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Conserved domains on  [gi|116667833]
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Chain D, Fab fragment, Light chain

Protein Classification

Ig and IgC_L domain-containing protein( domain architecture ID 10309407)

Ig and IgC_L domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 111-210 1.02e-46

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: 149.14  E-value: 1.02e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQS-DNTYSMSSYLTLSSSDWNKHKV 79

                         90       100
                 ....*....|....*....|
gi 116667833 191 YTCEATHKTSTSPIVKSFNR 210
Cdd:cd07699   80 YTCEVTHEGLSSTITKSFNR 99
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 2-105 2.43e-42

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


The actual alignment was detected with superfamily member cd04980:

Pssm-ID: 472250  Cd Length: 106  Bit Score: 138.29  E-value: 2.43e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   2 IVLTQSPAIMSAAPGDKVTMTCSASSSVS--YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSGSGSGTSYSLTINTMEA 79
Cdd:cd04980    1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                         90       100
                 ....*....|....*....|....*.
gi 116667833  80 EDAATYYCQQWSSHPQTFGGGTKLEI 105
Cdd:cd04980   81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
 
Name Accession Description Interval E-value
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 111-210 1.02e-46

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: 149.14  E-value: 1.02e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQS-DNTYSMSSYLTLSSSDWNKHKV 79

                         90       100
                 ....*....|....*....|
gi 116667833 191 YTCEATHKTSTSPIVKSFNR 210
Cdd:cd07699   80 YTCEVTHEGLSSTITKSFNR 99
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 2-105 2.43e-42

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: 138.29  E-value: 2.43e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   2 IVLTQSPAIMSAAPGDKVTMTCSASSSVS--YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSGSGSGTSYSLTINTMEA 79
Cdd:cd04980    1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                         90       100
                 ....*....|....*....|....*.
gi 116667833  80 EDAATYYCQQWSSHPQTFGGGTKLEI 105
Cdd:cd04980   81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
C1-set pfam07654
Immunoglobulin C1-set domain;
114-200 5.66e-30

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 106.18  E-value: 5.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833  114 VSIFPPSSEQLtSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 193
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78


                  ....*..
gi 116667833  194 EATHKTS 200
Cdd:pfam07654  79 RVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
129-203 1.77e-26

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 97.00  E-value: 1.77e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116667833   129 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDsKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSP 203
Cdd:smart00407   2 ATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKN-SDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 6-106 1.98e-12

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: 61.32  E-value: 1.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833    6 QSPAIMSAAPGDKVTMTCSASSSVS----YIHWYQQKSGTSPKRWIY----DTSKLTSGVPVRFSGSGSGTSYSLTINTM 77
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAyysnGSEEGVKKGRFSGRGDPSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 116667833   78 EAEDAATYYCQQWSSHPQTFGGGTKLEIL 106
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 8-105 3.80e-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: 57.13  E-value: 3.80e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833     8 PAIMSAAPGDKVTMTCSASSS-VSYIHWYQQKsgtspKRWIydtskltsGVPVRFSGSGSGTSYSLTINTMEAEDAATYY 86
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSpPPEVTWYKQG-----GKLL--------AESGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                           90
                   ....*....|....*....
gi 116667833    87 CQQWSSHPQTFgGGTKLEI 105
Cdd:smart00410  68 CAATNSSGSAS-SGTTLTV 85
 
Name Accession Description Interval E-value
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 111-210 1.02e-46

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: 149.14  E-value: 1.02e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQS-DNTYSMSSYLTLSSSDWNKHKV 79

                         90       100
                 ....*....|....*....|
gi 116667833 191 YTCEATHKTSTSPIVKSFNR 210
Cdd:cd07699   80 YTCEVTHEGLSSTITKSFNR 99
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 2-105 2.43e-42

