Table 4.
Computational Tools used in Studies of Shewanella
| Name | URL | Use | Limitations |
|---|---|---|---|
| LipoP | http://www.cbs.dtu.dk/services/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 | http://services.cbu.uib.no/tools/lipo | prediction of Sec signal peptides that are cleaved by LspA | does not detect Tat substrates |
| SignalP | http://www.cbs.dtu.dk/services/SignalP/ | prediction of Sec signal peptides that are cleaved by LepB | does not detect Tat substrates |
| Phobius | http://phobius.sbc.su.se/ | prediction of alpha helices in inner membrane proteins, distinguishing N-terminal TM from signal peptides | |
| TmHmm | http://www.cbs.dtu.dk/services/TMHMM/ | prediction of alpha helices in inner membrane proteins | Signal peptides are often erroneously counted as TM spans |
| Bomp | http://services.cbu.uib.no/tools/bomp | prediction of beta barrel spans in outer membrane proteins | |
| Cello | http://cello.life.nctu.edu.tw/ | 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 | http://www.bioinfo.tsinghua.edu.cn/SubLoc/ | prediction of localization (Cyt, Peri, Extra) | not appropriate for membrane bound proteins |
| PsortB | http://www.psort.org/psortb/index.html | prediction of localization (Cyt, IM, Peri, OM, Extra) | does not predict lipoprotein location in OM or IM, many proteins assigned |
| TatP | http://www.cbs.dtu.dk/services/TatP-1.0/ | 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) |
1 For correspondence. E-mail pohlschr@ sas.upenn.edu