Detailed view for Smp_170330

Basic information

TDR Targets ID: 285434
Schistosoma mansoni, Collagen alpha-1(V) chain precursor
Source Database / ID:  GeneDB

pI: 4.276 | Length (AA): 2991 | MW (Da): 295972 | Paralog Number: 6

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF01391   Collagen triple helix repeat (20 copies)
PF01413   C-terminal tandem repeated domain in type 4 procollagen

Gene Ontology

Mouse over links to read term descriptions.
GO:0005581   collagen  
GO:0005488   binding  
GO:0005201   extracellular matrix structural constituent  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 17 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
12 68 5cva (A) 3 59 28.00 0.25 0.01 0.258357 -0.12
163 339 4km7 (A) 37 222 6.00 0.1 0 0.0914775 -0.26
785 850 5cvw (A) 1529 1588 42.00 0.24 0.26 0.432866 -0.71
828 998 2ml3 (A) 2 179 21.00 0 0.07 0.279272 -0.87
830 1059 5c2m (A) 20 248 11.00 0 0.01 0.152997 -0.52
1172 1201 5cva (F) 12 41 47.00 0.069 0.03 0.68983 -2.13
1399 1607 5nb0 (A) 7 214 42.00 0 1 0.514676 0.39
1634 1664 5cva (E) 15 45 35.00 0 0.03 0.604464 -2.7
1667 2171 5jou (A) 309 813 7.00 0.36 0 0.18614 -0.01
2168 2197 4auo (C) 964 997 69.00 0.073 0.04 0.88883 -2.91
2186 2267 2pne (A) 2 81 39.00 0 0.92 0.628516 -1.73
2549 2717 3tiq (A) 433 609 34.00 0.54 0.13 0.151303 0.12
2693 2750 4mt2 (A) 3 60 7.00 0.34 0 0.180692 -1.45
2700 2816 2fj8 (A) 6 122 7.00 0.39 0 0.0714174 -0.16
2756 2984 5nb2 (B) 6 227 49.00 0 0.95 0.167663 1.05
2756 2983 1t60 (C) 5 225 43.00 0 1 0.559029 0.01
2756 2984 5nb2 (A) 6 227 48.00 0 1 0.392363 0.48

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

No expression data available for this gene

Orthologs

Ortholog group members (OG5_126592)

