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Conserved domains on  [gi|50872163|ref|NP_001002898|]
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signal-regulatory protein beta 1 [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 ...
 32-143 2.69e-64

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: 472250  Cd Length: 111  Bit Score: 200.86  E-value: 2.69e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  32 KVIQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYRGVGQSRLLIYPFTGEHSPRITNVSDVTKRNNMDFSIRISNVTPA 111
Cdd:cd16097   1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 50872163 112 DSGTYYCVKFQRGSSePDIEIQSGGGTELLVL 143
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 ...
 250-345 2.01e-61

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: 193.02  E-value: 2.01e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVWNVINVTCQIQKFYPPSFQLTWLENGNISRREVPFTLIVNKDGTYNWISCLLVNISALEENMVVTC 329
Cdd:cd16085   1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80

                        90
                ....*....|....*.
gi 50872163 330 KVEHDEQAEVIETHTV 345
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 ...
 145-247 5.30e-52

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: 168.66  E-value: 5.30e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 145 KPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQI 224
Cdd:cd05772   1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80

                        90       100
                ....*....|....*....|...
gi 50872163 225 ICEVDHVTLdRAPLRGIAHISEF 247
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 ...
 32-143 2.69e-64

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: 200.86  E-value: 2.69e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  32 KVIQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYRGVGQSRLLIYPFTGEHSPRITNVSDVTKRNNMDFSIRISNVTPA 111
Cdd:cd16097   1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 50872163 112 DSGTYYCVKFQRGSSePDIEIQSGGGTELLVL 143
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 ...
 250-345 2.01e-61

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: 193.02  E-value: 2.01e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVWNVINVTCQIQKFYPPSFQLTWLENGNISRREVPFTLIVNKDGTYNWISCLLVNISALEENMVVTC 329
Cdd:cd16085   1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80

                        90
                ....*....|....*.
gi 50872163 330 KVEHDEQAEVIETHTV 345
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 ...
 145-247 5.30e-52

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: 168.66  E-value: 5.30e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 145 KPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQI 224
Cdd:cd05772   1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80

                        90       100
                ....*....|....*....|...
gi 50872163 225 ICEVDHVTLdRAPLRGIAHISEF 247
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 ...
 38-143 3.83e-14

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 68.25  E-value: 3.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163    38 KSFFVGAGGSATLNCTVTSL--LPVGPIRWYRG--VGQSRLLIYPF-----TGEHSPRITNVSDVtkrNNMDFSIRISNV 108
Cdd:pfam07686   4 REVTVALGGSVTLPCTYSSSmsEASTSVYWYRQppGKGPTFLIAYYsngseEGVKKGRFSGRGDP---SNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 50872163   109 TPADSGTYYCVKFqrgssePDIEIQSGGGTELLVL 143
Cdd:pfam07686  81 TLSDSGTYTCAVI------PSGEGVFGKGTRLTVL 109
C1-set pfam07654
Immunoglobulin C1-set domain;
247-333 1.75e-10

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 56.87  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163   247 FIQVPPTLEIRQQPTmvwnvinVTCQIQKFYPPSFQLTWLENG-NISRREVPFTLIVNKDGTYNWISCLLVNISALEENM 325
Cdd:pfam07654   2 YVFPPSPEELGKPNT-------LTCLVTGFYPPDITVTWLKNGqEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGD 74


                  ....*...
gi 50872163   326 VVTCKVEH 333
Cdd:pfam07654  75 EYTCRVEH 82
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 42-119 4.82e-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: 52.89  E-value: 4.82e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50872163     42 VGAGGSATLNCTVTSLlPVGPIRWYRGVGQsrLLIYPftgehsPRITnvsdvTKRNNMDFSIRISNVTPADSGTYYCV 119
Cdd:smart00410   6 VKEGESVTLSCEASGS-PPPEVTWYKQGGK--LLAES------GRFS-----VSRSGSTSTLTISNVTPEDSGTYTCA 69
C1-set pfam07654
Immunoglobulin C1-set domain;
154-233 2.97e-08

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 50.71  E-value: 2.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163   154 PAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEI-SHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIICEVDHVT 232
Cdd:pfam07654   5 PPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHEG 84


                  .
gi 50872163   233 L 233
Cdd:pfam07654  85 L 85
IGc1 smart00407
Immunoglobulin C-Type;
269-333 7.61e-08

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 49.23  E-value: 7.61e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 50872163    269 VTCQIQKFYPPSFQLTWLENGNISRREV-PFTLIVNKDGTYNWISCLLVNISALEENMVVTCKVEH 333
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLRNGQEVTEGVsTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTH 69
IGc1 smart00407
Immunoglobulin C-Type;
163-234 4.43e-07

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 46.92  E-value: 4.43e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50872163    163 TVTFTCRSHGFFPRNLTLKWFKNGDE-ISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIICEVDHVTLD 234
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 ...
 32-143 2.69e-64

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: 200.86  E-value: 2.69e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  32 KVIQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYRGVGQSRLLIYPFTGEHSPRITNVSDVTKRNNMDFSIRISNVTPA 111
Cdd:cd16097   1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRISNITPA 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 50872163 112 DSGTYYCVKFQRGSSePDIEIQSGGGTELLVL 143
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 ...
 250-345 2.01e-61

