TB Genome Annotation Portal

Rv3659c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: helicase/secretion neighborhood ATPase
  • REFSEQ: hypothetical protein
  • PATRIC: Flp pilus assembly protein ATPase CpaF
  • TUBERCULIST: Conserved hypothetical protein
  • NCBI: hypothetical protein
  • updated information (H37Rv4):
    • gene name: -
    • function:
    • reference:
• Type: Not Target
• Start: 4096936
• End: 4097994
• Operon:


• Trans-membrane region:
  
• Role: II.C.5 - Other membrane proteins
• GO terms:
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0000746 - conjugation (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
  5FL3	38%	THERMUS THERMOPHILUS	PilT2 from Thermus thermophilus
  6OLM	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	CryoEM structure of PilT4 from Geobacter metallireducens with added ATP: C6cccccc conformation
  6OLL	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	CryoEM structure of PilT4 from Geobacter metallireducens without adding nucleotide: C2oocooc conformation
  6OLK	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	CryoEM structure of PilT4 from Geobacter metallireducens without adding nucleotide: C3ocococ conformation
  6OKV	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	PilT4 from Geobacter metallireducens bound to AMP-PNP: C2ccocco conformation
  6OK2	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	PilT4 from Geobacter metallireducens bound to ADP: C3ocococ conformation
  6OJZ	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	PilT4 from Geobacter metallireducens bound to ADP with partial occupancy: C3ocococ conformation
  6OJY	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	Methylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ conformation
  6OJY	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	Methylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ conformation
  6OJY	37%	Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)	Methylated PilT4 from Geobacter metallireducens bound to sulfate: C3ocococ conformation

• Links to additional information on Rv3659c:
  • KEGG - nucleotide and amino acid sequences of gene
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.618 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MLGDTEVLANLRVLQTELTGAGILEPLLSADGTTDVLVTAPDSVWVDDGNGLRRSQIRFADESAVRRLAQRLALAAGRRLDDAQPWVDGQLTGIGVGGFA
VRLHAVLPPVATQGTCLSLRVLRPATQDLAALAAAGAIDPAAAALVADIVTARLAFLVCGGTGAGKTTLLAAMLGAVSPDERIVCVEDAAELAPRHPHLV
KLVARRANVEGIGEVTVRQLVRQALRMRPDRIVVGEVRGAEVVDLLAALNTGHEGGAGTVHANNPGEVPARMEALGALGGLDRAALHSQLAAAVQVLLHV
ARDRAGRRRLAEIAVLRQAEGRVQAVTVWHADRGMSDDAAALHDLLRSRASA

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)	1.46 (0.21)	2.3 (1.16)
codons under selection		317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330
omega plots
genetic variants*	link	link
statistics at each codon	link	link