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Conserved domains on  [gi|564367094|ref|XP_006244487|]
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triggering receptor expressed on myeloid cells 2 isoform X2 [Rattus norvegicus]

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 ...
 21-128 1.97e-16

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 cd05716:

Pssm-ID: 472250  Cd Length: 100  Bit Score: 72.05  E-value: 1.97e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367094  21 TTVLQGVAGQSLRVSCTYDaLRHWGRRKAWCRQLAEEgpCQRVVSTHGVWllaflrkQNGSTVITDDTLAGTVTITLRNL 100
Cdd:cd05716    4 PEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG--CQTLVSSEGVV-------PGGRISLTDDPDNGVFTVTLNQL 73

                         90       100
                 ....*....|....*....|....*...
gi 564367094 101 QAGDAGLYQCQSlrGREAEVLQKVVVEV 128
Cdd:cd05716   74 RKEDAGWYWCGV--GDDGDRGLTVQVKL 99
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 21-128 1.97e-16

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: 72.05  E-value: 1.97e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367094  21 TTVLQGVAGQSLRVSCTYDaLRHWGRRKAWCRQLAEEgpCQRVVSTHGVWllaflrkQNGSTVITDDTLAGTVTITLRNL 100
Cdd:cd05716    4 PEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG--CQTLVSSEGVV-------PGGRISLTDDPDNGVFTVTLNQL 73

                         90       100
                 ....*....|....*....|....*...
gi 564367094 101 QAGDAGLYQCQSlrGREAEVLQKVVVEV 128
Cdd:cd05716   74 RKEDAGWYWCGV--GDDGDRGLTVQVKL 99
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 22-129 2.50e-05

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: 42.06  E-value: 2.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367094   22 TVLQGVAGQSLRVSCTYDALRHWGR-RKAWCRQLAEEGPcqrvvsthgvwLLAFLRKQNGSTV--------ITDDTLAGT 92
Cdd:pfam07686   4 REVTVALGGSVTLPCTYSSSMSEAStSVYWYRQPPGKGP-----------TFLIAYYSNGSEEgvkkgrfsGRGDPSNGD 72

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564367094   93 VTITLRNLQAGDAGLYQCQSlRGREAEVLQKVV-VEVL 129
Cdd:pfam07686  73 GSLTIQNLTLSDSGTYTCAV-IPSGEGVFGKGTrLTVL 109
IGv smart00406
Immunoglobulin V-Type;
84-111 3.32e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 35.44  E-value: 3.32e-03
                           10        20
                   ....*....|....*....|....*...
gi 564367094    84 ITDDTLAGTVTITLRNLQAGDAGLYQCQ 111
Cdd:smart00406  53 ISKDTSKNDVSLTISNLRVEDTGTYYCA 80
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 21-128 1.97e-16

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: 72.05  E-value: 1.97e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367094  21 TTVLQGVAGQSLRVSCTYDaLRHWGRRKAWCRQLAEEgpCQRVVSTHGVWllaflrkQNGSTVITDDTLAGTVTITLRNL 100
Cdd:cd05716    4 PEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG--CQTLVSSEGVV-------PGGRISLTDDPDNGVFTVTLNQL 73

                         90       100
                 ....*....|....*....|....*...
gi 564367094 101 QAGDAGLYQCQSlrGREAEVLQKVVVEV 128
Cdd:cd05716   74 RKEDAGWYWCGV--GDDGDRGLTVQVKL 99
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 22-129 2.50e-05

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: 42.06  E-value: 2.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564367094   22 TVLQGVAGQSLRVSCTYDALRHWGR-RKAWCRQLAEEGPcqrvvsthgvwLLAFLRKQNGSTV--------ITDDTLAGT 92
Cdd:pfam07686   4 REVTVALGGSVTLPCTYSSSMSEAStSVYWYRQPPGKGP-----------TFLIAYYSNGSEEgvkkgrfsGRGDPSNGD 72

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 564367094   93 VTITLRNLQAGDAGLYQCQSlRGREAEVLQKVV-VEVL 129
Cdd:pfam07686  73 GSLTIQNLTLSDSGTYTCAV-IPSGEGVFGKGTrLTVL 109
IGv smart00406
Immunoglobulin V-Type;
84-111 3.32e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 35.44  E-value: 3.32e-03
                           10        20
                   ....*....|....*....|....*...
gi 564367094    84 ITDDTLAGTVTITLRNLQAGDAGLYQCQ 111
Cdd:smart00406  53 ISKDTSKNDVSLTISNLRVEDTGTYYCA 80
Ig_Semaphorin_C cd04979
Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are ...
 69-130 3.39e-03

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


Pssm-ID: 409368  Cd Length: 88  Bit Score: 35.51  E-value: 3.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 564367094  69 VWLlaFLRKQNGSTVITDDTLAGTVTITLRNLQAGDAGLYQCQSLRGREAEVLQKVVVEVLE 130
Cdd:cd04979   28 TWI--HNGKKVPRYRSPRLVLKTERGLLIRSAQEADAGVYECHSGERVLGSTLRSVTLHVLE 87
 
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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