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Conserved domains on  [gi|13435879|gb|AAH04786|]
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Igh protein [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-142 2.47e-67

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: 211.78  E-value: 2.47e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  22 QLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 13435879 102 MSHLKSEDTAMYYCARDMGgspYGGYSRFDYWGQGTTITVS 142
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLG---GYGYSYFDYWGQGTTVTVS 118
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 261-352 8.33e-58

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: 186.05  E-value: 8.33e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLLGSDASLTCTLNGLRNPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 340
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 13435879 341 THPES-DTLTGTI 352
Cdd:cd04986  84 THPESkGTLTATI 96
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 362-469 4.39e-49

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: 163.66  E-value: 4.39e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQ 441
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDG---SFFVYSKLNVSTADWNS 77

                        90       100
                ....*....|....*....|....*...
gi 13435879 442 GDQYSCMVGHEALPMNFTQKTIDRLSGK 469
Cdd:cd05768  78 GDVFSCVVGHEALPLQFTQKSIDKSPGK 105
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 148-241 3.96e-43

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: 147.65  E-value: 3.96e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 148 NPTIYPLTLPRALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGGYTMSSQLTLPAVECPEGESVKC 227
Cdd:cd21818   1 SPTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKC 79

                        90
                ....*....|....
gi 13435879 228 SVQHDsNAVQELDV 241
Cdd:cd21818  80 SVQHY-SPSQDLNV 92
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-142 2.47e-67

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: 211.78  E-value: 2.47e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  22 QLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 13435879 102 MSHLKSEDTAMYYCARDMGgspYGGYSRFDYWGQGTTITVS 142
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLG---GYGYSYFDYWGQGTTVTVS 118
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 261-352 8.33e-58

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: 186.05  E-value: 8.33e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLLGSDASLTCTLNGLRNPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 340
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 13435879 341 THPES-DTLTGTI 352
Cdd:cd04986  84 THPESkGTLTATI 96
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 362-469 4.39e-49

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: 163.66  E-value: 4.39e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQ 441
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDG---SFFVYSKLNVSTADWNS 77

                        90       100
                ....*....|....*....|....*...
gi 13435879 442 GDQYSCMVGHEALPMNFTQKTIDRLSGK 469
Cdd:cd05768  78 GDVFSCVVGHEALPLQFTQKSIDKSPGK 105
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 148-241 3.96e-43

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: 147.65  E-value: 3.96e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 148 NPTIYPLTLPRALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGGYTMSSQLTLPAVECPEGESVKC 227
Cdd:cd21818   1 SPTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKC 79

                        90
                ....*....|....
gi 13435879 228 SVQHDsNAVQELDV 241
Cdd:cd21818  80 SVQHY-SPSQDLNV 92
IGv smart00406
Immunoglobulin V-Type;
36-117 3.53e-32

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 117.87  E-value: 3.53e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879     36 SLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSyTYYPDNVKGRFTISRDNAKNNLYLQMSHLKSEDTAMYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGS-SYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 13435879    116 AR 117
Cdd:smart00406  80 AV 81
C1-set pfam07654
Immunoglobulin C1-set domain;
364-454 2.55e-21

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 88.08  E-value: 2.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879   364 VHLLPPPSEELalNELVSLTCLVRAFNPKEVLVRWLHGNEELsPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQGD 443
Cdd:pfam07654   1 VYVFPPSPEEL--GKPNTLTCLVTGFYPPDITVTWLKNGQEV-TEGVKTTPPSPNSDW---TYQLSSYLTVTPSDWESGD 74

                          90
                  ....*....|.
gi 13435879   444 QYSCMVGHEAL 454
Cdd:pfam07654  75 EYTCRVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
380-455 4.04e-21

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 86.98  E-value: 4.04e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 13435879    380 VSLTCLVRAFNPKEVLVRWL-HGNEElsPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQGDQYSCMVGHEALP 455
Cdd:smart00407   2 ATLVCLVSGFYPPDITVTWLrNGQEV--TEGVSTTDPLKNSDG---TYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73
C1-set pfam07654
Immunoglobulin C1-set domain;
151-234 1.40e-19

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 83.07  E-value: 1.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879   151 IYPLTLPRALSSDPVIIGCLIHDYFPsGTMNVTWGKSGKDITT--VNFPPALASGGGYTMSSQLTLPAVECPEGESVKCS 228
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYP-PDITVTWLKNGQEVTEgvKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 13435879   229 VQHDSN 234
Cdd:pfam07654  80 VEHEGL 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 30-141 2.07e-10

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: 57.85  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879    30 LVKPGGSLKLSCAASGFTFS-SYAMSWVRQTPEKRLEWVATISDGGsYTYYPDnvKGRFTISRDNAKNNLYLQMSHLKSE 108
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEaSTSVYWYRQPPGKGPTFLIAYYSNG-SEEGVK--KGRFSGRGDPSNGDGSLTIQNLTLS 83

                          90       100       110
                  ....*....|....*....|....*....|...
gi 13435879   109 DTAMYYCArdMGGSPYGgysrfdYWGQGTTITV 141
Cdd:pfam07686  84 DSGTYTCA--VIPSGEG------VFGKGTRLTV 108
IGc1 smart00407
Immunoglobulin C-Type;
164-234 7.94e-09

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 52.32  E-value: 7.94e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 13435879    164 PVIIGCLIHDYFPSgTMNVTWGKSGKDIT--TVNFPPALASGGGYTMSSQLTLPAVECPEGESVKCSVQHDSN 234
Cdd:smart00407   1 KATLVCLVSGFYPP-DITVTWLRNGQEVTegVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGL 72
C1-set pfam07654
Immunoglobulin C1-set domain;
273-343 6.21e-06

