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Conserved domains on  [gi|1032530219|gb|ANG83989|]
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1F5-NQ-28-BB-z-2A-trCD19 [synthetic construct]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 147-265 5.75e-71

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: 231.43  E-value: 5.75e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  147 QLRQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQ 226
Cdd:cd04981      1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1032530219  227 LSSLTSEDSAVYYCARSHYGSNYvDYFDYWGQGTTLTVS 265
Cdd:cd04981     81 LNSLTSEDTAVYYCARGLGGYGY-SYFDYWGQGTTVTVS 118
CD19_protodomain_1_2 cd23999
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 ...
 762-853 2.87e-53

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 and 2; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 1 and 2 of the CD19 double Ig domain.


:

Pssm-ID: 467826  Cd Length: 92  Bit Score: 180.70  E-value: 2.87e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  762 LVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKPFLKLSLGLPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPS 841
Cdd:cd23999      1 LLVEVEEGDNAVLPCLIGPSDGPPEQLTWSRGGQLEPFLQLSLGSPGLGAQVGPLGIWLFIFNVSEQMGGFYLCELGPPS 80

                           90
                   ....*....|..
gi 1032530219  842 EKAWQPGWTVNV 853
Cdd:cd23999     81 KQAWQPGWTVSV 92
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 397-497 3.82e-48

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: 166.36  E-value: 3.82e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 473
Cdd:cd05768      1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                           90       100
                   ....*....|....*....|....
gi 1032530219  474 FSCSVMHEALHNHYTQKSLSLSPF 497
Cdd:cd05768     81 FSCVVGHEALPLQFTQKSIDKSPG 104
CD19_protodomain_3_4 cd23998
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 ...
 924-1012 6.19e-48

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain.


:

Pssm-ID: 467825  Cd Length: 95  Bit Score: 165.36  E-value: 6.19e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  924 QDLTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPK-GPKSLLSLELKDDRPARDMWVM-----ETGLLLPRATAQDAGKY 997
Cdd:cd23998      1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKpSNTSLLSLELKEDRPAREKWVLgtlrgGALLLLPRATAQDAGIY 80

                           90
                   ....*....|....*
gi 1032530219  998 YCHRGNLTMSFHLEI 1012
Cdd:cd23998     81 HCHLGNRTISMELTV 95
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 22-125 1.26e-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: 150.62  E-value: 1.26e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   22 IVLSQSPAILSASPGEKVTMTCRASSSLS--FMHWYQQKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEA 99
Cdd:cd04980      1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                           90       100
                   ....*....|....*....|....*.
gi 1032530219  100 EDAATYFCHQWSSNPLTFGAGTKLEL 125
Cdd:cd04980     81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 290-388 3.28e-39

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: 140.66  E-value: 3.28e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYQSTYRVVSVLTVLHQDWLNGK 368
Cdd:cd07696      2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                           90       100
                   ....*....|....*....|
gi 1032530219  369 EYKCKVSNKALPAPIEKTIS 388
Cdd:cd07696     79 TFKCKVTHPDLPSPIVKSIQ 98
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 624-644 1.94e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


:

Pssm-ID: 128390  Cd Length: 21  Bit Score: 39.29  E-value: 1.94e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   624 NQLYNELNLGRREEYDVLDKR 644
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 693-713 8.25e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


:

Pssm-ID: 128390  Cd Length: 21  Bit Score: 37.36  E-value: 8.25e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   693 DGLYQGLSTATKDTYDALHMQ 713
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 147-265 5.75e-71

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: 231.43  E-value: 5.75e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  147 QLRQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQ 226
Cdd:cd04981      1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1032530219  227 LSSLTSEDSAVYYCARSHYGSNYvDYFDYWGQGTTLTVS 265
Cdd:cd04981     81 LNSLTSEDTAVYYCARGLGGYGY-SYFDYWGQGTTVTVS 118
CD19_protodomain_1_2 cd23999
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 ...
 762-853 2.87e-53

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 and 2; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 1 and 2 of the CD19 double Ig domain.


Pssm-ID: 467826  Cd Length: 92  Bit Score: 180.70  E-value: 2.87e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  762 LVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKPFLKLSLGLPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPS 841
Cdd:cd23999      1 LLVEVEEGDNAVLPCLIGPSDGPPEQLTWSRGGQLEPFLQLSLGSPGLGAQVGPLGIWLFIFNVSEQMGGFYLCELGPPS 80

                           90
                   ....*....|..
gi 1032530219  842 EKAWQPGWTVNV 853
Cdd:cd23999     81 KQAWQPGWTVSV 92
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 397-497 3.82e-48

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: 166.36  E-value: 3.82e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 473
Cdd:cd05768      1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                           90       100
                   ....*....|....*....|....
gi 1032530219  474 FSCSVMHEALHNHYTQKSLSLSPF 497
Cdd:cd05768     81 FSCVVGHEALPLQFTQKSIDKSPG 104
CD19_protodomain_3_4 cd23998
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 ...
 924-1012 6.19e-48

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain.


Pssm-ID: 467825  Cd Length: 95  Bit Score: 165.36  E-value: 6.19e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  924 QDLTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPK-GPKSLLSLELKDDRPARDMWVM-----ETGLLLPRATAQDAGKY 997
Cdd:cd23998      1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKpSNTSLLSLELKEDRPAREKWVLgtlrgGALLLLPRATAQDAGIY 80

                           90
                   ....*....|....*
gi 1032530219  998 YCHRGNLTMSFHLEI 1012
Cdd:cd23998     81 HCHLGNRTISMELTV 95
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 22-125 1.26e-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: 150.62  E-value: 1.26e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   22 IVLSQSPAILSASPGEKVTMTCRASSSLS--FMHWYQQKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEA 99
Cdd:cd04980      1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                           90       100
                   ....*....|....*....|....*.
gi 1032530219  100 EDAATYFCHQWSSNPLTFGAGTKLEL 125
Cdd:cd04980     81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 290-388 3.28e-39

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: 140.66  E-value: 3.28e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYQSTYRVVSVLTVLHQDWLNGK 368
Cdd:cd07696      2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                           90       100
                   ....*....|....*....|
gi 1032530219  369 EYKCKVSNKALPAPIEKTIS 388
Cdd:cd07696     79 TFKCKVTHPDLPSPIVKSIQ 98
C1-set pfam07654
Immunoglobulin C1-set domain;
399-483 5.33e-36

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 130.83  E-value: 5.33e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  399 VYTLPPSRDELtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 477
Cdd:pfam07654    1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                   ....*.
gi 1032530219  478 VMHEAL 483
Cdd:pfam07654   80 VEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
413-486 1.17e-31

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 118.19  E-value: 1.17e-31
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1032530219   413 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 486
Cdd:smart00407    1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IGv smart00406
Immunoglobulin V-Type;
161-242 1.02e-28

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 110.16  E-value: 1.02e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   161 SVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYpGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYC 240
Cdd:smart00406    1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIG-SNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                    ..
gi 1032530219   241 AR 242
Cdd:smart00406   80 AV 81
C1-set pfam07654
Immunoglobulin C1-set domain;
291-379 1.54e-21

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 89.62  E-value: 1.54e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  291 VFLFPPKPKDTlmiSRTPEVTCVVVDVSHedPEVKFNWYVDGVEVHN-AKTKPREEQYQSTYRVVSVLTVLHQDWLNGKE 369
Cdd:pfam07654    1 VYVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75