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: 193.02  E-value: 2.01e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVWNVINVTCQIQKFYPPSFQLTWLENGNISRREVPFTLIVNKDGTYNWISCLLVNISALEENMVVTC 329
Cdd:cd16085   1 VPPTLEVTQQPTMVWNQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTC 80

                        90
                ....*....|....*.
gi 50872163 330 KVEHDEQAEVIETHTV 345
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 ...
 145-247 5.30e-52

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: 168.66  E-value: 5.30e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 145 KPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQI 224
Cdd:cd05772   1 KPSQPLVSGPSGRATPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTVFPEGDSVSYSVSSTVQVVLTKDDVHSQL 80

                        90       100
                ....*....|....*....|...
gi 50872163 225 ICEVDHVTLdRAPLRGIAHISEF 247
Cdd:cd05772  81 TCEVAHVTL-QAPLRGTANLSDI 102
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 33-142 8.68e-22

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: 89.32  E-value: 8.68e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  33 VIQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYRGV-GQSRLLIYPFTGEHSPRITNVSD---VTKRNNMDFSIRISNV 108
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKpGQGPEFLIYLSSSKGKTKGGVPGrfsGSRDGTSSFSLTISNL 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 50872163 109 TPADSGTYYCVKFQRGSSEPDIeiqSGGGTELLV 142
Cdd:cd00099  81 QPEDSGTYYCAVSESGGTDKLT---FGSGTRLTV 111
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 247-333 1.71e-14

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


Pssm-ID: 409354  Cd Length: 95  Bit Score: 68.64  E-value: 1.71e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 247 FIQVPPTLEIRQQPTmvwnviNVTCQIQKFYPPSFQLTWLENGN-ISRREVPFTLIVNKDGTYNWISCLLVNISALEENM 325
Cdd:cd00098   3 TLLPPSPEEKGGGKV------TLVCLVSGFYPKDITVTWLKNGVpLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGA 76


                ....*...
gi 50872163 326 VVTCKVEH 333
Cdd:cd00098  77 TYTCVVTH 84
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-143 3.83e-14

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 68.25  E-value: 3.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163    38 KSFFVGAGGSATLNCTVTSL--LPVGPIRWYRG--VGQSRLLIYPF-----TGEHSPRITNVSDVtkrNNMDFSIRISNV 108
Cdd:pfam07686   4 REVTVALGGSVTLPCTYSSSmsEASTSVYWYRQppGKGPTFLIAYYsngseEGVKKGRFSGRGDP---SNGDGSLTIQNL 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 50872163   109 TPADSGTYYCVKFqrgssePDIEIQSGGGTELLVL 143
Cdd:pfam07686  81 TLSDSGTYTCAVI------PSGEGVFGKGTRLTVL 109
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 148-234 8.34e-14

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


Pssm-ID: 409354  Cd Length: 95  Bit Score: 66.71  E-value: 8.34e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 148 SPMVSGPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETS-VSYRVSSTVQVVLEPRDVRSQIIC 226
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNdGTYSVTSSLTVPPSDWDEGATYTC 80


                ....*...
gi 50872163 227 EVDHVTLD 234
Cdd:cd00098  81 VVTHESLK 88
C1-set pfam07654
Immunoglobulin C1-set domain;
247-333 1.75e-10

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 56.87  E-value: 1.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163   247 FIQVPPTLEIRQQPTmvwnvinVTCQIQKFYPPSFQLTWLENG-NISRREVPFTLIVNKDGTYNWISCLLVNISALEENM 325
Cdd:pfam07654   2 YVFPPSPEELGKPNT-------LTCLVTGFYPPDITVTWLKNGqEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGD 74


                  ....*...
gi 50872163   326 VVTCKVEH 333
Cdd:pfam07654  75 EYTCRVEH 82
IgI_2_Necl-1-4 cd05761
Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of ...
 143-239 3.30e-09

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: 53.97  E-value: 3.30e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 143 LAKPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRNlTLKWFKNGDEIsHLETSVEPEETSVSYRVSSTVQVVLEPRDVRS 222
Cdd:cd05761   1 LGVPEKPVITGFTSPVVEGDEITLTCTTSGSKPAA-DIRWFKNDKEL-KGVKEVQESGAGKTFTVTSTLRFRVDRDDDGV 78

                        90
                ....*....|....*..
gi 50872163 223 QIICEVDHVTLDRAPLR 239
Cdd:cd05761  79 AVICRVDHESLTSTPKQ 95
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 42-119 4.82e-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: 52.89  E-value: 4.82e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50872163     42 VGAGGSATLNCTVTSLlPVGPIRWYRGVGQsrLLIYPftgehsPRITnvsdvTKRNNMDFSIRISNVTPADSGTYYCV 119
Cdd:smart00410   6 VKEGESVTLSCEASGS-PPPEVTWYKQGGK--LLAES------GRFS-----VSRSGSTSTLTISNVTPEDSGTYTCA 69
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 162-230 1.13e-08