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 44.16  E-value: 6.21e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 13435879   273 LGSDASLTCTLNGLrNPEGAVFTW----EPSTgKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTHP 343
Cdd:pfam07654  11 LGKPNTLTCLVTGF-YPPDITVTWlkngQEVT-EGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHE 83
IGc1 smart00407
Immunoglobulin C-Type;
277-343 1.31e-04

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 40.37  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 13435879    277 ASLTCTLNGLrNPEGAVFTW----EPSTgKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTHP 343
Cdd:smart00407   2 ATLVCLVSGF-YPPDITVTWlrngQEVT-EGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHE 70
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 22-142 2.47e-67

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: 211.78  E-value: 2.47e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  22 QLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQ 101
Cdd:cd04981   1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 13435879 102 MSHLKSEDTAMYYCARDMGgspYGGYSRFDYWGQGTTITVS 142
Cdd:cd04981  81 LNSLTSEDTAVYYCARGLG---GYGYSYFDYWGQGTTVTVS 118
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 261-352 8.33e-58

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: 186.05  E-value: 8.33e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLLGSDASLTCTLNGLRNPEGAVFTWEPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 340
Cdd:cd04986   4 LSLQRPALEDLLLGSNASLTCTLSGLKDPEGATFTWEPSGGKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDTFSCTV 83

                        90
                ....*....|...
gi 13435879 341 THPES-DTLTGTI 352
Cdd:cd04986  84 THPESkGTLTATI 96
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 362-469 4.39e-49

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: 163.66  E-value: 4.39e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQ 441
Cdd:cd05768   1 PSVYLLPPPEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDG---SFFVYSKLNVSTADWNS 77

                        90       100
                ....*....|....*....|....*...
gi 13435879 442 GDQYSCMVGHEALPMNFTQKTIDRLSGK 469
Cdd:cd05768  78 GDVFSCVVGHEALPLQFTQKSIDKSPGK 105
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 148-241 3.96e-43

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: 147.65  E-value: 3.96e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 148 NPTIYPLTLPRALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGGYTMSSQLTLPAVECPEGESVKC 227
Cdd:cd21818   1 SPTVFPLSLCPSLSSDPVVIGCLVQGFFPE-PVNVTWNYSGKGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKC 79

                        90
                ....*....|....
gi 13435879 228 SVQHDsNAVQELDV 241
Cdd:cd21818  80 SVQHY-SPSQDLNV 92
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 148-241 2.61e-35

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: 126.94  E-value: 2.61e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 148 NPTIYPLTLPRAL-SSDPVIIGCLIHDYFPSgTMNVTWGK---SGKDITTVNFPPALASGGGYTMSSQLTLPAVECPEGE 223
Cdd:cd04985   1 APTVFPLQSATKSqSNGPVALGCLISDYFPE-SITVSWQKntnSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGE 79

                        90
                ....*....|....*....
gi 13435879 224 SVKCSVQHD-SNAVQELDV 241
Cdd:cd04985  80 VYKCQVQHSaSNSKQEKDV 98
IGv smart00406
Immunoglobulin V-Type;
36-117 3.53e-32

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 117.87  E-value: 3.53e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879     36 SLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSyTYYPDNVKGRFTISRDNAKNNLYLQMSHLKSEDTAMYYC 115
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGSNGS-SYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 13435879    116 AR 117
Cdd:smart00406  80 AV 81
C1-set pfam07654
Immunoglobulin C1-set domain;
364-454 2.55e-21

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 88.08  E-value: 2.55e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879   364 VHLLPPPSEELalNELVSLTCLVRAFNPKEVLVRWLHGNEELsPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQGD 443
Cdd:pfam07654   1 VYVFPPSPEEL--GKPNTLTCLVTGFYPPDITVTWLKNGQEV-TEGVKTTPPSPNSDW---TYQLSSYLTVTPSDWESGD 74

                          90
                  ....*....|.
gi 13435879   444 QYSCMVGHEAL 454
Cdd:pfam07654  75 EYTCRVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
380-455 4.04e-21

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 86.98  E-value: 4.04e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 13435879    380 VSLTCLVRAFNPKEVLVRWL-HGNEElsPESYLVFEPLKEPGEgatTYLVTSVLRVSAETWKQGDQYSCMVGHEALP 455
Cdd:smart00407   2 ATLVCLVSGFYPPDITVTWLrNGQEV--TEGVSTTDPLKNSDG---TYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 30-141 1.77e-20

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: 86.62  E-value: 1.77e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  30 LVKPGGSLKLSCAASGFtFSSYAMSWVRQTPEKRLEWVATISdgGSYTYYPDNVKGRFTISRDNAKNnLYLQMSHLKSED 109
Cdd:cd00099   9 SVQEGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFLIYLS--SSKGKTKGGVPGRFSGSRDGTSS-FSLTISNLQPED 84

                        90       100       110
                ....*....|....*....|....*....|..
gi 13435879 110 TAMYYCARDMGGSPYGgysrfDYWGQGTTITV 141
Cdd:cd00099  85 SGTYYCAVSESGGTDK-----LTFGSGTRLTV 111
C1-set pfam07654
Immunoglobulin C1-set domain;
151-234 1.40e-19

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 83.07  E-value: 1.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879   151 IYPLTLPRALSSDPVIIGCLIHDYFPsGTMNVTWGKSGKDITT--VNFPPALASGGGYTMSSQLTLPAVECPEGESVKCS 228
Cdd:pfam07654   1 VYVFPPSPEELGKPNTLTCLVTGFYP-PDITVTWLKNGQEVTEgvKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                  ....*.
gi 13435879   229 VQHDSN 234
Cdd:pfam07654  80 VEHEGL 85
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 363-460 6.90e-18

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: 78.66  E-value: 6.90e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 363 QVHLLPPPSEELaLNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGegatTYLVTSVLRVSAETWKQG 442
Cdd:cd00098   1 TVTLLPPSPEEK-GGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNDG----TYSVTSSLTVPPSDWDEG 75

