFKCKVNNRALPSPIEKTIS 374
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 39-150 3.12e-55

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: 180.20  E-value: 3.12e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  39 AELVRPGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDTGYNQKFKGKAILTADKSSRTAYMELRSLTS 118
Cdd:cd04981    7 PGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQLNSLTS 86

                         90       100       110
                 ....*....|....*....|....*....|..
gi 418206463 119 EDSAVYYCTIPFYYSNYSPFAYWGQGTLVTVS 150
Cdd:cd04981   87 EDTAVYYCARGLGGYGYSYFDYWGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 156-248 1.27e-52

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


Pssm-ID: 409622  Cd Length: 94  Bit Score: 172.63  E-value: 1.27e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQ-SGLYTLSSSVTVTSNTWPSQTITCN 234
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQsSGLYTTSSQVTVPSSSWGSQTFTCN 80

                         90
                 ....*....|....
gi 418206463 235 VAHPASSTKVDKKI 248
Cdd:cd21817   81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 383-484 3.48e-43

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: 148.25  E-value: 3.48e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMTKKE-FSLTCMITGFLPAEIAVDWTSNGRT--EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSL 459
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                         90       100
                 ....*....|....*....|....*
gi 418206463 460 FACSVVHEGLHNHLTTKTISRSLGK 484
Cdd:cd05768   81 FSCVVGHEALPLQFTQKSIDKSPGK 105
C1-set pfam07654
Immunoglobulin C1-set domain;
385-469 4.88e-29

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 109.26  E-value: 4.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  385 VYVLPPPAEEMTKKeFSLTCMITGFLPAEIAVDWTSNGRTEQN-YKNTATVLDSDGSYFMYSKLRVQKSTWERGSLFACS 463
Cdd:pfam07654   1 VYVFPPSPEELGKP-NTLTCLVTGFYPPDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 418206463  464 VVHEGL 469
Cdd:pfam07654  80 VEHEGL 85
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 275-374 9.56e-29

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: 109.08  E-value: 9.56e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDVLMiSLSPMVTCVVVDVSEDDpDVQISWFV-NNVEVHTAQTQThREDYNSTLRVVSALPIQHQDWMSG 353
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLTSIE-EVNVTWSReDGNEVLASTTNP-EKHYNATLSVVSTLTVCADDWDNG 77

                         90       100
                 ....*....|....*....|.
gi 418206463 354 KEFKCKVNNRALPSPIEKTIS 374
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
IGc1 smart00407
Immunoglobulin C-Type;
401-472 2.90e-27

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 104.32  E-value: 2.90e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 418206463   401 SLTCMITGFLPAEIAVDWTSNGR-TEQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSLFACSVVHEGLHNH 472
Cdd:smart00407   3 TLVCLVSGFYPPDITVTWLRNGQeVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IGv smart00406
Immunoglobulin V-Type;
47-126 1.37e-22

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 91.29  E-value: 1.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463    47 SVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPEtGDTGYNQKFKGKAILTADKSSRTAYMELRSLTSEDSAVYYC 126
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSN-GSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
C1-set pfam07654
Immunoglobulin C1-set domain;
159-240 2.10e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.60  E-value: 2.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  159 VYPLAPVCGGTtGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQS-GLYTLSSSVTVTSNTWPS-QTITCN 234
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWlkNGQEVTEGVKTTPPSPNSdWTYQLSSYLTVTPSDWESgDEYTCR 79


                  ....*.
gi 418206463  235 VAHPAS 240
Cdd:pfam07654  80 VEHEGL 85
C1-set pfam07654
Immunoglobulin C1-set domain;
277-365 2.55e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.60  E-value: 2.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  277 VFIFPPKIKDvlmISLSPMVTCVVVDVSEddPDVQISWFVNNVEVHT-AQTQTHREDYNSTLRVVSALPIQHQDWMSGKE 355
Cdd:pfam07654   1 VYVFPPSPEE---LGKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 418206463  356 FKCKVNNRAL 365
Cdd:pfam07654  76 YTCRVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
173-241 7.38e-13

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 63.49  E-value: 7.38e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 418206463   173 SVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQS-GLYTLSSSVTVTSNTW-PSQTITCNVAHPASS 241
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWlrNGQEVTEGVSTTDPLKNSdGTYFLSSYLTVPASTWeSGDVYTCQVTHEGLK 73
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 45-149 1.02e-07

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: 50.15  E-value: 1.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463   45 GASVTLSCKASGYTFIDH-DMHWVQQTPVYGLEWIGAIdpetGDTGYNQKFKGKAI-LTADKSSRTAYMELRSLTSEDSA 122
Cdd:pfam07686  11 GGSVTLPCTYSSSMSEAStSVYWYRQPPGKGPTFLIAY----YSNGSEEGVKKGRFsGRGDPSNGDGSLTIQNLTLSDSG 86

                          90       100
                  ....*....|....*....|....*..
gi 418206463  123 VYYCTIpfyysNYSPFAYWGQGTLVTV 149
Cdd:pfam07686  87 TYTCAV-----IPSGEGVFGKGTRLTV 108
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 39-150 3.12e-55

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: 180.20  E-value: 3.12e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  39 AELVRPGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDTGYNQKFKGKAILTADKSSRTAYMELRSLTS 118
Cdd:cd04981    7 PGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQLNSLTS 86

                         90       100       110
                 ....*....|....*....|....*....|..
gi 418206463 119 EDSAVYYCTIPFYYSNYSPFAYWGQGTLVTVS 150
Cdd:cd04981   87 EDTAVYYCARGLGGYGYSYFDYWGQGTTVTVS 118
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 156-248 1.27e-52

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


Pssm-ID: 409622  Cd Length: 94  Bit Score: 172.63  E-value: 1.27e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQ-SGLYTLSSSVTVTSNTWPSQTITCN 234
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGSLTSGVKTFPAVLQsSGLYTTSSQVTVPSSSWGSQTFTCN 80

