Table 4

Computational Tools used in Studies of Shewanella

Name

URL

Use

Limitations


LipoP

http://www.cbs.dtu.dk/services/LipoP/ webcite

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 webcite

prediction of Sec signal peptides that are cleaved by LspA

does not detect Tat substrates

SignalP

http://www.cbs.dtu.dk/services/SignalP/ webcite

prediction of Sec signal peptides that are cleaved by LepB

does not detect Tat substrates

Phobius

http://phobius.sbc.su.se/ webcite

prediction of alpha helices in inner membrane proteins, distinguishing N-terminal TM from signal peptides

TmHmm

http://www.cbs.dtu.dk/services/TMHMM/ webcite

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 webcite

prediction of beta barrel spans in outer membrane proteins

Cello

http://cello.life.nctu.edu.tw/ webcite

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 webcite

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/ webcite

prediction of localization (Cyt, Peri, Extra)

not appropriate for membrane bound proteins

PsortB

http://www.psort.org/psortb/index.html webcite

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/ webcite

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

Romine BMC Genomics 2011 12(Suppl 1):S1   doi:10.1186/1471-2164-12-S1-S1

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