                        90
                ....*....|....*...
gi 13435879 443 DQYSCMVGHEALPMNFTQ 460
Cdd:cd00098  76 ATYTCVVTHESLKSPLSK 93
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 20-141 1.88e-17

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: 77.99  E-value: 1.88e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  20 EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSytyypDNVKGRFTISRDNAKNNLY 99
Cdd:cd16095   1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHIST-----KVSEDRITSSREDTNSQIF 75

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 13435879 100 LQMSHLKSEDTAMYYCARDMGgspYGGYSRFDYWGQGTTITV 141
Cdd:cd16095  76 LQIKGLGLRDSGQYHCARRVG---YGDDTDKLIFGPGTDVIV 114
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 149-233 1.71e-16

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: 74.67  E-value: 1.71e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 149 PTIYPLTLPRALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITT--VNFPPALaSGGGYTMSSQLTLPAVECPEGESVK 226
Cdd:cd21819   2 PTLFPLVSCGSSTSDPVTVGCLATDFLPD-SITFSWTDDNNSLTTgvKTYPSVL-TGGTYTASSQLQVPESEWKSKENFY 79


                ....*..
gi 13435879 227 CSVQHDS 233
Cdd:cd21819  80 CKVEHPG 86
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 361-454 1.16e-15

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: 72.43  E-value: 1.16e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPgeGATTYLVTSVLRVSAETWK 440
Cdd:cd16093   1 PPTVSLHAPSREEFLGNRTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEEPKED--GKTLYSATSFLTITESEWK 78

                        90
                ....*....|....
gi 13435879 441 QGDQYSCMVGHEAL 454
Cdd:cd16093  79 SQTEFTCEFKHKGE 92
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 30-141 8.28e-13

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: 64.61  E-value: 8.28e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  30 LVKPGGSLKLSCAAsgfTFSSYAMSWVRQTPEKRLEWVATiSDGGSYTYYPDNVKGRFTISRDNAKNnLYLQMSHLKSED 109
Cdd:cd05899   9 IKRRGQSVTLRCSQ---KSGHDNMYWYRQDPGKGLQLLFY-SYGGGLNEEGDLPGDRFSASRPSLTR-SSLTIKSAEPED 83

                        90       100       110
                ....*....|....*....|....*....|..
gi 13435879 110 TAMYYCARDMGGSPYGGysrfdYWGQGTTITV 141
Cdd:cd05899  84 SAVYLCASSLGGGADEA-----YFGPGTRLTV 110
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 33-142 9.07e-13

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: 64.69  E-value: 9.07e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  33 PGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQMSHLKSEDTAM 112
Cdd:cd04982  12 ESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSAT 91

                        90       100       110
                ....*....|....*....|....*....|
gi 13435879 113 YYCARDMGGSPYgGYSRFdywGQGTTITVS 142
Cdd:cd04982  92 YYCAYWESGSGY-YIKVF---GSGTKLIVT 117
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 149-231 2.16e-12

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: 62.85  E-value: 2.16e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 149 PTIYPLTLPRALSSDP-VIIGCLIHDYFPSGTMnVTWGKSGKDITTVNFPPALASGGGYTMSSQLTLPAVECPeGESVKC 227
Cdd:cd21817   2 PSVFPLAPCCKSTNGSsVTLGCLVTGYFPEPVT-VTWNSGSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWG-SQTFTC 79


                ....
gi 13435879 228 SVQH 231
Cdd:cd21817  80 NVEH 83
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 265-343 3.14e-12

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: 62.47  E-value: 3.14e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 265 RPALEDLLLGSDASLTCTLNGLRNPEGAVFTWEPSTGKD--AVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTH 342
Cdd:cd07696   7 PPSPKDLFLTKSAKVTCLVVDLTSIEEVNVTWSREDGNEvlASTTNPEKHYNATLSVVSTLTVCADDWDNGKTFKCKVTH 86


                .
gi 13435879 343 P 343
Cdd:cd07696  87 P 87
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 157-233 4.85e-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: 62.09  E-value: 4.85e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 13435879 157 PRALSSDPVIIGCLIHDYFPSGtMNVTWGKSGKDIT--TVNFPPALASGGGYTMSSQLTLPAVECPEGESVKCSVQHDS 233
Cdd:cd00098   9 PEEKGGGKVTLVCLVSGFYPKD-ITVTWLKNGVPLTsgVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTCVVTHES 86
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 26-141 2.05e-11

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 59.83  E-value: 2.05e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879     26 SGGGLVKPGGSLKLSCAASGFtfSSYAMSWVRQtpekRLEWVATisdggsytyypdnvKGRFTISRDNakNNLYLQMSHL 105
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLLAE--------------SGRFSVSRSG--STSTLTISNV 58

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 13435879    106 KSEDTAMYYCARdmggspygGYSRFDYWGqGTTITV 141
Cdd:smart00410  59 TPEDSGTYTCAA--------TNSSGSASS-GTTLTV 85
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 361-454 3.74e-11

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: 59.78  E-value: 3.74e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEELALNElVSLTCLVRAFNPKEVLVRWLHGNeelSPESYLVFE--PLKEPGEgatTYLVTSVLRVSAET 438
Cdd:cd07699   1 APSVTIFPPSSEELSSGK-ATLVCLINKFYPGFATVTWKVDG---STVSSGVTTskTEQQSDN---TYSMSSYLTLSSSD 73

                        90
                ....*....|....*.
gi 13435879 439 WKQGDQYSCMVGHEAL 454
Cdd:cd07699  74 WNKHKVYTCEVTHEGL 89
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 30-141 2.07e-10

