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Conserved domains on  [gi|1907136870|ref|XP_036015588|]
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tyrosine-protein phosphatase non-receptor type substrate 1 isoform X2 [Mus musculus]

Protein Classification

IgC1_SIRP_domain_2 and IgC1_SIRP_domain_3 domain-containing protein( domain architecture ID 11666212)

protein containing domains Ig, IgC1_SIRP_domain_2, and IgC1_SIRP_domain_3

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
28-139 5.13e-65

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 cd16097:

Pssm-ID: 448366  Cd Length: 111  Bit Score: 205.87  E-value: 5.13e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGVGPSRLLIYSFAGEYVPRIRNVSDTTKRNNMDFSIRISNVTPA 107
Cdd:cd16097     1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1907136870 108 DAGIYYCVKFQKGSSePDTEIQSGGGTEVYVL 139
Cdd:cd16097    81 DAGTYYCVKFRKGSP-DDVEFKSGAGTELSVR 111
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
246-341 3.28e-59

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: 190.33  E-value: 3.28e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTC 325
Cdd:cd16085     1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80
                          90
                  ....*....|....*.
gi 1907136870 326 QVKHDQQPAITRNHTV 341
Cdd:cd16085    81 QVEHDGQPAVTKNHTL 96
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
141-243 5.11e-50

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: 166.34  E-value: 5.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 141 KPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDVNSKV 220
Cdd:cd05772     1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80
                          90       100
                  ....*....|....*....|...
gi 1907136870 221 ICEVAHITLdRSPLRGIANLSNF 243
Cdd:cd05772    81 TCEVAHVTL-QAPLRGTANLSDI 102
 
Name Accession Description Interval E-value
IgV_SIRP cd16097
Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The ...
28-139 5.13e-65

Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). 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 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 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409516  Cd Length: 111  Bit Score: 205.87  E-value: 5.13e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGVGPSRLLIYSFAGEYVPRIRNVSDTTKRNNMDFSIRISNVTPA 107
Cdd:cd16097     1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1907136870 108 DAGIYYCVKFQKGSSePDTEIQSGGGTEVYVL 139
Cdd:cd16097    81 DAGTYYCVKFRKGSP-DDVEFKSGAGTELSVR 111
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
246-341 3.28e-59

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: 190.33  E-value: 3.28e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTC 325
Cdd:cd16085     1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80
                          90
                  ....*....|....*.
gi 1907136870 326 QVKHDQQPAITRNHTV 341
Cdd:cd16085    81 QVEHDGQPAVTKNHTL 96
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
141-243 5.11e-50

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: 166.34  E-value: 5.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 141 KPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDVNSKV 220
Cdd:cd05772     1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80
                          90       100
                  ....*....|....*....|...
gi 1907136870 221 ICEVAHITLdRSPLRGIANLSNF 243
Cdd:cd05772    81 TCEVAHVTL-QAPLRGTANLSDI 102
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
31-139 7.82e-16

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 429596  Cd Length: 109  Bit Score: 73.26  E-value: 7.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  31 QPEKSVSVAAGDSTVLNCTLTSL--LPVGPIRWYRG--VGPSRLLIYSFAGEYVPRIR--NVSDTTKRNNMDFSIRISNV 104
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQppGKGPTFLIAYYSNGSEEGVKkgRFSGRGDPSNGDGSLTIQNL 80
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1907136870 105 TPADAGIYYCVKFqkgssePDTEIQSGGGTEVYVL 139
Cdd:pfam07686  81 TLSDSGTYTCAVI------PSGEGVFGKGTRLTVL 109
IGc1 smart00407
Immunoglobulin C-Type;
262-329 5.24e-10

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 55.40  E-value: 5.24e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907136870  262 QVNLTCRAERFYPEDLQLIWLENGNVSRNDT-PKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTCQVKH 329
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVsTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTH 69
C1-set pfam07654
Immunoglobulin C1-set domain;
136-229 1.86e-09

Immunoglobulin C1-set domain;


Pssm-ID: 429576  Cd Length: 85  Bit Score: 54.17  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 136 VYVLAkPSPPEVSgpadrgipdQKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPS-GKNVSYNISSTVRVVLNSM 214
Cdd:pfam07654   1 VYVFP-PSPEELG---------KPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTTTPPSpNSDWTYQLSSYLTVTPSDW 70
                          90
                  ....*....|....*
gi 1907136870 215 DVNSKVICEVAHITL 229
Cdd:pfam07654  71 ESGDTYTCRVEHEGL 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
34-138 9.90e-09

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 52.12  E-value: 9.90e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870   34 KSVSVAAGDSTVLNCTLTSLlPVGPIRWYRGvgPSRLLIYSfageyvPRIrnvsdTTKRNNMDFSIRISNVTPADAGIYY 113
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGS-PPPEVTWYKQ--GGKLLAES------GRF-----SVSRSGSTSTLTISNVTPEDSGTYT 67
                           90       100
                   ....*....|....*....|....*.
gi 1907136870  114 C-VKFQKGSSEpdteiqsgGGTEVYV 138
Cdd:smart00410  68 CaATNSSGSAS--------SGTTLTV 85
C1-set pfam07654
Immunoglobulin C1-set domain;
250-329 1.26e-07

Immunoglobulin C1-set domain;


Pssm-ID: 429576  Cd Length: 85  Bit Score: 49.16  E-value: 1.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 250 VKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLENGNVSRND-TPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTCQV 327
Cdd:pfam07654   1 VYVFPPSPEELGKPNtLTCLVTGFYPPDITVTWLKNGQEVTEGvTTTPPSPNSDWTYQLSSYLTVTPSDWESGDTYTCRV 80

                  ..
gi 1907136870 328 KH 329
Cdd:pfam07654  81 EH 82
IGc1 smart00407
Immunoglobulin C-Type;
159-230 2.43e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 42.30  E-value: 2.43e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907136870  159 KVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSG-KNVSYNISSTVRVVLNSMDVNSKVICEVAHITLD 230
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKnSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73
 
Name Accession Description Interval E-value
IgV_SIRP cd16097
Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The ...
28-139 5.13e-65

Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). 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 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 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409516  Cd Length: 111  Bit Score: 205.87  E-value: 5.13e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGVGPSRLLIYSFAGEYVPRIRNVSDTTKRNNMDFSIRISNVTPA 107
Cdd:cd16097     1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1907136870 108 DAGIYYCVKFQKGSSePDTEIQSGGGTEVYVL 139
Cdd:cd16097    81 DAGTYYCVKFRKGSP-DDVEFKSGAGTELSVR 111
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
246-341 3.28e-59

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: 190.33  E-value: 3.28e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTC 325
Cdd:cd16085     1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80
                          90
                  ....*....|....*.
gi 1907136870 326 QVKHDQQPAITRNHTV 341
Cdd:cd16085    81 QVEHDGQPAVTKNHTL 96
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
141-243 5.11e-50

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: 166.34  E-value: 5.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 141 KPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDVNSKV 220
Cdd:cd05772     1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80
                          90       100
                  ....*....|....*....|...
gi 1907136870 221 ICEVAHITLdRSPLRGIANLSNF 243
Cdd:cd05772    81 TCEVAHVTL-QAPLRGTANLSDI 102
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
29-138 1.07e-21

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: 90.09  E-value: 1.07e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGV-GPSRLLIYSFAGEYVPRIRNVSD---TTKRNNMDFSIRISNV 104
Cdd:cd00099     1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKpGQGPEFLIYLSSSKGKTKGGVPGrfsGSRDGTSSFSLTISNL 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907136870 105 TPADAGIYYCVKFQKGSSEPDTeiqSGGGTEVYV 138
Cdd:cd00099    81 QPEDSGTYYCAVSESGGTDKLT---FGSGTRLTV 111
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
249-339 3.39e-17

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


Pssm-ID: 409354  Cd Length: 95  Bit Score: 76.73  E-value: 3.39e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 249 TVKVTQQSPTSM--NQVNLTCRAERFYPEDLQLIWLENGN-VSRNDTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTC 325
Cdd:cd00098     1 TVTLLPPSPEEKggGKVTLVCLVSGFYPKDITVTWLKNGVpLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80
                          90
                  ....*....|....*
gi 1907136870 326 QVKH-DQQPAITRNH 339
Cdd:cd00098    81 VVTHeSLKSPLSKTW 95
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
31-139 7.82e-16

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 429596  Cd Length: 109  Bit Score: 73.26  E-value: 7.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  31 QPEKSVSVAAGDSTVLNCTLTSL--LPVGPIRWYRG--VGPSRLLIYSFAGEYVPRIR--NVSDTTKRNNMDFSIRISNV 104
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQppGKGPTFLIAYYSNGSEEGVKkgRFSGRGDPSNGDGSLTIQNL 80
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1907136870 105 TPADAGIYYCVKFqkgssePDTEIQSGGGTEVYVL 139
Cdd:pfam07686  81 TLSDSGTYTCAVI------PSGEGVFGKGTRLTVL 109
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
145-232 9.14e-15

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


Pssm-ID: 409354  Cd Length: 95  Bit Score: 69.80  E-value: 9.14e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 145 PEVSGPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQELH----PLETTVNPSGknvSYNISSTVRVVLNSMDVNSKV 220
Cdd:cd00098     2 VTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTsgvsTSSPVEPNDG---TYSVTSSLTVPPSDWDEGATY 78
                          90
                  ....*....|..
gi 1907136870 221 ICEVAHITLDRS 232
Cdd:cd00098    79 TCVVTHESLKSP 90
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
29-138 3.55e-10

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 57.28  E-value: 3.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSLLPVGpIRWYR---GVGPSRLLIYSFAGEYVPRIRnVSDTTKRNNMDFSIRISNVT 105
Cdd:cd04983     1 VTQSPQSLSVQEGENVTLNCNYSTSTFYY-LFWYRqypGQGPQFLIYISSDSGNKKKGR-FSATLDKSRKSSSLHISAAQ 78
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907136870 106 PADAGIYYCVKFQKGSSEpdtEIQSGGGTEVYV 138
Cdd:cd04983    79 LSDSAVYFCALSESGGTG---KLTFGKGTRLTV 108
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
29-136 4.75e-10

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: 56.63  E-value: 4.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYR---GvGPSRLLIYS-----------FAGEYvprirnvSDTtkrnn 94
Cdd:cd04980     3 MTQSPASLSVSPGERVTISCKASQSISSNYLAWYQqkpG-QAPKLLIYYastlhsgvpsrFSGSG-------SGT----- 69
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1907136870  95 mDFSIRISNVTPADAGIYYCvkfQKGSSEPDTeiqSGGGTEV 136
Cdd:cd04980    70 -DFTLTISSVEPEDAAVYYC---QQGYTFPYT---FGGGTKL 104
IGc1 smart00407
Immunoglobulin C-Type;
262-329 5.24e-10

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 55.40  E-value: 5.24e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907136870  262 QVNLTCRAERFYPEDLQLIWLENGNVSRNDT-PKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTCQVKH 329
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVsTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTH 69
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
245-338 9.70e-10

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: 55.42  E-value: 9.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLENGNVSRND-TPKNLTKNTDGTYNYtsLFLVNSSAHREDvV 322
Cdd:cd05766     1 RVQPSVKVSPTKTGPLEHPNlLVCSVTGFYPAEIEVKWFRNGQEETAGvVSTELIPNGDWTFQI--LVMLETTPRRGD-V 77
                          90
                  ....*....|....*...
gi 1907136870 323 FTCQVKHD--QQPaITRN 338
Cdd:cd05766    78 YTCQVEHSslQSP-LTVD 94
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
246-329 1.09e-09

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: 55.31  E-value: 1.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQqSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTK-NTDGTYnYTSLFLVNSSAhrEDVVFT 324
Cdd:cd07698     1 DPPKVHVTH-HPRSDGESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVETRpNGDGTF-QKWAAVVVPSG--EEQRYT 76

                  ....*
gi 1907136870 325 CQVKH 329
Cdd:cd07698    77 CHVQH 81
C1-set pfam07654
Immunoglobulin C1-set domain;
136-229 1.86e-09

Immunoglobulin C1-set domain;


Pssm-ID: 429576  Cd Length: 85  Bit Score: 54.17  E-value: 1.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 136 VYVLAkPSPPEVSgpadrgipdQKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPS-GKNVSYNISSTVRVVLNSM 214
Cdd:pfam07654   1 VYVFP-PSPEELG---------KPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTTTPPSpNSDWTYQLSSYLTVTPSDW 70
                          90
                  ....*....|....*
gi 1907136870 215 DVNSKVICEVAHITL 229
Cdd:pfam07654  71 ESGDTYTCRVEHEGL 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
34-138 9.90e-09

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 52.12  E-value: 9.90e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870   34 KSVSVAAGDSTVLNCTLTSLlPVGPIRWYRGvgPSRLLIYSfageyvPRIrnvsdTTKRNNMDFSIRISNVTPADAGIYY 113
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGS-PPPEVTWYKQ--GGKLLAES------GRF-----SVSRSGSTSTLTISNVTPEDSGTYT 67
                           90       100
                   ....*....|....*....|....*.
gi 1907136870  114 C-VKFQKGSSEpdteiqsgGGTEVYV 138
Cdd:smart00410  68 CaATNSSGSAS--------SGTTLTV 85
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
145-226 4.56e-08

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 50.49  E-value: 4.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 145 PEVSGPA-DRGIPDQKVNFTCKSHGFSPRnITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDVNSKVICE 223
Cdd:pfam08205   1 PTIEPPAsLLEGEGPEVVATCSSAGGKPA-PRITWYLDGKPLEAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQ 79

                  ...
gi 1907136870 224 VAH 226
Cdd:pfam08205  80 VSY 82
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
245-335 5.87e-08

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


Pssm-ID: 409612  Cd Length: 94  Bit Score: 50.55  E-value: 5.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNqvNLTCRAERFYPEDLQLIWLENGNV--SRNDTPKNLTKNTDGTYN-YTSLFLVNSSAHRedv 321
Cdd:cd21021     2 QVPPLVKVTHHVTSSVT--TLRCRALNYYPQNITMKWLKDKQPmdAKEFEPKDVLPNGDGTYQgWITLAVPPGEEQR--- 76
                          90
                  ....*....|....*.
gi 1907136870 322 vFTCQVKHD--QQPAI 335
Cdd:cd21021    77 -YTCQVEHPglDQPLI 91
IgI_2_Necl-1-4 cd05761
Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of ...
139-235 6.81e-08

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


Pssm-ID: 409418  Cd Length: 102  Bit Score: 50.50  E-value: 6.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 139 LAKPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRnITLKWFKDGQELHPLeTTVNPSGKNVSYNISSTVRVVLNSMDVNS 218
Cdd:cd05761     1 LGVPEKPVITGFTSPVVEGDEITLTCTTSGSKPA-ADIRWFKNDKELKGV-KEVQESGAGKTFTVTSTLRFRVDRDDDGV 78
                          90
                  ....*....|....*..
gi 1907136870 219 KVICEVAHITLDRSPLR 235
Cdd:cd05761    79 AVICRVDHESLTSTPKQ 95
C1-set pfam07654
Immunoglobulin C1-set domain;
250-329 1.26e-07

Immunoglobulin C1-set domain;


Pssm-ID: 429576  Cd Length: 85  Bit Score: 49.16  E-value: 1.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 250 VKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLENGNVSRND-TPKNLTKNTDGTYNYTSLFLVNSSAHREDVVFTCQV 327
Cdd:pfam07654   1 VYVFPPSPEELGKPNtLTCLVTGFYPPDITVTWLKNGQEVTEGvTTTPPSPNSDWTYQLSSYLTVTPSDWESGDTYTCRV 80

                  ..
gi 1907136870 328 KH 329
Cdd:pfam07654  81 EH 82
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
246-330 2.86e-07

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: 48.47  E-value: 2.86e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDT-PKNLTKNTDGTYNYT-SLFLVNSSAHRedvvF 323
Cdd:cd21029     1 VKPRVRLSSRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTqSGGILPNHDGTYQLRkTLDIAPGEGAG----Y 76

                  ....*..
gi 1907136870 324 TCQVKHD 330
Cdd:cd21029    77 SCRVDHS 83
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
158-226 6.92e-07

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 47.39  E-value: 6.92e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907136870 158 QKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSGK---NVSYNISSTVRVVLNSMDVNSKVICEVAH 226
Cdd:cd16093    18 RTATFVCLATGFSPKTISFKWLRNGKEVTSSTGAVVEEPKedgKTLYSATSFLTITESEWKSQTEFTCEFKH 89
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
248-329 7.41e-07

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 47.39  E-value: 7.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVT--QQSPTSMNQ-VNLTCRAERFYPEDLQLIWLENGN--VSRND-TPKNLTKNTDGTYNYTSLFLVNSSAHREDV 321
Cdd:cd16093     2 PTVSLHapSREEFLGNRtATFVCLATGFSPKTISFKWLRNGKevTSSTGaVVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                  ....*...
gi 1907136870 322 VFTCQVKH 329
Cdd:cd16093    82 EFTCEFKH 89
IgI_2_Necl-3 cd05884
Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set ...
138-233 7.93e-07

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


Pssm-ID: 409467  Cd Length: 104  Bit Score: 47.62  E-value: 7.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 138 VLAKPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRnITLKWFKDGQELHPLEtTVNPSGKN-VSYNISSTVRVVLNSMDV 216
Cdd:cd05884     1 VLGVPEKPQISGFTSPVMEGDHIQLTCKTSGSKPA-ADIRWFKNDKEVKDVK-YLKAEDANrKTFTVSSSLDFHVDRDDD 78
                          90
                  ....*....|....*..
gi 1907136870 217 NSKVICEVAHITLDRSP 233
Cdd:cd05884    79 GVAITCRVDHESLTATP 95
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
244-329 1.00e-06