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


Pssm-ID: 409513  Cd Length: 99  Bit Score: 52.40  E-value: 1.13e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 50872163 162 QTVTFTCRSHGFFPRNLTLKWFKNGDEI--SHLETSVEP-EETSVSYRVSSTVQVVLEPRDVRSQIICEVDH 230
Cdd:cd16093  18 RTATFVCLATGFSPKTISFKWLRNGKEVtsSTGAVVEEPkEDGKTLYSATSFLTITESEWKSQTEFTCEFKH 89
IgI_2_Necl-3 cd05884
Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set ...
 142-237 1.37e-08

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: 52.24  E-value: 1.37e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 142 VLAKPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRnLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVR 221
Cdd:cd05884   1 VLGVPEKPQISGFTSPVMEGDHIQLTCKTSGSKPA-ADIRWFKNDKEVKDVKYLKAEDANRKTFTVSSSLDFHVDRDDDG 79

                        90
                ....*....|....*.
gi 50872163 222 SQIICEVDHVTLDRAP 237
Cdd:cd05884  80 VAITCRVDHESLTATP 95
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 33-142 1.53e-08

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: 52.01  E-value: 1.53e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  33 VIQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYR-GVGQS-RLLIYpftgEHSPRITNVSDvtkR-----NNMDFSIRI 105
Cdd:cd04980   3 MTQSPASLSVSPGERVTISCKASQSISSNYLAWYQqKPGQApKLLIY----YASTLHSGVPS---RfsgsgSGTDFTLTI 75

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 50872163 106 SNVTPADSGTYYCvkfQRGSSEPdieIQSGGGTELLV 142
Cdd:cd04980  76 SSVEPEDAAVYYC---QQGYTFP---YTFGGGTKLEI 106
C1-set pfam07654
Immunoglobulin C1-set domain;
154-233 2.97e-08

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 50.71  E-value: 2.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163   154 PAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEI-SHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIICEVDHVT 232
Cdd:pfam07654   5 PPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHEG 84


                  .
gi 50872163   233 L 233
Cdd:pfam07654  85 L 85
IGc1 smart00407
Immunoglobulin C-Type;
269-333 7.61e-08

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 49.23  E-value: 7.61e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 50872163    269 VTCQIQKFYPPSFQLTWLENGNISRREV-PFTLIVNKDGTYNWISCLLVNISALEENMVVTCKVEH 333
Cdd:smart00407   4 LVCLVSGFYPPDITVTWLRNGQEVTEGVsTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTH 69
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 147-235 1.88e-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: 1.88e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 147 SSPMVSGPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETS--VEPEETSvSYRVSSTVQVVLEPRDVRSqi 224
Cdd:cd21029   1 VKPRVRLSSRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSggILPNHDG-TYQLRKTLDIAPGEGAGYS-- 77

                        90
                ....*....|.
gi 50872163 225 iCEVDHVTLDR 235
Cdd:cd21029  78 -CRVDHSSLKQ 87
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 33-142 3.48e-07

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


Pssm-ID: 409480  Cd Length: 110  Bit Score: 48.43  E-value: 3.48e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  33 VIQPVKSFFVGAGGSATLNCTVTSLLPVgpIRWYRGV-GQSRLLIYPFTGEHSPRITNVS----DVTKRNNMDFSIRISN 107
Cdd:cd05899   1 VTQSPRYLIKRRGQSVTLRCSQKSGHDN--MYWYRQDpGKGLQLLFYSYGGGLNEEGDLPgdrfSASRPSLTRSSLTIKS 78

                        90       100       110
                ....*....|....*....|....*....|....*
gi 50872163 108 VTPADSGTYYCVKFQRGSSEpdiEIQSGGGTELLV 142
Cdd:cd05899  79 AEPEDSAVYLCASSLGGGAD---EAYFGPGTRLTV 110
IGv smart00406
Immunoglobulin V-Type;
47-118 3.51e-07

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 47.38  E-value: 3.51e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163     47 SATLNCTV-TSLLPVGPIRWYR---GVGQSRLLIYPFTGEH------SPRITNVSDVTKRnnmDFSIRISNVTPADSGTY 116
Cdd:smart00406   1 SVTLSCKFsGSTFSSYYVSWVRqppGKGLEWLGYIGSNGSSyyqesyKGRFTISKDTSKN---DVSLTISNLRVEDTGTY 77


                   ..
gi 50872163    117 YC 118
Cdd:smart00406  78 YC 79
IGc1 smart00407
Immunoglobulin C-Type;
163-234 4.43e-07

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 46.92  E-value: 4.43e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50872163    163 TVTFTCRSHGFFPRNLTLKWFKNGDE-ISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIICEVDHVTLD 234
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLK 73
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 33-142 5.26e-07

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


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 47.65  E-value: 5.26e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  33 VIQPVKSFFVGAGGSATLNCTVTSLLPVGpIRWYR---GVG-QSRLLIYPFTG-EHSPRITNVSDVTKRnnmDFSIRISN 107
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYY-LFWYRqypGQGpQFLIYISSDSGnKKKGRFSATLDKSRK---SSSLHISA 76

                        90       100       110
                ....*....|....*....|....*....|....*
gi 50872163 108 VTPADSGTYYCVKFQRGSSEpdiEIQSGGGTELLV 142
Cdd:cd04983  77 AQLSDSAVYFCALSESGGTG---KLTFGKGTRLTV 108
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 35-128 1.89e-06

