Detailed view for Rv3253c

Basic information

TDR Targets ID: 9031
Mycobacterium tuberculosis, Possible cationic amino acid transport integral membrane protein
Source Database / ID:  Tuberculist 

pI: 9.9249 | Length (AA): 495 | MW (Da): 52520 | Paralog Number: 1

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 12

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

PF13520   Amino acid permease

Gene Ontology

Mouse over links to read term descriptions.
GO:0022857   transmembrane transporter activity  
GO:0003333   GO:amino acid transmembrane transport  

GO:0016020   membrane  
GO:0015171   amino acid transmembrane transporter activity  
GO:0055085   transmembrane transport  
GO:0006865   amino acid transport  
GO:0006810   transport  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
6 480 5oqt (A) 5 458 48.00 0 1 1.4945 -0.53

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

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_126699)

Species Accession Gene Product
Arabidopsis thaliana AT3G03720   cationic amino acid transporter 4
Arabidopsis thaliana AT5G36940   cationic amino acid transporter 3
Arabidopsis thaliana AT1G05940   cationic amino acid transporter 9
Arabidopsis thaliana AT1G58030   cationic amino acid transporter 2
Brugia malayi Bm1_47115   Amino acid permease family protein
Caenorhabditis elegans CELE_F23F1.6   Protein F23F1.6
Caenorhabditis elegans CELE_C50D2.2   Protein C50D2.2
Caenorhabditis elegans CELE_B0454.6   Protein B0454.6
Dictyostelium discoideum DDB_G0291201   solute carrier family 7 member protein
Dictyostelium discoideum DDB_G0291227   solute carrier family 7 member protein
Dictyostelium discoideum DDB_G0279983   solute carrier family 7 member protein
Drosophila melanogaster Dmel_CG7255   CG7255 gene product from transcript CG7255-RE
Drosophila melanogaster Dmel_CG11128   slimfast
Drosophila melanogaster Dmel_CG5535   CG5535 gene product from transcript CG5535-RC
Drosophila melanogaster Dmel_CG13248   CG13248 gene product from transcript CG13248-RA
Escherichia coli b1296   putrescine importer
Escherichia coli b0486   putative amino acid transporter
Echinococcus granulosus EgrG_000873000   cationic amino acid transporter
Echinococcus multilocularis EmuJ_000873000   cationic amino acid transporter amino acid polyamine transporter i amino acid permease associated region
Homo sapiens ENSG00000099960   solute carrier family 7, member 4
Homo sapiens ENSG00000139514   solute carrier family 7 (cationic amino acid transporter, y+ system), member 1
Homo sapiens ENSG00000165349   solute carrier family 7 (cationic amino acid transporter, y+ system), member 3
Homo sapiens ENSG00000003989   solute carrier family 7 (cationic amino acid transporter, y+ system), member 2
Loa Loa (eye worm) LOAG_01548   hypothetical protein
Mus musculus ENSMUSG00000031596   solute carrier family 7 (cationic amino acid transporter, y+ system), member 2
Mus musculus ENSMUSG00000054753   expressed sequence AU018091
Mus musculus ENSMUSG00000031297   solute carrier family 7 (cationic amino acid transporter, y+ system), member 3
Mus musculus ENSMUSG00000022756   solute carrier family 7 (cationic amino acid transporter, y+ system), member 4
Mus musculus ENSMUSG00000041313   solute carrier family 7 (cationic amino acid transporter, y+ system), member 1
Mycobacterium tuberculosis Rv2320c   Probable cationic amino acid transport integral membrane protein RocE
Mycobacterium tuberculosis Rv3253c   Possible cationic amino acid transport integral membrane protein
Mycobacterium ulcerans MUL_2597   cationic amino acid transport integral membrane protein
Mycobacterium ulcerans MUL_1244   cationic amino acid transport integral membrane protein RocE
Oryza sativa 4352828   Os12g0623500
Oryza sativa 4348708   Os10g0437100
Oryza sativa 4330195   Os02g0655700
Oryza sativa 4333602   Os03g0654400
Onchocerca volvulus OVOC9937   Cationic amino acid transporter 4 homolog
Schistosoma japonicum Sjp_0210990   Cationic amino acid transporter 4, putative
Schistosoma japonicum Sjp_0005970   High affinity cationic amino acid transporter 1, putative
Schistosoma mansoni Smp_123010   cationic amino acid transporter
Schistosoma mansoni Smp_004190   cationic amino acid transporter
Schmidtea mediterranea mk4.025033.00  
Schmidtea mediterranea mk4.005443.00  
Trypanosoma brucei gambiense Tbg972.6.4480   cationic amino acid transporter, putative
Trypanosoma brucei Tb927.6.4660   cationic amino acid transporter, putative
Trypanosoma cruzi TcCLB.511729.70   cationic amino acid transporter, putative
Trypanosoma cruzi TcCLB.506833.70   cationic amino acid transporter, putative

Essentiality

Rv3253c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3312 this record Mycobacterium tuberculosis non-essential nmpdr
Tb927.6.4660 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.4660 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.4660 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.4660 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0486 Escherichia coli non-essential goodall
b1296 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • 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.
  • 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

Druggability index (range: 0 to 1): 0.4

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.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier Rv3253c (Mycobacterium tuberculosis), Possible cationic amino acid transport integral membrane protein
Title for this comment
Comment