Table 4 Computational Tools used in Studies of Shewanella
From: Genome-wide protein localization prediction strategies for gram negative bacteria
Name | URL | Use | Limitations |
|---|---|---|---|
LipoP | primarily prediction of Sec signal peptides that are cleaved by LspA but also provides prediction of inner membrane or cytoplasmic localization as well as LepB cleavage | does not detect Tat substrates | |
Lipo | prediction of Sec signal peptides that are cleaved by LspA | does not detect Tat substrates | |
SignalP | prediction of Sec signal peptides that are cleaved by LepB | does not detect Tat substrates | |
Phobius | prediction of alpha helices in inner membrane proteins, distinguishing N-terminal TM from signal peptides | Â | |
TmHmm | prediction of alpha helices in inner membrane proteins | Signal peptides are often erroneously counted as TM spans | |
Bomp | prediction of beta barrel spans in outer membrane proteins | Â | |
Cello | prediction of localization (Cyt, IM, Peri, OM, Extra) | does not predict lipoprotein location in OM or IM | |
Sosui-GramN | http://bp.nuap.nagoya-u.ac.jp/sosui/sosuigramn/sosuigramn_submit.html | prediction of localization (Cyt, IM, Peri, OM, Extra) in gram negatives only | does not predict lipoprotein location in OM or IM, no scores given |
Subloc | prediction of localization (Cyt, Peri, Extra) | not appropriate for membrane bound proteins | |
PsortB | prediction of localization (Cyt, IM, Peri, OM, Extra) | does not predict lipoprotein location in OM or IM, many proteins assigned | |
TatP | prediction of Tat and Sec signal peptides | does not detect lipoproteins that have Tat signal peptide; some very long signal peptides not detected | |
Tatfind | obtained from Dr. Pohlschroder 1 | Prediction of Tat signal peptides | does not require the presence of an adjacent LepB or LspA site or that it occurs at the protein N-terminus (though this can be advantageous when the start codon prediction is wrong) |