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: 45.65  E-value: 1.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163    35 QPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYRGVGQSRLLIYPFTGEhspritnvsdvtkRNNMDFSIRISNVTPADSG 114
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIESLKVKHDN-------------GRTTQSSLLISNVTKEDAG 67

                          90
                  ....*....|....
gi 50872163   115 TYYCVKFQRGSSEP 128
Cdd:pfam00047  68 TYTCVVNNPGGSAT 81
I-set pfam07679
Immunoglobulin I-set domain;
32-119 2.96e-06

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 44.94  E-value: 2.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163    32 KVIQPVKSFFVGAGGSATLNCTVTSLlPVGPIRWYRGvGQsrlliyPFTGEHSPRITNVSDVTkrnnmdfSIRISNVTPA 111
Cdd:pfam07679   2 KFTQKPKDVEVQEGESARFTCTVTGT-PDPEVSWFKD-GQ------PLRSSDRFKVTYEGGTY-------TLTISNVQPD 66


                  ....*...
gi 50872163   112 DSGTYYCV 119
Cdd:pfam07679  67 DSGKYTCV 74
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 157-198 3.32e-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: 44.91  E-value: 3.32e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 50872163 157 RAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEP 198
Cdd:cd07698  10 HPRSDGESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVET 51
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 32-119 8.67e-06

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 43.32  E-value: 8.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163    32 KVIQPVKSFFVGAGGSATLNCTVTSllpvGP---IRWYRGvgqsrlliypftgeHSPRITNVSDVTKRNNMDFSIRISNV 108
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCEATG----SPpptITWYKN--------------GEPISSGSTRSRSLSGSNSTLTISNV 64

                          90
                  ....*....|.
gi 50872163   109 TPADSGTYYCV 119
Cdd:pfam13927  65 TRSDAGTYTCV 75
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
 149-230 9.76e-06

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 43.56  E-value: 9.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163   149 PMVSGPAAR-AVPQQTVTFTCRSHGFFPR-NLTlkWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIIC 226
Cdd:pfam08205   1 PTIEPPASLlEGEGPEVVATCSSAGGKPApRIT--WYLDGKPLEAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTC 78


                  ....
gi 50872163   227 EVDH 230
Cdd:pfam08205  79 QVSY 82
IgC1_MHC_Ia_MIC-A_MIC-B cd21017
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; ...
 149-191 1.06e-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: 43.67  E-value: 1.06e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 50872163 149 PMVSGPAARaVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISH 191
Cdd:cd21017   5 PMVNVTRSE-ASEGNITVTCRASGFYPWNITLSWRQDGVSLSH 46
IgI_2_Necl-1 cd07705
Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set ...
 143-233 1.17e-05

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: 43.80  E-value: 1.17e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 143 LAKPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRnLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRS 222
Cdd:cd07705   1 LGIPQKPQITGYESAFKEKDKAKLRCTSSGSKPA-ANIKWRKGDQELEGAPTSVQEDGNGKTFTVSSSVEFQVTREDDGA 79

                        90
                ....*....|.
gi 50872163 223 QIICEVDHVTL 233
Cdd:cd07705  80 EITCSVGHESL 90
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
 161-213 1.22e-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: 43.86  E-value: 1.22e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 50872163 161 QQTVTFTCRSHGFFPRNLTLKWFKNGDEIS---HLETSVEPEETSvSYRVSSTVQV 213
Cdd:cd05768  16 NETVTLTCLVKGFYPEDIFVSWLQNGEPLPsadYKTTAPVPESDG-SFFVYSKLNV 70
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 149-239 1.42e-05

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


Pssm-ID: 409428  Cd Length: 100  Bit Score: 43.64  E-value: 1.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 149 PMVS-GPAARAVPQQTVTFTCRSHGFFPRNLTLKWFKngDEISHLETSVEPEETSVS---------YRVSSTVQVVLEPR 218
Cdd:cd05771   1 PRVRlSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLR--EEPGGSESQVSRDGVSLSshrqsvdgtYSISSYLTLEPGTE 78

                        90       100
                ....*....|....*....|.
gi 50872163 219 DVRSQIICEVDHVTLDrAPLR 239
Cdd:cd05771  79 NRGATYTCRVTHVSLE-EPLS 98
IgV_MOG_like cd05713
Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here ...
 32-126 3.21e-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: 42.95  E-value: 3.21e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  32 KVIQPVKSFFVGAGGSATLNCtvtSLLPVG-----PIRWYRGvgQSRLLIYPF------TGEHSP----RITNVSDVTKR 96
Cdd:cd05713   2 SVIGPTEPILALVGEDAELPC---HLSPKMsaehmEVRWFRS--QFSPVVHLYrdgqdqEEEQMPeyrgRTELLKDAIAE 76

                        90       100       110
                ....*....|....*....|....*....|
gi 50872163  97 NNMdfSIRISNVTPADSGTYYCVkFQRGSS 126
Cdd:cd05713  77 GSV--ALRIHNVRPSDEGQYTCF-FRSGSF 103
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 148-230 3.60e-05

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


Pssm-ID: 409374  Cd Length: 98  Bit Score: 42.19  E-value: 3.60e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 148 SPMVSGPaaRAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETSVSYRVSSTVQVVLEPRDVRSQ--II 225
Cdd:cd04985   5 FPLQSAT--KSQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGevYK 82


