TB Genome Annotation Portal

Rv1364c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: anti-anti-sigma factor
  • REFSEQ: hypothetical protein
  • PATRIC: Serine phosphatase RsbU regulator of sigma subunit
  • TUBERCULIST: Possible sigma factor regulatory protein
  • NCBI: Possible sigma factor regulatory protein
  • updated information (H37Rv4):
    • gene name: -
    • function:
    • reference:
• Type: Not Target
• Start: 1535683
• End: 1537644
• Operon:


• Trans-membrane region:
  
• Role: II.A.7 - RNA synthesis, RNA modification and DNA transcription
• GO terms:
  • GO:0042802 - identical protein binding (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0023014 - signal transduction by protein phosphorylation (Uniprot)
  • GO:0016791 - phosphatase activity (Uniprot)
  • GO:0016311 - dephosphorylation (Uniprot)
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0005622 - intracellular (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004035 - alkaline phosphatase activity (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0000287 - magnesium ion 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: 3k3d, 3kx0, 3ke6, 3k3c
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3KX0	100%	Mycobacterium tuberculosis	Crystal Structure of the PAS domain of Rv1364c
  3KE6	100%	Mycobacterium tuberculosis	The crystal structure of the RsbU and RsbW domains of Rv1364c from Mycobacterium tuberculosis
  3K3D	100%	Mycobacterium tuberculosis	The N-terminal PAS domain crystal structure of RV1364C from Mycobacterium Tuberculosis at 2.3 angstrom
  3K3C	100%	Mycobacterium tuberculosis	The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62

• Links to additional information on Rv1364c:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.865 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MAAEMDWDKTVGAAEDVRRIFEHIPAILVGLEGPDHRFVAVNAAYRGFSPLLDTVGQPAREVYPELEGQQIYEMLDRVYQTGEPQSGSEWRLQTDYDGSG
VEERYFDFVVTPRRRADGSIEGVQLIVDDVTSRVRARQAAEARVEELSERYRNVRDSATVMQQALLAASVPVVPGADIAAEYLVAAEDTAAGGDWFDALA
LGDRLVLVVGDVVGHGVEAAAVMSQLRTALRMQISAGYTVVEALEAVDRFHKQVPGSKSATMCVGSLDFTSGEFQYCTAGHPPPLLVTADASARYVEPTG
AGPLGSGTGFPVRSEVLNIGDAILFYTDGLIERPGRPLEASTAEFADLAASIASGSGGFVLDAPARPIDRLCSDTLELLLRSTGYNDDVTLLAMQRRAPT
PPLHITLDATINAARTVRAQLREWLAEIGADHSDIADIVHAISEFVENAVEHGYATDVSKGIVVAAALAGDGNVRASVIDRGQWKDHRDGARGRGRGLAM
AEALVSEARIMHGAGGTTATLTHRLSRPARFVTDTMVRRAAFQQTIDSEFVSLVESGRIVVRGDVDSTTAATLDRQIAVESRSGIAPVTIDLSAVTHLGS
AGVGALAAACDRARKQGTECVLVAPPGSPAHHVLSLVQLPVVGADTEDIFAQE

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	YES
omega peak height (95%CI lower bound)	1.93 (0.37)	3.02 (1.23)
codons under selection		62, 63, 64, 65, 66, 67, 68
omega plots
genetic variants*	link	link
statistics at each codon	link	link