TB Genome Annotation Portal

Rv1622c (cydB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: cytochrome d ubiquinol oxidase subunit II
  • REFSEQ: integral membrane cytochrome D ubiquinol oxidase (subunit II) cydB (cytochrome bd-I oxidase subunit II)
  • PATRIC: Cytochrome d ubiquinol oxidase subunit II (EC 1.10.3.-)
  • TUBERCULIST: Probable integral membrane cytochrome D ubiquinol oxidase (subunit II) CydB (cytochrome BD-I oxidase subunit II)
  • NCBI: Probable integral membrane cytochrome D ubiquinol oxidase (subunit II) CydB (cytochrome BD-I oxidase subunit II)
  • updated information (H37Rv4):
    • gene name: cydB
    • function:
    • reference:
• Type: Not Target
• Start: 1823360
• End: 1824400
• Operon:


• Trans-membrane region:
  
• Role: I.B.6.c - Electron transport
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • 0.5 O2[c] + 2 HEME_FE2[c] -> 2 H[c] + 2 HEME_FE3[c]
• 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): (none with >35% aa id)
• Links to additional information on cydB:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -2.688 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VVLQELWFGVIAALFLGFFILEGFDFGVGMLMAPFAHVGMGDPETHRRTALNTIGPVWDGNEVWLITAGAAIFAAFPGWYATVFSALYLPLLAILFGMIL
RAVAIEWRGKIDDPKWRTGADFGIAAGSWLPALLWGVAFAILVRGLPVDANGHVALSIPDVLNAYTLLGGLATAGLFSLYGAVFIALKTSGPIRDDAYRF
AVWLSLPVAGLVAGFGLWTQLAYGKDWTWLVLAVAGCAQAAATVLVWRRVSDGWAFMCTLIVVAAVVVLLFGALYPNLVPSTLNPQWSLTIHNASSTPYT
LKIMTWVTAFFAPLTVAYQTWTYWVFRQRISAERIPPPTGLARRAP

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)	1.41 (0.12)	1.16 (0.4)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link