Detailed view for Rv2920c

Basic information

TDR Targets ID: 980966
Mycobacterium tuberculosis, Probable ammonium-transport integral membrane protein Amt
Source Database / ID:  Tuberculist 

pI: 5.8822 | Length (AA): 477 | MW (Da): 49209 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 11

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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 4 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
9 442 2ns1 (A) 4 405 45.00 0 1 1.41045 -0.66
9 422 1xqf (A) 4 385 48.00 0 1 1.29752 -0.1
11 452 5aez (A) 24 445 31.00 0 1 1.26172 -0.22
11 441 2b2h (A) 2 390 43.00 0 1 1.34616 -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_126686)

Species Accession Gene Product
Arabidopsis thaliana AT4G28700   4
Arabidopsis thaliana AT3G24290   5
Arabidopsis thaliana AT2G38290   ammonium transporter 2
Arabidopsis thaliana AT3G24300   3
Arabidopsis thaliana AT4G13510   1
Arabidopsis thaliana AT1G64780   2
Brugia malayi Bm1_05640   Ammonium transporter 3
Candida albicans CaO19.9181   NH4+ transporter
Candida albicans CaO19.13117   similar to high affinity Ammonium permease involved in regulation of filamentous grouwth
Candida albicans CaO19.5672   similar to high affinity Ammonium permease involved in regulation of filamentous grouwth
Candida albicans CaO19.1614   NH4+ transporter
Caenorhabditis elegans CELE_C05E11.5   Protein AMT-4
Caenorhabditis elegans CELE_M195.3   Protein AMT-3
Caenorhabditis elegans CELE_C05E11.4   Protein AMT-1
Caenorhabditis elegans CELE_F49E11.3   Protein AMT-2
Dictyostelium discoideum DDB_G0277889   ammonium transporter
Dictyostelium discoideum DDB_G0267424   ammonium transporter
Dictyostelium discoideum DDB_G0277503   ammonium transporter
Drosophila melanogaster Dmel_CG6499   CG6499 gene product from transcript CG6499-RB
Escherichia coli b0451   ammonium transporter
Loa Loa (eye worm) LOAG_11758   ammonium transporter 3
Loa Loa (eye worm) LOAG_07480   hypothetical protein
Mycobacterium tuberculosis Rv2920c   Probable ammonium-transport integral membrane protein Amt
Mycobacterium ulcerans MUL_0037   ammonium-transport integral membrane protein, Amt
Oryza sativa 4339064   Os05g0468700
Oryza sativa 4330008   Os02g0620600
Oryza sativa 4336365   Os04g0509600
Oryza sativa 4329628   Os02g0550800
Oryza sativa 4330007   Os02g0620500
Oryza sativa 4334717   Os03g0838400
Oryza sativa 4327434   Os01g0831900
Oryza sativa 4324937   Os01g0870300
Saccharomyces cerevisiae YNL142W   ammonium permease MEP2
Saccharomyces cerevisiae YGR121C   ammonium permease MEP1
Saccharomyces cerevisiae YPR138C   ammonium permease MEP3
Trypanosoma cruzi TcCLB.509849.10   ammonium transporter, putative
Trypanosoma cruzi TcCLB.508317.50   ammonium transporter, putative

Essentiality

Rv2920c has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0451 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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
Species Known druggable target Linked compounds Reference
Saccharomyces cerevisiae ammonium permease MEP2 Compounds References
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

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Gene identifier Rv2920c (Mycobacterium tuberculosis), Probable ammonium-transport integral membrane protein Amt
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