TB Genome Annotation Portal

Rv0844c (narL)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: two-component system NarL family nitrate/nitrite response regulator NarL
  • REFSEQ: nitrate/nitrite response transcriptional regulatory protein NarL
  • PATRIC: DNA-binding response regulator LuxR family
  • TUBERCULIST: Possible nitrate/nitrite response transcriptional regulatory protein NarL
  • NCBI: Possible nitrate/nitrite response transcriptional regulatory protein NarL
  • updated information (H37Rv4):
    • gene name: narL
    • function:
    • reference:
• Type: Not Target
• Start: 940456
• End: 941106
• Operon:


• Trans-membrane region:
  
• Role: I.J.2 - Two component systems
• GO terms:
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0006351 - transcription, DNA-templated (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0003677 - DNA binding (Uniprot)
  • GO:0000160 - phosphorelay signal transduction system (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: 3eul
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3EUL	100%	Mycobacterium tuberculosis	Structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis
  4WSZ	45%	None	Crystal structure of the DNA binding domains of wild type LiaR from E. faecalis
  4WUL	43%	None	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 26bp DNA
  4WUH	43%	Enterococcus faecalis S613	Crystal structure of E. faecalis DNA binding domain LiaR wild type complexed with 22bp DNA
  4WU4	43%	None	Crystal structure of E. faecalis DNA binding domain LiaRD191N complexed with 22bp DNA
  4WT0	43%	None	Crystal structure of the DNA binding domains of LiaRD191N from E. faecalis
  3CLO	41%	Bacteroides thetaiotaomicron VPI-5482	Crystal structure of putative transcriptional regulator containing a LuxR DNA binding domain (NP_811094.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.04 A resolution
  2RNJ	37%	Staphylococcus aureus	NMR Structure of The S. Aureus VraR DNA Binding Domain
  1FSE	37%	Bacillus subtilis	CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS REGULATORY PROTEIN GERE
  4YN8	36%	Corynebacterium diphtheriae	Crystal Structure of Response Regulator ChrA in Heme-Sensing Two Component System

• Links to additional information on narL:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.986 (from Jeremy Rock's lab)

Amino Acid Sequence

MSNPQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQA
LQQGAAGFLLKDSTRTEIVKAVLDCAKGRDVVAPSLVGGLAGEIRQRAAPVAPVLSAREREVLNRIACGQSIPAIAAELYVAPSTVKTHVQRLYEKLGVS
DRAAAVAEAMRQRLLD

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)	1.38 (0.29)	1.83 (0.74)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link