Rv2003c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: FIG147732: hypothetical protein Rv2003c/MT2059
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 2248563
End: 2249420
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0032259 - methylation (Uniprot)
- GO:0008168 - methyltransferase activity (Uniprot)
- GO:0008152 - metabolic process (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):

PDB	aa ident	species	PDB title
2GS9	38%	Thermus thermophilus	Crystal structure of TT1324 from Thermus thermophilis HB8
1VLM	36%	Thermotoga maritima	Crystal structure of SAM-dependent methyltransferase, possible histamine N-methyltransferase (TM1293) from Thermotoga maritima at 2.20 A resolution

Links to additional information on Rv2003c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.94 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VVKRSRATRLSPSIWSGWESPQCRSIRARLLLPRGRSRPPNADCCWNQLAVTPDTRMPASSAAGRDAAAYDAWYDSPTGRPILATEVAALRPLIEVFAQP
RLEIGVGTGRFADLLGVRFGLDPSRDALMFARRRGVLVANAVGEAVPFVSRHFGAVLMAFTLCFVTDPAAIFRETRRLLADGGGLVIGFLPRGTPWADLY
ALRAARGQPGYRDARFYTAAELEQLLADSGFRVIARRCTLHQPPGLARYDIEAAHDGIQAGAGFVAISAVDQAHEPKDDHPLESE

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.154400; 4 non-insertions in a row out of 13 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 13 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 13 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 14 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 14 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: 0.45
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:
- No bindings to other targets were found.

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0576 (-)
- Rv2884 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv3133c	shahanup86	IEP		coexpression(Functional Linkage) authors,J. Bacon,BW. James,L. Wernisch,A. Williams,KA. Morley,GJ. Hatch,JA. Mangan,J. Hinds,NG. Stoker,PD. Butcher,PD. Marsh The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2004
Citation	The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. authors,J. Bacon,BW. James,L. Wernisch,A. Williams,KA. Morley,GJ. Hatch,JA. Mangan,J. Hinds,NG. Stoker,PD. Butcher,PD. Marsh Tuberculosis (Edinb) 2004	shahanup86	IEP	15207490	coexpression(Functional Linkage)
Interaction	RegulatedBy Rv3133c	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. HD. Park, KM. Guinn et al. Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol. Microbiol. 2003

TB Genome Annotation Portal