                           90
                   ....*....|
gi 1032530219  370 YKCKVSNKAL 379
Cdd:pfam07654   76 YTCRVEHEGL 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 26-123 3.86e-14

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: 69.41  E-value: 3.86e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   26 QSPAILSASPGEKVTMTCRASSSLS----FMHWYQQKPGSSPKPWIYATSNLA--SGVPARFSGSGSGTSY--SLTISRV 97
Cdd:pfam07686    1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAYYSNGSeeGVKKGRFSGRGDPSNGdgSLTIQNL 80

                           90       100
                   ....*....|....*....|....*.
gi 1032530219   98 EAEDAATYFCHQWSSNPLTFGAGTKL 123
Cdd:pfam07686   81 TLSDSGTYTCAVIPSGEGVFGKGTRL 106
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 155-264 8.11e-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: 62.86  E-value: 8.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  155 LVKPGASVKMSCKASGY-TFTSYNMHWVKQTPGQGLEWIGAIYPGNGDTSynqKFKGKATLTADKSSSTAYMQLSSLTSE 233
Cdd:pfam07686    7 TVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEG---VKKGRFSGRGDPSNGDGSLTIQNLTLS 83

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1032530219  234 DSAVYYCARSHYGSNyvdyfdYWGQGTTLTV 264
Cdd:pfam07686   84 DSGTYTCAVIPSGEG------VFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-124 1.20e-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: 61.75  E-value: 1.20e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219    28 PAILSASPGEKVTMTCRASSSLS-FMHWYQQKPgsspkPWIyatsnlasGVPARFSGSGSGTSYSLTISRVEAEDAATYF 106
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSPPpEVTWYKQGG-----KLL--------AESGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                            90
                    ....*....|....*...
gi 1032530219   107 CHQWSSNPLTFGaGTKLE 124
Cdd:smart00410   68 CAATNSSGSASS-GTTLT 84
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 761-853 1.73e-05

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: 44.03  E-value: 1.73e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   761 PLVVKVEEGDNAVLQCLkgTSDGPTQQLTWSRESPLKPFLKlslglPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPP 840
Cdd:smart00410    1 PPSVTVKEGESVTLSCE--ASGSPPPEVTWYKQGGKLLAES-----GRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNS 73

                            90
                    ....*....|...
gi 1032530219   841 SEKAWQpGWTVNV 853
Cdd:smart00410   74 SGSASS-GTTLTV 85
IGc1 smart00407
Immunoglobulin C-Type;
310-382 9.29e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.53  E-value: 9.29e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032530219   310 VTCVVVDVSHEDPEVKfnWYVDGVEVH-NAKTKPREEQYQSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAP 382
Cdd:smart00407    4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 624-644 1.94e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


Pssm-ID: 128390  Cd Length: 21  Bit Score: 39.29  E-value: 1.94e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   624 NQLYNELNLGRREEYDVLDKR 644
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 923-1012 7.70e-04

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: 39.41  E-value: 7.70e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   923 SQDLTMAPGSTLWLSCGVPPDSVSRgpLSWTHvhpKGPKSLLSlelkddrPARDMWVMETG---LLLPRATAQDAGKYYC 999
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSPPPE--VTWYK---QGGKLLAE-------SGRFSVSRSGStstLTISNVTPEDSGTYTC 68

                            90
                    ....*....|....*..
gi 1032530219  1000 HR----GNLTMSFHLEI 1012
Cdd:smart00410   69 AAtnssGSASSGTTLTV 85
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 693-713 8.25e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


Pssm-ID: 128390  Cd Length: 21  Bit Score: 37.36  E-value: 8.25e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   693 DGLYQGLSTATKDTYDALHMQ 713
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
ITAM pfam02189
Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex ...
 693-712 2.75e-03

Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains.


Pssm-ID: 426646  Cd Length: 20  Bit Score: 36.20  E-value: 2.75e-03
                           10        20
                   ....*....|....*....|
gi 1032530219  693 DGLYQGLSTATKDTYDALHM 712
Cdd:pfam02189    1 DQLYQPLNKRDDDTYSHLGM 20
ITAM pfam02189
Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex ...
 624-643 3.34e-03

Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains.


Pssm-ID: 426646  Cd Length: 20  Bit Score: 35.82  E-value: 3.34e-03
                           10        20
                   ....*....|....*....|
gi 1032530219  624 NQLYNELNLGRREEYDVLDK 643
Cdd:pfam02189    1 DQLYQPLNKRDDDTYSHLGM 20
 
Name Accession Description Interval E-value
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 147-265 5.75e-71

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: 231.43  E-value: 5.75e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  147 QLRQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQ 226
Cdd:cd04981      1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1032530219  227 LSSLTSEDSAVYYCARSHYGSNYvDYFDYWGQGTTLTVS 265
Cdd:cd04981     81 LNSLTSEDTAVYYCARGLGGYGY-SYFDYWGQGTTVTVS 118
CD19_protodomain_1_2 cd23999
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 ...
 762-853 2.87e-53

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 and 2; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 1 and 2 of the CD19 double Ig domain.


Pssm-ID: 467826  Cd Length: 92  Bit Score: 180.70  E-value: 2.87e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  762 LVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKPFLKLSLGLPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPS 841
Cdd:cd23999      1 LLVEVEEGDNAVLPCLIGPSDGPPEQLTWSRGGQLEPFLQLSLGSPGLGAQVGPLGIWLFIFNVSEQMGGFYLCELGPPS 80

                           90
                   ....*....|..
gi 1032530219  842 EKAWQPGWTVNV 853
Cdd:cd23999     81 KQAWQPGWTVSV 92
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 397-497 3.82e-48

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: 166.36  E-value: 3.82e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 473
Cdd:cd05768      1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                           90       100
                   ....*....|....*....|....
gi 1032530219  474 FSCSVMHEALHNHYTQKSLSLSPF 497
Cdd:cd05768     81 FSCVVGHEALPLQFTQKSIDKSPG 104
CD19_protodomain_3_4 cd23998
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 ...
 924-1012 6.19e-48

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain.


Pssm-ID: 467825  Cd Length: 95  Bit Score: 165.36  E-value: 6.19e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  924 QDLTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPK-GPKSLLSLELKDDRPARDMWVM-----ETGLLLPRATAQDAGKY 997
Cdd:cd23998      1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKpSNTSLLSLELKEDRPAREKWVLgtlrgGALLLLPRATAQDAGIY 80

                           90
                   ....*....|....*
gi 1032530219  998 YCHRGNLTMSFHLEI 1012
Cdd:cd23998     81 HCHLGNRTISMELTV 95
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 22-125 1.26e-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: 150.62  E-value: 1.26e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   22 IVLSQSPAILSASPGEKVTMTCRASSSLS--FMHWYQQKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEA 99
Cdd:cd04980      1 IVMTQSPASLSVSPGERVTISCKASQSISsnYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                           90       100
                   ....*....|....*....|....*.
gi 1032530219  100 EDAATYFCHQWSSNPLTFGAGTKLEL 125
Cdd:cd04980     81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
 290-388 3.28e-39

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: 140.66  E-value: 3.28e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYQSTYRVVSVLTVLHQDWLNGK 368
Cdd:cd07696      2 SVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNGK 78

                           90       100
                   ....*....|....*....|
gi 1032530219  369 EYKCKVSNKALPAPIEKTIS 388
Cdd:cd07696     79 TFKCKVTHPDLPSPIVKSIQ 98
CD19_double_Ig cd23997
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, ...
 762-853 2.49e-38

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding.


