PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.

TitlePROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins.
Publication TypeJournal Article
Year of Publication2006
AuthorsBigelow, H, Rost, B
JournalNucleic Acids Res
IssueWeb Server issue
Date Published2006 Jul 1
KeywordsBacterial Proteins, Genome, Bacterial, Gram-Negative Bacteria, Internet, Markov Chains, Membrane Proteins, Protein Structure, Secondary, Proteomics, Sequence Analysis, Protein, Software, User-Computer Interface

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. For each query protein, PROFtmb provides both a Z-value indicating that the protein actually contains a membrane barrel, and a four-state per-residue labeling of upward- and downward-facing strands, periplasmic hairpins and extracellular loops. While most users submit individual proteins known to contain TMBs, some groups submit entire proteomes to screen for potential TMBs. Response time is about 4 min for a 500-residue protein. PROFtmb is a profile-based Hidden Markov Model (HMM) with an architecture mirroring the structure of TMBs. The per-residue accuracy on the 8-fold cross-validated testing set is 86% while whole-protein discrimination accuracy was 70 at 60% coverage. The PROFtmb web server includes all source code, training data and whole-proteome predictions from 78 Gram-negative bacterial genomes and is available freely and without registration at

Alternate JournalNucleic Acids Res.
PubMed ID16844988
PubMed Central IDPMC1538807
Grant ListR01-LM07329-01 / LM / NLM NIH HHS / United States