TB Genome Annotation Portal

Rv0732 (secY)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: preprotein translocase subunit secY
  • REFSEQ: preprotein translocase subunit SecY
  • PATRIC: Preprotein translocase secY subunit (TC 3.A.5.1.1)
  • TUBERCULIST: Probable preprotein translocase SecY
  • NCBI: Probable preprotein translocase SecY
  • updated information (H37Rv4):
    • gene name: secY
    • function:
    • reference:
• Type: Not Target
• Start: 824800
• End: 826125
• Operon:


• Trans-membrane region:
  
• Role: III.D - Protein and peptide secretion
• GO terms:
  • GO:0052059 - evasion or tolerance by symbiont of host-produced reactive oxygen species (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0015031 - protein transport (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005576 - extracellular region (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):
  

  PDB	aa ident	species	PDB title
  6ITC	44%	Geobacillus thermodenitrificans (strain NG80-2)	Structure of a substrate engaged SecA-SecY protein translocation machine
  5EUL	44%	Geobacillus thermodenitrificans (strain NG80-2)	Structure of the SecA-SecY complex with a translocating polypeptide substrate
  6R7L	42%	Escherichia coli	Ribosome-bound SecYEG translocon in a nanodisc
  5MG3	42%	Escherichia coli	EM fitted model of bacterial holo-translocon
  5GAE	42%	Escherichia coli	RNC in complex with a translocating SecYEG
  5ABB	42%	ESCHERICHIA COLI	Visualization of a polytopic membrane protein during SecY-mediated membrane insertion
  4V6M	42%	Escherichia coli 536	Structure of the ribosome-SecYE complex in the membrane environment
  3J45	42%	Escherichia coli	Structure of a non-translocating SecY protein channel with the 70S ribosome
  5NCO	42%	Escherichia coli	Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome
  3J46	42%	Escherichia coli	Structure of the SecY protein translocation channel in action

• Links to additional information on secY:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -13.654 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VLSAFISSLRTVDLRRKILFTLGIVILYRVGAALPSPGVNFPNVQQCIKEASAGEAGQIYSLINLFSGGALLKLTVFAVGVMPYITASIIVQLLTVVIPR
FEELRKEGQAGQSKMTQYTRYLAIALAILQATSIVALAANGGLLQGCSLDIIADQSIFTLVVIVLVMTGGAALVMWMGELITERGIGNGMSLLIFVGIAA
RIPAEGQSILESRGGVVFTAVCAAALIIIVGVVFVEQGQRRIPVQYAKRMVGRRMYGGTSTYLPLKVNQAGVIPVIFASSLIYIPHLITQLIRSGSGVVG
NSWWDKFVGTYLSDPSNLVYIGIYFGLIIFFTYFYVSITFNPDERADEMKKFGGFIPGIRPGRPTADYLRYVLSRITLPGSIYLGVIAVLPNLFLQIGAG
GTVQNLPFGGTAVLIMIGVGLDTVKQIESQLMQRNYEGFLK

Additional Information

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)	1.52 (0.27)	1.79 (0.67)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link