Species Accession Gene Product
Brugia malayi Bm1_16850   collagen alpha 2(IV) chain precursor
Brugia malayi Bm1_57370   Collagen alpha
Caenorhabditis elegans CELE_F01G12.5   Protein LET-2, isoform B
Caenorhabditis elegans CELE_K04H4.1   Protein EMB-9, isoform B
Dictyostelium discoideum DDB_G0277909   calcium-binding protein
Drosophila melanogaster Dmel_CG42717   CG42717 gene product from transcript CG42717-RA
Drosophila melanogaster Dmel_CG4145   Collagen type IV
Drosophila melanogaster Dmel_CG16858   viking
Echinococcus granulosus EgrG_000948400   fibronectin type III domain-containing protein
Echinococcus granulosus EgrG_001060600   Type II collagen B
Echinococcus granulosus EgrG_000144300   Collagen alpha 1V chain
Echinococcus granulosus EgrG_000417600   collagen alpha 1IV chain
Echinococcus granulosus EgrG_000203400   Collagen alpha 1V chain
Echinococcus granulosus EgrG_000823800   collagen alpha 2I chain
Echinococcus granulosus EgrG_000144400   abnormal EMBroygenesis family member emb 9
Echinococcus granulosus EgrG_002068400   kunitz type serine protease inhibitor 6
Echinococcus granulosus EgrG_001060700   fibrillar collagen chain FAp1 alpha
Echinococcus granulosus EgrG_001190600   collagen type i ii iii v xi alpha
Echinococcus granulosus EgrG_000144350   collagen alpha 1(IV) chain
Echinococcus granulosus EgrG_000524200   collagen type XI alpha 2
Entamoeba histolytica EHI_059870   hypothetical protein
Echinococcus multilocularis EmuJ_000524200   collagen type XI alpha 2
Echinococcus multilocularis EmuJ_001060700   fibrillar collagen chain FAp1 alpha
Echinococcus multilocularis EmuJ_000144350  
Echinococcus multilocularis EmuJ_000203400   Collagen alpha 1(V) chain
Echinococcus multilocularis EmuJ_001060600   Type II collagen B
Echinococcus multilocularis EmuJ_000417600   collagen alpha 1(IV) chain
Echinococcus multilocularis EmuJ_000139900   abnormal EMBroygenesis family member (emb 9)
Echinococcus multilocularis EmuJ_000144400   abnormal EMBroygenesis family member (emb 9)
Echinococcus multilocularis EmuJ_000823800   collagen alpha 2(I) chain
Echinococcus multilocularis EmuJ_000140100   Collagen alpha 1(V) chain
Echinococcus multilocularis EmuJ_000140000   collagen alpha(iv) chain
Echinococcus multilocularis EmuJ_000144300   Collagen alpha 1(V) chain
Echinococcus multilocularis EmuJ_001190600   collagen type i II IIi v xi alpha collagen alpha (v) chain
Homo sapiens ENSG00000108821   collagen, type I, alpha 1
Homo sapiens ENSG00000114270   collagen, type VII, alpha 1
Homo sapiens ENSG00000188153   collagen, type IV, alpha 5
Homo sapiens ENSG00000171502   collagen, type XXIV, alpha 1
Homo sapiens ENSG00000169436   collagen, type XXII, alpha 1
Homo sapiens ENSG00000060718   collagen, type XI, alpha 1
Homo sapiens ENSG00000187498   collagen, type IV, alpha 1
Homo sapiens ENSG00000197565   collagen, type IV, alpha 6
Homo sapiens ENSG00000134871   collagen, type IV, alpha 2
Homo sapiens 1310   collagen, type XIX, alpha 1
Homo sapiens ENSG00000130635   collagen, type V, alpha 1
Homo sapiens ENSG00000080573   collagen, type V, alpha 3
Homo sapiens ENSG00000168542   collagen, type III, alpha 1
Homo sapiens ENSG00000204248   collagen, type XI, alpha 2
Homo sapiens 101929803   adhesive plaque matrix protein-like
Homo sapiens ENSG00000164692   collagen, type I, alpha 2
Homo sapiens ENSG00000204262   collagen, type V, alpha 2
Homo sapiens ENSG00000139219   collagen, type II, alpha 1
Homo sapiens ENSG00000169031   collagen, type IV, alpha 3 (Goodpasture antigen)
Homo sapiens ENSG00000196739   collagen, type XXVII, alpha 1
Homo sapiens ENSG00000084636   collagen, type XVI, alpha 1
Homo sapiens ENSG00000081052   collagen, type IV, alpha 4
Leishmania mexicana LmxM.14.1120b  
Loa Loa (eye worm) LOAG_09685   hypothetical protein
Loa Loa (eye worm) LOAG_03919   procollagen
Loa Loa (eye worm) LOAG_14600   hypothetical protein
Loa Loa (eye worm) LOAG_09684   hypothetical protein
Mus musculus 69700   collagen, type XXII, alpha 1
Mus musculus ENSMUSG00000026042   collagen, type V, alpha 2
Mus musculus ENSMUSG00000040690   collagen, type XVI, alpha 1
Mus musculus ENSMUSG00000031273   collagen, type IV, alpha 6
Mus musculus ENSMUSG00000031274   collagen, type IV, alpha 5
Mus musculus 12829   collagen, type IV, alpha 4
Mus musculus ENSMUSG00000031502   collagen, type IV, alpha 1
Mus musculus ENSMUSG00000025650   collagen, type VII, alpha 1
Mus musculus 12842   collagen, type I, alpha 1
Mus musculus ENSMUSG00000004098   collagen, type V, alpha 3
Mus musculus ENSMUSG00000027966   collagen, type XI, alpha 1
Mus musculus ENSMUSG00000031503   collagen, type IV, alpha 2
Mus musculus ENSMUSG00000026837   collagen, type V, alpha 1
Mus musculus ENSMUSG00000024330   collagen, type XI, alpha 2
Mus musculus 12823   collagen, type XIX, alpha 1
Mus musculus ENSMUSG00000079465   collagen, type IV, alpha 3
Mus musculus ENSMUSG00000022483   collagen, type II, alpha 1
Mus musculus ENSMUSG00000045672   collagen, type XXVII, alpha 1
Mus musculus ENSMUSG00000029661   collagen, type I, alpha 2
Mus musculus ENSMUSG00000028197   collagen, type XXIV, alpha 1