                ....*
gi 50872163 226 CEVDH 230
Cdd:cd04985  83 CQVQH 87
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 48-119 5.00e-05

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: 41.16  E-value: 5.00e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 50872163  48 ATLNCTVTSLlPVGPIRWYRGvgqsrlliypftgeHSPRITNVSDVTKRNNMDFSIRISNVTPADSGTYYCV 119
Cdd:cd00096   1 VTLTCSASGN-PPPTITWYKN--------------GKPLPPSSRDSRRSELGNGTLTISNVTLEDSGTYTCV 57
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 250-333 5.20e-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: 5.20e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVWNVIN-VTCQIQKFYPPSFQLTWLENGNI-SRREVPFTLIVNKDGTYNWISCLLVNISALEenmVV 327
Cdd:cd05766   2 VQPSVKVSPTKTGPLEHPNlLVCSVTGFYPAEIEVKWFRNGQEeTAGVVSTELIPNGDWTFQILVMLETTPRRGD---VY 78


                ....*.
gi 50872163 328 TCKVEH 333
Cdd:cd05766  79 TCQVEH 84
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 34-142 6.63e-05

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


Pssm-ID: 409497  Cd Length: 116  Bit Score: 42.05  E-value: 6.63e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  34 IQPVKSFFVGAGGSATLNCTVTSLLPVGPIRWYR---------------------------GVGQSRLLIYPFTGEHSPR 86
Cdd:cd07700   2 LQTPGSLLVQTNQTVKMSCEAKTSPKNTRIYWLRqrqapskdshfeflaswdpskgivygeGVDQEKLIILSDSDSSRYI 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 50872163  87 itnvsdvtkrnnmdfsIRISNVTPADSGTYYCVKFqrGSSepdiEIQSGGGTELLV 142
Cdd:cd07700  82 ----------------LSLMSVKPEDSGTYFCMTV--GSP----ELIFGTGTKLSV 115
IgV_P0-like cd05715
Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here ...
 41-135 1.29e-04

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.


Pssm-ID: 409380  Cd Length: 117  Bit Score: 41.26  E-value: 1.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  41 FVGAGGSATLNCTVTSLLPVG---PIRW-YR--GVGQSRLLIY-----PFTGEHSP---RITNVSDVTKRnnmDFSIRIS 106
Cdd:cd05715  10 NVLNGSDVRLTCTFTSCYTVGdafSVTWtYQpeGGNTTESMFHyskgkPYILKVGRfkdRVSWAGNPSKK---DASIVIS 86

                        90       100       110
                ....*....|....*....|....*....|
gi 50872163 107 NVTPADSGTYYC-VKfqrgsSEPDIEIQSG 135
Cdd:cd05715  87 NLQFSDNGTYTCdVK-----NPPDIVGGHG 111
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 250-333 1.37e-04

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: 40.68  E-value: 1.37e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVwnvinvTCQIQKFYPPSFQLTWLENGNI--SRREVPFTLIVNKDGTYNWISCLLVNISALEenmVV 327
Cdd:cd21002   9 APTTPFNTREPVML------ACHVWGFYPADVTITWLKNGDPvaPHSSAPKTAQPNGDWTYQTQVTLAVTPSPGD---TY 79


                ....*.
gi 50872163 328 TCKVEH 333
Cdd:cd21002  80 TCSVQH 85
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
 160-239 1.51e-04

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: 40.29  E-value: 1.51e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 160 PQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETsvePEETSVS-----YRVSSTVQVVLEPRDVRSqiiCEVDHVTLD 234
Cdd:cd21002  16 TREPVMLACHVWGFYPADVTITWLKNGDPVAPHSS---APKTAQPngdwtYQTQVTLAVTPSPGDTYT---CSVQHASLP 89


                ....*
gi 50872163 235 RaPLR 239
Cdd:cd21002  90 E-PLL 93
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 249-333 2.11e-04

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: 40.15  E-value: 2.11e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 249 QVPPTLEIRQQPTMvwNVINVTCQIQKFYPPSFQLTWLENGN-ISRREV-PFTLIVNKDGTYN-WIScllVNISALEENM 325
Cdd:cd21021   2 QVPPLVKVTHHVTS--SVTTLRCRALNYYPQNITMKWLKDKQpMDAKEFePKDVLPNGDGTYQgWIT---LAVPPGEEQR 76


                ....*...
gi 50872163 326 vVTCKVEH 333
Cdd:cd21021  77 -YTCQVEH 83
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
 250-333 2.79e-04

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: 39.52  E-value: 2.79e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVwNVINVTCQIQKFYPPSFQLTWLENG-----NISRREV-PftlivNKDGTYN-WIScllVNISALE 322
Cdd:cd07698   1 DPPKVHVTHHPRSD-GESTLRCWALGFYPAEITLTWQRDGedqtqDMELVETrP-----NGDGTFQkWAA---VVVPSGE 71

                        90
                ....*....|.
gi 50872163 323 ENmVVTCKVEH 333
Cdd:cd07698  72 EQ-RYTCHVQH 81
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 160-234 3.07e-04