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: 138.29  E-value: 2.43e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   2 IVLTQSPAIMSAAPGDKVTMTCSASSSVS--YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSGSGSGTSYSLTINTMEA 79
Cdd:cd04980    1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                         90       100
                 ....*....|....*....|....*.
gi 116667833  80 EDAATYYCQQWSSHPQTFGGGTKLEI 105
Cdd:cd04980   81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
C1-set pfam07654
Immunoglobulin C1-set domain;
114-200 5.66e-30

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 106.18  E-value: 5.66e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833  114 VSIFPPSSEQLtSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 193
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78


                  ....*..
gi 116667833  194 EATHKTS 200
Cdd:pfam07654  79 RVEHEGL 85
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 3-103 1.67e-28

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: 102.93  E-value: 1.67e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   3 VLTQSPAImSAAPGDKVTMTCSASSSVS---YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSGSGSGTSYSLTINTMEA 79
Cdd:cd04984    1 VLTQPSSL-SVSPGETVTITCTGSSGNIsgnYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                         90       100
                 ....*....|....*....|....
gi 116667833  80 EDAATYYCQQWSSHPQTFGGGTKL 103
Cdd:cd04984   80 EDEADYYCQVWDSNSYVFGGGTKL 103
IGc1 smart00407
Immunoglobulin C-Type;
129-203 1.77e-26

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 97.00  E-value: 1.77e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 116667833   129 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDsKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSP 203
Cdd:smart00407   2 ATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKN-SDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 113-208 2.27e-26

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: 97.15  E-value: 2.27e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 113 TVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTdQDSKDSTYSMSSTLTLTKDEYERHNSYT 192
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSP-VEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                         90
                 ....*....|....*.
gi 116667833 193 CEATHKTSTSPIVKSF 208
Cdd:cd00098   80 CVVTHESLKSPLSKTW 95
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 4-105 3.20e-25

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: 94.71  E-value: 3.20e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   4 LTQSPAIMSAAPGDKVTMTCSASSS--VSYIHWYQQKSGTSPKRWIY---DTSKLTSGVPVRFSGSGSGTSY-SLTINTM 77
Cdd:cd00099    1 VTQSPRSLSVQEGESVTLSCEVSSSfsSTYIYWYRQKPGQGPEFLIYlssSKGKTKGGVPGRFSGSRDGTSSfSLTISNL 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 116667833  78 EAEDAATYYCQQWSS---HPQTFGGGTKLEI 105
Cdd:cd00099   81 QPEDSGTYYCAVSESggtDKLTFGSGTRLTV 111
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 111-207 4.56e-21

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: 83.97  E-value: 4.56e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLnswTDQDSK---DSTYSMSSTLTLTKDEYE 186
Cdd:cd05769    2 PPTVALFPPSEaEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVA---TDPQALrenTSTYSLSSRLRVSATEWF 78

                         90       100
                 ....*....|....*....|....
gi 116667833 187 R-HNSYTCEATH--KTSTSPIVKS 207
Cdd:cd05769   79 NpRNTFTCIVKFygGTDTDTWTQG 102
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 112-210 1.50e-18

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: 77.38  E-value: 1.50e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGG-ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                         90       100
                 ....*....|....*....|.
gi 116667833 191 YTCEATHKTSTSPIV-KSFNR 210
Cdd:cd05768   81 FSCVVGHEALPLQFTqKSIDK 101
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 4-103 2.02e-15

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: 69.31  E-value: 2.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   4 LTQSPAIMSAAPGDKVTMTCSASS---SVSYIHWYQQKSGTSPKRWIY-----DTSKLTSGVPVRFSGS--GSGTSYSLT 73
Cdd:cd04982    1 LEQPQLSITREESKSVTISCKVSGidfSTTYIHWYRQKPGQALERLLYvsstsAVRKDSGKTKNKFEARkdVGKSTSTLT 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 116667833  74 INTMEAEDAATYYCQQWSSHPQT----FGGGTKL 103
Cdd:cd04982   81 ITNLEKEDSATYYCAYWESGSGYyikvFGSGTKL 114
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 4-103 6.11e-14

