Rv0950c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Phage peptidoglycan binding endopeptidase
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Conditional
Start: 1060656
End: 1061654
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0009405 - pathogenesis (FLUTE) (FLUTE Assigned!)
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
5J1M	47%	Helicobacter pylori	Crystal structure of Csd1-Csd2 dimer II
5J1L	47%	Helicobacter pylori	Crystal structure of Csd1-Csd2 dimer I
6MUK	43%	Neisseria gonorrhoeae	1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae.
3SLU	43%	Neisseria meningitidis	Crystal structure of NMB0315
2GU1	41%	Vibrio cholerae	Crystal structure of a zinc containing peptidase from vibrio cholerae
4ZYB	40%	Staphylococcus aureus subsp. aureus NCTC 8325	High resolution structure of M23 peptidase LytM with substrate analogue
2B44	40%	Staphylococcus aureus	Truncated S. aureus LytM, P 32 2 1 crystal form
2B13	40%	Staphylococcus aureus	Truncated S. aureus LytM, P41 crystal form
2B0P	40%	Staphylococcus aureus	truncated S. aureus LytM, P212121 crystal form
1QWY	40%	Staphylococcus aureus subsp. aureus NCTC 8325	Latent LytM at 1.3 A resolution

Links to additional information on Rv0950c:
- KEGG - nucleotide and amino acid sequences of gene
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.12 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MAAIRTPRDRWPHHHRNEVTEIIPLDGFLDGLALYDELDFAELDDLDLGDDCVFDYEAQLLAAPELDDLDDADDLAPEWLVAPTVVLTPEVTPVSRRVGQ
HRKQPIGAARGRLLISAMAAGAAAAAAHTAIQQSETPRTETVLTAHASALNEGSGSNPPRGVQVIAAQPAASAAVHNAEFARGVAFAEERAEREARLQRP
LYVMPTKGIFTSSFGYRWGVLHAGIDLANAIGTPIYAVSDGVVIDAGPTAGYGMWVKLLHADGTVTLYGHVNTTLVSVGERVMAGDQIATMGSRGFSTGP
HLHFEVLLGGTERVDPVPWLAKRGLSVGNYTG

(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; 2 non-insertions in a row out of 21 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000050; 8 non-insertions in a row out of 21 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.002700; 5 non-insertions in a row out of 21 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.684450; 6 non-insertions in a row out of 21 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 21 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: 1.65
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data

collected by: Rebecca Audette/Hesper Rego (Rubin lab) (5/3/2016)
SRA accession: PRJNA377978
counts: TnSeq_Mtb_Rv0950ko.wig
reference: TnSeq_H37Rv_CB.wig
resampling:resampling_H37Rv_Rv0950_day0_s10000_pc0.00.xlsx

RNASeq Data No data currently available.

collected by: Shoko Wakabayashi (Rubin lab) 2019
counts/RPKMs: RNAseq_Rv0950c_KO-1.expr, RNAseq_Rv0950c_KO-2.expr, RNAseq_Rv0950c_KO-3.expr
reference datasets: RNAseq_H37Rv_WT-1.expr, RNAseq_H37Rv_WT-2.expr, RNAseq_H37Rv_WT-3.expr
DeSeq analysis: DESeq_Rv0950c_KO.txt (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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0324 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv1255c (-) (Direct binding)
- Rv3246c (mtrA) (Direct binding)
- Rv3416 (whiB3) (Direct binding)
- Rv3597c (lsr2) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3416 (whiB3)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Citation	The Mycobacterium bovis BCG cyclic AMP receptor-like protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676. G. Bai, MA. Gazdik et al. Infect. Immun. 2007	sourish10	IPI	17785469	ChIP (Physical interaction)
Interaction	Transcription Rv3676	sourish10	IPI		ChIP (Physical interaction) G. Bai, MA. Gazdik et al. The Mycobacterium bovis BCG cyclic AMP receptor-like protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676. Infect. Immun. 2007
Interaction	RegulatedBy Rv3676	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

TB Genome Annotation Portal