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

Abstract

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.

Figure 1

True positive output example. PROFtmb prediction for OMPA from E.coli [PDB: 1g90 (5) chain A], a true TMB. Note that predicted strands have high contrast between state probabilities for a majority of their length.

Figure 2

False positive output example. Heme acquisition system protein A (HasA) from Serratia marcescens [PDB: 1B2V (6)], a secreted hemophore with architecture beta-alpha-beta (6)-alpha (2) according to SCOP (7). Predicted strands four, five and six show poor contrast in state probabilities and indicate a poor fit to the model.