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Conserved domains on  [gi|568974292|ref|XP_006533542|]
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T-cell immunoglobulin and mucin domain-containing protein 4 isoform X1 [Mus musculus]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

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 ...
 29-129 3.15e-35

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 cd20982:

Pssm-ID: 472250  Cd Length: 107  Bit Score: 123.34  E-value: 3.15e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292  29 IGFLGQPVTLPCHY-LSWSQSRNSMCWGKGSCPNSKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNTNRGDS 107
Cdd:cd20982    4 RAEVGHNAYLPCSYtTAAPGNLVPVCWGKGACPVSYCGNVLLRTDERDVTYQKSSRYQLKGDFSKGDVSLTIENVTLADS 83

                         90       100
                 ....*....|....*....|..
gi 568974292 108 GVYCCRIEVPGWFNDVKKNVRL 129
Cdd:cd20982   84 GIYCCRIQIPGIMNDEKFNLKL 105
 
Name Accession Description Interval E-value
IgV_TIM-3_like cd20982
Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3) ...
 29-129 3.15e-35

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: 123.34  E-value: 3.15e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292  29 IGFLGQPVTLPCHY-LSWSQSRNSMCWGKGSCPNSKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNTNRGDS 107
Cdd:cd20982    4 RAEVGHNAYLPCSYtTAAPGNLVPVCWGKGACPVSYCGNVLLRTDERDVTYQKSSRYQLKGDFSKGDVSLTIENVTLADS 83

                         90       100
                 ....*....|....*....|..
gi 568974292 108 GVYCCRIEVPGWFNDVKKNVRL 129
Cdd:cd20982   84 GIYCCRIQIPGIMNDEKFNLKL 105
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 24-114 8.33e-11

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: 58.24  E-value: 8.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292   24 SEDTIIGFLGQPVTLPCHYLSWSQSRN-SMCWGKGSCPNsKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNT 102
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSMSEAStSVYWYRQPPGK-GPTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNL 80

                          90
                  ....*....|..
gi 568974292  103 NRGDSGVYCCRI 114
Cdd:pfam07686  81 TLSDSGTYTCAV 92
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 27-130 1.66e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 39.80  E-value: 1.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292    27 TIIGFLGQPVTLPCHYlsWSQSRNSMCWgkgscpnSKCNAELLRTDGTRIISRKSTKYTLlgkvqfgevslTISNTNRGD 106
Cdd:smart00410   3 SVTVKEGESVTLSCEA--SGSPPPEVTW-------YKQGGKLLAESGRFSVSRSGSTSTL-----------TISNVTPED 62

                           90       100
                   ....*....|....*....|....
gi 568974292   107 SGVYCCRIEVPGwfNDVKKNVRLE 130
Cdd:smart00410  63 SGTYTCAATNSS--GSASSGTTLT 84
 
Name Accession Description Interval E-value
IgV_TIM-3_like cd20982
Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3) ...
 29-129 3.15e-35

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: 123.34  E-value: 3.15e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292  29 IGFLGQPVTLPCHY-LSWSQSRNSMCWGKGSCPNSKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNTNRGDS 107
Cdd:cd20982    4 RAEVGHNAYLPCSYtTAAPGNLVPVCWGKGACPVSYCGNVLLRTDERDVTYQKSSRYQLKGDFSKGDVSLTIENVTLADS 83

                         90       100
                 ....*....|....*....|..
gi 568974292 108 GVYCCRIEVPGWFNDVKKNVRL 129
Cdd:cd20982   84 GIYCCRIQIPGIMNDEKFNLKL 105
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 24-114 8.33e-11

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: 58.24  E-value: 8.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292   24 SEDTIIGFLGQPVTLPCHYLSWSQSRN-SMCWGKGSCPNsKCNAELLRTDGTRIISRKSTKYTLLGKVQFGEVSLTISNT 102
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSSMSEAStSVYWYRQPPGK-GPTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNL 80

                          90
                  ....*....|..
gi 568974292  103 NRGDSGVYCCRI 114
Cdd:pfam07686  81 TLSDSGTYTCAV 92
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 27-130 2.08e-06

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: 45.47  E-value: 2.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292  27 TIIGFLGQPVTLPCHY-LSWSQSRNSMC-WGKGSCpnskcnAELLRTDGtriiSRKSTKYTLLGKVQFGEVSLTISNTNR 104
Cdd:cd05716    6 VVTGVEGGSVTIQCPYpPKYASSRKYWCkWGSEGC------QTLVSSEG----VVPGGRISLTDDPDNGVFTVTLNQLRK 75

                         90       100
                 ....*....|....*....|....*.
gi 568974292 105 GDSGVYCCRIEVPGWFnDVKKNVRLE 130
Cdd:cd05716   76 EDAGWYWCGVGDDGDR-GLTVQVKLV 100
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 27-130 1.66e-04

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 39.80  E-value: 1.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292    27 TIIGFLGQPVTLPCHYlsWSQSRNSMCWgkgscpnSKCNAELLRTDGTRIISRKSTKYTLlgkvqfgevslTISNTNRGD 106
Cdd:smart00410   3 SVTVKEGESVTLSCEA--SGSPPPEVTW-------YKQGGKLLAESGRFSVSRSGSTSTL-----------TISNVTPED 62

                           90       100
                   ....*....|....*....|....
gi 568974292   107 SGVYCCRIEVPGwfNDVKKNVRLE 130
Cdd:smart00410  63 SGTYTCAATNSS--GSASSGTTLT 84
IGv smart00406
Immunoglobulin V-Type;
36-112 4.63e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 35.44  E-value: 4.63e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568974292    36 VTLPCHYLSWSQSRNSMCW-----GKGscpnskcnAELL---RTDGTRIISRKS-TKYTLLGKVQFGEVSLTISNTNRGD 106
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWvrqppGKG--------LEWLgyiGSNGSSYYQESYkGRFTISKDTSKNDVSLTISNLRVED 73


                   ....*.
gi 568974292   107 SGVYCC 112
Cdd:smart00406  74 TGTYYC 79
 
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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