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: 65.38  E-value: 6.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   4 LTQSPAIMSAAPGDKVTMTCSASSSVSYIHWYQQKSGTSPKRWIYDTSKLT---SGVPV-RFSGS-GSGTSYSLTINTME 78
Cdd:cd05899    1 VTQSPRYLIKRRGQSVTLRCSQKSGHDNMYWYRQDPGKGLQLLFYSYGGGLneeGDLPGdRFSASrPSLTRSSLTIKSAE 80

                         90       100
                 ....*....|....*....|....*...
gi 116667833  79 AEDAATYYC---QQWSSHPQTFGGGTKL 103
Cdd:cd05899   81 PEDSAVYLCassLGGGADEAYFGPGTRL 108
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 112-201 1.81e-13

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: 63.57  E-value: 1.81e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGG-ASVVCFLNNFYPKDINVKWKIDGSERQ--NGVLNSWTDQDSKdSTYSMSSTLTLTKDEYERH 188
Cdd:cd16093    2 PTVSLHAPSREEFLGNRtATFVCLATGFSPKTISFKWLRNGKEVTssTGAVVEEPKEDGK-TLYSATSFLTITESEWKSQ 80

                         90
                 ....*....|...
gi 116667833 189 NSYTCEATHKTST 201
Cdd:cd16093   81 TEFTCEFKHKGEI 93
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 5-103 6.94e-13

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: 62.29  E-value: 6.94e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   5 TQSPAIMSAAPGDKVTMTCSASSSVS-YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSGS--GSGTSYSLTINTMEAED 81
Cdd:cd04983    2 TQSPQSLSVQEGENVTLNCNYSTSTFyYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQLSD 81

                         90       100
                 ....*....|....*....|....*
gi 116667833  82 AATYYCQQWSSHPQ---TFGGGTKL 103
Cdd:cd04983   82 SAVYFCALSESGGTgklTFGKGTRL 106
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 6-106 1.98e-12

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: 61.32  E-value: 1.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833    6 QSPAIMSAAPGDKVTMTCSASSSVS----YIHWYQQKSGTSPKRWIY----DTSKLTSGVPVRFSGSGSGTSYSLTINTM 77
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAyysnGSEEGVKKGRFSGRGDPSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 116667833   78 EAEDAATYYCQQWSSHPQTFGGGTKLEIL 106
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 8-105 3.80e-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: 57.13  E-value: 3.80e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833     8 PAIMSAAPGDKVTMTCSASSS-VSYIHWYQQKsgtspKRWIydtskltsGVPVRFSGSGSGTSYSLTINTMEAEDAATYY 86
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSpPPEVTWYKQG-----GKLL--------AESGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                           90
                   ....*....|....*....
gi 116667833    87 CQQWSSHPQTFgGGTKLEI 105
Cdd:smart00410  68 CAATNSSGSAS-SGTTLTV 85
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 112-201 1.05e-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: 1.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd05847    1 PTVQILHSSCaSTLTSETIQLLCLISGYTPSTIEVEWLVDGQVATLSAASTAPQKEE-GGTFSTTSKLNVTQEDWKSGKT 79

                         90
                 ....*....|.
gi 116667833 191 YTCEATHKTST 201
Cdd:cd05847   80 YTCKVTHQGTT 90
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 112-204 4.39e-10

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409591  Cd Length: 96  Bit Score: 54.62  E-value: 4.39e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGGAsVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYsmsSTLTLTKDEYERHNSY 191
Cdd:cd21000    4 PKVTVYPAKTQPLQHHNL-LVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNG-DWTF---QTLVMLETVPRSGEVY 78

                         90
                 ....*....|...
gi 116667833 192 TCEATHKTSTSPI 204
Cdd:cd21000   79 TCQVEHPSVTSPL 91
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 112-207 2.29e-09

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: 52.88  E-value: 2.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPpSSEQLTSGGASVVCFLNNFYPKDINVKWKID---GSERQNGVLNSW--TDQDSKDSTYSMSSTLTLTKDEYE 186
Cdd:cd05771    1 PRVRLSP-KNLVKPDLPQTLSCHIAGYYPLDVDVEWLREepgGSESQVSRDGVSlsSHRQSVDGTYSISSYLTLEPGTEN 79

