Rv3005c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Membrane protein 2 distant similarity to thiosulphate:quinone oxidoreductase DoxD
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: doxX
  - function: oxidative stress response
  - reference: Nambi (2015) PMID: 26067605
Type: Conditional
Start: 3363693
End: 3364532
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0045454 - cell redox homeostasis (FLUTE) (FLUTE Assigned!Y1 report, Nambi et al.)
- GO:1902693 - superoxide dismutase complex (FLUTE) (FLUTE Assigned!Y1 report, Nambi et al.)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020): (none with >35% aa id)
Links to additional information on Rv3005c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.088 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VTSSNDSHWQRPDDSPGPMPGRPVSASLVDPEDDLTPARYAGDFGSGTTTVIPPYDAASSGVGNSGYSLIEAAEPLPYVQPQPGRQVPAGSAGIDMDDDE
RVRAAGRRGTQNLGLLILRVGLGAVLIAHGLQKLFGWWDGQGLAGFQNSLSDIGYQHAEILAYVSAGGEIVAGVLLVLGLFTPLAAAGALAFLINGLLAG
ISAQHSRPVAYFLQDGHEYQITLVVMAVAVILSGPGRYGLDAARGWAHRPFIGSFVALLGGIAAGIAVWVLLNGANPLA

(Nucleotide sequence available on KEGG)

Additional Information

DoxX
Nambi et al (2015). The oxidative stress network of Mycobacterium tuberculosis reveals coordination between radical detoxification systems. Cell Host Microbe, 17(6):829-837.

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 21 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 21 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 21 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 21 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 21 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.81
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data

collected by Subhalaxmi Nambi (Sassetti lab, ca. 2013)
insertion counts: H37Rv_day0_rep1.wig, H37Rv_day0_rep2.wig
reference data: H37Rv_day32_rep1.wig , H37Rv_day32_rep2.wig , H37Rv_day32_rep3.wig
resampling results: resampling_H37Rv_Rv3005c_day32_s10000_pc0.00.xlsx (significant conditionally essential genes are those with Padj<0.05)
pathway analysis: resampling_H37Rv_Rv3005c_day32_s10000_pc0.00.pathways-sanger-GSEA-p1.xlsx

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0022c (whiB5)
- Rv3223c (sigH)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0691c (-) (Direct binding)
- Rv3597c (lsr2) (Direct binding)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0022c (whiB5)
- Rv3223c (sigH)

TB Genome Annotation Portal