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

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; 25 non-insertions in a row out of 46 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 44 non-insertions in a row out of 46 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 44 non-insertions in a row out of 46 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999800; 14 non-insertions in a row out of 46 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 44 non-insertions in a row out of 46 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

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

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:
- Rv2887 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv2887 (-) (Direct binding)
- Rv3249c (-) (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:
- Rv2887 (-)

TB Genome Annotation Portal