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


Pssm-ID: 409593  Cd Length: 97  Bit Score: 46.84  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 244 IRVSPTvkvTQQSPTSmnQVNLTCRAERFYPEDLQLIWLENGNV--SRNDTPKNLTKNTDGTYNYTSLFLVNSSAhrEDv 321
Cdd:cd21002     6 VRVAPT---TPFNTRE--PVMLACHVWGFYPADVTITWLKNGDPvaPHSSAPKTAQPNGDWTYQTQVTLAVTPSP--GD- 77

                  ....*...
gi 1907136870 322 VFTCQVKH 329
Cdd:cd21002    78 TYTCSVQH 85
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
135-209 1.14e-06

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


Pssm-ID: 409495  Cd Length: 92  Bit Score: 46.45  E-value: 1.14e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907136870 135 EVYVLAKPSPPEvsgpadrgipdqKVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVN--PSGkNVSYNISSTVRV 209
Cdd:cd07698     4 KVHVTHHPRSDG------------ESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVEtrPNG-DGTFQKWAAVVV 67
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
248-329 1.82e-06

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: 46.25  E-value: 1.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQSPTSMNQ---VNLTCRAERFYPEDLQLIWLENGNVSRN-DTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVF 323
Cdd:cd05847     1 PTVQILHSSCASTLTsetIQLLCLISGYTPSTIEVEWLVDGQVATLsAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTY 80

                  ....*.
gi 1907136870 324 TCQVKH 329
Cdd:cd05847    81 TCKVTH 86
IgI_2_Necl-1 cd07705
Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set ...
139-232 3.03e-06

Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1; also known as cell adhesion molecule3 (CADM3)). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains is essential to cell-cell adhesion and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 409502  Cd Length: 103  Bit Score: 45.73  E-value: 3.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 139 LAKPSPPEVSGPADRGIPDQKVNFTCKSHGFSPRnITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDVNS 218
Cdd:cd07705     1 LGIPQKPQITGYESAFKEKDKAKLRCTSSGSKPA-ANIKWRKGDQELEGAPTSVQEDGNGKTFTVSSSVEFQVTREDDGA 79
                          90
                  ....*....|....*..
gi 1907136870 219 KVICEVAHITL---DRS 232
Cdd:cd07705    80 EITCSVGHESLhdsDRS 96
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
245-337 3.97e-06

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: 45.19  E-value: 3.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSahrEDVVF 323
Cdd:cd21023     2 RADPPKAHVAHHPISDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTELVETRPAgDGTFQKWAAVVVPPG---EEQRY 78
                          90
                  ....*....|....*.
gi 1907136870 324 TCQVKHD--QQPAITR 337
Cdd:cd21023    79 TCHVQHEglPQPLILR 94
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
29-122 4.47e-06

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: 45.82  E-value: 4.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSL-LPVGPIRWYR---GVGPSRLLIYSfageYVPRIRNVSDTTK--------RNNMD 96
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVSGIdFSTTYIHWYRqkpGQALERLLYVS----STSAVRKDSGKTKnkfearkdVGKST 76
                          90       100
                  ....*....|....*....|....*.
gi 1907136870  97 FSIRISNVTPADAGIYYCVKFQKGSS 122
Cdd:cd04982    77 STLTITNLEKEDSATYYCAYWESGSG 102
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
248-333 5.19e-06

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: 44.78  E-value: 5.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSahrEDVVFTCQ 326
Cdd:cd21024     6 PKTHVTHH-PISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAgDGTFQKWAAVVVPSG---EEQRYTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21024    82 VQHEGLP 88
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
245-341 5.55e-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: 45.15  E-value: 5.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKV--TQQSPTSMNQVnLTCRAERFYPEDLQLIWLENGNVSRND-TPKNLTKNTDGTYNytSLFLVNSSAHREDv 321
Cdd:cd20998     4 RVEPTVTVypTKTQPLEHHNL-LVCSVSDFYPGNIEVRWFRNGKEEKTGiVSTGLVRNGDWTFQ--TLVMLETVPQSGE- 79
                          90       100
                  ....*....|....*....|
gi 1907136870 322 VFTCQVKHdqqPAITRNHTV 341
Cdd:cd20998    80 VYTCQVEH---PSLTDPVTV 96
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
244-329 7.40e-06

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: 44.41  E-value: 7.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 244 IRVSPTVKVTQQSPTSmnqvnLTCRAERFYPEDLQLIWLEngnVSRNDTPKNLTK----------NTDGTYNYTSLFLVN 313
Cdd:cd05771     3 VRLSPKNLVKPDLPQT-----LSCHIAGYYPLDVDVEWLR---EEPGGSESQVSRdgvslsshrqSVDGTYSISSYLTLE 74
                          90
                  ....*....|....*.
gi 1907136870 314 SSAHREDVVFTCQVKH 329
Cdd:cd05771    75 PGTENRGATYTCRVTH 90
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
29-138 7.40e-06

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: 44.76  E-value: 7.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEkSVSVAAGDSTVLNCTLTSLLPVGP-IRWYRGVGPS--RLLIY--SFAGEYVP-RIRNVSDTTKRnnmdfSIRIS 102
Cdd:cd04984     2 LTQPS-SLSVSPGETVTITCTGSSGNISGNyVNWYQQKPGSapRYLIYedKHRPSGIPdRFSGSKSGNTA-----SLTIS 75
                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1907136870 103 NVTPADAGIYYCVKFQKGSsepdteIQSGGGTEVYV 138
Cdd:cd04984    76 GAQTEDEADYYCQVWDSNS------YVFGGGTKLTV 105
IGv smart00406
Immunoglobulin V-Type;
46-114 9.15e-06

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 43.91  E-value: 9.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907136870   46 LNCTL-TSLLPVGPIRWYR---GVGPSRLLIYSFAGE------YVPRIrNVSDTTKRNnmDFSIRISNVTPADAGIYYC 114
Cdd:smart00406   4 LSCKFsGSTFSSYYVSWVRqppGKGLEWLGYIGSNGSsyyqesYKGRF-TISKDTSKN--DVSLTISNLRVEDTGTYYC 79
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
135-232 1.12e-05

