Welcome to the PROFtmb server

A prediction service for Bacterial Transmembrane Beta Barrels

Whole-Protein prediction.     This service predicts whole-protein class (TMB/non-TMB) by providing a length-based z-score for a given protein. When tested on a representative set of known TMB and non-TMB proteins, the method detected 50% of TMBs at 80% accuracy (z-score>=10) and 70% of TMBs at 35% accuracy (z-score >= 6)

Four-state Residue prediction.     Secondly, it provides a four state (up-strand, down-strand, periplasmic loop, and outer loop) per-residue prediction for the protein. On a jackknifed test set of 8 families of TMBs of known structure, our method predicted 87.2% of residues correctly.

Download Predictions.     In addition to obtaining new predictions, you may download 4-state per residue predictions for all proteins in 78 Gram-Negative bacterial genomes.

Please cite:
Predicting transmembrane beta-barrels in proteomes
Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B.
Nucleic Acids Res. 2004 May 11;32(8):2566-77

Note: PROFtmb provides both whole-protein (TMB/non-TMB) and per-residue (up-strand,downstrand,periplasmic loop,extracellular loop) predictions. However, if the whole-protein score is below 0 (a value corresponding to 55% coverage and 55% accuracy, PROFtmb does not provide a per-residue 4-state prediction, since it is expected to be inaccurate. There is in general no use for a per-residue prediction if the protein turns out not to be a TMB. About half of TMBs receive low scores and are thus undetectable by statistical means.