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


Pssm-ID: 409423  Cd Length: 96  Bit Score: 39.62  E-value: 3.07e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 50872163 160 PQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVE----PEETsvsYRVSSTVQVVLEPRDVrsqIICEVDHVTLD 234
Cdd:cd05766  16 LEHPNLLVCSVTGFYPAEIEVKWFRNGQEETAGVVSTElipnGDWT---FQILVMLETTPRRGDV---YTCQVEHSSLQ 88
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 35-142 3.82e-04

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: 39.65  E-value: 3.82e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  35 QPVKSFFVGAGGSATLNCTVTSL-LPVGPIRWYR---GVGQSRLLIYPFTGEHSPRITNVS---DVTKRNNMD-FSIRIS 106
Cdd:cd04982   3 QPQLSITREESKSVTISCKVSGIdFSTTYIHWYRqkpGQALERLLYVSSTSAVRKDSGKTKnkfEARKDVGKStSTLTIT 82

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 50872163 107 NVTPADSGTYYCVKFQRGSSEpDIEIqSGGGTELLV 142
Cdd:cd04982  83 NLEKEDSATYYCAYWESGSGY-YIKV-FGSGTKLIV 116
IgI_2_Necl-2 cd05883
Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (Necl-2); member of the I-set ...
 143-230 5.28e-04

Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (Necl-2); 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 2 (Necl-2; also known as cell adhesion molecule 1 (CADM1)). Nectin-like molecules (Necls) 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-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 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: 409466  Cd Length: 99  Bit Score: 39.13  E-value: 5.28e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 143 LAKPSSPMVSGPAARAVPQQTVTFTCRSHGFFPRNlTLKWFKNGDEIShLETSVEPEETSVsYRVSSTVQVVLEPRDVRS 222
Cdd:cd05883   1 LVPPRNLVIDIQKDTAVEGEEIELNCTAMASKPAA-TIRWFKGNKELT-GKSEVEEWYSRM-FTVTSQLMLKVTKEDDGV 77


                ....*...
gi 50872163 223 QIICEVDH 230
Cdd:cd05883  78 PVICLVDH 85
IgV_EVA1 cd05880
Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are ...
 45-135 1.13e-03

Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development.


Pssm-ID: 409464  Cd Length: 116  Bit Score: 38.66  E-value: 1.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  45 GGSATLNCTVTSLLPVGP---IRW-YRGV--GQSRLLIY-------PFTGEHSPRITNVSDVTKRnnmDFSIRISNVTPA 111
Cdd:cd05880  14 GTDVRLKCTFSSSAPIGDtlvITWnFRPLdgGREESVFYyhkrpypPPDGRFKGRVVWDGNIMRR---DASILIWQLQPT 90

                        90       100
                ....*....|....*....|....*
gi 50872163 112 DSGTYYC-VKfqrgsSEPDIEIQSG 135
Cdd:cd05880  91 DNGTYTCqVK-----NPPDVHGPIG 110
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 33-142 1.14e-03

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: 38.21  E-value: 1.14e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  33 VIQPVkSFFVGAGGSATLNCTVTSLLPVGP-IRWYRGVGQS--RLLIYPFTGEHS--P-RITNVSDVTKRnnmdfSIRIS 106
Cdd:cd04984   2 LTQPS-SLSVSPGETVTITCTGSSGNISGNyVNWYQQKPGSapRYLIYEDKHRPSgiPdRFSGSKSGNTA-----SLTIS 75

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 50872163 107 NVTPADSGTYYCvkfQRGSSEPDIeiqSGGGTELLV 142
Cdd:cd04984  76 GAQTEDEADYYC---QVWDSNSYV---FGGGTKLTV 105
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 250-333 1.42e-03

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: 37.82  E-value: 1.42e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQptmvwNVINVTCQIQKFYPPSFQLTWLENGN-ISRREVPFTLIVNKDGTYNWISCLLVNISALEENMVVT 328
Cdd:cd07699   7 FPPSSEELSS-----GKATLVCLINKFYPGFATVTWKVDGStVSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVYT 81


                ....*
gi 50872163 329 CKVEH 333
Cdd:cd07699  82 CEVTH 86
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
 247-335 1.46e-03

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


Pssm-ID: 409513  Cd Length: 99  Bit Score: 37.76  E-value: 1.46e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 247 FIQVPPTLEIRQQPTMVwnvinVTCQIQKFYPPSFQLTWLENGNI---SRREVPFTLIVNKDGTYNWISCLLVNISALEE 323
Cdd:cd16093   5 SLHAPSREEFLGNRTAT-----FVCLATGFSPKTISFKWLRNGKEvtsSTGAVVEEPKEDGKTLYSATSFLTITESEWKS 79

                        90
                ....*....|..
gi 50872163 324 NMVVTCKVEHDE 335
Cdd:cd16093  80 QTEFTCEFKHKG 91
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
 269-334 1.55e-03

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


Pssm-ID: 409374  Cd Length: 98  Bit Score: 37.57  E-value: 1.55e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 50872163 269 VTCQIQKFYPPSFQLTW--LENGNISRREVPFTLIVNKDGTYNWISCLLVNISALEENMVVTCKVEHD 334
Cdd:cd04985  21 LGCLISDYFPESITVSWqkNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVYKCQVQHS 88
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
 267-344 1.56e-03