                         90       100
                 ....*....|....*....|.
gi 116667833 187 RHNSYTCEATHKTSTSPIVKS 207
Cdd:cd05771   80 RGATYTCRVTHVSLEEPLSVS 100
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 111-205 7.75e-09

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: 51.17  E-value: 7.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFppSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYErhnS 190
Cdd:cd21029    2 KPRVRLS--SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGT-QSGGILPNHDGTYQLRKTLDIAPGEGA---G 75

                         90
                 ....*....|....*
gi 116667833 191 YTCEATHKTSTSPIV 205
Cdd:cd21029   76 YSCRVDHSSLKQDLI 90
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 112-204 9.47e-09

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


Pssm-ID: 409590  Cd Length: 99  Bit Score: 51.31  E-value: 9.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGGAsVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYsmsSTLTLTKDEYERHNSY 191
Cdd:cd20998    7 PTVTVYPTKTQPLEHHNL-LVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNG-DWTF---QTLVMLETVPQSGEVY 81

                         90
                 ....*....|...
gi 116667833 192 TCEATHKTSTSPI 204
Cdd:cd20998   82 TCQVEHPSLTDPV 94
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 110-204 1.69e-08

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: 50.49  E-value: 1.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 110 AAPTVSIFPPSSEQLTSGGAsVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKdeyERHN 189
Cdd:cd21001    2 VEPTVTISPSRTEALNHHNL-LVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLIRNG-DWTFQILVMLEMTP---QRGD 76

                         90
                 ....*....|....*
gi 116667833 190 SYTCEATHKTSTSPI 204
Cdd:cd21001   77 VYTCHVEHPSLQSPI 91
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 111-202 2.53e-08

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


Pssm-ID: 409374  Cd Length: 98  Bit Score: 49.90  E-value: 2.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd04985    1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEV 80

                         90
                 ....*....|..
gi 116667833 191 YTCEATHKTSTS 202
Cdd:cd04985   81 YKCQVQHSASNS 92
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 112-204 3.34e-08

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


Pssm-ID: 409423  Cd Length: 96  Bit Score: 49.64  E-value: 3.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGgASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKdeyERHNSY 191
Cdd:cd05766    4 PSVKVSPTKTGPLEHP-NLLVCSVTGFYPAEIEVKWFRNGQEETAGV-VSTELIPNGDWTFQILVMLETTP---RRGDVY 78

                         90
                 ....*....|...
gi 116667833 192 TCEATHKTSTSPI 204
Cdd:cd05766   79 TCQVEHSSLQSPL 91
IGv smart00406
Immunoglobulin V-Type;
19-89 6.16e-08

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 48.53  E-value: 6.16e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833    19 VTMTCSASS---SVSYIHWYQQKSGTSPKRWIYDTSKLT----SGVPVRFSGSGSGTSY--SLTINTMEAEDAATYYCQQ 89
Cdd:smart00406   2 VTLSCKFSGstfSSYYVSWVRQPPGKGLEWLGYIGSNGSsyyqESYKGRFTISKDTSKNdvSLTISNLRVEDTGTYYCAV 81
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 112-207 8.63e-08

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: 48.60  E-value: 8.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQL-TSGGASVVCFLNNFYPKD-INVKWKidgseRQNG--VLNS-WTDQDSKDSTYSMSSTLTLTKDEYE 186
Cdd:cd07696    1 VSVFLIPPSPKDLfLTKSAKVTCLVVDLTSIEeVNVTWS-----REDGneVLAStTNPEKHYNATLSVVSTLTVCADDWD 75

                         90       100
                 ....*....|....*....|.
gi 116667833 187 RHNSYTCEATHKTSTSPIVKS 207
Cdd:cd07696   76 NGKTFKCKVTHPDLPSPIVKS 96
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
 117-197 3.48e-07

