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 
http://rostlab.org/services/proftmb.