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Conserved domains on  [gi|71361621|ref|NP_001025091|]
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V-set and transmembrane domain-containing protein 4 precursor [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 ...
 39-129 2.86e-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.


The actual alignment was detected with superfamily member cd20960:

Pssm-ID: 472250  Cd Length: 114  Bit Score: 37.05  E-value: 2.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71361621  39 GENATLLCHVSQKRRKDSLLAVRWFFAP-DGSQEAlmvkmtklrVIQYYGNfsRIANQqrlrLLEERRGVL-----YK-- 110
Cdd:cd20960  15 GENVTLPCHHQLGLEDQGTLDIEWLLLPsDKVEKV---------VITYSGD--RVYNH----YYPALKGRVaftsnDLsg 79

                        90       100
                ....*....|....*....|..
gi 71361621 111 ---LSVLMLRPADQGQYVCKVQ 129
Cdd:cd20960  80 dasLNISNLKLSDTGTYQCKVK 101
 
Name Accession Description Interval E-value
IgV_CAR_like cd20960
Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and ...
 39-129 2.86e-03

Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins; The members here are composed of the Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. CAR, which is encoded by human CXADR gene, is a cell adhesion molecule of the Immunoglobulin (Ig) superfamily. The CAR acts as a type I membrane receptor for group B1-B6 coxsackie viruses and subgroup C adenoviruses. For instance, adenovirus interacts with the coxsackievirus and adenovirus receptor to enter epithelial airway cells. The CAR is also shown to be involved in physiological processes such as neuronal and heart development, epithelial tight junction integrity, and tumor suppression. The CAR is a component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. The CAR is also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. The CAR is composed of one V-set and one C2-set Ig module, a single transmembrane helix, and an intracellular domain. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C" in the other


Pssm-ID: 409552  Cd Length: 114  Bit Score: 37.05  E-value: 2.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71361621  39 GENATLLCHVSQKRRKDSLLAVRWFFAP-DGSQEAlmvkmtklrVIQYYGNfsRIANQqrlrLLEERRGVL-----YK-- 110
Cdd:cd20960  15 GENVTLPCHHQLGLEDQGTLDIEWLLLPsDKVEKV---------VITYSGD--RVYNH----YYPALKGRVaftsnDLsg 79

                        90       100
                ....*....|....*....|..
gi 71361621 111 ---LSVLMLRPADQGQYVCKVQ 129
Cdd:cd20960  80 dasLNISNLKLSDTGTYQCKVK 101
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-128 9.08e-03

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: 35.51  E-value: 9.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71361621    38 EGENATLLCHVSqKRRKDSLLAVRWFFAPDGSQEALMVkmtkLRVIQYYGNFSRianQQRLRLLEERRGVLYKLSVLMLR 117
Cdd:pfam07686  10 LGGSVTLPCTYS-SSMSEASTSVYWYRQPPGKGPTFLI----AYYSNGSEEGVK---KGRFSGRGDPSNGDGSLTIQNLT 81

                          90
                  ....*....|.
gi 71361621   118 PADQGQYVCKV 128
Cdd:pfam07686  82 LSDSGTYTCAV 92
 
Name Accession Description Interval E-value
IgV_CAR_like cd20960
Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and ...
 39-129 2.86e-03

Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins; The members here are composed of the Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. CAR, which is encoded by human CXADR gene, is a cell adhesion molecule of the Immunoglobulin (Ig) superfamily. The CAR acts as a type I membrane receptor for group B1-B6 coxsackie viruses and subgroup C adenoviruses. For instance, adenovirus interacts with the coxsackievirus and adenovirus receptor to enter epithelial airway cells. The CAR is also shown to be involved in physiological processes such as neuronal and heart development, epithelial tight junction integrity, and tumor suppression. The CAR is a component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. The CAR is also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. The CAR is composed of one V-set and one C2-set Ig module, a single transmembrane helix, and an intracellular domain. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C" in the other


Pssm-ID: 409552  Cd Length: 114  Bit Score: 37.05  E-value: 2.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71361621  39 GENATLLCHVSQKRRKDSLLAVRWFFAP-DGSQEAlmvkmtklrVIQYYGNfsRIANQqrlrLLEERRGVL-----YK-- 110
Cdd:cd20960  15 GENVTLPCHHQLGLEDQGTLDIEWLLLPsDKVEKV---------VITYSGD--RVYNH----YYPALKGRVaftsnDLsg 79

                        90       100
                ....*....|....*....|..
gi 71361621 111 ---LSVLMLRPADQGQYVCKVQ 129
Cdd:cd20960  80 dasLNISNLKLSDTGTYQCKVK 101
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-128 9.08e-03

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: 35.51  E-value: 9.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71361621    38 EGENATLLCHVSqKRRKDSLLAVRWFFAPDGSQEALMVkmtkLRVIQYYGNFSRianQQRLRLLEERRGVLYKLSVLMLR 117
Cdd:pfam07686  10 LGGSVTLPCTYS-SSMSEASTSVYWYRQPPGKGPTFLI----AYYSNGSEEGVK---KGRFSGRGDPSNGDGSLTIQNLT 81

                          90
                  ....*....|.
gi 71361621   118 PADQGQYVCKV 128
Cdd:pfam07686  82 LSDSGTYTCAV 92
 
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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