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 409507  Cd Length: 96  Bit Score: 46.65  E-value: 3.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 117 FPPS---SEQLTSGG--ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDqdSKDSTYSMSSTLTLTKDEYERHNSY 191
Cdd:cd16085    1 VPPTlevTQQPTMVWnqVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTV--NKDGTYNWTSWLLVNVSAHREDVVL 78


                 ....*.
gi 116667833 192 TCEATH 197
Cdd:cd16085   79 TCQVEH 84
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 128-209 7.55e-07

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: 46.16  E-value: 7.55e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 128 GASVVCFLNNFYPKDINVKWKIDGSErqngVLNSWTD-QDSKDS-TYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIV 205
Cdd:cd05772   19 TVSFTCKSHGFSPRDITLKWFKNGNE----LSALQTTvFPEGDSvSYSVSSTVQVVLTKDDVHSQLTCEVAHVTLQAPLR 94


                 ....
gi 116667833 206 KSFN 209
Cdd:cd05772   95 GTAN 98
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 111-206 1.44e-06

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


Pssm-ID: 409424  Cd Length: 95  Bit Score: 44.99  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPpsSEQLTSGGASV-VCFLNNFYPKDINVKWKIDGSERQNGVlnSWTD-QDSKDSTYSMSSTLTLTKdeyERH 188
Cdd:cd05767    2 PPEVTVFP--KSPVELGEPNTlICFVDNFFPPVINVTWLRNGQPVTDGV--SETVfLPREDHSFRKFSYLPFTP---SEG 74

                         90
                 ....*....|....*...
gi 116667833 189 NSYTCEATHKTSTSPIVK 206
Cdd:cd05767   75 DIYDCRVEHWGLEEPLLK 92
IgC1_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig ...
 111-198 1.54e-06

T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 409494  Cd Length: 98  Bit Score: 44.94  E-value: 1.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSER--QNGVLNSWTDQDskdsTYSMSSTLTLTKDEYEr 187
Cdd:cd07697    1 SPKPTIFLPSIaETEKQKAGTYLCLLENFFPDVIKIHWREKKSDTilESQEGNTEKTKD----TYMKFSWLTVPKKSLG- 75

                         90
                 ....*....|.
gi 116667833 188 hNSYTCEATHK 198
Cdd:cd07697   76 -KEHRCIYKHE 85
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 5-105 2.03e-06

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: 45.20  E-value: 2.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   5 TQSPAIMSAAPGDKVTMTCSASSSVS--YIHWYQQKSGTSPKRWIYDTSKLTSGVPVRFSG--SGSGTSYSLTINTMEAE 80
Cdd:cd07706    3 TQAQPDVSVQVGEEVTLNCRYETSWTnyYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVnfQKAQKSISLTISALQLE 82

                         90       100
                 ....*....|....*....|....*...
gi 116667833  81 DAATYYCQQWSSHPQ---TFGGGTKLEI 105
Cdd:cd07706   83 DSAKYFCALSLPYDTdklIFGKGTRLTV 110
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 112-201 1.12e-05

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: 42.49  E-value: 1.12e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVsiFPPSSEQ-LTSGGASVVCFLNNFYPKDINVKWKIDGSErqnGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 190
Cdd:cd21818    2 PTV--FPLSLCPsLSSDPVVIGCLVQGFFPEPVNVTWNYSGKG---GTARNFPAMLASGGRYTQSSQLTLPADQCPEGEA 76

                         90
                 ....*....|.
gi 116667833 191 YTCEATHKTST 201
Cdd:cd21818   77 YKCSVQHYSPS 87
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 111-205 3.92e-05

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: 41.06  E-value: 3.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIF-PPSSEqltsGGASVVCFLNNFYPKDINVKWKIDGSE----------RQNGvlnswtdqdskDSTYSMSSTLT 179
Cdd:cd07698    2 PPKVHVThHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDqtqdmelvetRPNG-----------DGTFQKWAAVV 66

                         90       100
                 ....*....|....*....|....*.
gi 116667833 180 LTKDEYERhnsYTCEATHKTSTSPIV 205
Cdd:cd07698   67 VPSGEEQR---YTCHVQHEGLPEPLT 89
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 3-88 5.09e-05

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 40.24  E-value: 5.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833    3 VLTQSPAIMSAAPGDKVTMTCSASSS-VSYIHWYQQKSGTSPKRWIYDTSKLTSGVpvrfsgsgsgtsysLTINTMEAED 81
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCEATGSpPPTITWYKNGEPISSGSTRSRSLSGSNST--------------LTISNVTRSD 68


                  ....*..
gi 116667833   82 AATYYCQ 88
Cdd:pfam13927  69 AGTYTCV 75
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 132-204 6.65e-05

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


Pssm-ID: 409594  Cd Length: 96  Bit Score: 40.51  E-value: 6.65e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 116667833 132 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKdeyERHNSYTCEATHKTSTSPI 204
Cdd:cd21003   23 VCHVTDFYPGNIQVRWFLNGQEETAGVVSTNLIHNG-DWTFQILVMLEMTP---QQGDVYTCQVEHPSLDSPV 91
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 4-105 7.83e-05

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: 40.89  E-value: 7.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   4 LTQSPAIMSAAPGDKVTMTCSASSSVSY--IHWYQQKSGTSPKR-------WIyDTSKLTSGVPVR-----FSGSGSGTS 69
Cdd:cd07700    1 LLQTPGSLLVQTNQTVKMSCEAKTSPKNtrIYWLRQRQAPSKDShfeflasWD-PSKGIVYGEGVDqekliILSDSDSSR 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 116667833  70 YSLTINTMEAEDAATYYCQQWSSHPQTFGGGTKLEI 105
Cdd:cd07700   80 YILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKLSV 115
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 111-197 1.58e-04

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


Pssm-ID: 409624  Cd Length: 95  Bit Score: 39.23  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVsiFP-PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQdsKDSTYSMSSTLTLTKDEYERHN 189
Cdd:cd21819    1 APTL--FPlVSCGSSTSDPVTVGCLATDFLPDSITFSWTDDNNSLTTGVKTYPSVL--TGGTYTASSQLQVPESEWKSKE 76


                 ....*...
gi 116667833 190 SYTCEATH 197
Cdd:cd21819   77 NFYCKVEH 84
IgC1_MHC_II_alpha_I-A cd21006
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
 111-209 8.98e-04

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


Pssm-ID: 409597  Cd Length: 95  Bit Score: 37.36  E-value: 8.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPpSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSwTDQDSKDSTYSMSSTLTLTKDEyerHNS 190
Cdd:cd21006    2 APQATVFP-KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYET-SFLVNRDHSFHKLSYLTFIPSD---DDI 76

                         90
                 ....*....|....*....
gi 116667833 191 YTCEATHKTSTSPIVKSFN 209
Cdd:cd21006   77 YDCKVEHWGLEEPVLKHWE 95
IgI_PDGFR-alphabeta cd05861
Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha ...
 143-209 1.08e-03

Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (also known as cluster of differentiation (CD) 140a), and beta (also known as CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,PDGF-B, and PDGF-C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development.


Pssm-ID: 409447  Cd Length: 99  Bit Score: 37.20  E-value: 1.08e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 116667833 143 INVKWKIDGSERQNGVLNSwtdQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN 209
Cdd:cd05861   32 VDLEWTYPGKESGRGIEPV---EEFKVPPYHLVYTLTIPSATLEDSGTYECAVTEATNDHQDEKKIN 95
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 129-205 1.64e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409614  Cd Length: 98  Bit Score: 36.72  E-value: 1.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 116667833 129 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTdQDSKDSTYSMSSTLTLTKDEYERhnsYTCEATHKTSTSPIV 205
Cdd:cd21023   20 ATLRCWALGFYPAEITLTWQRDGEEQTQDTELVET-RPAGDGTFQKWAAVVVPPGEEQR---YTCHVQHEGLPQPLI 92
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 118-205 1.71e-03