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


Pssm-ID: 409434  Cd Length: 97  Bit Score: 37.78  E-value: 1.56e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 267 INVTCQIQKFYPPSFQLTWLENGNISRREVPFT-LIVNKDGTYNwiSCLLVNISALE--ENMVVTCKVEHdeQAEVIETH 343
Cdd:cd05847  19 IQLLCLISGYTPSTIEVEWLVDGQVATLSAASTaPQKEEGGTFS--TTSKLNVTQEDwkSGKTYTCKVTH--QGTTFEAH 94


                .
gi 50872163 344 T 344
Cdd:cd05847  95 T 95
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
 160-230 1.77e-03

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


Pssm-ID: 409607  Cd Length: 97  Bit Score: 37.39  E-value: 1.77e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 50872163 160 PQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVEPEETSvsyrvSSTVQ---VVLEPRDVRSQIICEVDH 230
Cdd:cd21016  16 PEGDVTLRCWALGFYPADITLTWQKDGEELTQDMEFVETRPAG-----DGTFQkwaAVVVPLGKEQSYTCHVYH 84
IgC1_MHC_II_alpha_HLA-DQ cd21008
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
 249-333 1.82e-03

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


Pssm-ID: 409599  Cd Length: 95  Bit Score: 37.23  E-value: 1.82e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 249 QVPPTLEIRQQPTMVWNVINVTCQIQKFYPPSFQLTWLENGNISRREVPFTLIVNK-DGTYNWISCLLVNISALEenmVV 327
Cdd:cd21008   1 EVPEVTVFPKSPVTLGQPNTLICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKsDHSFLKISYLTFLPSADD---IY 77


                ....*.
gi 50872163 328 TCKVEH 333
Cdd:cd21008  78 DCKVEH 83
IgV_1_Nectin-2_NecL-5_like_CD112_CD155 cd20989
First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar ...
 45-130 2.04e-03

First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'.


Pssm-ID: 409581  Cd Length: 112  Bit Score: 37.56  E-value: 2.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  45 GGSATLNCTVTS---LLPVGPIRWYR-GVGQSRLLIYPFTGEHSPRITNVSDVTKRNNMDF---SIRISNVTPADSGTYY 117
Cdd:cd20989  14 GGSVTLPCHLLPpnmVTHVSQVTWQRhDEHGSVAVFHPKQGPSFPESERLSFVAARLGAELrnaSLAMFGLRVEDEGNYT 93

                        90
                ....*....|....*
gi 50872163 118 C--VKFQRGSSEPDI 130
Cdd:cd20989  94 CefATFPQGSRSGDT 108
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 45-119 2.20e-03

Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their C-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620-residue extracellular region, a 23-residue transmembrane region, and a 103-residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions. This group also contains the Ig-like extracellular domains of other receptors such as NK cell receptor Nkp44 and myeloid receptors, among others.


Pssm-ID: 409381  Cd Length: 100  Bit Score: 37.38  E-value: 2.20e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 50872163  45 GGSATLNCTVTSLLPVGPIRWYRGVGQSRLLIYPFTGEHSPRITNVSDVTKRNNmdFSIRISNVTPADSGTYYCV 119
Cdd:cd05716  12 GGSVTIQCPYPPKYASSRKYWCKWGSEGCQTLVSSEGVVPGGRISLTDDPDNGV--FTVTLNQLRKEDAGWYWCG 84
IgC1_MHC_Ib_HLA-H cd21021
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
 159-238 3.09e-03

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


Pssm-ID: 409612  Cd Length: 94  Bit Score: 36.68  E-value: 3.09e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 159 VPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLEtsVEPEET----SVSYRVSSTVQVvlePRDVRSQIICEVDHVTLD 234
Cdd:cd21021  13 VTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKE--FEPKDVlpngDGTYQGWITLAV---PPGEEQRYTCQVEHPGLD 87


                ....
gi 50872163 235 RaPL 238
Cdd:cd21021  88 Q-PL 90
Ig3_L1-CAM_like cd05731
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar ...
 45-132 3.32e-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: 36.23  E-value: 3.32e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  45 GGSATLNCtVTSLLPVGPIRWYRGVGQsrLLiypftgehspritnvSDVTKRNNMDFSIRISNVTPADSGTYYCV-KFQR 123
Cdd:cd05731  10 GGVLLLEC-IAEGLPTPDIRWIKLGGE--LP---------------KGRTKFENFNKTLKIENVSEADSGEYQCTaSNTM 71


                ....*....
gi 50872163 124 GSSEPDIEI 132
Cdd:cd05731  72 GSARHTISV 80
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
 160-230 3.56e-03

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


Pssm-ID: 409611  Cd Length: 95  Bit Score: 36.66  E-value: 3.56e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50872163 160 PQQTVTFTCRSHGFFPRNLTLKWFKNGDEISHLETSVE--PEETSVSYRVSStvqvVLEPRDVRSQIICEVDH 230
Cdd:cd21020  16 PEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVEtrPAGDGTFQKWAS----VVVPLGKEQKYTCHVEH 84
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
 265-336 4.48e-03

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 409484  Cd Length: 80  Bit Score: 35.94  E-value: 4.48e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 50872163 265 NVINVTCQIQKFYPPSFQLTWLENGNISrrEVPFTLIVNKDGTYNwisclLVNISALEENMVVTCKVEHDEQ 336
Cdd:cd07687   9 NGTNVACLVKNFYPKEVTISLSSSKKII--EFDPAIVISPNGKYS-----AVKLGKYGDSDSVTCSVQHSNK 73
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
 45-130 5.43e-03

