TB Genome Annotation Portal

Rv1620c (cydC)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: thiol reductant ABC exporter CydC subunit
  • REFSEQ: cytochrome' transport transmembrane ATP-binding protein ABC transporter CydC
  • PATRIC: Transport ATP-binding protein CydC
  • TUBERCULIST: Probable 'component linked with the assembly of cytochrome' transport transmembrane ATP-binding protein ABC transporter CydC
  • NCBI: Probable 'component linked with the assembly of cytochrome' transport transmembrane ATP-binding protein ABC transporter CydC
  • updated information (H37Rv4):
    • gene name: cydC
    • function:
    • reference:
• Type: Not Target
• Start: 1819963
• End: 1821693
• Operon:


• Trans-membrane region:
  
• Role: I.B.6.c - Electron transport
• GO terms:
  • GO:0055085 - transmembrane transport (Uniprot)
  • GO:0045454 - cell redox homeostasis (Uniprot)
  • GO:0042626 - ATPase activity, coupled to transmembrane movement of substances (Uniprot)
  • GO:0034775 - glutathione transmembrane transport (Uniprot)
  • GO:0016887 - ATPase activity (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0000166 - nucleotide 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:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  6TEJ	38%	Mycolicibacterium thermoresistibile	Structure of apo IrtAB devoid SID in complex with sybody Syb_NL5
  5X41	36%	Rhodobacter capsulatus	3.5A resolution structure of a cobalt energy-coupling factor transporter using LCP method-CbiMQO
  5X3X	36%	Rhodobacter capsulatus	2.8A resolution structure of a cobalt energy-coupling factor transporter-CbiMQO
  5W81	35%	Danio rerio	Phosphorylated, ATP-bound structure of zebrafish cystic fibrosis transmembrane conductance regulator (CFTR)
  5UAR	35%	Danio rerio	Dephosphorylated, ATP-free cystic fibrosis transmembrane conductance regulator (CFTR) from zebrafish
  5X40	35%	Rhodobacter capsulatus	Structure of a CbiO dimer bound with AMPPCP

• Links to additional information on cydC:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.855 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MNRPSAVSRRQRDLLAASGLLGPRLPRILAAVALGVLSLGSALALAGVSAWLITRAWQMPPVLDLSVAVVAVRAFAISRGVLHYCERLATHDTALRAAGR
ARTLIYHRLAHGPAAAAVGLHSGDLAARVGADVDELANMLVRALVPIAVAAVLAVAATAVVAAVSVPAAVVLAVCLLVAGVVAPWLAGRTAAAQEAIARQ
HRGMRDTSAMIALEHAPELRVAGALRNVIADSQRRQHAWADALDAAARTGAIAEAMPTAAIGASLLGAVVAGIGMAPTVAPTTLAILMLLPLSAFEATVA
LPAAAVQLTRSRIAAARLLDLTGSNRVRETESTVSARLPVGTGVLAADVCCGHQEAQSIRVTIDLPPGARLAVTGASGAGKTTLLMTLAGLLPPVHGRVL
LDGTNLSDFDEDELRSAVSFFAEDAHIFATTVRDNLLTARGDCPDDELIEALDRVGLCGWLAGLPEGLSTVLIGGAQAVSAGQRRRLLLARAVLSPARIV
LLDEPVEHLDAANADLLRDLLAPNSGIMSAMRTVVVATHHLPNDIQCAELSIATDQRCRRRGTNSSDNNTNASAKT

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)	1.87 (0.31)	1.43 (0.63)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link