TB Genome Annotation Portal

Rv1821 (secA2)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: protein translocase subunit secA 2
  • REFSEQ: preprotein translocase subunit SecA
  • PATRIC: Protein export cytoplasm protein SecA ATPase RNA helicase (TC 3.A.5.1.1)
  • TUBERCULIST: Possible preprotein translocase ATPase SecA2
  • NCBI: Possible preprotein translocase ATPase SecA2
  • updated information (H37Rv4):
    • gene name: secA2
    • function:
    • reference:
• Type: Not Target
• Start: 2066457
• End: 2068883
• Operon:


• Trans-membrane region:
  
• Role: III.D - Protein and peptide secretion
• GO terms:
  • GO:0052553 - modulation by symbiont of host immune response (Uniprot)
  • GO:0052059 - evasion or tolerance by symbiont of host-produced reactive oxygen species (Uniprot)
  • GO:0044119 - growth of symbiont in host cell (Uniprot)
  • GO:0043952 - protein transport by the Sec complex (Uniprot)
  • GO:0031522 - cell envelope Sec protein transport complex (Uniprot)
  • GO:0017038 - protein import (Uniprot)
  • GO:0016887 - ATPase activity (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0015462 - ATPase-coupled protein transmembrane transporter activity (Uniprot)
  • GO:0015031 - protein transport (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0006886 - intracellular protein transport (Uniprot)
  • GO:0006605 - protein targeting (Uniprot)
  • GO:0005887 - integral component of plasma membrane (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0000166 - nucleotide binding (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
  4UAQ	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of the accessory translocation ATPase, SecA2, from Mycobacterium tuberculosis
  5K9T	40%	Escherichia coli (strain 55989 / EAEC)	SecA-N68, a C-terminal truncation of the SecA ATPase from E. coli
  5K94	38%	Escherichia coli O157:H7	Deletion-Insertion Chimera of MBP with the Preprotein Cross-Linking Domain of the SecA ATPase
  6ITC	37%	Bacillus subtilis (strain 168)	Structure of a substrate engaged SecA-SecY protein translocation machine
  3JV2	37%	Bacillus subtilis	Crystal Structure of B. subtilis SecA with bound peptide
  3DL8	37%	Bacillus subtilis	Structure of the complex of aquifex aeolicus SecYEG and bacillus subtilis SecA
  2IBM	37%	Bacillus subtilis	A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA
  1TF5	37%	Bacillus subtilis	Crystal structure of SecA in an open conformation from Bacillus Subtilis
  1TF2	37%	Bacillus subtilis	Crystal structure of SecA:ADP in an open conformation from Bacillus Subtilis
  1M74	37%	Bacillus subtilis	Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis

• Links to additional information on secA2:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.971 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VNVHGCPRIAACRCTDTHPRGRPAFAYRWFVPKTTRAQPGRLSSRFWRLLGASTEKNRSRSLADVTASAEYDKEAADLSDEKLRKAAGLLNLDDLAESAD
IPQFLAIAREAAERRTGLRPFDVQLLGALRMLAGDVIEMATGEGKTLAGAIAAAGYALAGRHVHVVTINDYLARRDAEWMGPLLDAMGLTVGWITADSTP
DERRTAYDRDVTYASVNEIGFDVLRDQLVTDVNDLVSPNPDVALIDEADSVLVDEALVPLVLAGTTHRETPRLEIIRLVAELVGDKDADEYFATDSDNRN
VHLTEHGARKVEKALGGIDLYSEEHVGTTLTEVNVALHAHVLLQRDVHYIVRDDAVHLINASRGRIAQLQRWPDGLQAAVEAKEGIETTETGEVLDTITV
QALINRYATVCGMTGTALAAGEQLRQFYQLGVSPIPPNKPNIREDEADRVYITTAAKNDGIVEHITEVHQRGQPVLVGTRDVAESEELHERLVRRGVPAV
VLNAKNDAEEARVIAEAGKYGAVTVSTQMAGRGTDIRLGGSDEADHDRVAELGGLHVVGTGRHHTERLDNQLRGRAGRQGDPGSSVFFSSWEDDVVAANL
DHNKLPMATDENGRIVSPRTGSLLDHAQRVAEGRLLDVHANTWRYNQLIAQQRAIIVERRNTLLRTVTAREELAELAPKRYEELSDKVSEERLETICRQI
MLYHLDRGWADHLAYLADIRESIHLRALGRQNPLDEFHRMAVDAFASLAADAIEAAQQTFETANVLDHEPGLDLSKLARPTSTWTYMVNDNPLSDDTLSA
LSLPGVFR

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)	2.08 (0.48)	1.2 (0.59)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link