                         90
                 ....*....|....
gi 418206463 235 VAHPASSTKVDKKI 248
Cdd:cd21817   81 VEHKPSSTKVDKKI 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 383-484 3.48e-43

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: 148.25  E-value: 3.48e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMTKKE-FSLTCMITGFLPAEIAVDWTSNGRT--EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSL 459
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                         90       100
                 ....*....|....*....|....*
gi 418206463 460 FACSVVHEGLHNHLTTKTISRSLGK 484
Cdd:cd05768   81 FSCVVGHEALPLQFTQKSIDKSPGK 105
C1-set pfam07654
Immunoglobulin C1-set domain;
385-469 4.88e-29

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 109.26  E-value: 4.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  385 VYVLPPPAEEMTKKeFSLTCMITGFLPAEIAVDWTSNGRTEQN-YKNTATVLDSDGSYFMYSKLRVQKSTWERGSLFACS 463
Cdd:pfam07654   1 VYVFPPSPEELGKP-NTLTCLVTGFYPPDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 418206463  464 VVHEGL 469
Cdd:pfam07654  80 VEHEGL 85
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 275-374 9.56e-29

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: 109.08  E-value: 9.56e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDVLMiSLSPMVTCVVVDVSEDDpDVQISWFV-NNVEVHTAQTQThREDYNSTLRVVSALPIQHQDWMSG 353
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLTSIE-EVNVTWSReDGNEVLASTTNP-EKHYNATLSVVSTLTVCADDWDNG 77

                         90       100
                 ....*....|....*....|.
gi 418206463 354 KEFKCKVNNRALPSPIEKTIS 374
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
IGc1 smart00407
Immunoglobulin C-Type;
401-472 2.90e-27

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 104.32  E-value: 2.90e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 418206463   401 SLTCMITGFLPAEIAVDWTSNGR-TEQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSLFACSVVHEGLHNH 472
Cdd:smart00407   3 TLVCLVSGFYPPDITVTWLRNGQeVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 156-248 2.86e-25

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: 99.59  E-value: 2.86e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTW---NSGSLSSGVHTFPALLQS-GLYTLSSSVTVTSNTWPS-QT 230
Cdd:cd04985    1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqknTNSITSGFTRTFPVVLRSgGDYSCSSQLTVPLQEWNSgEV 80

                         90
                 ....*....|....*...
gi 418206463 231 ITCNVAHPASSTKVDKKI 248
Cdd:cd04985   81 YKCQVQHSASNSKQEKDV 98
IGv smart00406
Immunoglobulin V-Type;
47-126 1.37e-22

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 91.29  E-value: 1.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463    47 SVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPEtGDTGYNQKFKGKAILTADKSSRTAYMELRSLTSEDSAVYYC 126
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSN-GSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 156-245 5.07e-22

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: 90.08  E-value: 5.07e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPvCGGTTGSSVTLGCLVKGYFPEPVTLTWNSG--SLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQT-IT 232
Cdd:cd21819    1 APTLFPLVS-CGSSTSDPVTVGCLATDFLPDSITFSWTDDnnSLTTGVKTYPSVLTGGTYTASSQLQVPESEWKSKEnFY 79

                         90
                 ....*....|...
gi 418206463 233 CNVAHPASSTKVD 245
Cdd:cd21819   80 CKVEHPGGNKEVP 92
C1-set pfam07654
Immunoglobulin C1-set domain;
159-240 2.10e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.60  E-value: 2.10e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  159 VYPLAPVCGGTtGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQS-GLYTLSSSVTVTSNTWPS-QTITCN 234
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWlkNGQEVTEGVKTTPPSPNSdWTYQLSSYLTVTPSDWESgDEYTCR 79


                  ....*.
gi 418206463  235 VAHPAS 240
Cdd:pfam07654  80 VEHEGL 85
C1-set pfam07654
Immunoglobulin C1-set domain;
277-365 2.55e-18

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 79.60  E-value: 2.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  277 VFIFPPKIKDvlmISLSPMVTCVVVDVSEddPDVQISWFVNNVEVHT-AQTQTHREDYNSTLRVVSALPIQHQDWMSGKE 355
Cdd:pfam07654   1 VYVFPPSPEE---LGKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75

                          90
                  ....*....|
gi 418206463  356 FKCKVNNRAL 365
Cdd:pfam07654  76 YTCRVEHEGL 85
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 384-469 2.36e-17

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 77.11  E-value: 2.36e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 384 QVYVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDWTSNG-RTEQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSLFAC 462
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGvPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80


                 ....*..
gi 418206463 463 SVVHEGL 469
Cdd:cd00098   81 VVTHESL 87
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 157-245 9.00e-17

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


Pssm-ID: 409623  Cd Length: 94  Bit Score: 75.62  E-value: 9.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 157 PSVYPLApVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSG-LYTLSSSVTVTSNTWP-SQTITCN 234
Cdd:cd21818    2 PTVFPLS-LCPSLSSDPVVIGCLVQGFFPEPVNVTWNYSGKGGTARNFPAMLASGgRYTQSSQLTLPADQCPeGEAYKCS 80

                         90
                 ....*....|.
gi 418206463 235 VAHPASSTKVD 245
Cdd:cd21818   81 VQHYSPSQDLN 91
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 382-484 5.94e-16

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


Pssm-ID: 409496  Cd Length: 99  Bit Score: 73.26  E-value: 5.94e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDWTSNGRTEQN-YKNTATVLDSDGSYFMYSKLRVQKSTWERGSLF 460
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTVSSgVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVY 80

                         90       100
                 ....*....|....*....|....
gi 418206463 461 ACSVVHEGLhnhltTKTISRSLGK 484
Cdd:cd07699   81 TCEVTHEGL-----SSTITKSFNR 99
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 158-248 1.50e-15

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: 72.11  E-value: 1.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 158 SVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGV-HTFPALLQSGLYTLSSSVTVTSNTWPSQTI-TC 233
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWlkNGVPLTSGVsTSSPVEPNDGTYSVTSSLTVPPSDWDEGATyTC 80

                         90
                 ....*....|....*
gi 418206463 234 NVAHPASSTKVDKKI 248
Cdd:cd00098   81 VVTHESLKSPLSKTW 95
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 41-149 2.34e-15

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: 71.98  E-value: 2.34e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  41 LVRPGASVTLSCKASgyTFIDHD-MHWVQQTPVYGLEWIGAIDPETGDTGynQKFKGKAILTADKSSrTAYMELRSLTSE 119
Cdd:cd00099    9 SVQEGESVTLSCEVS--SSFSSTyIYWYRQKPGQGPEFLIYLSSSKGKTK--GGVPGRFSGSRDGTS-SFSLTISNLQPE 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 418206463 120 DSAVYYCTIpFYYSNYSPFaYWGQGTLVTV 149
Cdd:cd00099   84 DSGTYYCAV-SESGGTDKL-TFGSGTRLTV 111
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 275-378 5.70e-15

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 70.83  E-value: 5.70e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDVLMISlspMV--TCVVVDVSEddPDVQISWFVNNVEVHTA--QTQTHREDYNSTLRVVSALPIQHQDW 350
Cdd:cd05768    1 PSVYLLPPPEEELSLNE---TVtlTCLVKGFYP--EDIFVSWLQNGEPLPSAdyKTTAPVPESDGSFFVYSKLNVSTADW 75

                         90       100
                 ....*....|....*....|....*....
gi 418206463 351 MSGKEFKCKVNNRALPSP-IEKTISKPRG 378
Cdd:cd05768   76 NSGDVFSCVVGHEALPLQfTQKSIDKSPG 104
IGc1 smart00407
Immunoglobulin C-Type;
173-241 7.38e-13

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 63.49  E-value: 7.38e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 418206463   173 SVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQS-GLYTLSSSVTVTSNTW-PSQTITCNVAHPASS 241
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWlrNGQEVTEGVSTTDPLKNSdGTYFLSSYLTVPASTWeSGDVYTCQVTHEGLK 73
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 276-373 6.05e-12

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: 61.71  E-value: 6.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 276 SVFIFPPKIKDvlMISLSPMVTCVVVDVSEddPDVQISWFVNNVEVHTAQTQTH-REDYNSTLRVVSALPIQHQDWMSGK 354
Cdd:cd00098    1 TVTLLPPSPEE--KGGGKVTLVCLVSGFYP--KDITVTWLKNGVPLTSGVSTSSpVEPNDGTYSVTSSLTVPPSDWDEGA 76

                         90
                 ....*....|....*....
gi 418206463 355 EFKCKVNNRALPSPIEKTI 373
Cdd:cd00098   77 TYTCVVTHESLKSPLSKTW 95
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 383-471 1.94e-10

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: 57.40  E-value: 1.94e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMT-KKEFSLTCMITGFLPAEIAVDWTSNGR--TEQNYK-NTATVLDSDGSYFMYSKLRVQKSTWERGS 458
Cdd:cd16093    2 PTVSLHAPSREEFLgNRTATFVCLATGFSPKTISFKWLRNGKevTSSTGAvVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                         90
                 ....*....|...
gi 418206463 459 LFACSVVHEGLHN 471
Cdd:cd16093   82 EFTCEFKHKGEIV 94
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 157-248 2.01e-10

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: 57.73  E-value: 2.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 157 PSVYPLAP-VCGGTTGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGVH--TFPALLQSGLYTLSSSVTVTSNTWPS-QT 230
Cdd:cd05768    1 PSVYLLPPpEEELSLNETVTLTCLVKGFYPEDIFVSWlqNGEPLPSADYktTAPVPESDGSFFVYSKLNVSTADWNSgDV 80

                         90
                 ....*....|....*...
gi 418206463 231 ITCNVAHPASSTKVDKKI 248
Cdd:cd05768   81 FSCVVGHEALPLQFTQKS 98
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 381-481 4.17e-10

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: 57.00  E-value: 4.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 381 RAPQVYVLPPPAEEMTKKEF-SLTCMITGFLPAEIAVDWTSNG--RTEQNYKNTATVLDSDGSYFMYSKLRVQKSTWER- 456
Cdd:cd05769    1 TPPTVALFPPSEAEIRNKRKaTLVCLATGFYPDHVSLSWKVNGkeVKDGVATDPQALRENTSTYSLSSRLRVSATEWFNp 80

                         90       100
                 ....*....|....*....|....*
gi 418206463 457 GSLFACSVVHEGLHNHLTTKTISRS 481
Cdd:cd05769   81 RNTFTCIVKFYGGTDTDTWTQGIAG 105
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 45-149 7.26e-10

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: 56.12  E-value: 7.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  45 GASVTLSCKASGYTFIDhdMHWVQQTPVYGLEWIGAIDPETGDtgynqKFKGKAILTADKSSRTAYMELRSLTSEDSAVY 124
Cdd:cd04983   13 GENVTLNCNYSTSTFYY--LFWYRQYPGQGPQFLIYISSDSGN-----KKKGRFSATLDKSRKSSSLHISAAQLSDSAVY 85

                         90       100
                 ....*....|....*....|....*
gi 418206463 125 YCTIPFYYSNYSPfaYWGQGTLVTV 149
Cdd:cd04983   86 FCALSESGGTGKL--TFGKGTRLTV 108
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 156-243 8.55e-10

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


Pssm-ID: 319341  Cd Length: 96  Bit Score: 55.62  E-value: 8.55e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSS-VTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTS-NTWPSQTITC 233
Cdd:cd16092    1 APDVFPIISGCRHPKDNSpVVLACLITGYHPTSVTVTWYMGTQSQPQRTFPEIQRRDSYYMTSSQLSTPlQQWRQGEYKC 80

                         90
                 ....*....|
gi 418206463 234 NVAHPASSTK 243
Cdd:cd16092   81 VVQHTASKSK 90
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 42-149 8.59e-10

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


Pssm-ID: 409373  Cd Length: 105  Bit Score: 55.93  E-value: 8.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  42 VRPGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDtGYNQKFKGKailtadKSSRTAYMELRSLTSEDS 121
Cdd:cd04984   10 VSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPS-GIPDRFSGS------KSGNTASLTISGAQTEDE 82

                         90       100
                 ....*....|....*....|....*...
gi 418206463 122 AVYYCTIpfYYSNYSPFaywGQGTLVTV 149
Cdd:cd04984   83 ADYYCQV--WDSNSYVF---GGGTKLTV 105
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 41-149 2.01e-09

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 54.43  E-value: 2.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463    41 LVRPGASVTLSCKASGYTfiDHDMHWVQQtpvyGLEWIGaidpetgdtgYNQKFKGkailtaDKSSRTAYMELRSLTSED 120
Cdd:smart00410   5 TVKEGESVTLSCEASGSP--PPEVTWYKQ----GGKLLA----------ESGRFSV------SRSGSTSTLTISNVTPED 62

                           90       100
                   ....*....|....*....|....*....
gi 418206463   121 SAVYYCTIPFYYSNYSpfaywgQGTLVTV 149
Cdd:smart00410  63 SGTYTCAATNSSGSAS------SGTTLTV 85
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 174-264 4.24e-09

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: 54.31  E-value: 4.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 174 VTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQSG--LYTLSSSVTVTSNTW--PSQTITCNVAH-PASSTKVDK 246
Cdd:cd05769   21 ATLVCLATGFYPDHVSLSWkvNGKEVKDGVATDPQALRENtsTYSLSSRLRVSATEWfnPRNTFTCIVKFyGGTDTDTWT 100

                         90
                 ....*....|....*...
gi 418206463 247 KIEPRVPItqnpCPPLKE 264
Cdd:cd05769  101 QGIAGPVT----CGVSAE 114
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 157-242 5.16e-09

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta, and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 53.57  E-value: 5.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 157 PSVYPLAPVCGGTTGS-SVTLGCLVKGYFPEPVTLTW---NSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQ-TI 231
Cdd:cd05847    1 PTVQILHSSCASTLTSeTIQLLCLISGYTPSTIEVEWlvdGQVATLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGkTY 80

                         90
                 ....*....|.
gi 418206463 232 TCNVAHPASST 242
Cdd:cd05847   81 TCKVTHQGTTF 91
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 383-469 1.13e-08

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: 52.41  E-value: 1.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPP-PAEEMTKKEFSLTCMITGFLPAEIAVDWTSNGR-TEQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSLF 460
Cdd:cd05847    1 PTVQILHSsCASTLTSETIQLLCLISGYTPSTIEVEWLVDGQvATLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTY 80


                 ....*....
gi 418206463 461 ACSVVHEGL 469
Cdd:cd05847   81 TCKVTHQGT 89
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 156-250 1.41e-08

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: 52.46  E-value: 1.41e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 156 APSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQSG-LYTLSSSVTVTSNTWPS-QTI 231
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWkvDGSTVSSGVTTSKTEQQSDnTYSMSSYLTLSSSDWNKhKVY 80

                         90
                 ....*....|....*....
gi 418206463 232 TCNVAHPASSTKVDKKIEP 250
Cdd:cd07699   81 TCEVTHEGLSSTITKSFNR 99
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 41-149 3.05e-08

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: 51.51  E-value: 3.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  41 LVRPGASVTLSCKASgytfIDHD-MHWVQQTPVYGLEWI----GAIDPETGDtGYNQKFKGKAIlTADKSSrtayMELRS 115
Cdd:cd05899    9 IKRRGQSVTLRCSQK----SGHDnMYWYRQDPGKGLQLLfysyGGGLNEEGD-LPGDRFSASRP-SLTRSS----LTIKS 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 418206463 116 LTSEDSAVYYCTIPFYYSNYSpfAYWGQGTLVTV 149
Cdd:cd05899   79 AEPEDSAVYLCASSLGGGADE--AYFGPGTRLTV 110
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 382-466 1.02e-07

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


Pssm-ID: 409622  Cd Length: 94  Bit Score: 49.75  E-value: 1.02e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDWTSnGRTEQNYKNTATVLDSDGSYFMYSKLRVQKSTWErGSLFA 461
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNS-GSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWG-SQTFT 78


                 ....*
gi 418206463 462 CSVVH 466
Cdd:cd21817   79 CNVEH 83
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 45-149 1.02e-07

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: 50.15  E-value: 1.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463   45 GASVTLSCKASGYTFIDH-DMHWVQQTPVYGLEWIGAIdpetGDTGYNQKFKGKAI-LTADKSSRTAYMELRSLTSEDSA 122
Cdd:pfam07686  11 GGSVTLPCTYSSSMSEAStSVYWYRQPPGKGPTFLIAY----YSNGSEEGVKKGRFsGRGDPSNGDGSLTIQNLTLSDSG 86

                          90       100
                  ....*....|....*....|....*..
gi 418206463  123 VYYCTIpfyysNYSPFAYWGQGTLVTV 149
Cdd:pfam07686  87 TYTCAV-----IPSGEGVFGKGTRLTV 108
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 275-360 1.71e-07

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: 49.33  E-value: 1.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDVLMiSLSPMVTCVVVDVSEddPDVQISWFVNNVEVH-TAQTQTHREDYNSTLRVVSALPIQHQDWMSG 353
Cdd:cd05847    1 PTVQILHSSCASTLT-SETIQLLCLISGYTP--STIEVEWLVDGQVATlSAASTAPQKEEGGTFSTTSKLNVTQEDWKSG 77


                 ....*..
gi 418206463 354 KEFKCKV 360
Cdd:cd05847   78 KTYTCKV 84
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 382-466 1.81e-07

