Rv3916c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: FIG007808: hypothetical protein
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Conditional
Start: 4404433
End: 4405167
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0051409 - response to nitrosative stress (Uniprot)
- GO:0005886 - plasma membrane (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 Rv3916c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -2.795 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VSARITALRLEAFEQLPKHARRCVFWEVDPAILGKDDHLADPEFEKEAWLSMVMLEWGSCGQVATAVPDERSHAEPPCLGYVLYAPPSAVPRAQRFPTAP
VSADAVLLTSMGIERGQADDDLPHSLIARVIEELVRRGVRALEAFGRTPAATDLQNPGAVTPDVRPVLEALGDCCVEHCIIDANFLMDVGFVVVAPHPYF
PRLRLELDKGLGWKAEVEAALERLLENARLQEPIAAGSTAGNTS

(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: 0.921300; 8 non-insertions in a row out of 11 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.998750; 10 non-insertions in a row out of 11 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000400; 3 non-insertions in a row out of 11 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.162150; 5 non-insertions in a row out of 12 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999950; 12 non-insertions in a row out of 12 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: 1.4
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: Rv3916c_day0_rep1.wig, Rv3916c_day0_rep2.wig
reference datasets: H37Rv_day0_rep1.wig, H37Rv_day0_rep2.wig
resampling results: resampling_H37Rv_Rv3916c_day0_s10000_pc0.00.xlsx (conditionally essential genes are marked in yellow, with Padj<0.05)

RNASeq Data No data currently available.

collected by: Shoko Wakabayashi (Rubin lab) 2019
counts/RPKMs: RNAseq_Rv3916c_KO-1.expr, RNAseq_Rv3916c_KO-2.expr, RNAseq_Rv3916c_KO-3.expr
reference datasets: RNAseq_H37Rv_WT-1.expr, RNAseq_H37Rv_WT-2.expr, RNAseq_H37Rv_WT-3.expr
DeSeq analysis: DESeq_Rv3916c_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:
- 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:
- Rv0047c (-) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv3133c (devR) (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.

TB Genome Annotation Portal