TB Genome Annotation Portal

Rv0735 (sigL)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: sigma-70 family RNA polymerase sigma factor
  • REFSEQ: RNA polymerase sigma factor SigL
  • PATRIC: RNA polymerase sigma-70 factor
  • TUBERCULIST: Probable alternative RNA polymerase sigma factor SigL
  • NCBI: Probable alternative RNA polymerase sigma factor SigL
  • updated information (H37Rv4):
    • gene name: sigL
    • function:
    • reference:
• Type: Not Target
• Start: 827543
• End: 828076
• Operon:


• Trans-membrane region:
  
• Role: II.A.7 - RNA synthesis, RNA modification and DNA transcription
• GO terms:
  • GO:2000142 - regulation of DNA-templated transcription, initiation (Uniprot)
  • GO:0016987 - bacterial sigma factor activity (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0006352 - DNA-templated transcription, initiation (Uniprot)
  • GO:0006351 - transcription, DNA-templated (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003700 - DNA binding transcription factor activity (Uniprot)
  • GO:0003677 - DNA 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: 3hug
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  6TYG	99%	Mycobacterium tuberculosis	Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer
  6TYF	99%	Mycobacterium tuberculosis	Crystal structure of MTB sigma L transcription initiation complex with 6 nt long RNA primer
  6TYE	99%	Mycobacterium tuberculosis	Crystal structure of MTB sigma L transcription initiation complex with 5 nt long RNA primer
  6DVE	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF selenomethionine-labelled sigma factor L) with 6 nt spacer
  6DVD	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) with 6 nt spacer and bromine labelled in position "-11
  6DVC	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 6nt spacer
  6DVB	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer
  6DV9	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 4nt spacer
  3HUG	97%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis anti-sigma factor RslA in complex with -35 promoter binding domain of sigL
  5XE7	49%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigJ

• Links to additional information on sigL:
  • 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 = 0.389 (from Jeremy Rock's lab)

Amino Acid Sequence

VARVSGAAAAEAALMRALYDEHAAVLWRYALRLTGDAAQAEDVVQETLLRAWQHPEVIGDTARPARAWLFTVARNMIIDERRSARFRNVVGSTDQSGTPE
QSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR

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)	1.04 (0.12)	1.27 (0.52)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link