Rv1565c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: O-antigen acetylase
- TUBERCULIST: Conserved hypothetical membrane protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function: involved in adding mannose cap on LAM
  - reference: Driessen (2010) PMID: 20688818
Type: Essential
Start: 1771640
End: 1773829
Operon:

Trans-membrane region:
Role: II.C.5 - Other membrane proteins
GO terms:
- GO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0009103 - lipopolysaccharide biosynthetic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0009405 - pathogenesis (FLUTE) (FLUTE Assigned!)
- GO:0071468 - cellular response to acidic pH (FLUTE) (FLUTE Assigned!)
- GO:0009252 - peptidoglycan biosynthetic process (FLUTE) (FLUTE Assigned!Y2 report, Kieser 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 Rv1565c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -1.32 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MLTLSPPRPPALTPEPALPPVTMGTRTTGFYRHDLDGLRGVAIALVAVFHVWFGRVSGGVDVFLALSGFFFGGKILRAALNPDLSLSPIAEVIRLIRRLL
PALVVVLAGCALLTIAIQPQTRWEAFANQSLASLGYYQNWELASTVSNYLRAGEAVSPLQHIWSMSVQGQFYLAFLLLVAGCAYLLRRLFRGPRAPYLRT
MFVVLLSTLTLASFIYAIVAHHAYQATAYYNTFARAWELLAGALVGAVVPHVRWPMWLRTAVATAALAAILSCGALIDGVKEFPGPWALVPVGATMLMIL
AGANRQGHPGTRDRLPLPNRLLATAPLVALGAMAYSWYLWHWPLLIFWLSYTGHRHANFVEGAAVLLVSGLLAYLTTRLVEDPLRYRAPAGVRSPAAVPP
IPWRLRLRRPTIVLGSVVALLGVALTATSFTWREHVIVQRAAGKELSGLSSRDYPGARALIDHVRVPKLRMRPTVLEVRHDLPTSTKDGCISDFVNPAII
NCTYGDVDAPRTIALAGGSHAEHWLTALDLLGRMHHFKVVTYLKMGCPLSTEEVPLIMGNNAPYPQCHQWVQAAMAKLVADHPDYVFTTSTRPWNIKPGD
VMPATYVGIWQTFADNNIPVLAMRDTPWLVKDGQPFIPADCLAKGGNPQSCGIARSKVLVDRNPTLDFVARFPLLKPLDMSDAICRTDTCRAVEGNVLVY
RDSHHLTPTYMRTMTSELGRQIAANTDWW

(Nucleotide sequence available on KEGG)

Additional Information

involved in adding mannose cap on LAM
Driessen et al (2010). Microbiology. http://www.ncbi.nlm.nih.gov/pubmed/20688818
synthetic lethal in presence of imipenem (Lun..Bishai ,2014, Mbio) http://mbio.asm.org/content/5/5/e01767-14.full

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.81 (0.32)	1.59 (0.8)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

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

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv1565c/-, gene len: 2189 bp, num TA sites: 46

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	no data	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	uncertain	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.94)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=-0.278)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	YES (LFC=-3.64)	YM rich vs minimal medium	resampling

TnSeq Data

collected by: Subhalaxmi Nambi (Sassetti lab) c. 2015
insertion counts: Rv1565c_day0_rep1.wig, Rv1565c_day0_rep2.wig
reference datasets: H37Rv_day0_rep1.wig, H37Rv_day0_rep2.wig
resampling results: resampling_Rv1565c_vs_H37Rv_day0.xlsx (conditionally essential genes are marked in yellow, with Padj<0.05)
pathway analysis: resampling_Rv1565c_vs_H37Rv_day0.pathways-sanger-GSEA-p1.xlsx

RNASeq Data No data currently available.

collected by: Shoko Wakabayashi (Rubin lab) 2019
counts/RPKMs: RNAseq_Rv1565c_KO-1.expr, RNAseq_Rv1565c_KO-2.expr, RNAseq_Rv1565c_KO-3.expr
reference datasets: RNAseq_H37Rv_WT-1.expr, RNAseq_H37Rv_WT-2.expr, RNAseq_H37Rv_WT-3.expr
DeSeq analysis: DESeq_Rv1565c_KO.xlsx (differentially expressed genes, qval<0.05, marked in yellow)
BioProject accession: PRJNA511742

TB Genome Annotation Portal

Rv1565c (-)

Amino Acid Sequence

Additional Information

Analysis of Positive Selection in Clinical Isolates new

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

Interactions based on ChIPSeq data

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

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

TBCAP

Comments

TB Genome Annotation Portal

Rv1565c (-)

Amino Acid Sequence

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

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

Interactions based on ChIPSeq data

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

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

TBCAP

Comments

Analysis of Positive Selection in Clinical Isolates new