Rv0086 (hycQ)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hydrogenase-4 component F
- REFSEQ: hydrogenase HycQ
- PATRIC: Hydrogenase-4 component F (EC 1.-.-.-)
- TUBERCULIST: Possible hydrogenase HycQ
- NCBI: Possible hydrogenase HycQ
- updated information (H37Rv4):
  - gene name: hycQ
  - function:
  - reference:
Type: Not Target
Start: 93951
End: 95417
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
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 hycQ:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.884 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTGLLLAAILAPLAASIASLITGWRRTTATLTALSATTVLACAVAMGFWMGSGAQFGLGGLLRADALTVVMLVVIGIVGTLATAASIGYIDTELAHGHID
GRSARLYGVLTPAFLCAMVLAVCANNIGVIWVAIEATTVITAFLVGHRRTRTALEATWKYVVICSVGIAVAFLGTVLLYFAARDSGAAAAGALNLDILAE
HAAGLDPGVARLAGGLLLIGYGAKAGLFPFHTWLADAHSQAPAPVSALMSGVLLAVAFSVLIRLRPILDAVSGPAYLRNGLLVVGLATLLVAVLMLTVTG
DVKRMLAYSSMEHMGLIAIAAAAGTTLAIAALLLHVLAHGIGKTVLFLAGGQLQAAHDSTAIADITGVMRRSRLIGVSFAVGLIVLLGLPPFAMFASELA
IARSLANERLAWVLGAALLLIAIGFTALARNSGRMLLGTPAAGAPAITVPATAAAALMVGIVVSAALGITAGPLADLLGIAASNVGLP

(Nucleotide sequence available on KEGG)

Additional Information

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 15 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 15 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 15 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 15 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 15 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.2
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1990c (-) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv2827c (-)
- Rv3133c (devR)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv0085	vmevada102	IGC		Operon(Functional Linkage) authors,M. Berney,GM. Cook Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS ONE 2010
Interaction	PhysicalInteraction Rv0085	vmevada102	IGC		Operon(Functional Linkage) authors,F. Veyrier,D. Pletzer,C. Turenne,MA. Behr Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis. BMC Evol. Biol. 2009
Citation	Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis. authors,F. Veyrier,D. Pletzer,C. Turenne,MA. Behr BMC Evol. Biol. 2009	vmevada102	IGC	19664275	Operon(Functional Linkage)
Interaction	PhysicalInteraction Rv0085	vmevada102	IGC		Operon(Functional Linkage) authors,F. Veyrier,D. Pletzer,C. Turenne,MA. Behr Phylogenetic detection of horizontal gene transfer during the step-wise genesis of Mycobacterium tuberculosis. BMC Evol. Biol. 2009

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