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: 43.85  E-value: 1.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 135 EVYVLAKPSPPevsgpadrgipDQKVNFTCKSHGFSPRNITLKWFKDGQELHP-LETT-VNPSGkNVSYNISSTVRVVLN 212
Cdd:cd21029     4 RVRLSSRPSPG-----------DGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDgTQSGgILPNH-DGTYQLRKTLDIAPG 71
                          90       100
                  ....*....|....*....|
gi 1907136870 213 SMDvnsKVICEVAHITLDRS 232
Cdd:cd21029    72 EGA---GYSCRVDHSSLKQD 88
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
246-335 1.26e-05

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


Pssm-ID: 409424  Cd Length: 95  Bit Score: 43.83  E-value: 1.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLENG-NVSRNDTPKNLTKNTDGTYN---YTSlFLvnssAHRED 320
Cdd:cd05767     1 VPPEVTVFPKSPVELGEPNtLICFVDNFFPPVINVTWLRNGqPVTDGVSETVFLPREDHSFRkfsYLP-FT----PSEGD 75
                          90
                  ....*....|....*..
gi 1907136870 321 vVFTCQVKH--DQQPAI 335
Cdd:cd05767    76 -IYDCRVEHwgLEEPLL 91
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
245-329 1.48e-05

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


Pssm-ID: 409592  Cd Length: 97  Bit Score: 43.56  E-value: 1.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLEN------GNVSrndTPknLTKNTDGTYNYtsLFLVNSSAH 317
Cdd:cd21001     1 RVEPTVTISPSRTEALNHHNlLVCSVTDFYPGQIKVRWFRNdqeetaGVVS---TP--LIRNGDWTFQI--LVMLEMTPQ 73
                          90
                  ....*....|..
gi 1907136870 318 REDvVFTCQVKH 329
Cdd:cd21001    74 RGD-VYTCHVEH 84
Ig_Semaphorin_C cd04979
Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are ...
31-114 1.88e-05

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: 43.22  E-value: 1.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  31 QPEKSVSVAAGDSTVLNCTLTSLLpvGPIRWY--RGVGPsrlliysfaGEYVPRIRNVSDTtkrnnmdfSIRISNVTPAD 108
Cdd:cd04979     1 TSFKQISVKEGDTVILSCSVKSNN--APVTWIhnGKKVP---------RYRSPRLVLKTER--------GLLIRSAQEAD 61

                  ....*.
gi 1907136870 109 AGIYYC 114
Cdd:cd04979    62 AGVYEC 67
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
245-341 2.05e-05

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 [Multi-domain]  Cd Length: 96  Bit Score: 43.07  E-value: 2.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNQVNL-TCRAERFYPEDLQLIWLENGNVSRNDT-PKNLTKNTDGTYNYTSLFlvnSSAHREDVV 322
Cdd:cd21000     1 RVEPKVTVYPAKTQPLQHHNLlVCSVNGFYPGSIEVRWFRNGQEEKAGVvSTGLIQNGDWTFQTLVML---ETVPRSGEV 77
                          90
                  ....*....|....*....
gi 1907136870 323 FTCQVKHdqqPAITRNHTV 341
Cdd:cd21000    78 YTCQVEH---PSVTSPLTV 93
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
29-126 2.31e-05

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 43.59  E-value: 2.31e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSLLP--VGPIRWYRGVGPSRLLI--------YSFAGEYVPRIRNVSDTTKRNNMdfS 98
Cdd:cd05718     2 RVQVPTEVTGFLGGSVTLPCSLTSPGTtkITQVTWMKIGAGSSQNVavfhpqygPSVPNPYAERVEFLAARLGLRNA--T 79
                          90       100       110
                  ....*....|....*....|....*....|
gi 1907136870  99 IRISNVTPADAGIYYC--VKFQKGSSEPDT 126
Cdd:cd05718    80 LRIRNLRVEDEGNYICefATFPQGNRQGTT 109
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
263-330 2.38e-05

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


Pssm-ID: 409429  Cd Length: 102  Bit Score: 43.08  E-value: 2.38e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 263 VNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNTDGTYNYTSLFLVnsSAHREDVV--FTCQVKHD 330
Cdd:cd05772    20 VSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQV--VLTKDDVHsqLTCEVAHV 87
IGc1 smart00407
Immunoglobulin C-Type;
159-230 2.43e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 42.30  E-value: 2.43e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907136870  159 KVNFTCKSHGFSPRNITLKWFKDGQELHPLETTVNPSG-KNVSYNISSTVRVVLNSMDVNSKVICEVAHITLD 230
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKnSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
248-333 3.01e-05

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


Pssm-ID: 409616  Cd Length: 96  Bit Score: 42.87  E-value: 3.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSahrEDVVFTCQ 326
Cdd:cd21025     6 PKTHVTHH-PVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAgDGTFQKWAAVVVPSG---EEQRYTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21025    82 VQHEGLP 88
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
247-329 3.90e-05

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


Pssm-ID: 409496  Cd Length: 99  Bit Score: 42.44  E-value: 3.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 247 SPTVKVTQQSPT--SMNQVNLTCRAERFYPEDLQLIWLENGN-VSRNDTPKNLTKNTDGTYNYTSLFLVNSSAHREDVVF 323
Cdd:cd07699     1 APSVTIFPPSSEelSSGKATLVCLINKFYPGFATVTWKVDGStVSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVY 80

