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Conserved domains on  [gi|38348215|ref|NP_940851|]
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embigin precursor [Homo sapiens]

Protein Classification

immunoglobulin domain-containing protein( domain architecture ID 11669303)

immunoglobulin (Ig) domain-containing protein adopts a fold comprised of a sandwich of two beta sheets, which is often involved in functions such as cell adhesion, immune recognition, and protein-protein interactions; similar to Homo sapiens V-set and immunoglobulin domain containing 8 (VSIG8) endothelial cell-selective adhesion molecule (ESAM), and Embigin/basigin subgroup, all of which are members of the immunoglobulin superfamily (IgSF)

CATH:  2.60.40.10
PubMed:  9417933|7932691
SCOP:  3000071

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 ...
84-142 9.21e-04

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 pfam07679:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 90  Bit Score: 37.62  E-value: 9.21e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 38348215    84 VNLTCQFTTSGDLNavnVTWKKDGEQLENN--YLVSATGSTlytqYRFTIINSKQ--MGSYSC 142
Cdd:pfam07679  18 ARFTCTVTGTPDPE---VSWFKDGQPLRSSdrFKVTYEGGT----YTLTISNVQPddSGKYTC 73
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
172-254 9.71e-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: 37.48  E-value: 9.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38348215    172 VGDSTVLTCKCQNCFPLNWTWYSSNGS-VKVPVGVQMNKYVINGTyanetkLKITQLLEEDGESYWCRALFQLGESEEHI 250
Cdd:smart00410   8 EGESVTLSCEASGSPPPEVTWYKQGGKlLAESGRFSVSRSGSTST------LTISNVTPEDSGTYTCAATNSSGSASSGT 81

                   ....
gi 38348215    251 ELVV 254
Cdd:smart00410  82 TLTV 85
 
Name Accession Description Interval E-value
I-set pfam07679
Immunoglobulin I-set domain;
84-142 9.21e-04

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 37.62  E-value: 9.21e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 38348215    84 VNLTCQFTTSGDLNavnVTWKKDGEQLENN--YLVSATGSTlytqYRFTIINSKQ--MGSYSC 142
Cdd:pfam07679  18 ARFTCTVTGTPDPE---VSWFKDGQPLRSSdrFKVTYEGGT----YTLTISNVQPddSGKYTC 73
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
172-254 9.71e-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: 37.48  E-value: 9.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38348215    172 VGDSTVLTCKCQNCFPLNWTWYSSNGS-VKVPVGVQMNKYVINGTyanetkLKITQLLEEDGESYWCRALFQLGESEEHI 250
Cdd:smart00410   8 EGESVTLSCEASGSPPPEVTWYKQGGKlLAESGRFSVSRSGSTST------LTISNVTPEDSGTYTCAATNSSGSASSGT 81

                   ....
gi 38348215    251 ELVV 254
Cdd:smart00410  82 TLTV 85
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
159-239 1.85e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.77  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38348215   159 PELHGKNKPLISYVGDSTVLTCKCQNCFPLNWTWYsSNGSVKVPvgvqmNKYVINGTYANETKLKITQLLEEDGESYWCR 238
Cdd:pfam13927   2 PVITVSPSSVTVREGETVTLTCEATGSPPPTITWY-KNGEPISS-----GSTRSRSLSGSNSTLTISNVTRSDAGTYTCV 75

                  .
gi 38348215   239 A 239
Cdd:pfam13927  76 A 76
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
177-250 2.64e-03

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.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 36.15  E-value: 2.64e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 38348215 177 VLTCKCQNCFPLNWTWYssngsvKVPVGVQMNKYVINGTYANETKLKITQLLEEDGESYWCRALFQLGESEEHI 250
Cdd:cd00096   2 TLTCSASGNPPPTITWY------KNGKPLPPSSRDSRRSELGNGTLTISNVTLEDSGTYTCVASNSAGGSASAS 69
IgC2_3_Dscam cd20957
Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
86-150 3.13e-03

Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the Constant 2 (C2)-set of IgSF domains; The members here are composed of the third immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. 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, and C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409549 [Multi-domain]  Cd Length: 88  Bit Score: 36.36  E-value: 3.13e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38348215  86 LTCQFTTSGdlnAVNVTWKKDGEQLENNYLVSATG-STLytqyRFTIINSKQMGSYSCFFREEKEQ 150
Cdd:cd20957  21 FNCSVTGNP---IHTVLWMKDGKPLGHSSRVQILSeDVL----VIPSVKREDKGMYQCFVRNDGDS 79
 
Name Accession Description Interval E-value
I-set pfam07679
Immunoglobulin I-set domain;
84-142 9.21e-04

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 37.62  E-value: 9.21e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 38348215    84 VNLTCQFTTSGDLNavnVTWKKDGEQLENN--YLVSATGSTlytqYRFTIINSKQ--MGSYSC 142
Cdd:pfam07679  18 ARFTCTVTGTPDPE---VSWFKDGQPLRSSdrFKVTYEGGT----YTLTISNVQPddSGKYTC 73
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
172-254 9.71e-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: 37.48  E-value: 9.71e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38348215    172 VGDSTVLTCKCQNCFPLNWTWYSSNGS-VKVPVGVQMNKYVINGTyanetkLKITQLLEEDGESYWCRALFQLGESEEHI 250
Cdd:smart00410   8 EGESVTLSCEASGSPPPEVTWYKQGGKlLAESGRFSVSRSGSTST------LTISNVTPEDSGTYTCAATNSSGSASSGT 81

                   ....
gi 38348215    251 ELVV 254
Cdd:smart00410  82 TLTV 85
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
82-142 1.45e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.77  E-value: 1.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 38348215    82 SNVNLTCQFTTSgdlNAVNVTWKKDGEQLENNYLVSATGSTLYTQYRFTIINSKQMGSYSC 142
Cdd:pfam13927  17 ETVTLTCEATGS---PPPTITWYKNGEPISSGSTRSRSLSGSNSTLTISNVTRSDAGTYTC 74
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
159-239 1.85e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.77  E-value: 1.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 38348215   159 PELHGKNKPLISYVGDSTVLTCKCQNCFPLNWTWYsSNGSVKVPvgvqmNKYVINGTYANETKLKITQLLEEDGESYWCR 238
Cdd:pfam13927   2 PVITVSPSSVTVREGETVTLTCEATGSPPPTITWY-KNGEPISS-----GSTRSRSLSGSNSTLTISNVTRSDAGTYTCV 75

                  .
gi 38348215   239 A 239
Cdd:pfam13927  76 A 76
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
177-250 2.64e-03

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.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 36.15  E-value: 2.64e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 38348215 177 VLTCKCQNCFPLNWTWYssngsvKVPVGVQMNKYVINGTYANETKLKITQLLEEDGESYWCRALFQLGESEEHI 250
Cdd:cd00096   2 TLTCSASGNPPPTITWY------KNGKPLPPSSRDSRRSELGNGTLTISNVTLEDSGTYTCVASNSAGGSASAS 69
IgC2_3_Dscam cd20957
Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
86-150 3.13e-03

Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the Constant 2 (C2)-set of IgSF domains; The members here are composed of the third immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. 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, and C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409549 [Multi-domain]  Cd Length: 88  Bit Score: 36.36  E-value: 3.13e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 38348215  86 LTCQFTTSGdlnAVNVTWKKDGEQLENNYLVSATG-STLytqyRFTIINSKQMGSYSCFFREEKEQ 150
Cdd:cd20957  21 FNCSVTGNP---IHTVLWMKDGKPLGHSSRVQILSeDVL----VIPSVKREDKGMYQCFVRNDGDS 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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