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: 57.85  E-value: 2.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879    30 LVKPGGSLKLSCAASGFTFS-SYAMSWVRQTPEKRLEWVATISDGGsYTYYPDnvKGRFTISRDNAKNNLYLQMSHLKSE 108
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEaSTSVYWYRQPPGKGPTFLIAYYSNG-SEEGVK--KGRFSGRGDPSNGDGSLTIQNLTLS 83

                          90       100       110
                  ....*....|....*....|....*....|...
gi 13435879   109 DTAMYYCArdMGGSPYGgysrfdYWGQGTTITV 141
Cdd:pfam07686  84 DSGTYTCA--VIPSGEG------VFGKGTRLTV 108
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 362-454 4.80e-10

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: 56.27  E-value: 4.80e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWL-HGNEELSPESYLVfePLKEPGEgatTYLVTSVLRVSAETWK 440
Cdd:cd05847   1 PTVQILHSSCASTLTSETIQLLCLISGYTPSTIEVEWLvDGQVATLSAASTA--PQKEEGG---TFSTTSKLNVTQEDWK 75

                        90
                ....*....|....
gi 13435879 441 QGDQYSCMVGHEAL 454
Cdd:cd05847  76 SGKTYTCKVTHQGT 89
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 31-141 7.09e-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: 56.32  E-value: 7.09e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  31 VKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVATISDGgsytyYPDNVKGRFTISRDNakNNLYLQMSHLKSEDT 110
Cdd:cd04984  10 VSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKH-----RPSGIPDRFSGSKSG--NTASLTISGAQTEDE 82

                        90       100       110
                ....*....|....*....|....*....|.
gi 13435879 111 AMYYCARdmggspygGYSRFDYWGQGTTITV 141
Cdd:cd04984  83 ADYYCQV--------WDSNSYVFGGGTKLTV 105
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 261-347 1.89e-09

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: 54.77  E-value: 1.89e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLlGSDASLTCTLNGLRnPEGAVFTWEP---STGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFK 337
Cdd:cd00098   2 VTLLPPSPEEKG-GGKVTLVCLVSGFY-PKDITVTWLKngvPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                        90
                ....*....|
gi 13435879 338 CTVTHPESDT 347
Cdd:cd00098  80 CVVTHESLKS 89
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 362-455 2.99e-09

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: 53.99  E-value: 2.99e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELALNELVSLTCLV-RAFNPKEVLVRWLH--GNEELSPESYlvfePLKEPGEgatTYLVTSVLRVSAET 438
Cdd:cd07696   1 VSVFLIPPSPKDLFLTKSAKVTCLVvDLTSIEEVNVTWSRedGNEVLASTTN----PEKHYNA---TLSVVSTLTVCADD 73

                        90
                ....*....|....*..
gi 13435879 439 WKQGDQYSCMVGHEALP 455
Cdd:cd07696  74 WDNGKTFKCKVTHPDLP 90
IGc1 smart00407
Immunoglobulin C-Type;
164-234 7.94e-09

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 52.32  E-value: 7.94e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 13435879    164 PVIIGCLIHDYFPSgTMNVTWGKSGKDIT--TVNFPPALASGGGYTMSSQLTLPAVECPEGESVKCSVQHDSN 234
Cdd:smart00407   1 KATLVCLVSGFYPP-DITVTWLRNGQEVTegVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGL 72
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 266-360 1.36e-08

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: 52.34  E-value: 1.36e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 266 PALEDLLLGSDASLTCTLNGLrNPEGAVFTW----EPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVT 341
Cdd:cd05768   8 PPEEELSLNETVTLTCLVKGF-YPEDIFVSWlqngEPLPSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDVFSCVVG 86

                        90
                ....*....|....*....
gi 13435879 342 HpESDTLTGTIAKITVNTF 360
Cdd:cd05768  87 H-EALPLQFTQKSIDKSPG 104
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 261-345 1.59e-07

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: 49.32  E-value: 1.59e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLLGSDASLTCTLNGLRnPEGAVFTW-----EPSTGKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGAS 335
Cdd:cd16093   4 VSLHAPSREEFLGNRTATFVCLATGFS-PKTISFKWlrngkEVTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQTE 82

                        90
                ....*....|
gi 13435879 336 FKCTVTHPES 345
Cdd:cd16093  83 FTCEFKHKGE 92
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 30-123 1.94e-07

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


Pssm-ID: 409497  Cd Length: 116  Bit Score: 49.37  E-value: 1.94e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  30 LVKPGGSLKLSCAASGFTfSSYAMSWVRQ----TPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQMSHL 105
Cdd:cd07700   9 LVQTNQTVKMSCEAKTSP-KNTRIYWLRQrqapSKDSHFEFLASWDPSKGIVYGEGVDQEKLIILSDSDSSRYILSLMSV 87

                        90
                ....*....|....*...
gi 13435879 106 KSEDTAMYYCArdMGGSP 123
Cdd:cd07700  88 KPEDSGTYFCM--TVGSP 103
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 34-141 2.93e-07

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: 48.81  E-value: 2.93e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  34 GGSLKLSCAASgfTFSSYAMSWVRQTPEKRLEWVATI-SDGGSYTyypdnvKGRFTISRDNAKNNLYLQMSHLKSEDTAM 112
Cdd:cd04983  13 GENVTLNCNYS--TSTFYYLFWYRQYPGQGPQFLIYIsSDSGNKK------KGRFSATLDKSRKSSSLHISAAQLSDSAV 84

                        90       100
                ....*....|....*....|....*....
gi 13435879 113 YYCArdmgGSPYGGYSRFdYWGQGTTITV 141
Cdd:cd04983  85 YFCA----LSESGGTGKL-TFGKGTRLTV 108
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 360-452 5.28e-07

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


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 48.14  E-value: 5.28e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 360 FPPQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRW-LHGNEE---LSPESYlvfePLKepgEGATTYLVTSVLRVS 435
Cdd:cd05769   1 TPPTVALFPPSEAEIRNKRKATLVCLATGFYPDHVSLSWkVNGKEVkdgVATDPQ----ALR---ENTSTYSLSSRLRVS 73