Mus musculus ENSMUSG00000026043   collagen, type III, alpha 1
Mycobacterium ulcerans MUL_4367   PE-PGRS family protein
Neospora caninum NCLIV_049870   GH22120, related
Neospora caninum NCLIV_035900   RNA binding motif-containing protein, putative
Neospora caninum NCLIV_009210   hypothetical protein
Oryza sativa 4328242   Os02g0138000
Oryza sativa 4343091   Os07g0440100
Plasmodium knowlesi PKNH_0946500   SICAvar, type II
Plasmodium knowlesi PKNH_0300400   SICAvar, type II
Plasmodium vivax PVX_118360   TRAP-like protein
Plasmodium yoelii PY07368   circumsporozoite protein precursor-related
Schistosoma japonicum Sjp_0011650   ko:K06237 collagen, type IV, alpha, putative
Schistosoma japonicum Sjp_0034140   ko:K06237 collagen, type IV, alpha, putative
Schistosoma japonicum Sjp_0003010   Collagen alpha-2(I) chain precursor, putative
Schistosoma japonicum Sjp_0099350   Collagen alpha-2(XI) chain precursor, putative
Schistosoma japonicum Sjp_0003000   Collagen alpha-2(V) chain precursor, putative
Schistosoma japonicum Sjp_0034120   ko:K06237 collagen, type IV, alpha, putative
Schistosoma japonicum Sjp_0000750   Collagen alpha-2(V) chain precursor, putative
Schistosoma japonicum Sjp_0098850   Collagen alpha-1(VI) chain precursor, putative
Schistosoma japonicum Sjp_0120520   Collagen alpha-1(XXVII) chain precursor, putative
Schistosoma japonicum Sjp_0000760   Collagen alpha-2(V) chain precursor, putative
Schistosoma japonicum Sjp_0081590   Collagen alpha-3(V) chain precursor, putative
Schistosoma japonicum Sjp_0071880   Collagen alpha-2(I) chain precursor, putative
Schistosoma japonicum Sjp_0034130   Collagen alpha-1(IV) chain precursor, putative
Schistosoma japonicum Sjp_0300670   Collagen alpha-2(I) chain precursor, putative
Schistosoma japonicum Sjp_0099360   expressed protein
Schistosoma mansoni Smp_123830   Collagen alpha-1(V) chain precursor
Schistosoma mansoni Smp_083630   hypothetical protein
Schistosoma mansoni Smp_159600   Collagen alpha-1(V) chain precursor
Schistosoma mansoni Smp_164590   Collagen alpha-1(V) chain precursor
Schistosoma mansoni Smp_144910   Collagen alpha-1(V) chain precursor
Schistosoma mansoni Smp_170340   Collagen alpha-1(V) chain precursor
Schistosoma mansoni Smp_170330   Collagen alpha-1(V) chain precursor
Schmidtea mediterranea mk4.003416.05  
Schmidtea mediterranea mk4.001322.02  
Schmidtea mediterranea mk4.000017.05  
Schmidtea mediterranea mk4.013024.02  
Schmidtea mediterranea mk4.001322.03  
Schmidtea mediterranea mk4.008247.01  
Schmidtea mediterranea mk4.000017.06  
Schmidtea mediterranea mk4.000373.10  
Schmidtea mediterranea mk4.000363.01  
Schmidtea mediterranea mk4.003634.05  
Schmidtea mediterranea mk4.004716.04  
Schmidtea mediterranea mk4.005629.01  
Schmidtea mediterranea mk4.010742.01  
Schmidtea mediterranea mk4.003647.02  
Schmidtea mediterranea mk4.005629.00  
Schmidtea mediterranea mk4.016703.01  
Schmidtea mediterranea mk4.013024.00   Putative cuticle collagen 99
Schmidtea mediterranea mk4.008247.00   Putative cuticle collagen 99
Schmidtea mediterranea mk4.005498.05  
Schmidtea mediterranea mk4.012654.00  
Schmidtea mediterranea mk4.016703.00  
Schmidtea mediterranea mk4.005498.04  
Schmidtea mediterranea mk4.000017.23   Putative cuticle collagen 75
Schmidtea mediterranea mk4.002029.01  
Trypanosoma brucei Tb927.7.6580   hypothetical protein
Trypanosoma brucei Tb927.7.6590   hypothetical protein, conserved
Toxoplasma gondii TGME49_322700   collagen, putative
Toxoplasma gondii TGME49_278800   zinc finger protein 36 family 3 protein
Toxoplasma gondii TGME49_235420   hypothetical protein
Theileria parva TP02_0895   hypothetical protein
Theileria parva TP01_0967   hypothetical protein
Trichomonas vaginalis TVAG_276200   conserved hypothetical protein

Essentiality

Smp_170330 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.7.6580 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.6580 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.6580 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.6580 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.7.6590 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.7.6590 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.7.6590 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.7.6590 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_K04H4.1 Caenorhabditis elegans adult lethal wormbase
CELE_K04H4.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_K04H4.1 Caenorhabditis elegans larval arrest wormbase
CELE_K04H4.1 Caenorhabditis elegans slow growth wormbase
CELE_K04H4.1 Caenorhabditis elegans sterile wormbase
CELE_F01G12.5 Caenorhabditis elegans embryonic lethal wormbase
CELE_F01G12.5 Caenorhabditis elegans larval arrest wormbase
TGME49_235420 Toxoplasma gondii Probably essential sidik
TGME49_278800 Toxoplasma gondii Probably essential sidik
TGME49_322700 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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User comments

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Gene identifier Smp_170330 (Schistosoma mansoni), Collagen alpha-1(V) chain precursor
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