TB Genome Annotation Portal

Rv0490 (senX3)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: sensor-like histidine kinase senX3
  • REFSEQ: putative two component sensor histidine kinase SENX3
  • PATRIC: Phosphate regulon sensor protein PhoR (SphS) (EC 2.7.13.3); Sensor-like histidine kinase senX3 (EC 2.7.13.3)
  • TUBERCULIST: Putative two component sensor histidine kinase SenX3
  • NCBI: Putative two component sensor histidine kinase SenX3
  • updated information (H37Rv4):
    • gene name: senX3
    • function:
    • reference:
• Type: Not Target
• Start: 579349
• End: 580581
• Operon:


• Trans-membrane region:
  
• Role: I.J.2 - Two component systems
• GO terms:
  • GO:0046777 - protein autophosphorylation (Uniprot)
  • GO:0023014 - signal transduction by protein phosphorylation (Uniprot)
  • GO:0018106 - peptidyl-histidine phosphorylation (Uniprot)
  • GO:0016772 - transferase activity, transferring phosphorus-containing groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016310 - phosphorylation (Uniprot)
  • GO:0016301 - kinase activity (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0007165 - signal transduction (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005622 - intracellular (Uniprot)
  • GO:0005576 - extracellular region (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0004673 - protein histidine kinase activity (Uniprot)
  • GO:0000166 - nucleotide binding (Uniprot)
  • GO:0000160 - phosphorelay signal transduction system (Uniprot)
  • GO:0000155 - phosphorelay sensor kinase activity (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
  3SL2	44%	Bacillus subtilis	ATP Forms a Stable Complex with the Essential Histidine Kinase WalK (YycG) Domain
  6BLK	36%	Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)	Mycobacterial sensor histidine kinase MprB
  5C93	35%	Lactobacillus plantarum 16	Histidine kinase with ATP
  4ZKI	35%	Lactobacillus plantarum JDM1	The crystal structure of Histidine Kinase YycG with ADP
  4U7O	35%	Lactobacillus plantarum	Active histidine kinase bound with ATP
  4U7N	35%	Lactobacillus plantarum	Inactive structure of histidine kinase

• Links to additional information on senX3:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.984 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VTVFSALLLAGVLSALALAVGGAVGMRLTSRVVEQRQRVATEWSGITVSQMLQCIVTLMPLGAAVVDTHRDVVYLNERAKELGLVRDRQLDDQAWRAARQ
ALGGEDVEFDLSPRKRSATGRSGLSVHGHARLLSEEDRRFAVVFVHDQSDYARMEAARRDFVANVSHELKTPVGAMALLAEALLASADDSETVRRFAEKV
LIEANRLGDMVAELIELSRLQGAERLPNMTDVDVDTIVSEAISRHKVAADNADIEVRTDAPSNLRVLGDQTLLVTALANLVSNAIAYSPRGSLVSISRRR
RGANIEIAVTDRGIGIAPEDQERVFERFFRGDKARSRATGGSGLGLAIVKHVAANHDGTIRVWSKPGTGSTFTLALPALIEAYHDDERPEQAREPELRSN
RSQREEELSR

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)	1.71 (0.33)	1.07 (0.39)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link