                        90
                ....*....|....*...
gi 13435879 436 AETW-KQGDQYSCMVGHE 452
Cdd:cd05769  74 ATEWfNPRNTFTCIVKFY 91
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 149-237 5.95e-07

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: 47.72  E-value: 5.95e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 149 PTIYPLTLPR--ALSSDPVIIGCLIHDYFPSGtMNVTWGKSGKDITTVNF---PPALASGGGYTMSSQLTLPAVECPEGE 223
Cdd:cd05768   1 PSVYLLPPPEeeLSLNETVTLTCLVKGFYPED-IFVSWLQNGEPLPSADYkttAPVPESDGSFFVYSKLNVSTADWNSGD 79

                        90
                ....*....|....
gi 13435879 224 SVKCSVQHDSNAVQ 237
Cdd:cd05768  80 VFSCVVGHEALPLQ 93
IgC1_CH3_IgD cd16094
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 373-452 6.17e-07

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


Pssm-ID: 319343  Cd Length: 100  Bit Score: 47.54  E-value: 6.17e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 373 ELALNELVS---------LTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGegATTYLVTSVLRVSAETWKQGD 443
Cdd:cd16094   1 KLSLNLLASsdppeaaswLLCEVSGFSPPNILLMWLEDQREVNTSGFAPARPPPQPG--STTFWAWSVLRVPAPPSPQPA 78


                ....*....
gi 13435879 444 QYSCMVGHE 452
Cdd:cd16094  79 TYTCVVSHE 87
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 361-456 1.90e-06

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: 46.07  E-value: 1.90e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEElalnELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfEPLkeP-GEGatTYLVTSVLRVSAETW 439
Cdd:cd07698   2 PPKVHVTHHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELV-ETR--PnGDG--TFQKWAAVVVPSGEE 72

                        90
                ....*....|....*..
gi 13435879 440 KQgdqYSCMVGHEALPM 456
Cdd:cd07698  73 QR---YTCHVQHEGLPE 86
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 361-455 3.80e-06

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: 45.30  E-value: 3.80e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPseelALN--ELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYlvfEPLKEPGEGATTYLVTSVLRVSAet 438
Cdd:cd21002   3 PPSVRVAPTT----PFNtrEPVMLACHVWGFYPADVTITWLKNGDPVAPHSS---APKTAQPNGDWTYQTQVTLAVTP-- 73

                        90
                ....*....|....*..
gi 13435879 439 wKQGDQYSCMVGHEALP 455
Cdd:cd21002  74 -SPGDTYTCSVQHASLP 89
C1-set pfam07654
Immunoglobulin C1-set domain;
273-343 6.21e-06

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 44.16  E-value: 6.21e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 13435879   273 LGSDASLTCTLNGLrNPEGAVFTW----EPSTgKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTHP 343
Cdd:pfam07654  11 LGKPNTLTCLVTGF-YPPDITVTWlkngQEVT-EGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHE 83
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 149-234 7.88e-06

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


Pssm-ID: 319341  Cd Length: 96  Bit Score: 44.44  E-value: 7.88e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 149 PTIYPLTL----PRalSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALASGGGYTMSSQLTLPAVECPEGEs 224
Cdd:cd16092   2 PDVFPIISgcrhPK--DNSPVVLACLITGYHPT-SVTVTWYMGTQSQPQRTFPEIQRRDSYYMTSSQLSTPLQQWRQGE- 77

                        90
                ....*....|
gi 13435879 225 VKCSVQHDSN 234
Cdd:cd16092  78 YKCVVQHTAS 87
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 361-454 8.81e-06

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: 44.24  E-value: 8.81e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPesylvFEPLKEPGEGATTYLVTSVLRVSAETWK 440
Cdd:cd05772   1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSA-----LQTTVFPEGDSVSYSVSSTVQVVLTKDD 75

                        90
                ....*....|....
gi 13435879 441 QGDQYSCMVGHEAL 454
Cdd:cd05772  76 VHSQLTCEVAHVTL 89
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 370-454 1.00e-05

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of human histocompatibility antigen (HLA) DQ and mouse I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. Human HLA-DR, -DQ, and -DP are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes; these peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC, and bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409592  Cd Length: 97  Bit Score: 43.95  E-value: 1.00e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 370 PSEELALNELVSLTCLVRAFNPKEVLVRWLHGNEELSpeSYLVFEPLKEPGEgaTTYLVTSVLRVsaeTWKQGDQYSCMV 449
Cdd:cd21001  10 PSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEET--AGVVSTPLIRNGD--WTFQILVMLEM---TPQRGDVYTCHV 82


                ....*
gi 13435879 450 GHEAL 454
Cdd:cd21001  83 EHPSL 87
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 261-354 1.32e-05

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: 43.98  E-value: 1.32e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 261 LSLQRPALEDLLLGSdASLTCTLNGLrNPEGAVFTW--EPSTGKDAVQK-KAVQNSCGCYSVSSVLPGCAERWNSGASFK 337
Cdd:cd07699   4 VTIFPPSSEELSSGK-ATLVCLINKF-YPGFATVTWkvDGSTVSSGVTTsKTEQQSDNTYSMSSYLTLSSSDWNKHKVYT 81

                        90
                ....*....|....*..
gi 13435879 338 CTVTHPesdTLTGTIAK 354
Cdd:cd07699  82 CEVTHE---GLSSTITK 95
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 31-141 2.97e-05

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: 43.31  E-value: 2.97e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  31 VKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVatISDGGsyTYYPdNVKGRFTISRDNAKNNLYLQMSHLKSEDT 110
Cdd:cd20988  10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFI--YREGG--IYGP-GFKDNFRGDIDSSNNLAVLKILEASERDE 84

                        90       100       110
                ....*....|....*....|....*....|.
gi 13435879 111 AMYYCARDMGGSpyGGYSRFDYWGQGTTITV 141
Cdd:cd20988  85 GSYYCASDTPGG--GREYDPLIFGKGTYLTV 113
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 361-455 3.10e-05

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: 42.71  E-value: 3.10e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEelALNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESylVFEPLKEPGEgaTTYLVTSVLRVsaeTWK 440
Cdd:cd05766   3 QPSVKVSPTKTG--PLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGV--VSTELIPNGD--WTFQILVMLET---TPR 73

                        90
                ....*....|....*
gi 13435879 441 QGDQYSCMVGHEALP 455
Cdd:cd05766  74 RGDVYTCQVEHSSLQ 88
IgI_2_Necl-1-4 cd05761
Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of ...
 378-455 3.46e-05

Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 or CADM3), Necl-2 (also known as CADM1), Necl-3 (also known as CADM2) and Necl-4 (also known as CADM4). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues, and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression.


Pssm-ID: 409418  Cd Length: 102  Bit Score: 42.80  E-value: 3.46e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 13435879 378 ELVSLTCLVRAFNPKEVLvRWLHGNEELSPESYLVFEPLKEpgegatTYLVTSVLRVSAETWKQGDQYSCMVGHEALP 455
Cdd:cd05761  20 DEITLTCTTSGSKPAADI-RWFKNDKELKGVKEVQESGAGK------TFTVTSTLRFRVDRDDDGVAVICRVDHESLT 90
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
 361-459 6.04e-05

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


Pssm-ID: 409625  Cd Length: 98  Bit Score: 42.06  E-value: 6.04e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEElalnELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAETWk 440
Cdd:cd21820   5 PPKAHVTHHPRSE----DEVTLRCWALGFYPADITLTWQLNGEELTQDMELV--ETRPAGDGTFQKWAAVVVPLGKEQY- 77

                        90
                ....*....|....*....
gi 13435879 441 qgdqYSCMVGHEALPMNFT 459
Cdd:cd21820  78 ----YTCHVYHEGLPEPLT 92
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 362-455 6.75e-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: 41.71  E-value: 6.75e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPppsEELALNELVS-LTCLVRAFNPKEVLVRWLH----GNEELSPESYLVFEPLKEPGEGatTYLVTSVLRVSA 436
Cdd:cd05771   1 PRVRLSP---KNLVKPDLPQtLSCHIAGYYPLDVDVEWLReepgGSESQVSRDGVSLSSHRQSVDG--TYSISSYLTLEP 75

                        90
                ....*....|....*....
gi 13435879 437 ETWKQGDQYSCMVGHEALP 455
Cdd:cd05771  76 GTENRGATYTCRVTHVSLE 94
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 362-465 1.01e-04

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: 41.42  E-value: 1.01e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEELAlNELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVFEPLKEPGegaTTYLVTSVLRVSAETWKQ 441
Cdd:cd04985   2 PTVFPLQSATKSQS-NGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSG---GDYSCSSQLTVPLQEWNS 77

                        90       100
                ....*....|....*....|....
gi 13435879 442 GDQYSCMVGHEAlpmNFTQKTIDR 465
Cdd:cd04985  78 GEVYKCQVQHSA---SNSKQEKDV 98
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 377-453 1.06e-04

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


Pssm-ID: 319341  Cd Length: 96  Bit Score: 41.36  E-value: 1.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 13435879 377 NELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYlvfeplKEPGEGATTYLVTSVLRVSAETWKQGdQYSCMVGHEA 453
Cdd:cd16092  17 NSPVVLACLITGYHPTSVTVTWYMGTQSQPQRTF------PEIQRRDSYYMTSSQLSTPLQQWRQG-EYKCVVQHTA 86
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
 361-459 1.18e-04

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: 41.26  E-value: 1.18e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEElalnELVSLTCLVRAFNPKEVLVRWLHGNEELSPEsyLVFEPLKEPGEGATTYLVTSVLRVSAEtwk 440
Cdd:cd21013   4 PPKAHVTHHPRSE----GYVTLRCWALGFYPADITLTWQLNGEELTQD--MEFVETRPAGDGTFQKWASVVVPLGKE--- 74

                        90
                ....*....|....*....
gi 13435879 441 qgDQYSCMVGHEALPMNFT 459
Cdd:cd21013  75 --QKYTCHVEHEGLPEPLT 91
IgC1_MHC_Ia_RT1-Aa cd21015
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the ...
 361-461 1.25e-04

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


Pssm-ID: 409606  Cd Length: 95  Bit Score: 40.90  E-value: 1.25e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEELAlnelVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAEtwk 440
Cdd:cd21015   4 PPEAHVTLHPRPEGD----VTLRCWALGFYPADITLTWQLNGEDLTQDMELV--ETRPAGDGTFQKWASVVVPLGKE--- 74

                        90       100
                ....*....|....*....|.
gi 13435879 441 qgDQYSCMVGHEALPMNFTQK 461
Cdd:cd21015  75 --QNYTCRVEHEGLPKPLSQR 93
IGc1 smart00407
Immunoglobulin C-Type;
277-343 1.31e-04

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 40.37  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 13435879    277 ASLTCTLNGLrNPEGAVFTW----EPSTgKDAVQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTVTHP 343
Cdd:smart00407   2 ATLVCLVSGF-YPPDITVTWlrngQEVT-EGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHE 70
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
 359-459 2.44e-04

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


Pssm-ID: 409605  Cd Length: 94  Bit Score: 40.12  E-value: 2.44e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 359 TFPPQVHLLPPPSEELAlnelVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAEt 438
Cdd:cd21014   2 TDPPKAHVTHHPRSYGA----VTLRCWALGFYPADITLTWQLNGEELTQDMELV--ETRPAGDGTFQKWASVVVPLGKE- 74