Pssm-ID: 467824  Cd Length: 89  Bit Score: 137.85  E-value: 2.49e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  762 LVVKVEEGDNAVLQCLKGTSDGPTQQLTWSRESPLKPFLKLSLGLPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPPS 841
Cdd:cd23997      1 LDVTVAEGSTLWLPCLVPPSDGPRGPLTWSRGHPKTPLLSLELGSPGLWVLVGPLGILLLLPNVSAQMGGFYLCELGNLS 80

                           90
                   ....*....|..
gi 1032530219  842 ekaWQPGWTVNV 853
Cdd:cd23997     81 ---WTIGWTVSV 89
C1-set pfam07654
Immunoglobulin C1-set domain;
399-483 5.33e-36

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 130.83  E-value: 5.33e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  399 VYTLPPSRDELtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 477
Cdd:pfam07654    1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79


                   ....*.
gi 1032530219  478 VMHEAL 483
Cdd:pfam07654   80 VEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
413-486 1.17e-31

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 118.19  E-value: 1.17e-31
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1032530219   413 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 486
Cdd:smart00407    1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 23-123 5.00e-29

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: 111.78  E-value: 5.00e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   23 VLSQSPAiLSASPGEKVTMTCRASSSLS---FMHWYQQKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEA 99
Cdd:cd04984      1 VLTQPSS-LSVSPGETVTITCTGSSGNIsgnYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                           90       100
                   ....*....|....*....|....
gi 1032530219  100 EDAATYFCHQWSSNPLTFGAGTKL 123
Cdd:cd04984     80 EDEADYYCQVWDSNSYVFGGGTKL 103
IGv smart00406
Immunoglobulin V-Type;
161-242 1.02e-28

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 110.16  E-value: 1.02e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   161 SVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIYpGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYC 240
Cdd:smart00406    1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIG-SNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                    ..
gi 1032530219   241 AR 242
Cdd:smart00406   80 AV 81
CD19_double_Ig cd23997
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, ...
 924-1012 3.79e-28

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding.


Pssm-ID: 467824  Cd Length: 89  Bit Score: 108.58  E-value: 3.79e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  924 QDLTMAPGSTLWLSCGVPPDSVSRGPLSWTHVHPKgpKSLLSLELKDdrpaRDMWVMET----GLLLPRATAQDAGKYYC 999
Cdd:cd23997      1 LDVTVAEGSTLWLPCLVPPSDGPRGPLTWSRGHPK--TPLLSLELGS----PGLWVLVGplgiLLLLPNVSAQMGGFYLC 74

                           90
                   ....*....|....*
gi 1032530219 1000 HRGNL--TMSFHLEI 1012
Cdd:cd23997     75 ELGNLswTIGWTVSV 89
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 148-264 8.32e-28

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: 108.58  E-value: 8.32e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  148 LRQPGAEL-VKPGASVKMSCKASGyTFTSYNMHWVKQTPGQGLEWIgaIYPGNGDTSYNQKFKGKATLTADKSSStAYMQ 226
Cdd:cd00099      1 VTQSPRSLsVQEGESVTLSCEVSS-SFSSTYIYWYRQKPGQGPEFL--IYLSSSKGKTKGGVPGRFSGSRDGTSS-FSLT 76

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1032530219  227 LSSLTSEDSAVYYCARSHYGSNYVDYFdywGQGTTLTV 264
Cdd:cd00099     77 ISNLQPEDSGTYYCAVSESGGTDKLTF---GSGTRLTV 111
Ig_Semaphorin_C cd04979
Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are ...
 920-1024 1.67e-26

Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are composed of the immunoglobulin (Ig)-like domain in semaphorins. Semaphorins are transmembrane protein that have important roles in a variety of tissues. Functionally, semaphorins were initially characterized for their importance in the development of the nervous system and in axonal guidance. Later they have been found to be important for the formation and functioning of the cardiovascular, endocrine, gastrointestinal, hepatic, immune, musculoskeletal, renal, reproductive, and respiratory systems. Semaphorins function through binding to their receptors and transmembrane semaphorins also serves as receptors themselves. Although molecular mechanism of semaphorins is poorly understood, the Ig-like domains may be involved in ligand binding or dimerization.


Pssm-ID: 409368  Cd Length: 88  Bit Score: 104.08  E-value: 1.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  920 QSLSQDLTMaPGSTLWLSCGVPPdsvSRGPLSWTHVHPKGPKSllslelkddRPARDMWVMETGLLLPRATAQDAGKYYC 999
Cdd:cd04979      1 TSFKQISVK-EGDTVILSCSVKS---NNAPVTWIHNGKKVPRY---------RSPRLVLKTERGLLIRSAQEADAGVYEC 67

                           90       100
                   ....*....|....*....|....*
gi 1032530219 1000 HRGNLTmsfhLEITARPVLWHWLLR 1024
Cdd:cd04979     68 HSGERV----LGSTLRSVTLHVLER 88
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 24-124 6.38e-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: 100.49  E-value: 6.38e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   24 LSQSPAILSASPGEKVTMTCRASSSLSF--MHWYQQKPGSSPKPWIYATSNLAS---GVPARFSGSGSGTSY-SLTISRV 97
Cdd:cd00099      1 VTQSPRSLSVQEGESVTLSCEVSSSFSStyIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGTSSfSLTISNL 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1032530219   98 EAEDAATYFCHQWSS---NPLTFGAGTKLE 124
Cdd:cd00099     81 QPEDSGTYYCAVSESggtDKLTFGSGTRLT 110
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 398-483 1.08e-22

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: 93.29  E-value: 1.08e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  398 QVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSC 476
Cdd:cd00098      1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTsGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80


                   ....*..
gi 1032530219  477 SVMHEAL 483
Cdd:cd00098     81 VVTHESL 87
C1-set pfam07654
Immunoglobulin C1-set domain;
291-379 1.54e-21

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 89.62  E-value: 1.54e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  291 VFLFPPKPKDTlmiSRTPEVTCVVVDVSHedPEVKFNWYVDGVEVHN-AKTKPREEQYQSTYRVVSVLTVLHQDWLNGKE 369
Cdd:pfam07654    1 VYVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75

                           90
                   ....*....|
gi 1032530219  370 YKCKVSNKAL 379
Cdd:pfam07654   76 YTCRVEHEGL 85
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 396-483 1.83e-19

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: 84.43  E-value: 1.83e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  396 EPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 474
Cdd:cd07699      1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTvSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVY 80


                   ....*....
gi 1032530219  475 SCSVMHEAL 483
Cdd:cd07699     81 TCEVTHEGL 89
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 150-264 1.72e-18

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: 81.93  E-value: 1.72e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  150 QPGAEL-VKPGASVKMSCKASgyTFTSYNMHWVKQTPGQGLEWIGAIYPGNGDtsynqKFKGKATLTADKSSSTAYMQLS 228
Cdd:cd04983      3 QSPQSLsVQEGENVTLNCNYS--TSTFYYLFWYRQYPGQGPQFLIYISSDSGN-----KKKGRFSATLDKSRKSSSLHIS 75

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1032530219  229 SLTSEDSAVYYCARSHYGSNYVDYFdywGQGTTLTV 264
Cdd:cd04983     76 AAQLSDSAVYFCALSESGGTGKLTF---GKGTRLTV 108
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 24-123 1.45e-17

