Detailed view for Rv1899c

Basic information

TDR Targets ID: 6327
Mycobacterium tuberculosis, Possible lipoprotein LppD
Source Database / ID:  Tuberculist 

pI: 10.5859 | Length (AA): 343 | MW (Da): 35072 | Paralog Number: 0

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

Druggability Group : DG2

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

PF01661   Macro domain

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
118 334 2x47 (A) 91 318 27.00 0.00019 1 0.941853 -0.02
174 335 1vhu (A) 19 196 31.00 0 1 0.839003 -0.86
191 247 5dus (A) 33 92 42.00 0.0015 0.93 0.605281 -0.12
191 265 2acf (A) 217 294 32.00 0.056 0.93 0.538759 0.27

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
Mid 40-60% 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_127054)

Species Accession Gene Product
Arabidopsis thaliana AT2G40600   appr-1-p processing enzyme family protein
Brugia malayi Bm1_50500   Appr-1-p processing enzyme family protein
Candida albicans CaO19.2285   potential Appr-1-p processing enzyme family member
Candida albicans CaO19.9825   potential Appr-1-p processing enzyme family member
Caenorhabditis elegans CELE_B0035.3   Protein B0035.3
Dictyostelium discoideum DDB_G0278229   hypothetical protein
Escherichia coli b1045   O-acetyl-ADP-ribose deacetylase
Echinococcus granulosus EgrG_001094800   MACRO domain containing protein 2
Echinococcus granulosus EgrG_001095000   MACRO domain containing protein 2
Entamoeba histolytica EHI_054700   hypothetical protein, conserved
Entamoeba histolytica EHI_131910   hypothetical protein, conserved
Entamoeba histolytica EHI_114350   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001094800   MACRO domain containing protein 2
Echinococcus multilocularis EmuJ_001095000   MACRO domain containing protein 2
Giardia lamblia GL50803_14730   Protein LRP16
Homo sapiens ENSG00000138496   poly (ADP-ribose) polymerase family, member 9
Homo sapiens ENSG00000133315   MACRO domain containing 1
Homo sapiens ENSG00000172264   MACRO domain containing 2
Loa Loa (eye worm) LOAG_03200   hypothetical protein
Mus musculus ENSMUSG00000036278   MACRO domain containing 1
Mus musculus ENSMUSG00000022906   poly (ADP-ribose) polymerase family, member 9
Mus musculus ENSMUSG00000068205   MACRO domain containing 2
Mycobacterium tuberculosis Rv1899c   Possible lipoprotein LppD
Mycobacterium ulcerans MUL_2958   lipoprotein LppD
Neospora caninum NCLIV_016520   hypothetical protein
Oryza sativa 4332764   Os03g0336500
Plasmodium berghei PBANKA_1312500   Appr-1-p processing domain protein
Plasmodium falciparum PF3D7_1448800   Appr-1-p processing domain protein
Plasmodium knowlesi PKNH_1233300   Appr-1-p processing domain protein
Plasmodium vivax PVX_118050   hypothetical protein, conserved
Plasmodium yoelii PY05109   ATPase associated with chromosome architecture/replication
Schistosoma mansoni Smp_140900.2   hypothetical protein
Schistosoma mansoni Smp_140900.1   hypothetical protein
Schmidtea mediterranea mk4.005647.00  
Schmidtea mediterranea mk4.003806.01  
Trypanosoma brucei gambiense Tbg972.5.3640   hypothetical protein, conserved
Trypanosoma brucei Tb927.5.2590   Macro domain containing protein, putative
Trypanosoma congolense TcIL3000_5_2540   Macro domain containing protein, putative
Trypanosoma congolense TcIL3000_5_2610   Macro domain containing protein, putative
Trypanosoma cruzi TcCLB.509179.20   Macro domain containing protein, putative
Trypanosoma cruzi TcCLB.511303.34   Macro domain containing protein, putative
Toxoplasma gondii TGME49_240250   macro domain-containing protein
Trichomonas vaginalis TVAG_246760   ganglioside induced differentiation associated protein, putative
Trichomonas vaginalis TVAG_307230   ganglioside induced differentiation associated protein, putative
Trichomonas vaginalis TVAG_423290   ganglioside induced differentiation associated protein, putative

Essentiality

Rv1899c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1930 this record Mycobacterium tuberculosis non-essential nmpdr
Tb927.5.2590 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.2590 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.2590 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.2590 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1045 Escherichia coli non-essential goodall
PBANKA_1312500 Plasmodium berghei Essential plasmo
TGME49_240250 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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
Human coronavirus NL63 Replicase polyprotein 1a Compounds References
SARS coronavirus SARS coronavirus 3C-like proteinase Compounds References
SARS coronavirus Replicase polyprotein 1ab Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0017 0.4134 0
0.003 0.5 0.5
0.0013 0.5 0.5
0.003 0.5 0.5
0.0014 0.5 0.5
0.0013 0.5 0.5
0.003 0.5 0.5
0.0013 0.5 0.5
0.0032 0.5 0.5
0.0044 0.5 0.5
0.0017 0.5 0.5
0.0062 0.4763 1
0.0031 0.5 0.5

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 Rv1899c (Mycobacterium tuberculosis), Possible lipoprotein LppD
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