NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958801385|ref|XP_038939102|]
View 

triggering receptor expressed on myeloid cells 1 isoform X1 [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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 24-132 1.06e-15

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: 70.12  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  24 PEEERYDLVEGQTLTVNCPFNiMKYARSRKAWQRLSAGKePLTLVVTERSsttsseVRVGKYTLKDDPTEAMLFVQMTDL 103
Cdd:cd05716     2 VGPEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG-CQTLVSSEGV------VPGGRISLTDDPDNGVFTVTLNQL 73

                          90       100
                  ....*....|....*....|....*....
gi 1958801385 104 QVTDSGLYRCVIYHPPndPVLLFHPVRLV 132
Cdd:cd05716    74 RKEDAGWYWCGVGDDG--DRGLTVQVKLV 100
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 24-132 1.06e-15

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: 70.12  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  24 PEEERYDLVEGQTLTVNCPFNiMKYARSRKAWQRLSAGKePLTLVVTERSsttsseVRVGKYTLKDDPTEAMLFVQMTDL 103
Cdd:cd05716     2 VGPEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG-CQTLVSSEGV------VPGGRISLTDDPDNGVFTVTLNQL 73

                          90       100
                  ....*....|....*....|....*....
gi 1958801385 104 QVTDSGLYRCVIYHPPndPVLLFHPVRLV 132
Cdd:cd05716    74 RKEDAGWYWCGVGDDG--DRGLTVQVKLV 100
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 32-134 8.95e-12

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 59.78  E-value: 8.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  32 VEGQTLTVNCPF-NIMKYARSRKAWQRLSAGKEPlTLVVTERSSTTSSEVRVGKYTLKDDPTEAMLFVQMTDLQVTDSGL 110
Cdd:pfam07686   9 ALGGSVTLPCTYsSSMSEASTSVYWYRQPPGKGP-TFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGT 87

                          90       100
                  ....*....|....*....|....
gi 1958801385 111 YRCVIYhpPNDPVLLFHPVRLVVT 134
Cdd:pfam07686  88 YTCAVI--PSGEGVFGKGTRLTVL 109
IGv smart00406
Immunoglobulin V-Type;
36-113 1.33e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 39.29  E-value: 1.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385   36 TLTVNCPFNIMKYARSRKAWQRLSAGKePLTLVVTERSSTTS---SEVRvGKYTLKDDPTEAMLFVQMTDLQVTDSGLYR 112
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGK-GLEWLGYIGSNGSSyyqESYK-GRFTISKDTSKNDVSLTISNLRVEDTGTYY 78


                   .
gi 1958801385  113 C 113
Cdd:smart00406  79 C 79
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 24-132 1.06e-15

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: 70.12  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  24 PEEERYDLVEGQTLTVNCPFNiMKYARSRKAWQRLSAGKePLTLVVTERSsttsseVRVGKYTLKDDPTEAMLFVQMTDL 103
Cdd:cd05716     2 VGPEVVTGVEGGSVTIQCPYP-PKYASSRKYWCKWGSEG-CQTLVSSEGV------VPGGRISLTDDPDNGVFTVTLNQL 73

                          90       100
                  ....*....|....*....|....*....
gi 1958801385 104 QVTDSGLYRCVIYHPPndPVLLFHPVRLV 132
Cdd:cd05716    74 RKEDAGWYWCGVGDDG--DRGLTVQVKLV 100
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 32-134 8.95e-12

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 59.78  E-value: 8.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  32 VEGQTLTVNCPF-NIMKYARSRKAWQRLSAGKEPlTLVVTERSSTTSSEVRVGKYTLKDDPTEAMLFVQMTDLQVTDSGL 110
Cdd:pfam07686   9 ALGGSVTLPCTYsSSMSEASTSVYWYRQPPGKGP-TFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGT 87

                          90       100
                  ....*....|....*....|....
gi 1958801385 111 YRCVIYhpPNDPVLLFHPVRLVVT 134
Cdd:pfam07686  88 YTCAVI--PSGEGVFGKGTRLTVL 109
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 34-114 4.25e-06

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


Pssm-ID: 409514  Cd Length: 115  Bit Score: 44.47  E-value: 4.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  34 GQTLTVNCPFNIMKYARSRKAWQRLSAGKEPLTLVVTERSSTTSSEVRVgkyTLKDDPTEAMLFVQMTDLQVTDSGLYRC 113
Cdd:cd16095    15 GKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVSEDRI---TSSREDTNSQIFLQIKGLGLRDSGQYHC 91


                  .
gi 1958801385 114 V 114
Cdd:cd16095    92 A 92
IGv smart00406
Immunoglobulin V-Type;
36-113 1.33e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 39.29  E-value: 1.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385   36 TLTVNCPFNIMKYARSRKAWQRLSAGKePLTLVVTERSSTTS---SEVRvGKYTLKDDPTEAMLFVQMTDLQVTDSGLYR 112
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGK-GLEWLGYIGSNGSSyyqESYK-GRFTISKDTSKNDVSLTISNLRVEDTGTYY 78


                   .
gi 1958801385  113 C 113
Cdd:smart00406  79 C 79
Ig_Aggrecan cd05900
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 23-117 3.10e-04

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggrecan has a wide distribution in connective tissue and extracellular matrices. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409481  Cd Length: 123  Bit Score: 39.54  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  23 VPEEERYDLVEGQTLTVNCPFNIMKYARS----------RKAWQRLSAGKEPLTLVVTERSSTTSSEVRvGKYTLKDDP- 91
Cdd:cd05900     1 IPLESPLRVVLGSSLLIPCYFQDPIAKDPgaptvaplspRIKWSFISKEKESVLLVATEGKVRVNTEYL-DRVSLPNYPa 79

                          90       100
                  ....*....|....*....|....*...
gi 1958801385  92 --TEAMLfvQMTDLQVTDSGLYRCVIYH 117
Cdd:cd05900    80 ipSDATL--EITELRSNDSGTYRCEVMH 105
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 33-126 9.76e-03

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: 34.62  E-value: 9.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958801385  33 EGQTLTVNCPFNiMKYARSRKAWQRLSAGKEPlTLVVTERSSTTSSEVRV-GKYTL-KDDPTEAMLfvQMTDLQVTDSGL 110
Cdd:cd00099    12 EGESVTLSCEVS-SSFSSTYIYWYRQKPGQGP-EFLIYLSSSKGKTKGGVpGRFSGsRDGTSSFSL--TISNLQPEDSGT 87

                          90
                  ....*....|....*.
gi 1958801385 111 YRCVIYHPPNDPVLLF 126
Cdd:cd00099    88 YYCAVSESGGTDKLTF 103
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH