NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|39545679|gb|AAR27943|]
View 

CLM6 [Mus musculus]

Protein Classification

immunoglobulin domain-containing protein( domain architecture ID 10146027)

immunoglobulin (Ig) domain-containing protein with one or more Ig domains, which adopt a fold comprised of a sandwich of two beta sheets and may function in cell adhesion and/or pattern recognition; similar to polymeric immunoglobulin receptor

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 26-125 4.75e-24

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: 91.69  E-value: 4.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  26 RGPSTVTGTVGESLSVSCQYEKKLKTKKKIWCKWKSNVlCKDIVKTSASEeaRNGRVSIRDHPDNLTFTVTLENLTLEDA 105
Cdd:cd05716   2 VGPEVVTGVEGGSVTIQCPYPPKYASSRKYWCKWGSEG-CQTLVSSEGVV--PGGRISLTDDPDNGVFTVTLNQLRKEDA 78

                        90       100
                ....*....|....*....|
gi 39545679 106 GTYMCMVDIGFFYDAYLQID 125
Cdd:cd05716  79 GWYWCGVGDDGDRGLTVQVK 98
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 26-125 4.75e-24

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: 91.69  E-value: 4.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  26 RGPSTVTGTVGESLSVSCQYEKKLKTKKKIWCKWKSNVlCKDIVKTSASEeaRNGRVSIRDHPDNLTFTVTLENLTLEDA 105
Cdd:cd05716   2 VGPEVVTGVEGGSVTIQCPYPPKYASSRKYWCKWGSEG-CQTLVSSEGVV--PGGRISLTDDPDNGVFTVTLNQLRKEDA 78

                        90       100
                ....*....|....*....|
gi 39545679 106 GTYMCMVDIGFFYDAYLQID 125
Cdd:cd05716  79 GWYWCGVGDDGDRGLTVQVK 98
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 27-132 2.22e-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: 58.62  E-value: 2.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679    27 GPSTVTGTVGESLSVSCQY--EKKLKTKKKIWCKWKSNVLCKDIV---KTSASEEARNGRVSIRDHPDNLTFTVTLENLT 101
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYssSMSEASTSVYWYRQPPGKGPTFLIayySNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 39545679   102 LEDAGTYMCMVdigfFYDAYLQIDKSFKVEV 132
Cdd:pfam07686  82 LSDSGTYTCAV----IPSGEGVFGKGTRLTV 108
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-132 5.92e-08

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: 48.66  E-value: 5.92e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679     28 PSTVTGTVGESLSVSCQYEKKLKTKKKiWCKWKSNVLCKDivktsaseearnGRVSIRdhPDNLTFTVTLENLTLEDAGT 107
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVT-WYKQGGKLLAES------------GRFSVS--RSGSTSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|....*
gi 39545679    108 YMCMVdigffYDAYLQIDKSFKVEV 132
Cdd:smart00410  66 YTCAA-----TNSSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 26-125 4.75e-24

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: 91.69  E-value: 4.75e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  26 RGPSTVTGTVGESLSVSCQYEKKLKTKKKIWCKWKSNVlCKDIVKTSASEeaRNGRVSIRDHPDNLTFTVTLENLTLEDA 105
Cdd:cd05716   2 VGPEVVTGVEGGSVTIQCPYPPKYASSRKYWCKWGSEG-CQTLVSSEGVV--PGGRISLTDDPDNGVFTVTLNQLRKEDA 78

                        90       100
                ....*....|....*....|
gi 39545679 106 GTYMCMVDIGFFYDAYLQID 125
Cdd:cd05716  79 GWYWCGVGDDGDRGLTVQVK 98
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 27-132 2.22e-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: 58.62  E-value: 2.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679    27 GPSTVTGTVGESLSVSCQY--EKKLKTKKKIWCKWKSNVLCKDIV---KTSASEEARNGRVSIRDHPDNLTFTVTLENLT 101
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYssSMSEASTSVYWYRQPPGKGPTFLIayySNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 39545679   102 LEDAGTYMCMVdigfFYDAYLQIDKSFKVEV 132
Cdd:pfam07686  82 LSDSGTYTCAV----IPSGEGVFGKGTRLTV 108
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 28-119 4.46e-08

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: 49.64  E-value: 4.46e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  28 PSTVTGTVGESLSVSCQYEKKLKTKKKIWCKWKSNVLCKDIVKTSASEEARNGRVSIR---DHPDNLTFTVTLENLTLED 104
Cdd:cd00099   5 PRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKPGQGPEFLIYLSSSKGKTKGGVPGRfsgSRDGTSSFSLTISNLQPED 84

                        90
                ....*....|....*
gi 39545679 105 AGTYMCMVDIGFFYD 119
Cdd:cd00099  85 SGTYYCAVSESGGTD 99
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 28-132 5.92e-08

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: 48.66  E-value: 5.92e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679     28 PSTVTGTVGESLSVSCQYEKKLKTKKKiWCKWKSNVLCKDivktsaseearnGRVSIRdhPDNLTFTVTLENLTLEDAGT 107
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVT-WYKQGGKLLAES------------GRFSVS--RSGSTSTLTISNVTPEDSGT 65

                           90       100
                   ....*....|....*....|....*
gi 39545679    108 YMCMVdigffYDAYLQIDKSFKVEV 132
Cdd:smart00410  66 YTCAA-----TNSSGSASSGTTLTV 85
IGv smart00406
Immunoglobulin V-Type;
80-112 2.31e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 38.90  E-value: 2.31e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 39545679     80 GRVSIRDHPDNLTFTVTLENLTLEDAGTYMCMV 112
Cdd:smart00406  49 GRFTISKDTSKNDVSLTISNLRVEDTGTYYCAV 81
IgI_2_FGFRL1-like cd05856
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1 ...
 93-132 3.99e-04

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1); member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.