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: 49.13  E-value: 1.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDW--TSNGRTEQNYKNTATVLDSDGSYFMYSKLRVQKSTWERGSL 459
Cdd:cd04985    1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqkNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEV 80


                 ....*..
gi 418206463 460 FACSVVH 466
Cdd:cd04985   81 YKCQVQH 87
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 382-476 3.75e-07

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: 48.00  E-value: 3.75e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVL--PPPAEEMTkkefsLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERgs 458
Cdd:cd07698    2 PPKVHVThhPRSDGEST-----LRCWALGFYPAEITLTWQRDGEDqTQDMELVETRPNGDGTFQKWAAVVVPSGEEQR-- 74

                         90
                 ....*....|....*...
gi 418206463 459 lFACSVVHEGLHNHLTTK 476
Cdd:cd07698   75 -YTCHVQHEGLPEPLTLR 91
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 382-468 4.07e-07

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


Pssm-ID: 409624  Cd Length: 95  Bit Score: 48.09  E-value: 4.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPpAEEMTKKEFSLTCMITGFLPAEIAVDWTSNGRTEQ-NYKNTATVLdSDGSYFMYSKLRVQKSTWERGSLF 460
Cdd:cd21819    1 APTLFPLVS-CGSSTSDPVTVGCLATDFLPDSITFSWTDDNNSLTtGVKTYPSVL-TGGTYTASSQLQVPESEWKSKENF 78


                 ....*...
gi 418206463 461 ACSVVHEG 468
Cdd:cd21819   79 YCKVEHPG 86
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 44-155 9.82e-07

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: 47.36  E-value: 9.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  44 PGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDTGYNQKFKGKAILTADKSSRTAYMELRSLTSEDSAV 123
Cdd:cd04982   12 ESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSAT 91

                         90       100       110
                 ....*....|....*....|....*....|....
gi 418206463 124 YYCtipfyysnyspfAYW--GQGTLVTVSAAKTT 155
Cdd:cd04982   92 YYC------------AYWesGSGYYIKVFGSGTK 113
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 275-375 1.56e-06

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: 46.30  E-value: 1.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 275 PSVFIFPPKIKDvlMISLSPMVTCVVVDVSEDDPDVQisWFVNNVEVHTA-QTQTHREDYNSTLRVVSALPIQHQDWMSG 353
Cdd:cd07699    2 PSVTIFPPSSEE--LSSGKATLVCLINKFYPGFATVT--WKVDGSTVSSGvTTSKTEQQSDNTYSMSSYLTLSSSDWNKH 77

                         90       100
                 ....*....|....*....|..
gi 418206463 354 KEFKCKVNNRALPSPIEKTISK 375
Cdd:cd07699   78 KVYTCEVTHEGLSSTITKSFNR 99
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
 390-468 2.86e-06

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: 45.49  E-value: 2.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 390 PPAEEMTKK------EFSLTCMITGFLPAEIAVDWTSNG---RTEQNYknTATVlDSDGSYFMYSKLRVQKSTWERGSLF 460
Cdd:cd16085    2 PPTLEVTQQptmvwnQVNVTCQVEKFYPQRLQLTWLENGnvsRTETPS--TLTV-NKDGTYNWTSWLLVNVSAHREDVVL 78


                 ....*...
gi 418206463 461 ACSVVHEG 468
Cdd:cd16085   79 TCQVEHDG 86
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 382-474 4.34e-06

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: 45.01  E-value: 4.34e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPPAEEMTKKEfsLTCMITGFLPAEIAVDWTSNGRTEQNYKNTATVL-DSDGSYFMYSKLRVQKstwERGSLF 460
Cdd:cd21029    2 KPRVRLSSRPSPGDGHLQ--LSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILpNHDGTYQLRKTLDIAP---GEGAGY 76

                         90
                 ....*....|....
gi 418206463 461 ACSVVHEGLHNHLT 474
Cdd:cd21029   77 SCRVDHSSLKQDLI 90
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 42-145 5.02e-06

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


Pssm-ID: 409369  Cd Length: 106  Bit Score: 45.07  E-value: 5.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  42 VRPGASVTLSCKASGyTFIDHDMHWVQQTP-------VYGlewigaidPETGDTGYNQKFKGKAiltadksSRTAY-MEL 113
Cdd:cd04980   12 VSPGERVTISCKASQ-SISSNYLAWYQQKPgqapkllIYY--------ASTLHSGVPSRFSGSG-------SGTDFtLTI 75

                         90       100       110
                 ....*....|....*....|....*....|...
gi 418206463 114 RSLTSEDSAVYYCtipfyySNYSPFAY-WGQGT 145
Cdd:cd04980   76 SSVEPEDAAVYYC------QQGYTFPYtFGGGT 102
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 157-242 9.12e-06

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: 44.31  E-value: 9.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 157 PSVYPLAPVCGGTTGS-SVTLGCLVKGYFPEPVTLTW--NSGSLSSG---VHTFPALLQSGLYTLSSSVTVTSNTWPSQT 230
Cdd:cd16093    2 PTVSLHAPSREEFLGNrTATFVCLATGFSPKTISFKWlrNGKEVTSStgaVVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                         90
                 ....*....|...
gi 418206463 231 -ITCNVAHPASST 242
Cdd:cd16093   82 eFTCEFKHKGEIV 94
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 383-469 4.39e-05

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: 42.48  E-value: 4.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVyVLPPPAEEMTKKEFSLTCMITGFLPAEIAVDWT--SNGRTEQNYKNTATVLDS-----DGSYFMYSKLRVQKSTWE 455
Cdd:cd05771    1 PRV-RLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLreEPGGSESQVSRDGVSLSShrqsvDGTYSISSYLTLEPGTEN 79

                         90
                 ....*....|....
gi 418206463 456 RGSLFACSVVHEGL 469
Cdd:cd05771   80 RGATYTCRVTHVSL 93
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 381-469 7.20e-05