                  ....*.
gi 1907136870 324 TCQVKH 329
Cdd:cd07699    81 TCEVTH 86
IgC1_MHC_Ia_MIC-A_MIC-B cd21017
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; ...
246-329 3.99e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B. MIC-A and MIC-B are homologs that serve as stress-inducible antigens on epithelial and epithelially derived cells. Both serve as ligands for the widely expressed activating immunoreceptor NKG2D, a C-type lectin-like activating immunoreceptor. MIC-B is very similar in structure to MIC-A and likely interacts with NKG2D in an analogous manner. The interdomain flexibility observed in the MIC-A structures, a feature unique to MIC proteins among MHC class I proteins and homologs, is also displayed by MIC-B, with an interdomain relationship intermediate between the two examples of MIC-A structures. Mapping sequence variations onto the structures of MIC-A and MIC-B reveals patterns completely distinct from those displayed by classical MHC class I proteins, with a number of substitutions falling on positions likely to affect interactions with NKG2D, but with other positions lying distant from the NKG2D binding sites or buried within the core of the proteins. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409608  Cd Length: 95  Bit Score: 42.51  E-value: 3.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 246 VSPTVKVTQqSPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPK--NLTKNTDGTYNytsLFLVNSSAHREDVVF 323
Cdd:cd21017     3 VPPMVNVTR-SEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQwgDVLPDGNGTYQ---TWVATRICQGEEQRF 78

                  ....*.
gi 1907136870 324 TCQVKH 329
Cdd:cd21017    79 TCYMEH 84
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
28-115 4.01e-05

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 433584 [Multi-domain]  Cd Length: 75  Bit Score: 41.80  E-value: 4.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLlPVGPIRWYRGvgpsrlliysfageyvpRIRNVSDTTKRNNMDFSIRISNVTPA 107
Cdd:pfam13927   3 VITVSPSSVVVVEGETVTLTCEASGS-PPPTITWYKN-----------------GGKLSSGRTSLVGGNGTLTISNVTRE 64

                  ....*...
gi 1907136870 108 DAGIYYCV 115
Cdd:pfam13927  65 DSGTYTCT 72
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
31-115 4.48e-05

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


Pssm-ID: 395002  Cd Length: 86  Bit Score: 41.80  E-value: 4.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  31 QPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWyrgvgpsrlliySFAGEYVPRIRNVSDTTKRNnMDFSIRISNVTPADAG 110
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPGPDVTW------------SKEGGTLIESLKVKHDNGRT-TQSSLLISNVTKEDAG 67

                  ....*
gi 1907136870 111 IYYCV 115
Cdd:pfam00047  68 TYTCV 72
IgV_MOG_like cd05713
Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here ...
28-122 4.79e-05

Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here are composed of the immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the CNS on the outermost lamellae of the myelin sheath, and on the surface of oligodendrocytes, and may participate in the completion, compaction, and/or maintenance of myelin. This group also includes butyrophilin (BTN). BTN is the most abundant protein in bovine milk-fat globule membrane (MFGM).


Pssm-ID: 409378  Cd Length: 114  Bit Score: 42.56  E-value: 4.79e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTsllpvgP--------IRWYRGvGPSRL-LIY----SFAGEYVPRIRN----VSDTT 90
Cdd:cd05713     2 SVIGPTEPILALVGEDAELPCHLS------PkmsaehmeVRWFRS-QFSPVvHLYrdgqDQEEEQMPEYRGrtelLKDAI 74
                          90       100       110
                  ....*....|....*....|....*....|..
gi 1907136870  91 KRNNMdfSIRISNVTPADAGIYYCVkFQKGSS 122
Cdd:cd05713    75 AEGSV--ALRIHNVRPSDEGQYTCF-FRSGSF 103
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
150-235 5.16e-05

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


Pssm-ID: 409423  Cd Length: 96  Bit Score: 41.93  E-value: 5.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 150 PADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQELHP--LETTVNPSGkNVSYNISSTVRVVLNSMDVnskVICEVAHI 227
Cdd:cd05766    10 PTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAgvVSTELIPNG-DWTFQILVMLETTPRRGDV---YTCQVEHS 85

                  ....*...
gi 1907136870 228 TLDrSPLR 235
Cdd:cd05766    86 SLQ-SPLT 92
I-set pfam07679
Immunoglobulin I-set domain;
28-115 7.13e-05

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 41.47  E-value: 7.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLlPVGPIRWYRG---VGPSRLLiysfageyvpRIRNVSDTTkrnnmdfSIRISNV 104
Cdd:pfam07679   2 KFTQKPKDVEVQEGESARFTCTVTGT-PDPEVSWFKDgqpLRSSDRF----------KVTYEGGTY-------TLTISNV 63
                          90
                  ....*....|.
gi 1907136870 105 TPADAGIYYCV 115
Cdd:pfam07679  64 QPDDSGKYTCV 74
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
262-350 7.57e-05

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: 41.94  E-value: 7.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 262 QVNLTCRAERFYPEDLQLIWLENG-----NVSRNDTPknlTKNTDGTYNYTSLFLVNSSAHREDVVFTCQVKHDqqpAIT 336
Cdd:cd05768    18 TVTLTCLVKGFYPEDIFVSWLQNGeplpsADYKTTAP---VPESDGSFFVYSKLNVSTADWNSGDVFSCVVGHE---ALP 91
                          90
                  ....*....|....
gi 1907136870 337 RNHTVLGFAHSSDQ 350
Cdd:cd05768    92 LQFTQKSIDKSPGK 105
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
247-333 8.09e-05

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


Pssm-ID: 409609  Cd Length: 95  Bit Score: 41.65  E-value: 8.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 247 SPTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTC 325
Cdd:cd21018     5 SPKAHVTHH-PRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAgDGTFQKWASVVVPLGKEQN---YTC 80

                  ....*...
gi 1907136870 326 QVKHDQQP 333
Cdd:cd21018    81 RVYHEGLP 88
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
135-226 1.08e-04

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: 41.55  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 135 EVYVLakpsPPevsgPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGQEL---HPLETTVNPSGKNvSYNISSTVRVVL 211
Cdd:cd05768     2 SVYLL----PP----PEEELSLNETVTLTCLVKGFYPEDIFVSWLQNGEPLpsaDYKTTAPVPESDG-SFFVYSKLNVST 72
                          90
                  ....*....|....*
gi 1907136870 212 NSMDVNSKVICEVAH 226
Cdd:cd05768    73 ADWNSGDVFSCVVGH 87
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
248-333 1.26e-04

