Rv3660c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: helicase/secretion neighborhood CpaE-like protein
- REFSEQ: hypothetical protein
- PATRIC: Septum site-determining protein MinD @ possible CpaE
- TUBERCULIST: Conserved hypothetical protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: ssd
  - function: septum site-determining protein (cell division)
  - reference: England (2011) PMID: 21504606
Type: Not Target
Start: 4098096
End: 4099148
Operon:

Trans-membrane region:
Role: IV.E - Bacteriocin-like proteins
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0005829 - cytosol (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 Rv3660c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.526 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MLTDPGLRDELDRVAAAVGVRVVHLGGRHPVSRKTWSAAAAVVLDHAAADRCGRLALPRRTHVSVLTGTEAATATWAAAITVGAQHVLRMPEQEGELVRE
LAEAAESARDDGICGAVVAVIGGRGGAGASLFAVALAQAAADALLVDLDPWAGGIDLLVGGETAPGLRWPDLALQGGRLNWSAVRAALPRPRGISVLSGT
RRGYELDAGPVDAVIDAGRRGGVTVVCDLPRRLTDATQAALDAADLVVLVSPCDVRACAAAATMAPVLTAINPNLGLVVRGPSPGGLRAAEVADVAGVPL
LASMRAQPRLAEQLEHGGLRLRRRSVLASAARRVLGVLPRAGSGRHGRAA

(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: 0.903300; 7 non-insertions in a row out of 9 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.162950; 3 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.385700; 4 non-insertions in a row out of 9 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.161150; 3 non-insertions in a row out of 9 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.19
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

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:
- Rv0047c (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0135c (-) (Direct binding)
- Rv0576 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv0827c (kmtR) (Direct binding)
- Rv0967 (csoR) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1049 (-) (Direct binding)
- Rv1353c (-) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv2324 (-) (Direct binding)
- Rv2887 (-) (Direct binding)
- Rv3249c (-) (Direct binding)
- Rv3736 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0576 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv0491	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.. T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Name	Septum site determining protein	mjackson	ISS		Cell division
Symbol	ssd	mjackson	IMP		Cell division
Name	Septum site determining protein	mjackson	IMP		Cell division
Symbol	ssd	mjackson	ISS		Cell division
Symbol	Ssd	rslayden			dormancy response regulator authors,K. England,R. Crew,RA. Slayden Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response. BMC Microbiol. 2011
Name	Septum site determining protein, ssd	rslayden			dormancy response regulator authors,K. England,R. Crew,RA. Slayden Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response. BMC Microbiol. 2011
Citation	Mycobacterium tuberculosis septum site determining protein, Ssd encoded by rv3660c, promotes filamentation and elicits an alternative metabolic and dormancy stress response. authors,K. England,R. Crew,RA. Slayden BMC Microbiol. 2011	rslayden		21504606	dormancy response regulator
Symbol	Ssd	rslayden			dormancy response regulator RA. Slayden, DL. Knudson et al. Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis. Microbiology (Reading, Engl.) 2006
Name	Septum site determining protein, ssd	rslayden			dormancy response regulator RA. Slayden, DL. Knudson et al. Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis. Microbiology (Reading, Engl.) 2006
Citation	Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis. RA. Slayden, DL. Knudson et al. Microbiology (Reading, Engl.) 2006	rslayden		16735741	dormancy response regulator

TB Genome Annotation Portal