The Helicobacter pylori genome: From sequence analysis to structural and functional predictions

Krzysztof Pawłowski, Baohong Zhang, Leszek Rychlewski, Adam Godzik

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

Abstract

Fold assignments for proteins from the Helicobacter pylori genome are carried out using BASIC, a profile-profile alignment algorithm recently tested on the Mycoplasma genitalium and Escherichia coli genomes. The fold assignments are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. Over 40% of the proteins encoded in the H. pylori genome can be recognized as belonging to a protein family with known structure. Previous estimates suggested that only 10-15% of genome proteins could be characterized this way. This dramatic increase in the number of recognized homologies between H. pylori proteins and structurally characterized protein families is partly due to the rapid increase of the database of known protein structures, but mostly it is due to the significant improvement in prediction algorithms. Knowledge of a protein fold adds a new dimension to our understanding of its function and, similarly, structure prediction can also add to understanding, verification, and/or prediction of function for uncharacterized proteins. Several examples analyzed in more detail in this article illustrate insights that can be achieved from structure and detailed function prediction.

Original languageEnglish (US)
Pages (from-to)20-30
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume36
Issue number1
DOIs
StatePublished - Jul 1 1999
Externally publishedYes

Keywords

  • Bacterial genomes
  • Fold assignment
  • Function prediction
  • Sequence profiles
  • Structure prediction

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Fingerprint Dive into the research topics of 'The Helicobacter pylori genome: From sequence analysis to structural and functional predictions'. Together they form a unique fingerprint.

Cite this