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: 41.52  E-value: 7.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 381 RAPQVYVLPPPAEEMTKKEFsLTCMITGFLPAEIAVDWTSNG-RTEQNYKNTATVLDSDGSYFMYSKLRVqksTWERGSL 459
Cdd:cd05767    1 VPPEVTVFPKSPVELGEPNT-LICFVDNFFPPVINVTWLRNGqPVTDGVSETVFLPREDHSFRKFSYLPF---TPSEGDI 76

                         90
                 ....*....|
gi 418206463 460 FACSVVHEGL 469
Cdd:cd05767   77 YDCRVEHWGL 86
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 382-476 7.98e-05

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: 7.98e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 382 APQVYVLPPPaeeMTKKEFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslF 460
Cdd:cd21018    5 SPKAHVTHHP---RSKGEVTLRCWALGFYPADITLTWQLNGEElTQDMELVETRPAGDGTFQKWASVVVPLGKEQN---Y 78

                         90
                 ....*....|....*.
gi 418206463 461 ACSVVHEGLHNHLTTK 476
Cdd:cd21018   79 TCRVYHEGLPEPLTLR 94
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 153-237 8.41e-05

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: 41.54  E-value: 8.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 153 KTTAPSVypLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTW-NSGSLSSGVHT--FPaLLQSGLYTLSSSVTVTSNTWP-- 227
Cdd:cd05772    1 KPSQPLV--SGPSGRATPGQTVSFTCKSHGFSPRDITLKWfKNGNELSALQTtvFP-EGDSVSYSVSSTVQVVLTKDDvh 77

                         90
                 ....*....|
gi 418206463 228 SQtITCNVAH 237
Cdd:cd05772   78 SQ-LTCEVAH 86
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 389-469 9.03e-05

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: 41.34  E-value: 9.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 389 PPPAE----EMTKKEFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFACS 463
Cdd:cd21023    5 PPKAHvahhPISDHEATLRCWALGFYPAEITLTWQRDGEEQtQDTELVETRPAGDGTFQKWAAVVVPPGEEQR---YTCH 81


                 ....*.
gi 418206463 464 VVHEGL 469
Cdd:cd21023   82 VQHEGL 87
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
 383-476 9.58e-05

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: 41.33  E-value: 9.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPaeeMTKKEFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFA 461
Cdd:cd21025    6 PKTHVTHHP---VSDHEATLRCWALGFYPAEITLTWQWDGEDQtQDTELVETRPAGDGTFQKWAAVVVPSGEEQR---YT 79

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21025   80 CHVQHEGLPEPLTLR 94
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
 383-476 1.09e-04

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: 41.29  E-value: 1.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEmtkKEFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKStweRGSLFA 461
Cdd:cd21820    6 PKAHVTHHPRSE---DEVTLRCWALGFYPADITLTWQLNGEElTQDMELVETRPAGDGTFQKWAAVVVPLG---KEQYYT 79

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21820   80 CHVYHEGLPEPLTLR 94
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 383-474 1.67e-04

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: 40.78  E-value: 1.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEmTKKEFSLTCMITGFLPAEIAVDWTSNGRTEQNYKNTATVL-DSDGSYFMYSKLRVqksTWERGSLFA 461
Cdd:cd05766    4 PSVKVSPTKTGP-LEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTELIpNGDWTFQILVMLET---TPRRGDVYT 79

                         90
                 ....*....|...
gi 418206463 462 CSVVHEGLHNHLT 474
Cdd:cd05766   80 CQVEHSSLQSPLT 92
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 171-244 1.77e-04

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


Pssm-ID: 409428  Cd Length: 100  Bit Score: 40.56  E-value: 1.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 171 GSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFP---ALLQS------GLYTLSSSVTVTSNTWPS-QTITCNVAHPAS 240
Cdd:cd05771   14 DLPQTLSCHIAGYYPLDVDVEWLREEPGGSESQVSrdgVSLSShrqsvdGTYSISSYLTLEPGTENRgATYTCRVTHVSL 93


                 ....
gi 418206463 241 STKV 244
Cdd:cd05771   94 EEPL 97
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 375-474 1.90e-04

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: 40.77  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 375 KPRGP-VRAPQVYVLPppaeemtKKEFSLTCMITGFLPAEIAVDWTSNGRTEQNYKNTATVLDSDGSYFMYSKLRVQKST 453
Cdd:cd05772    1 KPSQPlVSGPSGRATP-------GQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTK 73

                         90       100
                 ....*....|....*....|.
gi 418206463 454 WERGSLFACSVVHEGLHNHLT 474
Cdd:cd05772   74 DDVHSQLTCEVAHVTLQAPLR 94
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 383-476 2.06e-04

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: 40.37  E-value: 2.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMTKKEFsLTCMITGFLPAEIAVDWTSNGRTEQ-NYKNTATVLDSDgsyFMYSKLRVQKSTWERGSLFA 461
Cdd:cd21000    4 PKVTVYPAKTQPLQHHNL-LVCSVNGFYPGSIEVRWFRNGQEEKaGVVSTGLIQNGD---WTFQTLVMLETVPRSGEVYT 79

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21000   80 CQVEHPSVTSPLTVE 94
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 390-469 3.90e-04

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


Pssm-ID: 409613  Cd Length: 94  Bit Score: 39.74  E-value: 3.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 390 PPAEEMTKK-----EFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFACS 463
Cdd:cd21022    4 PPKTHVTHHpvfdyEATLRCWALGFYPAEIILTWQRDGEDQtQDVELVETRPAGDGTFQKWAAVVVPSGEEQR---YTCH 80


                 ....*.
gi 418206463 464 VVHEGL 469
Cdd:cd21022   81 VQHEGL 86
IgC1_MHC_Ia_HLA-B cd21026
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 383-476 3.97e-04