                        90       100
                ....*....|....*....|.
gi 13435879 439 wkqgDQYSCMVGHEALPMNFT 459
Cdd:cd21014  75 ----QNYTCHVNHEGLPEPLT 91
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 150-233 2.58e-04

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: 40.13  E-value: 2.58e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 150 TIYPLTlPRALSSDPVIIGCLIHDYFPSGtMNVTWGKSGKDITT--VNFPPALASGGGYTMSSQLTLPAVECPEGESVKC 227
Cdd:cd07699   5 TIFPPS-SEELSSGKATLVCLINKFYPGF-ATVTWKVDGSTVSSgvTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVYTC 82


                ....*.
gi 13435879 228 SVQHDS 233
Cdd:cd07699  83 EVTHEG 88
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 21-115 3.80e-04

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: 39.68  E-value: 3.80e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  21 VQLVESGGGL-VKPGGSLKLSCAASGfTFSSYAMSWVRQTP---EKRLEWVATISDGGsytyypdnVKGRFTISrdNAKN 96
Cdd:cd04980   1 IVMTQSPASLsVSPGERVTISCKASQ-SISSNYLAWYQQKPgqaPKLLIYYASTLHSG--------VPSRFSGS--GSGT 69

                        90
                ....*....|....*....
gi 13435879  97 NLYLQMSHLKSEDTAMYYC 115
Cdd:cd04980  70 DFTLTISSVEPEDAAVYYC 88
IgI_2_Necl-3 cd05884
Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set ...
 362-454 4.16e-04

Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3; also known as cell adhesion molecule 2 (CADM2)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 409467  Cd Length: 104  Bit Score: 39.91  E-value: 4.16e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 362 PQVHLLPPPSEElalNELVSLTCLVRAFNPKeVLVRWLHGNEELSPESYLvfeplKEPGEGATTYLVTSVLRVSAETWKQ 441
Cdd:cd05884   8 PQISGFTSPVME---GDHIQLTCKTSGSKPA-ADIRWFKNDKEVKDVKYL-----KAEDANRKTFTVSSSLDFHVDRDDD 78

                        90
                ....*....|...
gi 13435879 442 GDQYSCMVGHEAL 454
Cdd:cd05884  79 GVAITCRVDHESL 91
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 380-455 5.85e-04

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: 38.84  E-value: 5.85e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 380 VSLTCLVRAFNPKEVLVRWLHGNEELSPESylvfeplkEPGE----GATTYLVTSVLRVSAEtwkQGDQYSCMVGHEALP 455
Cdd:cd21029  18 LQLSCHVTGFYPRPIEVTWLRDGQEQMDGT--------QSGGilpnHDGTYQLRKTLDIAPG---EGAGYSCRVDHSSLK 86
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
 359-459 8.98e-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: 38.59  E-value: 8.98e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 359 TFPPQVHLLPPPSEELAlnelVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAEt 438
Cdd:cd21020   3 TDPPKAHVTHHRRPEGD----VTLRCWALGFYPADITLTWQLNGEELTQEMELV--ETRPAGDGTFQKWASVVVPLGKE- 75

                        90       100
                ....*....|....*....|.
gi 13435879 439 wkqgDQYSCMVGHEALPMNFT 459
Cdd:cd21020  76 ----QKYTCHVEHEGLPEPLT 92
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 48-141 9.78e-04

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


Pssm-ID: 409503  Cd Length: 112  Bit Score: 39.04  E-value: 9.78e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879  48 FSSYAMSWVRQTPEKRLEWVatISDGGSYTyypDNVKGRFTISRDNAKNNLYLQMSHLKSEDTAMYYCArdMGGSPYGGY 127
Cdd:cd07706  27 WTNYYLFWYKQLPSGEMTFL--IRQDSSEQ---NAKSGRYSVNFQKAQKSISLTISALQLEDSAKYFCA--LSLPYDTDK 99

                        90
                ....*....|....
gi 13435879 128 SRFdywGQGTTITV 141
Cdd:cd07706 100 LIF---GKGTRLTV 110
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 361-449 1.46e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 37.55  E-value: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879   361 PPQVhLLPPPSEELALNELVSLTCLVRAFNPKEvlVRWLHGNEELSPESYLVFeplkepgegaTTYLVTSVLRVSAETWK 440
Cdd:pfam13927   1 KPVI-TVSPSSVTVREGETVTLTCEATGSPPPT--ITWYKNGEPISSGSTRSR----------SLSGSNSTLTISNVTRS 67


                  ....*....
gi 13435879   441 QGDQYSCMV 449
Cdd:pfam13927  68 DAGTYTCVA 76
IgC2_2_ICAM-1_like cd05755
Second immunoglobulin (Ig)-like C2-set domain of intercellular cell adhesion molecule 1 ...
 360-428 1.74e-03

Second immunoglobulin (Ig)-like C2-set domain of intercellular cell adhesion molecule 1 (ICAM-1), and similar domains; The members here are composed of the second immunoglobulin (Ig)-like domain of intercellular cell adhesion molecule 1 (ICAM-1; also known as domain of cluster of differentiation (CD) 54) and similar proteins. During the inflammation process, these molecules recruit leukocytes onto the vascular endothelium before extravasation to the injured tissues. ICAM-1 may be involved in organ targeted tumor metastasis. The interaction of ICAM-1 with leukocyte function-associated antigen-1 (LFA-1) plays a part in leukocyte-endothelial cell recognition. This group also contains ICAM-2 which also interacts with LFA-1. Transmigration of immature dendritic cells across resting endothelium is dependent on the interaction of ICAM-2 with, yet unidentified, ligand(s) on the dendritic cells. ICAM-1 has five Ig-like domains and ICAM-2 has two. ICAM-1 may also act as host receptor for viruses and parasites. The structures of this group show that the second Ig domain lacks a D strand and thus belonging to the C2-set of the IgSF


