Detailed view for Rv1354c

Basic information

TDR Targets ID: 7892
Mycobacterium tuberculosis, Conserved hypothetical protein
Source Database / ID:  Tuberculist 

pI: 4.9935 | Length (AA): 623 | MW (Da): 67653 | Paralog Number: 0

Signal peptide: N | 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

PF00563   EAL domain
PF00990   Diguanylate cyclase, GGDEF domain
PF13185   GAF domain
PF13492  

Gene Ontology

Mouse over links to read term descriptions.
GO:0005515   protein binding  

Metabolic Pathways

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

Structural information

Modbase 3D models:

There are 7 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
11 340 4zmu (A) 9 338 29.00 0 1 0.742395 0.15
22 340 1w25 (A) 124 449 33.00 0 1 0.850739 -0.21
28 171 5w10 (A) 22 164 20.00 0.85 1 0.53884 -1.1
106 597 5xgb (A) 271 794 31.00 0 1 1.15443 -0.17
185 612 5m3c (A) 809 1233 39.00 0 1 1.1857 -0.51
187 345 3icl (A) 1 161 35.00 0 1 0.836917 -1.54
369 611 5yrp (A) 364 606 61.00 0 1 1.10065 -0.93

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. murphy
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
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_128712)

Species Accession Gene Product
Escherichia coli b1285   cyclic-di-GMP phosphodiesterase
Escherichia coli b3529   cyclic-di-GMP phosphodiesterase
Escherichia coli b1489   oxygen sensor, c-di-GMP phosphodiesterase, heme-regulated
Mycobacterium leprae ML1750c   conserved hypothetical protein
Mycobacterium tuberculosis Rv1354c   Conserved hypothetical protein
Schmidtea mediterranea mk4.047695.00  

Essentiality

Rv1354c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1377 this record Mycobacterium tuberculosis non-essential nmpdr
b1285 Escherichia coli non-essential goodall
b1489 Escherichia coli non-essential goodall
b3529 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.211 0.3494 0.7069
0.1293 0.3533 0.6179
0.1293 0.3533 0.6179
0.0235 0.3315 0.6554
0.0826 0.3555 0.7193
0.2698 0.3006 0.5947
0.2563 0.2566 0.6179
0.2178 0.2964 0.5902
0.2071 0.3498 0.7061
0.1123 0.3528 0.6179
0.0902 0.3512 0.7173
0.0968 0.3511 0.6179
0.1849 0.2909 0.5845
0.1615 0.3563 0.7214
0.2022 0.3349 0.6774
0.1227 0.2566 0.6179
0.2514 0.2991 0.5931
0.0607 0.3312 0.6179
0.0151 0.2615 0.6179
0.2256 0.2948 0.5886
0.1107 0.3562 0.7201
0.211 0.3494 0.7069
0.0479 0.2566 0.6179
0.1078 0.2723 0.5653
0.0413 0.3161 0.6407
0.0036 0.5 0.5
0.0109 0.408 0.4149
0.1429 0.3543 0.7185
0.1429 0.3543 0.7185
0.2601 0.2997 0.5937
0.165 0.2894 0.583
0.2396 0.3482 0.5924
0.1221 0.3559 0.7206
0.2596 0.2993 0.5933
0.1221 0.3559 0.7206
0.0072 0.8353 1
0.1388 0.2566 0.6179
0.1807 0.2909 0.5846
0.1507 0.286 0.5795
0.2089 0.3472 0.5897
0.2573 0.2983 0.5922
0.1107 0.3562 0.7201
0.0383 0.2566 0.6179
0.1293 0.3533 0.6179
0.2532 0.2981 0.5921
0.0109 0.408 0.4149
0.0035 0.5 0.5
0.1293 0.3533 0.6179
0.2978 0.3014 0.5955
0.2832 0.3014 0.5938
0.1403 0.3573 0.7226
0.2503 0.3013 0.5936
0.1896 0.2913 0.585
0.2367 0.2985 0.5925
0.1546 0.3218 0.5855
0.1617 0.3564 0.6179
0.1947 0.34 0.5867
0.0320809 0.508055 0.51811
0.1385 0.2566 0.6179
0.1615 0.3563 0.7214
0.1391 0.3542 0.6179
0.2307 0.2981 0.5921
0.1417 0.2566 0.6179
0.1293 0.3533 0.6179
0.2018 0.2953 0.6198
0.1293 0.3539 0.6179
0.149 0.3568 0.7219
0.127 0.2566 0.6179
0.1615 0.3563 0.7214
0.1401 0.3556 0.7183
0.2545 0.2996 0.5937
0.2416 0.299 0.593
0.0849 0.2566 0.6179
0.0072 0.3543 0.3847
0.1447 0.2566 0.6179
0.2614 0.3191 0.6353
0.1623 0.3007 0.582
0.1615 0.3563 0.7214
0.0785 0.2566 0.6179
0.2243 0.2974 0.5913
0.1437 0.2839 0.5773
0.1879 0.2905 0.5842
0.1072 0.3535 0.7192
0.2468 0.2984 0.5924
0.2789 0.3321 0.6818
0.1338 0.2566 0.6179
0.1898 0.2938 0.5876
0.2825 0.3009 0.595
0.119 0.3493 0.6799
0.2979 0.3015 0.5957
0.0209 0.3006 0.6045
0.2789 0.3321 0.6818
0.2921 0.3018 0.596
0.1123 0.3528 0.6179
0.1615 0.3563 0.7214
0.211 0.3494 0.7069
0.2574 0.3427 0.5921
0.2018 0.2953 0.6198
0.2227 0.2965 0.5903
0.2789 0.3321 0.6818
0.1743 0.3024 0.5847
0.2733 0.3005 0.5946
0.1342 0.3563 0.7205
0.255 0.2995 0.5935
0.1903 0.3022 0.6099
0.2584 0.3484 0.7047
0.0826 0.3555 0.7193
0.2773 0.3007 0.5948
0.2574 0.3427 0.5921
0.1039 0.2566 0.6179
0.1591 0.3574 0.7226
0.1979 0.3497 0.7056
0.2789 0.3321 0.6818
0.2392 0.2982 0.5921
0.2089 0.3472 0.5897
0.2437 0.296 0.5898
0.2614 0.3191 0.6353
0.2574 0.3427 0.5921
0.0046 0.2566 0.6179
0.2249 0.3486 0.706
0.1615 0.3563 0.7214
0.1256 0.2566 0.6179
0.0629 0.3167 0.6179
0.2937 0.3014 0.5956
0.2789 0.3321 0.6818
0.2563 0.2566 0.6179
0.099 0.3226 0.6179
0.0129 0.2774 0.6179
0.251 0.2975 0.5915
0.2503 0.3013 0.5936
0.0849 0.2566 0.6179
0.2725 0.3504 0.7086
0.2082 0.2944 0.5882
0.2435 0.2988 0.5928
0.2392 0.2987 0.5927
0.1892 0.293 0.5868
0.27 0.2983 0.5923
0.1175 0.3154 0.6179
0.0785 0.2566 0.6179
0.2789 0.3321 0.6818
0.2541 0.2994 0.5934

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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Gene identifier Rv1354c (Mycobacterium tuberculosis), Conserved hypothetical protein
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