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Conserved domains on  [gi|62078457|ref|NP_001013883|]
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Ig-like V-type domain-containing protein FAM187A 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
V-set super family cl46292
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 49-135 1.23e-06

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


The actual alignment was detected with superfamily member pfam07686:

Pssm-ID: 462230  Cd Length: 109  Bit Score: 46.68  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457    49 SFELPCHCKPEDVSAVV---WYYQKyLGSSHTTVLTDFDGrllTEAAHVRVGssmlaRFSIRM------FSLLVFRAQPE 119
Cdd:pfam07686  13 SVTLPCTYSSSMSEASTsvyWYRQP-PGKGPTFLIAYYSN---GSEEGVKKG-----RFSGRGdpsngdGSLTIQNLTLS 83

                          90
                  ....*....|....*.
gi 62078457   120 DSGLYFCGTRNGDYFY 135
Cdd:pfam07686  84 DSGTYTCAVIPSGEGV 99
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 281-345 7.36e-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 cd05724:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 87  Bit Score: 38.15  E-value: 7.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078457 281 LGHGLIISC--PGARPEHAVAWDKDSQPLyrtqylkgVNRSMRVFIDHGNHLHIRFTQLSDRGIYYC 345
Cdd:cd05724  11 VGEMAVLECspPRGHPEPTVSWRKDGQPL--------NLDNERVRIVDDGNLLIAEARKSDEGTYKC 69
 
Name Accession Description Interval E-value
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 49-135 1.23e-06

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: 46.68  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457    49 SFELPCHCKPEDVSAVV---WYYQKyLGSSHTTVLTDFDGrllTEAAHVRVGssmlaRFSIRM------FSLLVFRAQPE 119
Cdd:pfam07686  13 SVTLPCTYSSSMSEASTsvyWYRQP-PGKGPTFLIAYYSN---GSEEGVKKG-----RFSGRGdpsngdGSLTIQNLTLS 83

                          90
                  ....*....|....*.
gi 62078457   120 DSGLYFCGTRNGDYFY 135
Cdd:pfam07686  84 DSGTYTCAVIPSGEGV 99
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 55-137 1.73e-05

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: 43.48  E-value: 1.73e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457  55 HCKPED---VSAVVWYYQK---------YLGSSHTTVLTDFDGRLLTEaahvrvgssmlaRFSIRMFSLLVFRAQPEDSG 122
Cdd:cd00099  19 SCEVSSsfsSTYIYWYRQKpgqgpefliYLSSSKGKTKGGVPGRFSGS------------RDGTSSFSLTISNLQPEDSG 86

                        90
                ....*....|....*.
gi 62078457 123 LYFC-GTRNGDYFYAY 137
Cdd:cd00099  87 TYYCaVSESGGTDKLT 102
IgI_2_Robo cd05724
Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
 281-345 7.36e-04

Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409389 [Multi-domain]  Cd Length: 87  Bit Score: 38.15  E-value: 7.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078457 281 LGHGLIISC--PGARPEHAVAWDKDSQPLyrtqylkgVNRSMRVFIDHGNHLHIRFTQLSDRGIYYC 345
Cdd:cd05724  11 VGEMAVLECspPRGHPEPTVSWRKDGQPL--------NLDNERVRIVDDGNLLIAEARKSDEGTYKC 69
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 49-131 2.31e-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: 36.71  E-value: 2.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457     49 SFELPCHCKPEDVSAVVWYYQkylgsshttvltdfDGRLLTEAAHVRVgssmlaRFSIRMFSLLVFRAQPEDSGLYFCGT 128
Cdd:smart00410  11 SVTLSCEASGSPPPEVTWYKQ--------------GGKLLAESGRFSV------SRSGSTSTLTISNVTPEDSGTYTCAA 70


                   ...
gi 62078457    129 RNG 131
Cdd:smart00410  71 TNS 73
 
Name Accession Description Interval E-value
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 49-135 1.23e-06

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: 46.68  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457    49 SFELPCHCKPEDVSAVV---WYYQKyLGSSHTTVLTDFDGrllTEAAHVRVGssmlaRFSIRM------FSLLVFRAQPE 119
Cdd:pfam07686  13 SVTLPCTYSSSMSEASTsvyWYRQP-PGKGPTFLIAYYSN---GSEEGVKKG-----RFSGRGdpsngdGSLTIQNLTLS 83

                          90
                  ....*....|....*.
gi 62078457   120 DSGLYFCGTRNGDYFY 135
Cdd:pfam07686  84 DSGTYTCAVIPSGEGV 99
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 55-137 1.73e-05

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: 43.48  E-value: 1.73e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457  55 HCKPED---VSAVVWYYQK---------YLGSSHTTVLTDFDGRLLTEaahvrvgssmlaRFSIRMFSLLVFRAQPEDSG 122
Cdd:cd00099  19 SCEVSSsfsSTYIYWYRQKpgqgpefliYLSSSKGKTKGGVPGRFSGS------------RDGTSSFSLTISNLQPEDSG 86

                        90
                ....*....|....*.
gi 62078457 123 LYFC-GTRNGDYFYAY 137
Cdd:cd00099  87 TYYCaVSESGGTDKLT 102
IgI_2_Robo cd05724
Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
 281-345 7.36e-04

Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409389 [Multi-domain]  Cd Length: 87  Bit Score: 38.15  E-value: 7.36e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 62078457 281 LGHGLIISC--PGARPEHAVAWDKDSQPLyrtqylkgVNRSMRVFIDHGNHLHIRFTQLSDRGIYYC 345
Cdd:cd05724  11 VGEMAVLECspPRGHPEPTVSWRKDGQPL--------NLDNERVRIVDDGNLLIAEARKSDEGTYKC 69
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 49-131 2.31e-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: 36.71  E-value: 2.31e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457     49 SFELPCHCKPEDVSAVVWYYQkylgsshttvltdfDGRLLTEAAHVRVgssmlaRFSIRMFSLLVFRAQPEDSGLYFCGT 128
Cdd:smart00410  11 SVTLSCEASGSPPPEVTWYKQ--------------GGKLLAESGRFSV------SRSGSTSTLTISNVTPEDSGTYTCAA 70


                   ...
gi 62078457    129 RNG 131
Cdd:smart00410  71 TNS 73
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 55-126 2.73e-03

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 37.25  E-value: 2.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62078457  55 HCKPEDVS--AVVWYYQK------YLGSSHTTVLTDFDGRLlteaahvrvgSSMLARfSIRMFSLLVFRAQPEDSGLYFC 126
Cdd:cd04983  19 NCNYSTSTfyYLFWYRQYpgqgpqFLIYISSDSGNKKKGRF----------SATLDK-SRKSSSLHISAAQLSDSAVYFC 87
 
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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