Pssm-ID: 409413  Cd Length: 101  Bit Score: 37.93  E-value: 1.74e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 360 FPPQVHLLPPPSEElALNELVSLTCLVRAFNPKEVL-VRWLHGNEELSPESYLVFEPLKEPGEGATTYLV 428
Cdd:cd05755   1 PPERVELTPLPSWQ-PVGKNFTLRCRVPGGAPRASLtLVLLRGNETLHRETFGGAAPAPQPAEATFTVLA 69
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
 359-459 1.98e-03

H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the major histocompatibility complex (MHC) H-2 class I histocompatibility complex TLA (thymus leukemia antigen). The murine MHC class I histocompatibility TLA (Thymus leukemia antigen), which is encoded in the T region by T3 and T18 genes, is expressed mainly by intestinal epithelial cells and thymocytes. The murine TLAs are class I, beta-2-microglobulin-associated glycoproteins. The TLA function is not defined by antigen presentation, but rather by its relatively high affinity binding to CD8-alpha-alpha compared with CD8-alpha-beta. The existence of a human homolog for murine TLA remains unresolved. This group is a member of the C1-set Ig domains, which have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409603  Cd Length: 95  Bit Score: 37.79  E-value: 1.98e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 359 TFPPQVHLLPPPSEElalnELVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAEt 438
Cdd:cd21012   3 TDPPKTHVTHHPRPE----GYVTLRCWALGFYPAHITLTWQLNGEELIQDTELV--ETRPAGDGTFQKWAAVVVPSGEE- 75

                        90       100
                ....*....|....*....|.
gi 13435879 439 wkqgDQYSCMVGHEALPMNFT 459
Cdd:cd21012  76 ----QKYTCHVYHEGLPEPLT 92
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
 361-455 2.74e-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: 37.39  E-value: 2.74e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLLPPPSEELAlnelVSLTCLVRAFNPKEVLVRWLHGNEELSPESYLVfePLKEPGEGATTYLVTSVLRVSAEtwk 440
Cdd:cd21016   5 PPKAHVTRHPRPEGD----VTLRCWALGFYPADITLTWQKDGEELTQDMEFV--ETRPAGDGTFQKWAAVVVPLGKE--- 75

                        90
                ....*....|....*
gi 13435879 441 qgDQYSCMVGHEALP 455
Cdd:cd21016  76 --QSYTCHVYHEGLP 88
IgC1_CH2_IgD cd16084
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; ...
 266-343 3.17e-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: 37.03  E-value: 3.17e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 266 PALEDLLLGSDASLTCTLNGlRNPEGAVFTWE-----PSTGKDavQKKAVQNSCGCYSVSSVLPGCAERWNSGASFKCTV 340
Cdd:cd16084   7 PAVQDLWLRDKATFTCFVVG-SDLKDAHLTWEvagkvPTGGVE--EGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTCTL 83


                ...
gi 13435879 341 THP 343
Cdd:cd16084  84 NHP 86
IgV_CAR_like cd20960
Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and ...
 55-115 4.68e-03

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


Pssm-ID: 409552  Cd Length: 114  Bit Score: 37.05  E-value: 4.68e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 13435879  55 WVRQTPEKRLEWVATISDGGSYTYYPDNVKGRFTISRDNAKNNLYLQMSHLKSEDTAMYYC 115
Cdd:cd20960  38 WLLLPSDKVEKVVITYSGDRVYNHYYPALKGRVAFTSNDLSGDASLNISNLKLSDTGTYQC 98
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 169-231 4.74e-03

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: 36.62  E-value: 4.74e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 13435879 169 CLIHDYFPsGTMNVTWGKSGK--DITTVNFPPALASGGGYTMSSQLTLPAVECPEGESVKCSVQH 231
Cdd:cd05847  23 CLISGYTP-STIEVEWLVDGQvaTLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTYTCKVTH 86
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 361-454 4.89e-03

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409594  Cd Length: 96  Bit Score: 36.27  E-value: 4.89e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 361 PPQVHLlpPPSEELALNELVSLTCLVRAFNPKEVLVRW-LHGNEELSpeSYLVFEPLKEpgeGATTYLVTSVLRVsaeTW 439
Cdd:cd21003   3 QPKVNV--SPSKKGPLQHHNLLVCHVTDFYPGNIQVRWfLNGQEETA--GVVSTNLIHN---GDWTFQILVMLEM---TP 72

                        90
                ....*....|....*
gi 13435879 440 KQGDQYSCMVGHEAL 454
Cdd:cd21003  73 QQGDVYTCQVEHPSL 87
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 150-237 8.54e-03

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: 35.83  E-value: 8.54e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 13435879 150 TIYPLTLPRALSSDPVIIGCLIHDYFPSgTMNVTWGKSGKDITT----VNFPPALASGGGYTMSSQLTLPAVECPEGESV 225
Cdd:cd16093   5 SLHAPSREEFLGNRTATFVCLATGFSPK-TISFKWLRNGKEVTSstgaVVEEPKEDGKTLYSATSFLTITESEWKSQTEF 83

                        90
                ....*....|..
gi 13435879 226 KCSVQHDSNAVQ 237
Cdd:cd16093  84 TCEFKHKGEIVE 95
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 163-233 9.36e-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: 35.67  E-value: 9.36e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 13435879 163 DPVIIGCLIHDYFPSgTMNVTWGKSGKDITTVNFPPALA-SGGGYTMSSQLTLPAVECPeGESVKCSVQHDS 233
Cdd:cd21002  18 EPVMLACHVWGFYPA-DVTITWLKNGDPVAPHSSAPKTAqPNGDWTYQTQVTLAVTPSP-GDTYTCSVQHAS 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.
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