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: 79.25  E-value: 1.45e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   24 LSQSPAILSASPGEKVTMTCRASSSLSFMHWYQQKPGSSPKPWIYATSNLA---SGVPA-RFSGS-GSGTSYSLTISRVE 98
Cdd:cd05899      1 VTQSPRYLIKRRGQSVTLRCSQKSGHDNMYWYRQDPGKGLQLLFYSYGGGLneeGDLPGdRFSASrPSLTRSSLTIKSAE 80

                           90       100
                   ....*....|....*....|....*...
gi 1032530219   99 AEDAATYFC---HQWSSNPLTFGAGTKL 123
Cdd:cd05899     81 PEDSAVYLCassLGGGADEAYFGPGTRL 108
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 155-264 8.17e-17

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: 77.32  E-value: 8.17e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  155 LVKPGASVKMSC-KASGYtftsYNMHWVKQTPGQGLEWIGaiypgngdTSYNQKFKGKATLTADK------SSSTAYMQL 227
Cdd:cd05899      9 IKRRGQSVTLRCsQKSGH----DNMYWYRQDPGKGLQLLF--------YSYGGGLNEEGDLPGDRfsasrpSLTRSSLTI 76

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1032530219  228 SSLTSEDSAVYYCARSHYGSNYVDYFdywGQGTTLTV 264
Cdd:cd05899     77 KSAEPEDSAVYLCASSLGGGADEAYF---GPGTRLTV 110
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 148-264 1.18e-16

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: 76.35  E-value: 1.18e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  148 LRQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLewIGAIYPGNGDTS-YNQKFKGKatltadKSSSTAYMQ 226
Cdd:cd04984      2 LTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAP--RYLIYEDKHRPSgIPDRFSGS------KSGNTASLT 73

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1032530219  227 LSSLTSEDSAVYYCArSHYGSNYVdyfdyWGQGTTLTV 264
Cdd:cd04984     74 ISGAQTEDEADYYCQ-VWDSNSYV-----FGGGTKLTV 105
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 397-493 2.68e-16

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: 75.12  E-value: 2.68e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNG---QPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGN 472
Cdd:cd16093      2 PTVSLHAPSREEFLGNRtATFVCLATGFSPKTISFKWLRNGkevTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                           90       100
                   ....*....|....*....|.
gi 1032530219  473 VFSCSVMHEalhNHYTQKSLS 493
Cdd:cd16093     82 EFTCEFKHK---GEIVEKNAS 99
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 290-393 1.81e-15

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


Pssm-ID: 409425  Cd Length: 105  Bit Score: 73.14  E-value: 1.81e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPkPKDTLMISRTPEVTCVVVDVSHEDPEVKfnWYVDGVEVHNAK---TKPREEQyQSTYRVVSVLTVLHQDWLN 366
Cdd:cd05768      2 SVYLLPP-PEEELSLNETVTLTCLVKGFYPEDIFVS--WLQNGEPLPSADyktTAPVPES-DGSFFVYSKLNVSTADWNS 77

                           90       100
                   ....*....|....*....|....*...
gi 1032530219  367 GKEYKCKVSNKALPAP-IEKTISKAKGQ 393
Cdd:cd05768     78 GDVFSCVVGHEALPLQfTQKSIDKSPGK 105
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 26-123 3.04e-15

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: 72.69  E-value: 3.04e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   26 QSPAILSASPGEKVTMTCRASSSLS-FMHWYQQKPGSSPKPWIYATS---NLASGvpaRFSGS--GSGTSYSLTISRVEA 99
Cdd:cd04983      3 QSPQSLSVQEGENVTLNCNYSTSTFyYLFWYRQYPGQGPQFLIYISSdsgNKKKG---RFSATldKSRKSSSLHISAAQL 79

                           90       100
                   ....*....|....*....|....*..
gi 1032530219  100 EDAATYFC---HQWSSNPLTFGAGTKL 123
Cdd:cd04983     80 SDSAVYFCalsESGGTGKLTFGKGTRL 106
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 148-265 6.42e-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: 72.01  E-value: 6.42e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  148 LRQPGAELVKP-GASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIgAIYPGNGDTSYNQKF-KGKATLTADKSSSTAYM 225
Cdd:cd04982      1 LEQPQLSITREeSKSVTISCKVSGIDFSTTYIHWYRQKPGQALERL-LYVSSTSAVRKDSGKtKNKFEARKDVGKSTSTL 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1032530219  226 QLSSLTSEDSAVYYCARSHYGSNYvdYFDYWGQGTTLTVS 265
Cdd:cd04982     80 TITNLEKEDSATYYCAYWESGSGY--YIKVFGSGTKLIVT 117
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
 397-482 9.33e-15

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: 70.55  E-value: 9.33e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESnGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWqQGNVFSC 476
Cdd:cd21817      2 PSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNS-GSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSW-GSQTFTC 79


                   ....*.
gi 1032530219  477 SVMHEA 482
Cdd:cd21817     80 NVEHKP 85
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 290-387 1.12e-14

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: 70.57  E-value: 1.12e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDTLmiSRTPEVTCVVVDVSHEDpeVKFNWYVDGVEVHNAKTKPRE-EQYQSTYRVVSVLTVLHQDWLNGK 368
Cdd:cd00098      1 TVTLLPPSPEEKG--GGKVTLVCLVSGFYPKD--ITVTWLKNGVPLTSGVSTSSPvEPNDGTYSVTSSLTVPPSDWDEGA 76

                           90
                   ....*....|....*....
gi 1032530219  369 EYKCKVSNKALPAPIEKTI 387
Cdd:cd00098     77 TYTCVVTHESLKSPLSKTW 95
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 397-483 2.06e-14

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: 69.75  E-value: 2.06e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPS-RDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 474
Cdd:cd05847      1 PTVQILHSScASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVaTLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTY 80


                   ....*....
gi 1032530219  475 SCSVMHEAL 483
Cdd:cd05847     81 TCKVTHQGT 89
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 26-123 3.86e-14

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: 69.41  E-value: 3.86e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   26 QSPAILSASPGEKVTMTCRASSSLS----FMHWYQQKPGSSPKPWIYATSNLA--SGVPARFSGSGSGTSY--SLTISRV 97
Cdd:pfam07686    1 QTPREVTVALGGSVTLPCTYSSSMSeastSVYWYRQPPGKGPTFLIAYYSNGSeeGVKKGRFSGRGDPSNGdgSLTIQNL 80

                           90       100
                   ....*....|....*....|....*.
gi 1032530219   98 EAEDAATYFCHQWSSNPLTFGAGTKL 123
Cdd:pfam07686   81 TLSDSGTYTCAVIPSGEGVFGKGTRL 106
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 24-123 1.54e-13

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


Pssm-ID: 409371  Cd Length: 117  Bit Score: 68.16  E-value: 1.54e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   24 LSQSPAILSASPGEKVTMTCRASS---SLSFMHWYQQKPGSSPKPWIYATSNLA----SGVPA-RFSGSGSGTSYS--LT 93
Cdd:cd04982      1 LEQPQLSITREESKSVTISCKVSGidfSTTYIHWYRQKPGQALERLLYVSSTSAvrkdSGKTKnKFEARKDVGKSTstLT 80

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1032530219   94 ISRVEAEDAATYFCHQWSSNPLT----FGAGTKL 123
Cdd:cd04982     81 ITNLEKEDSATYYCAYWESGSGYyikvFGSGTKL 114
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 151-264 2.80e-13

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: 66.37  E-value: 2.80e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   151 PGAELVKPGASVKMSCKASGytFTSYNMHWVKQtpgqGLEWIgaiypgngdtSYNQKFKGkatltaDKSSSTAYMQLSSL 230
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASG--SPPPEVTWYKQ----GGKLL----------AESGRFSV------SRSGSTSTLTISNV 58

                            90       100       110
                    ....*....|....*....|....*....|....
gi 1032530219   231 TSEDSAVYYCARShygsnyVDYFDYWGqGTTLTV 264
Cdd:smart00410   59 TPEDSGTYTCAAT------NSSGSASS-GTTLTV 85
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 397-482 4.43e-13

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: 66.07  E-value: 4.43e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 474
Cdd:cd04985      2 PTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqkNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVY 81


                   ....*...
gi 1032530219  475 SCSVMHEA 482
Cdd:cd04985     82 KCQVQHSA 89
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 395-484 9.01e-13

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: 65.86  E-value: 9.01e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  395 REPQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFF-LYSKLTVDKSRWQQ- 470
Cdd:cd05769      1 TPPTVALFPPSEAEIRNKRkATLVCLATGFYPDHVSLSWKVNGKEvKDGVATDPQALRENTSTYsLSSRLRVSATEWFNp 80

                           90
                   ....*....|....
gi 1032530219  471 GNVFSCSVMHEALH 484
Cdd:cd05769     81 RNTFTCIVKFYGGT 94
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 155-264 8.11e-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: 62.86  E-value: 8.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  155 LVKPGASVKMSCKASGY-TFTSYNMHWVKQTPGQGLEWIGAIYPGNGDTSynqKFKGKATLTADKSSSTAYMQLSSLTSE 233
Cdd:pfam07686    7 TVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIAYYSNGSEEG---VKKGRFSGRGDPSNGDGSLTIQNLTLS 83

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1032530219  234 DSAVYYCARSHYGSNyvdyfdYWGQGTTLTV 264
Cdd:pfam07686   84 DSGTYTCAVIPSGEG------VFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-124 1.20e-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: 61.75  E-value: 1.20e-11
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219    28 PAILSASPGEKVTMTCRASSSLS-FMHWYQQKPgsspkPWIyatsnlasGVPARFSGSGSGTSYSLTISRVEAEDAATYF 106
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSPPpEVTWYKQGG-----KLL--------AESGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                            90
                    ....*....|....*...
gi 1032530219   107 CHQWSSNPLTFGaGTKLE 124
Cdd:smart00410   68 CAATNSSGSASS-GTTLT 84
IGv smart00406
Immunoglobulin V-Type;
39-107 2.96e-10

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 57.39  E-value: 2.96e-10
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1032530219    39 VTMTCRASS---SLSFMHWYQQKPGSSPKPWIY----ATSNLASGVPARFSGSGSGTSY--SLTISRVEAEDAATYFC 107
Cdd:smart00406    2 VTLSCKFSGstfSSYYVSWVRQPPGKGLEWLGYigsnGSSYYQESYKGRFTISKDTSKNdvSLTISNLRVEDTGTYYC 79
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 290-379 7.54e-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: 57.04  E-value: 7.54e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDTLMiSRTPEVTCVVVdvSHEDPEVKFNWYVDGVEVHN--AKTKPREEQyQSTYRVVSVLTVLHQDWLNG 367
Cdd:cd05847      2 TVQILHSSCASTLT-SETIQLLCLIS--GYTPSTIEVEWLVDGQVATLsaASTAPQKEE-GGTFSTTSKLNVTQEDWKSG 77

                           90
                   ....*....|..
gi 1032530219  368 KEYKCKVSNKAL 379
Cdd:cd05847     78 KTYTCKVTHQGT 89
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 405-483 1.93e-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: 55.41  E-value: 1.93e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  405 SRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL-DSDGSFFLYSKLTVDKsrwQQGNVFSCSVMHEAL 483
Cdd:cd21029      9 SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILpNHDGTYQLRKTLDIAP---GEGAGYSCRVDHSSL 85
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
 412-481 2.15e-09

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: 55.51  E-value: 2.15e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  412 NQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHE 481
Cdd:cd16085     16 NQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTCQVEHD 85
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 410-482 7.56e-09

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: 53.87  E-value: 7.56e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032530219  410 TKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLdSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEA 482
Cdd:cd21819     14 TSDPVTVGCLATDFLPDSITFSWTDDNNSLtTGVKTYPSVL-TGGTYTASSQLQVPESEWKSKENFYCKVEHPG 86
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 290-389 9.99e-09

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: 53.61  E-value: 9.99e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDtlMISRTPEVTCVVVDVSHEDPEVkfNWYVDGVEVHNA-KTKPREEQYQSTYRVVSVLTVLHQDWLNGK 368
Cdd:cd07699      3 SVTIFPPSSEE--LSSGKATLVCLINKFYPGFATV--TWKVDGSTVSSGvTTSKTEQQSDNTYSMSSYLTLSSSDWNKHK 78

                           90       100
                   ....*....|....*....|.
gi 1032530219  369 EYKCKVSNKALPAPIEKTISK 389
Cdd:cd07699     79 VYTCEVTHEGLSSTITKSFNR 99
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 397-483 1.26e-08

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: 53.65  E-value: 1.26e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPE-----NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ 469
Cdd:cd05771      1 PRV-RLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWlrEEPGGSEsqvsrDGVSLSSHRQSVDGTYSISSYLTLEPGTEN 79

                           90
                   ....*....|....
gi 1032530219  470 QGNVFSCSVMHEAL 483
Cdd:cd05771     80 RGATYTCRVTHVSL 93
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 397-480 1.30e-08

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: 53.28  E-value: 1.30e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVY--TLPPSRdelTKNQVSLTCLVKGFYPSDIAVEWESNGQpENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 474
Cdd:cd21818      2 PTVFplSLCPSL---SSDPVVIGCLVQGFFPEPVNVTWNYSGK-GGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAY 77


                   ....*.
gi 1032530219  475 SCSVMH 480
Cdd:cd21818     78 KCSVQH 83
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 145-264 1.31e-08

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


Pssm-ID: 409514  Cd Length: 115  Bit Score: 54.10  E-value: 1.31e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  145 QVQLRQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGAIypgngDTSYNQKFKGKATLTADKSSSTAY 224
Cdd:cd16095      1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSL-----DHISTKVSEDRITSSREDTNSQIF 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1032530219  225 MQLSSLTSEDSAVYYCARSHYGSNYVDYFDYwGQGTTLTV 264
Cdd:cd16095     76 LQIKGLGLRDSGQYHCARRVGYGDDTDKLIF-GPGTDVIV 114
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 397-483 1.69e-08

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: 53.08  E-value: 1.69e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDELTKNQVsLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRwqqGNVFS 475
Cdd:cd05767      3 PEVTVFPKSPVELGEPNT-LICFVDNFFPPVINVTWLRNGQPvTDGVSETVFLPREDHSFRKFSYLPFTPSE---GDIYD 78


                   ....*...
gi 1032530219  476 CSVMHEAL 483
Cdd:cd05767     79 CRVEHWGL 86
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 25-123 3.25e-08

