TB Genome Annotation Portal

Rv2916c (ffh)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: signal recognition particle protein
  • REFSEQ: signal recognition particle protein
  • PATRIC: Signal recognition particle subunit Ffh SRP54 (TC 3.A.5.1.1)
  • TUBERCULIST: Probable signal recognition particle protein Ffh (fifty-four homolog) (SRP protein)
  • NCBI: Probable signal recognition particle protein Ffh (fifty-four homolog) (SRP protein)
  • updated information (H37Rv4):
    • gene name: ffh
    • function:
    • reference:
• Type: Not Target
• Start: 3224708
• End: 3226285
• Operon:


• Trans-membrane region:
  
• Role: III.D - Protein and peptide secretion
• GO terms:
  • GO:0048500 - signal recognition particle (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0030529 - not-found (Uniprot)
  • GO:0008312 - 7S RNA binding (Uniprot)
  • GO:0006614 - SRP-dependent cotranslational protein targeting to membrane (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005525 - GTP binding (Uniprot)
  • GO:0003924 - GTPase activity (Uniprot)
  • GO:0003723 - RNA 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
  4UE4	56%	BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168	Structural basis for targeting and elongation arrest of Bacillus signal recognition particle
  1RJ9	52%	Thermus aquaticus	Structure of the heterodimer of the conserved GTPase domains of the Signal Recognition Particle (Ffh) and Its Receptor (FtsY)
  2J46	52%	THERMUS AQUATICUS	Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
  2J45	52%	THERMUS AQUATICUS	Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
  2C04	52%	THERMUS AQUATICUS	GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
  2C03	52%	THERMUS AQUATICUS	GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN
  1O87	52%	THERMUS AQUATICUS	A new MgGDP complex of the Ffh NG domain
  3ZN8	52%	ESCHERICHIA COLI	Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex
  1RY1	52%	Canis lupus familiaris	Structure of the signal recognition particle interacting with the elongation-arrested ribosome
  1JPN	52%	Thermus aquaticus	GMPPNP Complex of SRP GTPase NG Domain

• Links to additional information on ffh:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -10.202 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VFESLSDRLTAALQGLRGKGRLTDADIDATTREIRLALLEADVSLPVVRAFIHRIKERARGAEVSSALNPAQQVVKIVNEELISILGGETRELAFAKTPP
TVVMLAGLQGSGKTTLAGKLAARLRGQGHTPLLVACDLQRPAAVNQLQVVGERAGVPVFAPHPGASPESGPGDPVAVAAAGLAEARAKHFDVVIVDTAGR
LGIDEELMAQAAAIRDAINPDEVLFVLDAMIGQDAVTTAAAFGEGVGFTGVALTKLDGDARGGAALSVREVTGVPILFASTGEKLEDFDVFHPDRMASRI
LGMGDVLSLIEQAEQVFDAQQAEEAAAKIGAGELTLEDFLEQMLAVRKMGPIGNLLGMLPGAAQMKDALAEVDDKQLDRVQAIIRGMTPQERADPKIINA
SRRLRIANGSGVTVSEVNQLVERFFEARKMMSSMLGGMGIPGIGRKSATRKSKGAKGKSGKKSKKGTRGPTPPKVKSPFGVPGMPGLAGLPGGLPDLSQM
PKGLDELPPGLADFDLSKLKFPGKK

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)	1.63 (0.17)	1.38 (0.53)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link