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: 40.87  E-value: 1.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTCQ 326
Cdd:cd21012     6 PKTHVTHH-PRPEGYVTLRCWALGFYPAHITLTWQLNGEELIQDTELVETRPAgDGTFQKWAAVVVPSGEEQK---YTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21012    82 VYHEGLP 88
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
145-235 2.13e-04

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


Pssm-ID: 409428  Cd Length: 100  Bit Score: 40.56  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 145 PEVS-GPADRGIPDQKVNFTCKSHGFSPRNITLKWFKDGqelhPLETTVNPSGKNVS-----------YNISSTVRVVLN 212
Cdd:cd05771     1 PRVRlSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLREE----PGGSESQVSRDGVSlsshrqsvdgtYSISSYLTLEPG 76
                          90       100
                  ....*....|....*....|...
gi 1907136870 213 SMDVNSKVICEVAHITLDrSPLR 235
Cdd:cd05771    77 TENRGATYTCRVTHVSLE-EPLS 98
IgC1_MHC_Ia_HLA-B cd21026
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
248-333 2.24e-04

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


Pssm-ID: 409617  Cd Length: 97  Bit Score: 40.18  E-value: 2.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSahrEDVVFTCQ 326
Cdd:cd21026     6 PKTHVTHH-PISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAgDRTFQKWAAVVVPSG---EEQRYTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21026    82 VQHEGLP 88
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
248-333 2.39e-04

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


Pssm-ID: 409625  Cd Length: 98  Bit Score: 40.14  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHRedvVFTCQ 326
Cdd:cd21820     6 PKAHVTHH-PRSEDEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAgDGTFQKWAAVVVPLGKEQ---YYTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21820    82 VYHEGLP 88
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
245-329 2.75e-04

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


Pssm-ID: 409594  Cd Length: 96  Bit Score: 40.13  E-value: 2.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 245 RVSPTVKVTQQSPTSMNQVN-LTCRAERFYPEDLQLIWLENGnvsRNDTPKNLTKNT--DGTYNYTSLFLVNSSAHREDv 321
Cdd:cd21003     1 RVQPKVNVSPSKKGPLQHHNlLVCHVTDFYPGNIQVRWFLNG---QEETAGVVSTNLihNGDWTFQILVMLEMTPQQGD- 76

                  ....*...
gi 1907136870 322 VFTCQVKH 329
Cdd:cd21003    77 VYTCQVEH 84
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
247-333 3.12e-04

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


Pssm-ID: 409618  Cd Length: 95  Bit Score: 39.82  E-value: 3.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 247 SPTVKVTQQSpTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTC 325
Cdd:cd21027     5 APKTHMTHHA-VSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAgDGTFQKWAAVVVPSGQEQR---YTC 80

                  ....*...
gi 1907136870 326 QVKHDQQP 333
Cdd:cd21027    81 HVQHEGLP 88
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
248-333 5.85e-04

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


Pssm-ID: 409604  Cd Length: 97  Bit Score: 39.33  E-value: 5.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTCQ 326
Cdd:cd21013     5 PKAHVTHH-PRSEGYVTLRCWALGFYPADITLTWQLNGEELTQDMEFVETRPAgDGTFQKWASVVVPLGKEQK---YTCH 80

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21013    81 VEHEGLP 87
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
248-333 7.22e-04

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


Pssm-ID: 409605  Cd Length: 94  Bit Score: 38.96  E-value: 7.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTCQ 326
Cdd:cd21014     5 PKAHVTHH-PRSYGAVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAgDGTFQKWASVVVPLGKEQN---YTCH 80

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21014    81 VNHEGLP 87
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
28-138 9.15e-04

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


Pssm-ID: 409503  Cd Length: 112  Bit Score: 39.04  E-value: 9.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  28 KVTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGV--GPSRLLIYSFAGEYVPRIRNVSDTTKRNNMDFSIRISNVT 105
Cdd:cd07706     1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNYYLFWYKQLpsGEMTFLIRQDSSEQNAKSGRYSVNFQKAQKSISLTISALQ 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1907136870 106 PADAGIYYCVKfqkgSSEPDTE-IQSGGGTEVYV 138
Cdd:cd07706    81 LEDSAKYFCAL----SLPYDTDkLIFGKGTRLTV 110
IgI_2_Necl-4 cd05885
Second immunoglobulin (Ig)-like domain of nectin-like molecule-4 (Necl-4); member of the ...
159-229 1.33e-03

Second immunoglobulin (Ig)-like domain of nectin-like molecule-4 (Necl-4); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule-4 (Necl-4; also known as cell adhesion molecule 4 (CADM4)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1-Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Ig domains are likely to participate in ligand binding and recognition. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. In injured peripheral nerve cells, the mRNA signal for both Necl-4 and Necl-5 was observed to be elevated. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression.


Pssm-ID: 409468  Cd Length: 100  Bit Score: 38.01  E-value: 1.33e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907136870 159 KVNFTCkshgFSPRN---ITLKWFKDGQELhPLETTVNPSGKNVSynISSTVRVVLNSMDVNSKVICEVAHITL 229
Cdd:cd05885    20 EVELSC----LVPRSrpaATLRWYRDRKEL-KGVSSGQENGKVWS--VASTVRFRVDRKDDGGIVICEAQNQAL 86
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
248-330 1.59e-03

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  Cd Length: 116  Bit Score: 38.51  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQSPTSMNQ---VNLTCRAERFYPEDLQLIWLENGNVSRND--TPKNLTKNTDGTYNYTS-LFLVNSSAHREDV 321
Cdd:cd05769     3 PTVALFPPSEAEIRNkrkATLVCLATGFYPDHVSLSWKVNGKEVKDGvaTDPQALRENTSTYSLSSrLRVSATEWFNPRN 82

                  ....*....
gi 1907136870 322 VFTCQVKHD 330
Cdd:cd05769    83 TFTCIVKFY 91
Ig3_L1-CAM_like cd05731
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar ...
32-115 1.90e-03

Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar domains; The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM and human neurofascin.