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: 52.52  E-value: 3.25e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   25 SQSPAILSASPGEKVTMTCRASSSLS--FMHWYQQKPGSSPKPWIYATSNLASGVPARFSG--SGSGTSYSLTISRVEAE 100
Cdd:cd07706      3 TQAQPDVSVQVGEEVTLNCRYETSWTnyYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVnfQKAQKSISLTISALQLE 82

                           90       100
                   ....*....|....*....|....*.
gi 1032530219  101 DAATYFCHQWSSNP---LTFGAGTKL 123
Cdd:cd07706     83 DSAKYFCALSLPYDtdkLIFGKGTRL 108
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 396-483 3.56e-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: 52.04  E-value: 3.56e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  396 EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKsrwQQGNVF 474
Cdd:cd21001      3 EPTV-TISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETaGVVSTPLIRNGDWTFQILVMLEMTP---QRGDVY 78


                   ....*....
gi 1032530219  475 SCSVMHEAL 483
Cdd:cd21001     79 TCHVEHPSL 87
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 290-388 3.59e-08

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: 52.01  E-value: 3.59e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPkPKDTLMISRTPEVTCVVVDVSHEDPEVKfnWYVDGVEVHNAKTKPREEQYQS---TYRVVSVLTVLHQDWLN 366
Cdd:cd16093      3 TVSLHAP-SREEFLGNRTATFVCLATGFSPKTISFK--WLRNGKEVTSSTGAVVEEPKEDgktLYSATSFLTITESEWKS 79

                           90       100
                   ....*....|....*....|..
gi 1032530219  367 GKEYKCKVSNKAlpAPIEKTIS 388
Cdd:cd16093     80 QTEFTCEFKHKG--EIVEKNAS 99
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
 398-483 4.00e-08

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


Pssm-ID: 409427  Cd Length: 94  Bit Score: 51.71  E-value: 4.00e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  398 QVYTLPPSrDELTKNQvsLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFL--YSKLTVDKsrwqqGNVFS 475
Cdd:cd05770      6 QVYSRFPA-ENGKPNV--LNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYLlkYTEFTPTK-----GDEYA 77


                   ....*...
gi 1032530219  476 CSVMHEAL 483
Cdd:cd05770     78 CRVRHNTL 85
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 397-488 3.14e-07

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 49.15  E-value: 3.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDEltkNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL-DSDGSFFLYSKLTVDKSRWQqgnVFS 475
Cdd:cd07698      3 PKVHVTHHPRSD---GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVETRpNGDGTFQKWAAVVVPSGEEQ---RYT 76

                           90
                   ....*....|...
gi 1032530219  476 CSVMHEALHNHYT 488
Cdd:cd07698     77 CHVQHEGLPEPLT 89
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 395-483 3.68e-07

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: 49.25  E-value: 3.68e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  395 REPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN---NYKTTPPVLDsdgsfFLYSKLTVDKSRWQQG 471
Cdd:cd05766      2 VQPSV-KVSPTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETagvVSTELIPNGD-----WTFQILVMLETTPRRG 75

                           90
                   ....*....|..
gi 1032530219  472 NVFSCSVMHEAL 483
Cdd:cd05766     76 DVYTCQVEHSSL 87
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 396-483 5.18e-07

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: 48.85  E-value: 5.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  396 EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKL-TVDKSrwqqGNV 473
Cdd:cd21000      3 EPKV-TVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKaGVVSTGLIQNGDWTFQTLVMLeTVPRS----GEV 77

                           90
                   ....*....|
gi 1032530219  474 FSCSVMHEAL 483
Cdd:cd21000     78 YTCQVEHPSV 87
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 410-483 8.16e-07

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: 48.38  E-value: 8.16e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1032530219  410 TKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG--SFFLYSKLTVDKSrwqQGNVFSCSVMHEAL 483
Cdd:cd21002     16 TREPVMLACHVWGFYPADVTITWLKNGDPVAPHSSAPKTAQPNGdwTYQTQVTLAVTPS---PGDTYTCSVQHASL 88
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 396-483 8.39e-07

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: 48.21  E-value: 8.39e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  396 EPQVYtLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKsrwQQGNVF 474
Cdd:cd21003      3 QPKVN-VSPSKKGPLQHHNLLVCHVTDFYPGNIQVRWFLNGQEETaGVVSTNLIHNGDWTFQILVMLEMTP---QQGDVY 78


                   ....*....
gi 1032530219  475 SCSVMHEAL 483
Cdd:cd21003     79 TCQVEHPSL 87
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 24-123 1.30e-06

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: 48.21  E-value: 1.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   24 LSQSPAILSASPGEKVTMTCRASSSLSFM--HWYQQKPGSSPKPW--IYATSNLASGV-------PARFSGSGSGTSY-- 90
Cdd:cd07700      1 LLQTPGSLLVQTNQTVKMSCEAKTSPKNTriYWLRQRQAPSKDSHfeFLASWDPSKGIvygegvdQEKLIILSDSDSSry 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1032530219   91 SLTISRVEAEDAATYFCHQWSSNPLTFGAGTKL 123
Cdd:cd07700     81 ILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKL 113
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 394-488 6.51e-06

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: 45.92  E-value: 6.51e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  394 PR--EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN-YKTTPPVLDSDGSFflySKLTVDKSRWQQ 470
Cdd:cd20998      2 PRrvEPTV-TVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTgIVSTGLVRNGDWTF---QTLVMLETVPQS 77

                           90
                   ....*....|....*...
gi 1032530219  471 GNVFSCSVMHEALHNHYT 488
Cdd:cd20998     78 GEVYTCQVEHPSLTDPVT 95
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 148-264 7.00e-06

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: 46.29  E-value: 7.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  148 LRQPGAELVKPGASVKMSCKASGYTfTSYNMHWVKQ----TPGQGLEWIgAIYPGNGDTSYNQKFKG-KATLTADKSSST 222
Cdd:cd07700      2 LQTPGSLLVQTNQTVKMSCEAKTSP-KNTRIYWLRQrqapSKDSHFEFL-ASWDPSKGIVYGEGVDQeKLIILSDSDSSR 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1032530219  223 AYMQLSSLTSEDSAVYYCARshYGSNYVDYfdywGQGTTLTV 264
Cdd:cd07700     80 YILSLMSVKPEDSGTYFCMT--VGSPELIF----GTGTKLSV 115
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 410-483 1.06e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409609  Cd Length: 95  Bit Score: 45.12  E-value: 1.06e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1032530219  410 TKNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21018     16 SKGEVTLRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCRVYHEGL 87
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 156-264 1.19e-05

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


Pssm-ID: 409580  Cd Length: 114  Bit Score: 45.63  E-value: 1.19e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  156 VKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWI---GAIY-PGngdtsYNQKFKGKatltADKSSSTAYMQLSSLT 231
Cdd:cd20988     10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFIyreGGIYgPG-----FKDNFRGD----IDSSNNLAVLKILEAS 80

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1032530219  232 SEDSAVYYCARSHYGSNYVDYFDYWGQGTTLTV 264
Cdd:cd20988     81 ERDEGSYYCASDTPGGGREYDPLIFGKGTYLTV 113
IgC1_CH2_IgD cd16084
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; ...
 399-483 1.71e-05

