Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q

Proteins. 2004 May 1;55(2):464-73. doi: 10.1002/prot.20044.


The genome scale threading of five complete microbial genomes is revisited using our state-of-the-art threading algorithm, PROSPECTOR_Q. Considering that structure assignment to an ORF could be useful for predicting biochemical function as well as for analyzing pathways, it is important to assess the current status of genome scale threading. The fraction of ORFs to which we could assign protein structures with a reasonably good confidence level to each genome sequences is over 72%, which is significantly higher than earlier studies. Using the assigned structures, we have predicted the function of several ORFs through "single-function" template structures, obtained from an analysis of the relationship between protein fold and function. The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms*
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Computational Biology / methods*
  • Genome, Bacterial*
  • Genome, Fungal*
  • Molecular Sequence Data
  • Open Reading Frames
  • Protein Conformation
  • Protein Folding
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Software*
  • Structure-Activity Relationship


  • Bacterial Proteins
  • Saccharomyces cerevisiae Proteins