Pssm-ID: 409442  Cd Length: 92  Bit Score: 38.30  E-value: 3.99e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 39545679  93 FTVTLENLTLEDAGTYMCMVdigffYDAYLQIDKSFKVEV 132
Cdd:cd05856  58 WTLSLKNLKPEDSGKYTCHV-----SNRAGEINATYKVDV 92
IgV_VISTA cd20980
Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell ...
 69-112 5.61e-04

Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA); The members here are composed of the immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA; also known as B7-H5, PD-1H, Gi24, Dies1, SISP1 and DD1alpha). VISTA is an immune checkpoint protein involved in the regulation of T cell activity and inhibits the T cell response against cancer. VISTA is a type I transmembrane protein with a single IgV domain with sequence homology to the IgV domains of the members of B7 family. VISTA is the only B7 family member that lacks an IgC domain. VISTA is primarily expressed in white blood cells and its transcription is partially controlled by p53. Similar to PD-1/PD-L1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Unlike the B7 family members, VISTA contains 10 beta-strands, instead of the nine that typically comprises of an IgV fold. Moreover, human VISTA contains the 21-residue extended loop between stands C and C', which does not align with any B7 family structure.


Pssm-ID: 409572  Cd Length: 147  Bit Score: 39.14  E-value: 5.61e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 39545679  69 VKTSASEEARNGRVSIRDHPDNltFTVTLENLTLEDAGTYMCMV 112
Cdd:cd20980  73 ANTSHDLAQRHGLESASDHHGN--FSITMRNLTLLDSGLYCCLV 114
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 28-113 9.28e-04

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: 37.17  E-value: 9.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679    28 PSTVTGTVGESLSVSCQYEKKLKTKKKIWckWKSNvlckDIVKTSASEEARNGRVSIrdhpdnltFTVTLENLTLEDAGT 107
Cdd:pfam00047   3 PPTVTVLEGDSATLTCSASTGSPGPDVTW--SKEG----GTLIESLKVKHDNGRTTQ--------SSLLISNVTKEDAGT 68


                  ....*.
gi 39545679   108 YMCMVD 113
Cdd:pfam00047  69 YTCVVN 74
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 29-110 1.20e-03

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


Pssm-ID: 409503  Cd Length: 112  Bit Score: 37.50  E-value: 1.20e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  29 STVTGTVGESLSVSCQYEKKLKTKKKIWCKWK-SNVLCKDIVKTSASEEARNGRVSIRDHPDNLTFTVTLENLTLEDAGT 107
Cdd:cd07706   7 PDVSVQVGEEVTLNCRYETSWTNYYLFWYKQLpSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQKSISLTISALQLEDSAK 86


                ...
gi 39545679 108 YMC 110
Cdd:cd07706  87 YFC 89
IgV_1_MRC-OX-2_like cd05846
First immunoglobulin (Ig) variable (V) domain of rat MRC OX-2 antigen, and similar domains; ...
 25-110 1.47e-03

First immunoglobulin (Ig) variable (V) domain of rat MRC OX-2 antigen, and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200) and similar proteins. MRC OX-2 is a membrane glycoprotein expressed in a variety of lymphoid and non-lymphoid cells in rats. It has a similar broad distribution pattern in humans. MRC OX-2 may regulate myeloid cell activity. The protein has an extracellular portion containing two Ig-like domains, a transmembrane portion, and a cytoplasmic portion.


Pssm-ID: 409433  Cd Length: 108  Bit Score: 36.94  E-value: 1.47e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  25 VRGPSTVTGtvGESLSVSCQYEKKLKTKKKIWCKwKSNVLCKDIVKTSAS-----EEARNGRVSIRdHPDNLTFTVTLEN 99
Cdd:cd05846   4 HTGDTRAVL--GGNATLSCNLTLPEEVLQVTWQK-IKASSPENIVTYSKKygvkiQPSYVRRISFT-SSGLNSTSITIWN 79

                        90
                ....*....|.
gi 39545679 100 LTLEDAGTYMC 110
Cdd:cd05846  80 VTLEDEGCYKC 90
Ig_SLAM-like_N cd16842
N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule ...
 30-108 7.46e-03

N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family and similar proteins. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. Members of this group include proteins such as CD84, SLAM (CD150), Ly-9 (CD229), NTB-A (ly-108, SLAM6), 19A (CRACC), and SLAMF9. The genes coding for the SLAM family are nested on chromosome 1, in humans at 1q23, and in mice at 1H2. The SLAM family is a subset of the CD2 family, which also includes CD2 and CD58 located on chromosome 1 at 1p13 in humans. In mice, CD2 is located on chromosome 3, and there is no CD58 homolog. The SLAM family proteins are organized as an extracellular domain with either two or four Ig-like domains, a single transmembrane segment, and a cytoplasmic region having Tyr-based motifs. The extracellular domain is organized as a membrane-distal Ig variable (IgV) domain that is responsible for ligand recognition and a membrane-proximal truncated Ig constant-2 (IgC2) domain.


Pssm-ID: 409517  Cd Length: 102  Bit Score: 34.99  E-value: 7.46e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39545679  30 TVTGTVGESLSVSCQYEKKLKTKKKIWcKWKSNVLCKDIVKTSASE-----EARNGRVSIRDHPDNLTftvtLENLTLED 104
Cdd:cd16842   2 EVNGILGGSVTFPLNISDGQEIENITW-SFKTSLAVIAPGEGGAPEiiitdKSYKERLNISQNDYSLQ----ISNLTMED 76


                ....
gi 39545679 105 AGTY 108
Cdd:cd16842  77 AGSY 80
 
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