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-B gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. Human leukocyte antigen (HLA) B*3501 (B35) is a common human allele involved in mediating protective immunity against HIV. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409617  Cd Length: 97  Bit Score: 39.80  E-value: 3.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPaeeMTKKEFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFA 461
Cdd:cd21026    6 PKTHVTHHP---ISDHEATLRCWALGFYPAEITLTWQRDGEDQtQDTELVETRPAGDRTFQKWAAVVVPSGEEQR---YT 79

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21026   80 CHVQHEGLPKPLTLR 94
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 395-476 4.05e-04

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


Pssm-ID: 409618  Cd Length: 95  Bit Score: 39.43  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 395 MTKKEFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFACSVVHEGLHNHL 473
Cdd:cd21027   15 VSDHEATLRCWALSFYPAEITLTWQRDGEDQtQDTELVETRPAGDGTFQKWAAVVVPSGQEQR---YTCHVQHEGLPKPL 91


                 ...
gi 418206463 474 TTK 476
Cdd:cd21027   92 TLR 94
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 383-476 7.22e-04

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409590  Cd Length: 99  Bit Score: 38.98  E-value: 7.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEMTKKEFsLTCMITGFLPAEIAVDWTSNGRTEQN-YKNTATVLDSDgsyFMYSKLRVQKSTWERGSLFA 461
Cdd:cd20998    7 PTVTVYPTKTQPLEHHNL-LVCSVSDFYPGNIEVRWFRNGKEEKTgIVSTGLVRNGD---WTFQTLVMLETVPQSGEVYT 82

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd20998   83 CQVEHPSLTDPVTVE 97
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
 390-476 7.52e-04

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


Pssm-ID: 409611  Cd Length: 95  Bit Score: 38.97  E-value: 7.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 390 PPAEEMT-----KKEFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFACS 463
Cdd:cd21020    5 PPKAHVThhrrpEGDVTLRCWALGFYPADITLTWQLNGEElTQEMELVETRPAGDGTFQKWASVVVPLGKEQK---YTCH 81

                         90
                 ....*....|...
gi 418206463 464 VVHEGLHNHLTTK 476
Cdd:cd21020   82 VEHEGLPEPLTLR 94
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 388-478 9.38e-04

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: 38.51  E-value: 9.38e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 388 LPPPAEE--MTKKEFSLTCMITGFLPAEIAV-DWTSNGRTEQNYKntATVLDSDGSYFMYSKLRVQKSTWERGSLFACSV 464
Cdd:cd04986    6 LQRPALEdlLLGSNASLTCTLSGLKDPEGATfTWEPSGGKEAIQG--PPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                         90
                 ....*....|....
gi 418206463 465 VHEGLHNHLtTKTI 478
Cdd:cd04986   84 THPESKGTL-TATI 96
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
 383-476 1.09e-03

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: 38.56  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 383 PQVYVLPPPAEEmtkKEFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFA 461
Cdd:cd21013    5 PKAHVTHHPRSE---GYVTLRCWALGFYPADITLTWQLNGEElTQDMEFVETRPAGDGTFQKWASVVVPLGKEQK---YT 78

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21013   79 CHVEHEGLPEPLTLR 93
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 42-149 1.14e-03

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: 38.69  E-value: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  42 VRPGASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWI----GAIDPetgdtGYNQKFKGKailtADKSSRTAYMELRSLT 117
Cdd:cd20988   10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFIyregGIYGP-----GFKDNFRGD----IDSSNNLAVLKILEAS 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 418206463 118 SEDSAVYYC--TIPFYYSNYSPFAYwGQGTLVTV 149
Cdd:cd20988   81 ERDEGSYYCasDTPGGGREYDPLIF-GKGTYLTV 113
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 154-241 1.38e-03

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: 37.98  E-value: 1.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 154 TTAPSVYpLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTI 231
Cdd:cd21002    1 RRPPSVR-VAPTTPFNTREPVMLACHVWGFYPADVTITWlkNGDPVAPHSSAPKTAQPNGDWTYQTQVTLAVTPSPGDTY 79

                         90
                 ....*....|
gi 418206463 232 TCNVAHPASS 241
Cdd:cd21002   80 TCSVQHASLP 89
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 45-149 1.41e-03

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: 38.31  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463  45 GASVTLSCKASGYTFIDHDMHWVQQTPVYGLEWIGAIDPETGDTGynqkfKGKAILTADKSSRTAYMELRSLTSEDSAVY 124
Cdd:cd16095   15 GKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVS-----EDRITSSREDTNSQIFLQIKGLGLRDSGQY 89

                         90       100
                 ....*....|....*....|....*
gi 418206463 125 YCTIPFYYSNYSPFAYWGQGTLVTV 149
Cdd:cd16095   90 HCARRVGYGDDTDKLIFGPGTDVIV 114
IgC1_MHC_Ia_MIC-A_MIC-B cd21017
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; ...
 394-470 2.22e-03

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: 37.50  E-value: 2.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418206463 394 EMTKKEFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVL-DSDGSYFMYSKLRVQKSTWERgslFACSVVHEGLH 470
Cdd:cd21017   13 EASEGNITVTCRASGFYPWNITLSWRQDGVSlSHDTQQWGDVLpDGNGTYQTWVATRICQGEEQR---FTCYMEHSGNH 88
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 388-476 2.24e-03

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


Pssm-ID: 409615  Cd Length: 95  Bit Score: 37.46  E-value: 2.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 388 LPPPAEEMTKK-----EFSLTCMITGFLPAEIAVDWTSNGRTE-QNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFA 461
Cdd:cd21024    3 LEPPKTHVTHHpisdhEATLRCWALGFYPAEITLTWQQDGEGHtQDTELVETRPAGDGTFQKWAAVVVPSGEEQR---YT 79

                         90
                 ....*....|....*
gi 418206463 462 CSVVHEGLHNHLTTK 476
Cdd:cd21024   80 CHVQHEGLPEPVTLR 94
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 171-241 2.49e-03

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409375  Cd Length: 96  Bit Score: 37.36  E-value: 2.49e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 418206463 171 GSSVTLGCLVKGYF-PEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPS-QTITCNVAHPASS 241
Cdd:cd04986   17 GSNASLTCTLSGLKdPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSgDTFSCTVTHPESK 89
IgI_2_KIRREL3-like cd05759
Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar ...
 297-374 2.89e-03

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: 2.89e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 418206463 297 TCVVvdvSEDDPDVQISWFVNNVEVHTA-QTQTHREDYNSTlRVVSALPIQHQDWMSGKEFKCKVNNRALPSPIEKTIS 374
Cdd:cd05759   21 TCRA---RGAKPAAEIIWFRDGEQLEGAvYSKELLKDGKRE-TTVSTLLITPSDLDTGRTFTCRARNEAIPNGKETSIT 95
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 381-469 3.39e-03

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: 36.83  E-value: 3.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 381 RAPQVYVLPPPAEEmTKKEFSLTCMITGFLPAEIAVDWTSNGR-TEQNYKNTATVLDS-DGSYFMYSKLRVqksTWERGS 458
Cdd:cd21002    2 RPPSVRVAPTTPFN-TREPVMLACHVWGFYPADVTITWLKNGDpVAPHSSAPKTAQPNgDWTYQTQVTLAV---TPSPGD 77

                         90
                 ....*....|.
gi 418206463 459 LFACSVVHEGL 469
Cdd:cd21002   78 TYTCSVQHASL 88
IgC1_CH2_IgD cd16084
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; ...
 385-469 4.45e-03

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: 36.65  E-value: 4.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 385 VYVLPPPAEEM-TKKEFSLTCMITGFLPAEIAVDWTSNGRTEQNYKNTATV-LDSDGSYFMYSKLRVQKSTWERGSLFAC 462
Cdd:cd16084    2 VYLLTPAVQDLwLRDKATFTCFVVGSDLKDAHLTWEVAGKVPTGGVEEGLLeRHSNGSQSQHSRLTLPRSLWNAGTSVTC 81


                 ....*..
gi 418206463 463 SVVHEGL 469
Cdd:cd16084   82 TLNHPSL 88
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 159-239 4.46e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H (HLA-H). HLA-H (also known as hereditary hemochromatosis protein; HFE) is a major histocompatibility complex (MHC) class I-like protein that is mutated in Hereditary Hemochromatosis. HFE is a protein of 343 amino acids that includes a signal peptide, an extracellular transferrin receptor-binding region (a1 and a2), an immunoglobulin-like domain (a3), a transmembrane region, and a short cytoplasmic tail. HFE binds beta-2-microglobulin to form a heterodimer expressed at the cell surface. It binds transferrin receptor (TFRC) in its extracellular alpha1-alpha2 domain. HFE plays an important part in the regulation of hepcidin expression in response to iron overload and the liver is important in the pathophysiology of HFE-associated hemochromatosis. Nine HFE splicing variants have been reported with transcripts lacking exon 2 or exon 3, or exons 2-3, 2-4, or 2-5. Diverse mutations involving HFE introns and exons discovered in persons with hemochromatosis or their family members cause or probably cause high iron phenotypes. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409612  Cd Length: 94  Bit Score: 36.68  E-value: 4.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 159 VYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPA--LLQSGLYTLSSSVTVTSNTWPSQTITCNVA 236
Cdd:cd21021    3 VPPLVKVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPkdVLPNGDGTYQGWITLAVPPGEEQRYTCQVE 82


                 ...
gi 418206463 237 HPA 239
Cdd:cd21021   83 HPG 85
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 159-237 5.12e-03

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


Pssm-ID: 409424  Cd Length: 95  Bit Score: 36.52  E-value: 5.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 159 VYPLAPVcggTTGSSVTLGCLVKGYFPEPVTLTW--NSGSLSSGV-HTFPALLQSGLYTLSSSVTVTSNtwPSQTITCNV 235
Cdd:cd05767    7 VFPKSPV---ELGEPNTLICFVDNFFPPVINVTWlrNGQPVTDGVsETVFLPREDHSFRKFSYLPFTPS--EGDIYDCRV 81


                 ..
gi 418206463 236 AH 237
Cdd:cd05767   82 EH 83
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
 390-476 5.69e-03

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: 36.23  E-value: 5.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 390 PPAEEMTKK-----EFSLTCMITGFLPAEIAVDWTSNGRT-EQNYKNTATVLDSDGSYFMYSKLRVQKSTWERgslFACS 463
Cdd:cd21016    5 PPKAHVTRHprpegDVTLRCWALGFYPADITLTWQKDGEElTQDMEFVETRPAGDGTFQKWAAVVVPLGKEQS---YTCH 81

                         90
                 ....*....|...
gi 418206463 464 VVHEGLHNHLTTK 476
Cdd:cd21016   82 VYHEGLPEPLTLR 94
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
 381-469 7.04e-03

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: 35.92  E-value: 7.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 418206463 381 RAPQVYVLPP-PAEEMTKKEfsLTCMITGFLPAEIAVDWTSNGRTEQNYKNTATVLDSDGSYFMyskLRVQKSTWERGSL 459
Cdd:cd05770    1 STPKVQVYSRfPAENGKPNV--LNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYL---LKYTEFTPTKGDE 75

                         90
                 ....*....|
gi 418206463 460 FACSVVHEGL 469
Cdd:cd05770   76 YACRVRHNTL 85
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
 168-242 7.86e-03

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 35.86  E-value: 7.86e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 418206463  168 GTTGSSVTLGCLVKGYFPEPvTLTW--NSGSLSSGVHTFPALLQSGLYTLSSSVTVT-SNTWPSQTITCNVAHPASST 242
Cdd:pfam08205  11 EGEGPEVVATCSSAGGKPAP-RITWylDGKPLEAAETSSEQDPESGLVTVTSELKLVpSRSDHGQSLTCQVSYGALRG 87
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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