Rv0338c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: oxidoreductase
- REFSEQ: iron-sulfur-binding reductase
- PATRIC: Iron-sulphur-binding reductase
- TUBERCULIST: Probable iron-sulfur-binding reductase
- NCBI: Probable iron-sulfur-binding reductase
- updated information (H37Rv4):
  - gene name: etfD
  - function: involved in beta-oxidataion of fatty acids (interacts with acyl-CoA dehydrogenase)
  - reference: Beites (2021) PMID: 34782606
Type: Essential
Start: 403193
End: 405841
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0051536 - iron-sulfur cluster binding (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005887 - integral component of plasma membrane (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (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 Rv0338c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -5.232 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VTTQTLIRLILGMSMTAVVGVFALRRVWWLYKLVMSGQPASGRTDNLGTRIWTQISEVLGQRRLLKWSIPGLAHFFTMWGFFILLTVYIEAYGLLFEERF
HIPVIGRWDALGFLQDFFATAVFLGITTFAIIRILRNPREIGRSSRFYGSHNGGAWLVLLMIFNVIWTYVLVRGSAVNNGTLPYGNGAFLSQLFGAILRP
LGQPANEIIETTALLLHIGVMLAFLILVLHSKHLHIFLAPINVTFKRLPDGLGPLLPLEADGKPIDFENPSEDAVFGRGKIEDFTWKGMLDFATCTECGR
CQSQCPAWNTGKPLSPKLVIMDLRDHWMAKAPYILGQKDASAGGEAGHQEHHHVPESGFGRVPGHGPEQATRPLVGTEEQGGVIDPDVLWSCVTCGACVE
QCPVDIEHVDHIVDMRRYQVMMESEFPSELSVLFKNLETKGNPWGQNASDRTNWIDEVDFDVPVYGQDVDSFDGYEYLFWVGCAGAYDDKAKKTTKAVAE
LLAVARVKYLVLGAGETCNGDSARRSGNEFLFQQLAQQAVETLDGLFEGVETVDRKIVVTCPHCFNTIGKEYRQLGANYTVLHHTQLLNRLVRDKRLVPV
TPVSQDITYHDPCYLGRHNKAYEAPRELIGAAGASLTEMPRHADRSFCCGAGGARMWMEEHIGKRINHERVDEALATDATAIATACPFCRVMVTDGVNDR
QEEAGRSGVEVLDVAQVLLGSLDHDKAQLPAKGTAAKQAQERAPKAAPKAAAPVTPVEAPAEAPQAPAPAAPAAPVKGLGMAAGAKRPGAKKAAPTPAAP
AAPAAPVKGLGIAAGAKRPGAKKTPPPAPGLAEPAAQPQPEAKPQPEPAAPPKPQTDGDPAAPAAPVKGLGIARGARPPGKR

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 37 non-insertions in a row out of 37 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 36 non-insertions in a row out of 37 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 36 non-insertions in a row out of 37 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 36 non-insertions in a row out of 37 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 36 non-insertions in a row out of 37 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.03
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:
- Rv0576 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0678 (-) (Direct binding)
- Rv1674c (-) (Direct binding)
- Rv1776c (-) (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:
- Rv0576 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv2711	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv2711	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.. GM. Rodriguez, MI. Voskuil et al. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002

TB Genome Annotation Portal