Rv3620c (esxW)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ESAT-6-like protein esxJ
- REFSEQ: putative ESAT-6 like protein ESXW (ESAT-6 like protein 10)
- PATRIC: ESAT-6-like protein EsxK
- TUBERCULIST: Putative ESAT-6 like protein EsxW (ESAT-6 like protein 10)
- NCBI: Putative ESAT-6 like protein EsxW (ESAT-6 like protein 10)
- updated information (H37Rv4):
  - gene name: esxW
  - function:
  - reference:
Type: Not Target
Start: 4060295
End: 4060591
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0005576 - extracellular region (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
4GZR	96%	Mycobacterium tuberculosis	Crystal structure of the Mycobacterium tuberculosis H37Rv EsxOP (Rv2346c-Rv2347c) complex in space group C2221
3OGI	96%	Mycobacterium tuberculosis	Crystal structure of the Mycobacterium tuberculosis H37Rv EsxOP complex (Rv2346c-Rv2347c)

Links to additional information on esxW:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.134 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTSRFMTDPHAMRDMAGRFEVHAQTVEDEARRMWASAQNISGAGWSGMAEATSLDTMTQMNQAFRNIVNMLHGVRDGLVRDANNYEQQEQASQQILSS

(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; 0 non-insertions in a row out of 3 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 3 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 3 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0324 (-) (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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) authors,B. Sidders,M. Withers,SL. Kendall,J. Bacon,SJ. Waddell,J. Hinds,P. Golby,F. Movahedzadeh,RA. Cox,R. Frita,AM. Ten Bokum,L. Wernisch,NG. Stoker Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biol. 2007
Citation	ESAT-6-like protein secretion in Bacillus anthracis. G. Garufi, E. Butler et al. J. Bacteriol. 2008	sourish10	ISO	18723613	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv3874	sourish10	ISO		Yeast two-hybrid (Physical interaction) G. Garufi, E. Butler et al. ESAT-6-like protein secretion in Bacillus anthracis. J. Bacteriol. 2008
Citation	ESAT-6-like protein secretion in Bacillus anthracis. G. Garufi, E. Butler et al. J. Bacteriol. 2008	ahal4789	ISO	18723613	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv3874	ahal4789	ISO		Yeast two-hybrid (Physical interaction) G. Garufi, E. Butler et al. ESAT-6-like protein secretion in Bacillus anthracis. J. Bacteriol. 2008
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) authors,UN. Wiesmann,S. DiDonato,NN. Herschkowitz Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. Biochem. Biophys. Res. Commun. 1975
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) authors,K. Moroi,T. Sato Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase. Biochem. Pharmacol. 1975
Interaction	Activation Rv3619c	shahanup86	IGC		Co-expression (Functional linkage) M. Marmiesse, P. Brodin et al. Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex. Microbiology (Reading, Engl.) 2004
Interaction	RegulatedBy Rv1221	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.. R. Manganelli, MI. Voskuil et al. The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol. Microbiol. 2001

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