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin constant domain (IgC) in delta heavy chains. The IgC family includes immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409506  Cd Length: 97  Bit Score: 44.74  E-value: 1.71e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  399 VYTLPPSRDEL-TKNQVSLTCLVKGFYPSDIAVEWESNGQ-PENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSC 476
Cdd:cd16084      2 VYLLTPAVQDLwLRDKATFTCFVVGSDLKDAHLTWEVAGKvPTGGVEEGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTC 81


                   ....*..
gi 1032530219  477 SVMHEAL 483
Cdd:cd16084     82 TLNHPSL 88
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 761-853 1.73e-05

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: 44.03  E-value: 1.73e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   761 PLVVKVEEGDNAVLQCLkgTSDGPTQQLTWSRESPLKPFLKlslglPGLGIHMRPLAIWLFIFNVSQQMGGFYLCQPGPP 840
Cdd:smart00410    1 PPSVTVKEGESVTLSCE--ASGSPPPEVTWYKQGGKLLAES-----GRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNS 73

                            90
                    ....*....|...
gi 1032530219   841 SEKAWQpGWTVNV 853
Cdd:smart00410   74 SGSASS-GTTLTV 85
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
 391-483 1.90e-05

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


Pssm-ID: 409625  Cd Length: 98  Bit Score: 44.37  E-value: 1.90e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  391 KGQPREPQVYTLPPSRDELTknqvsLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKS 466
Cdd:cd21820      2 RSDPPKAHVTHHPRSEDEVT-----LRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWAAVVVPLG 73

                           90
                   ....*....|....*..
gi 1032530219  467 RWQqgnVFSCSVMHEAL 483
Cdd:cd21820     74 KEQ---YYTCHVYHEGL 87
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
 414-482 2.92e-05

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


Pssm-ID: 319341  Cd Length: 96  Bit Score: 44.06  E-value: 2.92e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1032530219  414 VSLTCLVKGFYPSDIAVEWE--SNGQPEnnyKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNvFSCSVMHEA 482
Cdd:cd16092     20 VVLACLITGYHPTSVTVTWYmgTQSQPQ---RTFPEIQRRDSYYMTSSQLSTPLQQWRQGE-YKCVVQHTA 86
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
 397-483 6.70e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409610  Cd Length: 94  Bit Score: 42.79  E-value: 6.70e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  397 PQVYTLPPSRDEltkNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQqgn 472
Cdd:cd21019      5 PKAHVTHHSRPE---DKVTLRCWALGFYPADITLTWQLNGeeliQDMELVETRPA---GDGTFQKWASVVVPLGKEQ--- 75

                           90
                   ....*....|.
gi 1032530219  473 VFSCSVMHEAL 483
Cdd:cd21019     76 YYTCHVYHQGL 86
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
 391-483 8.93e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins. Qa-1 presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vbeta8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409604  Cd Length: 97  Bit Score: 42.42  E-value: 8.93e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  391 KGQPREPQVYTLPPSRDELTknqvsLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSR 467
Cdd:cd21013      1 RSDPPKAHVTHHPRSEGYVT-----LRCWALGFYPADITLTWQLNGEEltqDMEFVETRPA--GDGTFQKWASVVVPLGK 73

                           90
                   ....*....|....*.
gi 1032530219  468 WQQgnvFSCSVMHEAL 483
Cdd:cd21013     74 EQK---YTCHVEHEGL 86
IGc1 smart00407
Immunoglobulin C-Type;
310-382 9.29e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.53  E-value: 9.29e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032530219   310 VTCVVVDVSHEDPEVKfnWYVDGVEVH-NAKTKPREEQYQSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAP 382
Cdd:smart00407    4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 624-644 1.94e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


Pssm-ID: 128390  Cd Length: 21  Bit Score: 39.29  E-value: 1.94e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   624 NQLYNELNLGRREEYDVLDKR 644
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
 394-485 3.07e-04

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


Pssm-ID: 409429  Cd Length: 102  Bit Score: 41.15  E-value: 3.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  394 PREPQVyTLPPSRDELTKnQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTT-PPVLDSDgSFFLYSKLTVDKSRWQQGN 472
Cdd:cd05772      2 PSQPLV-SGPSGRATPGQ-TVSFTCKSHGFSPRDITLKWFKNGNELSALQTTvFPEGDSV-SYSVSSTVQVVLTKDDVHS 78

                           90
                   ....*....|...
gi 1032530219  473 VFSCSVMHEALHN 485
Cdd:cd05772     79 QLTCEVAHVTLQA 91
IgC1_MHC_Ia_RT1-Aa cd21015
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the ...
 411-490 3.12e-04

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


Pssm-ID: 409606  Cd Length: 95  Bit Score: 40.90  E-value: 3.12e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  411 KNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEALHNH 486
Cdd:cd21015     16 EGDVTLRCWALGFYPADITLTWQLNGedltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCRVEHEGLPKP 89


                   ....
gi 1032530219  487 YTQK 490
Cdd:cd21015     90 LSQR 93
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 24-107 4.14e-04

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: 41.14  E-value: 4.14e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   24 LSQSPAILsASPGEKVTMTCRASSsLSF----MHWYQQKPGSSPK--PWIY---ATSNLASGVPARF--SGSGSGTSYSL 92
Cdd:cd04981      2 LQESGPGL-VKPGQSLKLSCKASG-FTFtsygMGWVRQAPGKGLEwiGLIYpggGDTYYADSFKGRFtiTRDTSKSTAYL 79

                           90
                   ....*....|....*
gi 1032530219   93 TISRVEAEDAATYFC 107
Cdd:cd04981     80 QLNSLTSEDTAVYYC 94
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
 396-480 4.85e-04

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


Pssm-ID: 409375  Cd Length: 96  Bit Score: 40.44  E-value: 4.85e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  396 EPQVYTLPPS-RDELTKNQVSLTCLVKGFYPSDIAV-EWESNGqpENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 473
Cdd:cd04986      1 QPRLSLQRPAlEDLLLGSNASLTCTLSGLKDPEGATfTWEPSG--GKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDT 78


                   ....*..
gi 1032530219  474 FSCSVMH 480
Cdd:cd04986     79 FSCTVTH 85
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
 401-484 4.86e-04

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 40.09  E-value: 4.86e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  401 TLPPSRDELTKNQVSLTCLVKGFYPsDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH 480
Cdd:pfam08205    4 EPPASLLEGEGPEVVATCSSAGGKP-APRITWYLDGKPLEAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSY 82


                   ....
gi 1032530219  481 EALH 484
Cdd:pfam08205   83 GALR 86
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 156-264 4.88e-04

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


Pssm-ID: 409503  Cd Length: 112  Bit Score: 40.97  E-value: 4.88e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  156 VKPGASVKMSCKASgYTFTSYNMHWVKQTPGQGLEWIgaIYpgnGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDS 235
Cdd:cd07706     11 VQVGEEVTLNCRYE-TSWTNYYLFWYKQLPSGEMTFL--IR---QDSSEQNAKSGRYSVNFQKAQKSISLTISALQLEDS 84

                           90       100
                   ....*....|....*....|....*....
gi 1032530219  236 AVYYCARSHYGSNYVDYFdywGQGTTLTV 264
Cdd:cd07706     85 AKYFCALSLPYDTDKLIF---GKGTRLTV 110
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 409-483 5.57e-04