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: 36.27  E-value: 5.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  45 GGSATLNCTVTSLLP--VGPIRWYRGVGQSRLLIYPFTGEHSPRITN--------VSDVTKRNNMdfSIRISNVTPADSG 114
Cdd:cd05718  14 GGSVTLPCSLTSPGTtkITQVTWMKIGAGSSQNVAVFHPQYGPSVPNpyaervefLAARLGLRNA--TLRIRNLRVEDEG 91

                        90
                ....*....|....*...
gi 50872163 115 TYYC--VKFQRGSSEPDI 130
Cdd:cd05718  92 NYICefATFPQGNRQGTT 109
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 269-340 6.28e-03

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: 35.76  E-value: 6.28e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 50872163 269 VTCQIQKFYPPSFQLTWLENGNISRREVPFTLIV-NKDGTYNWISCLLVnisALEENMVVTCKVEHDEQAEVI 340
Cdd:cd21029  20 LSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILpNHDGTYQLRKTLDI---APGEGAGYSCRVDHSSLKQDL 89
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
 250-333 6.36e-03

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


Pssm-ID: 409424  Cd Length: 95  Bit Score: 35.75  E-value: 6.36e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 250 VPPTLEIRQQPTMVWNVINV-TCQIQKFYPPSFQLTWLENG-NISRREVPFTLIVNKDGTYNWISCLlvNISALEENmVV 327
Cdd:cd05767   1 VPPEVTVFPKSPVELGEPNTlICFVDNFFPPVINVTWLRNGqPVTDGVSETVFLPREDHSFRKFSYL--PFTPSEGD-IY 77


                ....*.
gi 50872163 328 TCKVEH 333
Cdd:cd05767  78 DCRVEH 83
IgV_TIM-3_like cd20982
Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3) ...
 44-119 6.71e-03

Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3), and similar domains; The members here are composed of the immunoglobulin variable (IgV) domain of T cell immunoglobulin domain and mucin domain 3 (Tim-3; also known as Hepatitis A virus cellular receptor 2 (HAVcr-2) and Cluster of Differentiation 366 (CD366)) and similar proteins. TIM-3 is a checkpoint inhibitor in immune responses to tumors, as well as involved in chronic viral infections. Thus, Tim-3 has emerged as one of most promising immune checkpoint targets for cancer immunotherapy. Tim-3 is highly expressed on Th1 lymphocytes and CD11b(+) macrophages and is upregulated on activated T and myeloid cells. TIM-3 regulates macrophage, activation and inhibits Th1 mediated immune responses to promote immunological tolerance. There are three TIM family members in humans (TIM-1, TIM-3, and TIM-4) and eight members in mice (TIM-1 to TIM-8). The IgV domain of human TIM-3 has been shown to bind ligands such as carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1), high mobility group protein B1 (HMGB1)and galectin-9 (GAL9). The binding of GAL9 to TIM-3 can negatively regulate Th1 immune response, enhance immune tolerance and inhibit anti#tumor immunity. Dysregulation of the TIM-3/GAL9 pathway is implicated in numerous chronic autoimmune diseases, such as multiple sclerosis and systemic lupus erythematosus.


Pssm-ID: 409574  Cd Length: 107  Bit Score: 35.90  E-value: 6.71e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163  44 AGGSATLNCTVTSLLPVG--PIRWYRGVGQS----RLLIYpftgehspriTNVSDVTKRNNM-----------DFSIRIS 106
Cdd:cd20982   7 VGHNAYLPCSYTTAAPGNlvPVCWGKGACPVsycgNVLLR----------TDERDVTYQKSSryqlkgdfskgDVSLTIE 76

                        90
                ....*....|...
gi 50872163 107 NVTPADSGTYYCV 119
Cdd:cd20982  77 NVTLADSGIYCCR 89
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
 160-189 7.20e-03

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


Pssm-ID: 409610  Cd Length: 94  Bit Score: 35.86  E-value: 7.20e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 50872163 160 PQQTVTFTCRSHGFFPRNLTLKWFKNGDEI 189
Cdd:cd21019  15 PEDKVTLRCWALGFYPADITLTWQLNGEEL 44
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
 154-233 7.94e-03

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: 35.51  E-value: 7.94e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50872163 154 PAARAVPQQTVTFTCRSHGFFPRNLTLKWFKNGDEISH-LETSVEPEETSVSYRVSSTVQVVLEPRDVRSQIICEVDHVT 232
Cdd:cd07699   9 PSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTVSSgVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVYTCEVTHEG 88


                .
gi 50872163 233 L 233
Cdd:cd07699  89 L 89
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
 163-230 9.53e-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: 35.38  E-value: 9.53e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 50872163 163 TVTFTCRSHGFFPRNLTLKWFKNG-DEISHLET--SVepeETSVSYRVSSTVQVVLEPRDVRSQIICEVDH 230
Cdd:cd21819  17 PVTVGCLATDFLPDSITFSWTDDNnSLTTGVKTypSV---LTGGTYTASSQLQVPESEWKSKENFYCKVEH 84
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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