Pssm-ID: 409394 [Multi-domain]  Cd Length: 83  Bit Score: 37.39  E-value: 1.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  32 PEKSVSVAAGDSTVLNCtLTSLLPVGPIRWYRGVGPsrlliysfageyVPrirnvSDTTKRNNMDFSIRISNVTPADAGI 111
Cdd:cd05731     1 SESSTMVLRGGVLLLEC-IAEGLPTPDIRWIKLGGE------------LP-----KGRTKFENFNKTLKIENVSEADSGE 62

                  ....
gi 1907136870 112 YYCV 115
Cdd:cd05731    63 YQCT 66
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
248-333 2.20e-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: 37.43  E-value: 2.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSahrEDVVFTCQ 326
Cdd:cd21022     5 PKTHVTHH-PVFDYEATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAgDGTFQKWAAVVVPSG---EEQRYTCH 80

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21022    81 VQHEGLP 87
IgC1_MHC-like_FcRn cd21011
immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; ...
265-329 2.55e-03

immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of neonatal Fc receptor (FcRn). FcRn performs two distinct functions: the transport of maternal immunoglobulin G (IgG) to pre- or neonatal mammals which provides passive immunity and protection of IgG from normal serum protein catabolism. FcRn is related to class I MHC proteins, but lacks a functional peptide binding groove. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409602  Cd Length: 93  Bit Score: 37.02  E-value: 2.55e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907136870 265 LTCRAERFYPEDLQLIWLENGNVSRNDTpKNLTKNTDGTYNYTSLFLVNS-SAHRedvvFTCQVKH 329
Cdd:cd21011    22 LTCSAFSFYPPELQLRFLRNGLAAGSGE-GDFGPNGDGSFHAWSSLTVKSgDEHH----YRCVVQH 82
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
247-334 3.77e-03

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: 36.54  E-value: 3.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 247 SPTV-KVTQQSPTSMNQVNLTCRAERFYPEDLQLIWLENGN--VSRNDT-PKNLTKntdGTYNYTSLFLVNSSAHREDVV 322
Cdd:cd21819     1 APTLfPLVSCGSSTSDPVTVGCLATDFLPDSITFSWTDDNNslTTGVKTyPSVLTG---GTYTASSQLQVPESEWKSKEN 77
                          90
                  ....*....|..
gi 1907136870 323 FTCQVKHDQQPA 334
Cdd:cd21819    78 FYCKVEHPGGNK 89
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
45-115 4.91e-03

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.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 35.77  E-value: 4.91e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907136870  45 VLNCTLTSLlPVGPIRWYRGvgpsrlliysfaGEYVPRIRNVSDTTKRNNmdFSIRISNVTPADAGIYYCV 115
Cdd:cd00096     2 TLTCSASGN-PPPTITWYKN------------GKPLPPSSRDSRRSELGN--GTLTISNVTLEDSGTYTCV 57
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
143-229 5.59e-03

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


Pssm-ID: 409427  Cd Length: 94  Bit Score: 36.30  E-value: 5.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 143 SPPEV----SGPADRGipdqKVNF-TCKSHGFSPRNITLKWFKDGQELHPLETTVNPSGKNVSYNISSTVRVVLNSMDvn 217
Cdd:cd05770     1 STPKVqvysRFPAENG----KPNVlNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYLLKYTEFTPTKGD-- 74
                          90
                  ....*....|..
gi 1907136870 218 sKVICEVAHITL 229
Cdd:cd05770    75 -EYACRVRHNTL 85
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
248-333 5.59e-03

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


Pssm-ID: 409607  Cd Length: 97  Bit Score: 36.23  E-value: 5.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870 248 PTVKVTQQsPTSMNQVNLTCRAERFYPEDLQLIWLENGNVSRNDTPKNLTKNT-DGTYNYTSLFLVNSSAHREdvvFTCQ 326
Cdd:cd21016     6 PKAHVTRH-PRPEGDVTLRCWALGFYPADITLTWQKDGEELTQDMEFVETRPAgDGTFQKWAAVVVPLGKEQS---YTCH 81

                  ....*..
gi 1907136870 327 VKHDQQP 333
Cdd:cd21016    82 VYHEGLP 88
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
31-138 6.45e-03

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: 36.66  E-value: 6.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  31 QPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYR-GVGPSR------LLIYSFA-----GEYVPRIRNV--SDTTKRNnmd 96
Cdd:cd07700     3 QTPGSLLVQTNQTVKMSCEAKTSPKNTRIYWLRqRQAPSKdshfefLASWDPSkgivyGEGVDQEKLIilSDSDSSR--- 79
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1907136870  97 FSIRISNVTPADAGIYYCVKFqkGSSepdtEIQSGGGTEVYV 138
Cdd:cd07700    80 YILSLMSVKPEDSGTYFCMTV--GSP----ELIFGTGTKLSV 115
IgI_Perlecan_like cd05754
Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of ...
29-115 6.49e-03

Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain found in Perlecan. Perlecan is a large multi-domain heparin sulfate proteoglycan, important in tissue development and organogenesis. Perlecan can be represented as 5 major portions; its fourth major portion (domain IV) is a tandem repeat of immunoglobulin-like domains (Ig2-Ig15) which can vary in size due to alternative splicing. Perlecan binds many cellular and extracellular ligands. Its domain IV region has many binding sites. Some of these have been mapped at the level of individual Ig-like domains, including a site restricted to the Ig5 domain for heparin/sulfatide, a site restricted to the Ig3 domain for nidogen-1 and nidogen-2, a site restricted to Ig4-5 for fibronectin, and sites restricted to Ig2 and to Ig13-15 for fibulin-2. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409412  Cd Length: 85  Bit Score: 36.00  E-value: 6.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907136870  29 VTQPEKSVSVAAGDSTVLNCTLTSLLPVGPIRWYRGVGPsrlliysfageyVPRirnvsdttkrNNMDFS--IRISNVTP 106
Cdd:cd05754     4 TVEEPRSQEVRPGADVSFICRAKSKSPAYTLVWTRVNGT------------LPS----------RAMDFNgiLTIRNVQL 61

                  ....*....
gi 1907136870 107 ADAGIYYCV 115
Cdd:cd05754    62 SDAGTYVCT 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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