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: 40.18  E-value: 5.57e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1032530219  409 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21023     15 ISDHEATLRCWALGFYPAEITLTWQRDGEEQTQdtelVETRPA---GDGTFQKWAAVVVPPGEEQR---YTCHVQHEGL 87
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
 403-483 5.84e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409607  Cd Length: 97  Bit Score: 40.08  E-value: 5.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  403 PP----SRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFS 475
Cdd:cd21016      5 PPkahvTRHPRPEGDVTLRCWALGFYPADITLTWQKDGEEltqDMEFVETRPA--GDGTFQKWAAVVVPLGKEQS---YT 79


                   ....*...
gi 1032530219  476 CSVMHEAL 483
Cdd:cd21016     80 CHVYHEGL 87
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
 290-400 7.24e-04

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: 40.44  E-value: 7.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  290 SVFLFPPKPKDtlmISRTPEVTCVVVdVSHEDPE-VKFNWYVDGVEVH-NAKTKP---REEqyQSTYRVVSVLTVLHQDW 364
Cdd:cd05769      4 TVALFPPSEAE---IRNKRKATLVCL-ATGFYPDhVSLSWKVNGKEVKdGVATDPqalREN--TSTYSLSSRLRVSATEW 77

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1032530219  365 LN-GKEYKCKVS--NKALPAPIEKTISKAKGQPREPQVY 400
Cdd:cd05769     78 FNpRNTFTCIVKfyGGTDTDTWTQGIAGPVTCGVSAEEL 116
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 923-1012 7.70e-04

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: 39.41  E-value: 7.70e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   923 SQDLTMAPGSTLWLSCGVPPDSVSRgpLSWTHvhpKGPKSLLSlelkddrPARDMWVMETG---LLLPRATAQDAGKYYC 999
Cdd:smart00410    1 PPSVTVKEGESVTLSCEASGSPPPE--VTWYK---QGGKLLAE-------SGRFSVSRSGStstLTISNVTPEDSGTYTC 68

                            90
                    ....*....|....*..
gi 1032530219  1000 HR----GNLTMSFHLEI 1012
Cdd:smart00410   69 AAtnssGSASSGTTLTV 85
ITAM smart00077
Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on ...
 693-713 8.25e-04

Immunoreceptor tyrosine-based activation motif; Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery.


Pssm-ID: 128390  Cd Length: 21  Bit Score: 37.36  E-value: 8.25e-04
                            10        20
                    ....*....|....*....|.
gi 1032530219   693 DGLYQGLSTATKDTYDALHMQ 713
Cdd:smart00077    1 DQLYQPLNKRQRDTYSDLNTR 21
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
 411-483 8.47e-04

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


Pssm-ID: 409611  Cd Length: 95  Bit Score: 39.74  E-value: 8.47e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1032530219  411 KNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21020     17 EGDVTLRCWALGFYPADITLTWQLNGEEltqEMELVETRPA--GDGTFQKWASVVVPLGKEQK---YTCHVEHEGL 87
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 23-107 9.49e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 39.09  E-value: 9.49e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   23 VLSQSPAILSASPGEKVTMTCRASSS-LSFMHWYQQKPGSSPKPWIYATSNLASGVparfsgsgsgtsysLTISRVEAED 101
Cdd:pfam13927    3 VITVSPSSVTVREGETVTLTCEATGSpPPTITWYKNGEPISSGSTRSRSLSGSNST--------------LTISNVTRSD 68


                   ....*.
gi 1032530219  102 AATYFC 107
Cdd:pfam13927   69 AGTYTC 74
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
 414-483 1.32e-03

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


Pssm-ID: 409605  Cd Length: 94  Bit Score: 38.96  E-value: 1.32e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032530219  414 VSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21014     19 VTLRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCHVNHEGL 86
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
 414-483 1.39e-03

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


Pssm-ID: 409603  Cd Length: 95  Bit Score: 38.94  E-value: 1.39e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1032530219  414 VSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21012     20 VTLRCWALGFYPAHITLTWQLNGEEliqDTELVETRPA--GDGTFQKWAAVVVPSGEEQK---YTCHVYHEGL 87
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 409-483 2.05e-03

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


Pssm-ID: 409618  Cd Length: 95  Bit Score: 38.66  E-value: 2.05e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1032530219  409 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21027     15 VSDHEATLRCWALSFYPAEITLTWQRDGEDQTQdtelVETRPA---GDGTFQKWAAVVVPSGQEQR---YTCHVQHEGL 87
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 409-483 2.09e-03

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


Pssm-ID: 409615  Cd Length: 95  Bit Score: 38.62  E-value: 2.09e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1032530219  409 LTKNQVSLTCLVKGFYPSDIAVEWESNGQ---PENNYKTTPPVldSDGSFFLYSKLTVDKSRWQqgnVFSCSVMHEAL 483
Cdd:cd21024     15 ISDHEATLRCWALGFYPAEITLTWQQDGEghtQDTELVETRPA--GDGTFQKWAAVVVPSGEEQ---RYTCHVQHEGL 87
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
 409-483 2.57e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409616  Cd Length: 96  Bit Score: 38.25  E-value: 2.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1032530219  409 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21025     15 VSDHEATLRCWALGFYPAEITLTWQWDGEDQTQdtelVETRPA---GDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 87
ITAM pfam02189
Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex ...
 693-712 2.75e-03

Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains.


Pssm-ID: 426646  Cd Length: 20  Bit Score: 36.20  E-value: 2.75e-03
                           10        20
                   ....*....|....*....|
gi 1032530219  693 DGLYQGLSTATKDTYDALHM 712
Cdd:pfam02189    1 DQLYQPLNKRDDDTYSHLGM 20
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 413-483 3.09e-03

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


Pssm-ID: 409613  Cd Length: 94  Bit Score: 38.20  E-value: 3.09e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1032530219  413 QVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 483
Cdd:cd21022     18 EATLRCWALGFYPAEIILTWQRDGEDQTQdvelVETRPA---GDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 86
ITAM pfam02189
Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex ...
 624-643 3.34e-03

Immunoreceptor tyrosine-based activation motif; T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains.


Pssm-ID: 426646  Cd Length: 20  Bit Score: 35.82  E-value: 3.34e-03
                           10        20
                   ....*....|....*....|
gi 1032530219  624 NQLYNELNLGRREEYDVLDK 643
Cdd:pfam02189    1 DQLYQPLNKRDDDTYSHLGM 20
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
 409-488 5.30e-03

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma 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. 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: 409484  Cd Length: 80  Bit Score: 37.10  E-value: 5.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219  409 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPennYKTTP-PVLDSDGSfflYSklTVDKSRWQQGNVFSCSVMHEALHNHY 487
Cdd:cd07687      6 VMKNGTNVACLVKNFYPKEVTISLSSSKKI---IEFDPaIVISPNGK---YS--AVKLGKYGDSDSVTCSVQHSNKTVHS 77


                   .
gi 1032530219  488 T 488
Cdd:cd07687     78 T 78
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 26-117 5.97e-03

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 36.79  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032530219   26 QSPAILSASPGEKVTMTCRASSSLSF--MHWY---QQKPGSSPKPWIYATSNLASgvparfsgsgsgtsysLTISRVEAE 100
Cdd:pfam00047    1 SAPPTVTVLEGDSATLTCSASTGSPGpdVTWSkegGTLIESLKVKHDNGRTTQSS----------------LLISNVTKE 64

                           90       100
                   ....*....|....*....|
gi 1032530219  101 DAATYFC---HQWSSNPLTF 117
Cdd:pfam00047   65 DAGTYTCvvnNPGGSATLST 84
 
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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