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


Pssm-ID: 409612  Cd Length: 94  Bit Score: 36.68  E-value: 1.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 118 PP---SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERhnsYTCE 194
Cdd:cd21021    4 PPlvkVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQR---YTCQ 80

                         90
                 ....*....|.
gi 116667833 195 ATHKTSTSPIV 205
Cdd:cd21021   81 VEHPGLDQPLI 91
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 15-87 2.08e-03

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: 36.90  E-value: 2.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833  15 PGDKVTMTCSASS---SVSYIHWYQQKSGTSPKrWI----YDTSKLTSGVPVR----FSGSGSGTSYSLTINTMEAEDAA 83
Cdd:cd04981   12 PGQSLKLSCKASGftfTSYGMGWVRQAPGKGLE-WIgliyPGGGDTYYADSFKgrftITRDTSKSTAYLQLNSLTSEDTA 90


                 ....
gi 116667833  84 TYYC 87
Cdd:cd04981   91 VYYC 94
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 111-206 3.60e-03

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: 35.50  E-value: 3.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 111 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKidgSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERhNS 190
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWN---SGSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSWGS-QT 76

                         90
                 ....*....|....*.
gi 116667833 191 YTCEATHKTSTSPIVK 206
Cdd:cd21817   77 FTCNVEHKPSSTKVDK 92
IgC1_MHC_II_alpha_HLA-DQ cd21008
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
 112-206 7.05e-03

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


Pssm-ID: 409599  Cd Length: 95  Bit Score: 34.92  E-value: 7.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPPSSEQLTSGGaSVVCFLNNFYPKDINVKWKIDGSERQNGVlnSWTDQDSK-DSTYSMSSTLTLTKDEYErhnS 190
Cdd:cd21008    3 PEVTVFPKSPVTLGQPN-TLICLVDNIFPPVINITWLSNGHSVTEGV--SETSFLSKsDHSFLKISYLTFLPSADD---I 76

                         90
                 ....*....|....*.
gi 116667833 191 YTCEATHKTSTSPIVK 206
Cdd:cd21008   77 YDCKVEHWGLDKPLLK 92
IgV_CD79b_beta cd16096
Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are ...
 6-105 8.37e-03

Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are composed of the immunoglobulin variable domain (IgV) of the Cluster of Differentiation (CD) 79B (also known as CD79b molecule, immunoglobulin-associated beta (Ig-beta), and B29). The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. Members of the IgV family 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409515  Cd Length: 96  Bit Score: 34.54  E-value: 8.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833   6 QSPAIMSAAPGDKVTMTCSASSSvSYIHWYQQKSGTSPKRWiydtsKLTSGvpvRFSGSGSGTSYSLTINTMEAEDAATY 85
Cdd:cd16096    3 QHPRFAAKKRSSMVKFHCYTNYS-GVMTWFRKKGNQRPQEL-----FPEDG---RISQTQNGSVYTLTIQNIQYEDNGIY 73

                         90       100
                 ....*....|....*....|...
gi 116667833  86 YCQQW---SSHPQTFGGGTKLEI 105
Cdd:cd16096   74 FCQQKcnsTEPDVTDGCGTELLV 96
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 112-206 9.79e-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: 34.51  E-value: 9.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 116667833 112 PTVSIFPpSSEQLTSGGASVVCFLNNFYPKDINVKWkidgseRQNGVLNSWTDQDSK------DSTYSMSSTLTLT---K 182
Cdd:cd21002    4 PSVRVAP-TTPFNTREPVMLACHVWGFYPADVTITW------LKNGDPVAPHSSAPKtaqpngDWTYQTQVTLAVTpspG 76

                         90       100
                 ....*....|....*....|....
gi 116667833 183 DeyerhnSYTCEATHKTSTSPIVK 206
Cdd:cd21002   77 D------TYTCSVQHASLPEPLLE 94
 
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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