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Conserved domains on  [gi|1958794637|ref|XP_038936766|]
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thy-1 membrane glycoprotein isoform X4 [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 ...
9-107 1.12e-11

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 cd20948:

Pssm-ID: 448366  Cd Length: 76  Bit Score: 56.74  E-value: 1.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   9 SLTACLVNQNLRLDCRHENNTNLPIQHEFSLTREKKKHVLSgtlgvpehtyrsrvnlfsdrfikvltLANFTTKDEGDYM 88
Cdd:cd20948     3 SDTYYLSGENLNLSCHAASNPPAQYSWTINGTFQTSSQELF--------------------------LPAITENNEGTYT 56
                          90       100
                  ....*....|....*....|
gi 1958794637  89 CELRVSGQN-PTSSNKTINV 107
Cdd:cd20948    57 CSAHNSLTGkNISLVLSVTV 76
 
Name Accession Description Interval E-value
IgC2_CEACAM5-like cd20948
Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell ...
9-107 1.12e-11

Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains; member of the C2-set IgSF domains; The members here are composed of the fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), also known as CD66e (Cluster of Differentiation 66e), is a cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression. Diseases associated with CEACAM5 include lung cancer and rectum cancer. 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. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409540  Cd Length: 76  Bit Score: 56.74  E-value: 1.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   9 SLTACLVNQNLRLDCRHENNTNLPIQHEFSLTREKKKHVLSgtlgvpehtyrsrvnlfsdrfikvltLANFTTKDEGDYM 88
Cdd:cd20948     3 SDTYYLSGENLNLSCHAASNPPAQYSWTINGTFQTSSQELF--------------------------LPAITENNEGTYT 56
                          90       100
                  ....*....|....*....|
gi 1958794637  89 CELRVSGQN-PTSSNKTINV 107
Cdd:cd20948    57 CSAHNSLTGkNISLVLSVTV 76
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
7-101 4.19e-05

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: 39.87  E-value: 4.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   7 VISLTACLVNQNLRLDCRHENNTNLPiqhEFSLTREKKKHVLSgtLGVPEHTYRsrvnlfsdRFIKVLTLANFTTKDEGD 86
Cdd:pfam00047   2 APPTVTVLEGDSATLTCSASTGSPGP---DVTWSKEGGTLIES--LKVKHDNGR--------TTQSSLLISNVTKEDAGT 68
                          90
                  ....*....|....*
gi 1958794637  87 YMCELRVSGQNPTSS 101
Cdd:pfam00047  69 YTCVVNNPGGSATLS 83
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
15-101 1.40e-03

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: 35.56  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   15 VNQNLRLDCRHENNTNlpiqHEFSLTREKKKHVLsgtlgvpehtYRSRVNLFSDRFIKVLTLANFTTKDEGDYMCELRVS 94
Cdd:smart00410   8 EGESVTLSCEASGSPP----PEVTWYKQGGKLLA----------ESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNS 73

                   ....*..
gi 1958794637   95 GQNPTSS 101
Cdd:smart00410  74 SGSASSG 80
 
Name Accession Description Interval E-value
IgC2_CEACAM5-like cd20948
Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell ...
9-107 1.12e-11

Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains; member of the C2-set IgSF domains; The members here are composed of the fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), also known as CD66e (Cluster of Differentiation 66e), is a cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression. Diseases associated with CEACAM5 include lung cancer and rectum cancer. 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. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409540  Cd Length: 76  Bit Score: 56.74  E-value: 1.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   9 SLTACLVNQNLRLDCRHENNTNLPIQHEFSLTREKKKHVLSgtlgvpehtyrsrvnlfsdrfikvltLANFTTKDEGDYM 88
Cdd:cd20948     3 SDTYYLSGENLNLSCHAASNPPAQYSWTINGTFQTSSQELF--------------------------LPAITENNEGTYT 56
                          90       100
                  ....*....|....*....|
gi 1958794637  89 CELRVSGQN-PTSSNKTINV 107
Cdd:cd20948    57 CSAHNSLTGkNISLVLSVTV 76
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
7-101 4.19e-05

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: 39.87  E-value: 4.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   7 VISLTACLVNQNLRLDCRHENNTNLPiqhEFSLTREKKKHVLSgtLGVPEHTYRsrvnlfsdRFIKVLTLANFTTKDEGD 86
Cdd:pfam00047   2 APPTVTVLEGDSATLTCSASTGSPGP---DVTWSKEGGTLIES--LKVKHDNGR--------TTQSSLLISNVTKEDAGT 68
                          90
                  ....*....|....*
gi 1958794637  87 YMCELRVSGQNPTSS 101
Cdd:pfam00047  69 YTCVVNNPGGSATLS 83
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
15-101 1.40e-03

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: 35.56  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   15 VNQNLRLDCRHENNTNlpiqHEFSLTREKKKHVLsgtlgvpehtYRSRVNLFSDRFIKVLTLANFTTKDEGDYMCELRVS 94
Cdd:smart00410   8 EGESVTLSCEASGSPP----PEVTWYKQGGKLLA----------ESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNS 73

                   ....*..
gi 1958794637   95 GQNPTSS 101
Cdd:smart00410  74 SGSASSG 80
IGv smart00406
Immunoglobulin V-Type;
18-90 4.26e-03

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 34.28  E-value: 4.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637   18 NLRLDCRHENNTNlPIQHEFSLTREKKKHV------LSGTLGVPEHTYRSRVNLFSD--RFIKVLTLANFTTKDEGDYMC 89
Cdd:smart00406   1 SVTLSCKFSGSTF-SSYYVSWVRQPPGKGLewlgyiGSNGSSYYQESYKGRFTISKDtsKNDVSLTISNLRVEDTGTYYC 79

                   .
gi 1958794637   90 E 90
Cdd:smart00406  80 A 80
IgI_VEGFR_like cd05742
Immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and ...
14-108 6.19e-03

Immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and similar proteins; member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and related proteins. The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members: VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF-A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF; VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angiogenic, and microvascular permeability-enhancing effects of VEGF-A. VEGFR-1 may play an inhibitory part in these processes by binding VEGF and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. VEGFR-3 has been shown to be involved in tumor angiogenesis and growth. This group also contains alpha-type platelet-derived growth factor receptor precursor (PDGFR)-alpha (CD140a), and PDGFR-beta (CD140b). PDGFRs alpha and beta have an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion that has protein tyrosine kinase activity.


Pssm-ID: 409404  Cd Length: 102  Bit Score: 34.44  E-value: 6.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958794637  14 LVNQNLRLDCRHENNTNLPIQHEFSLTREKKKHvlsGTLGVPEhtyRSRVNLFSDRFIKVLTLANFTTKDEGDYMCELRv 93
Cdd:cd05742    15 PQGETLVLNCTANVNLNEVVDFQWTYPSEKEGK---LALLKPD---IKVDWSEPGEFVSTLTIPEATLKDSGTYTCAAR- 87
                          90
                  ....*....|....*
gi 1958794637  94 sgQNPTSSNKTINVI 108
Cdd:cd05742    88 --SGVMKKEKQTSVS 100
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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