LocateP: Genome-scale subcellular-location predictor for bacterial proteins-1

By 2D gel electrophoresis) which have a putative SPI-cleavage site motif in the C-region that follows the transmembrane helix H-region (see Fig. 1B). A sequence composition chart, made using WebLogo [47], based on multiple-sequence alignment of the H- and C-regions (see Fig. 1B) of the N-anchored and secreted protein sets. The red arrow indicates the cleavage position of true SPI-site motifs (see Figure 1B), and the green dashed arrow represents the corresponding position in N-anchored proteins that is not cleaved. The specificity of HMMs of different lengths containing the putative cleavage site A* = the Alanine after which cleavage takes place. Mod1: residues -9 to A*; Mod2: residues -11 to A*; Mod3: residues -14 to A*; Mod4: residues -8 to +3 of A*; Mod5: residues -13 to +10 of A*; Mod6: residues -8 to +17 of A*; Mod7: residues -3 to +10 of A*; Mod8: residues -3 to +17 of A*; Mod9: residues +1 to +25.<p><b>Copyright information:</b></p><p>Taken from "LocateP: Genome-scale subcellular-location predictor for bacterial proteins"</p><p>http://www.biomedcentral.com/1471-2105/9/173</p><p>BMC Bioinformatics 2008;9():173-173.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2375117.</p><p></p

LocateP: Genome-scale subcellular-location predictor for bacterial proteins-2

by combining Tat-find v1.2 [91] and our Tat-specific HMMs (RR-HMM, CS-HMM). Bacteriocin-like proteins were identified using Bagel [149]. Secondly, Phobius [14], PrediSi [98], SignalP 3.0 [18] and TMHMM 2.0 [12] were combined to identify transmembrane regions. Those proteins without any predicted TM segments were considered intracellular, whereas those with TM segments were divided into multi-TM membrane proteins, N-anchored membrane proteins or secreted/released proteins (single N-terminal TM segment, possibly signal peptide), and C-anchored membrane proteins (signal peptide and single C-terminal TM segment). Thirdly, a sortase-substrate HMM [165] was used to distinguish LPxTG-type peptidoglycan-anchored proteins from C-anchored membrane proteins. Subsequently, signal peptidase type II (SPII) substrates were predicted by combining existing lipoprotein motif models [41, 157] and new lipoprotein HMMs. The remaining proteins were classified into the categories secreted/released or N-anchored membrane proteins. See Methods and additional file for more details. Abbreviation: A-S = Anchored-Secreted; TMS = TransMembrane Segment; SP = Signal Peptide; C/N-TM = C/N-terminally transmembrane anchored; LPxTG = LPxTG cell-wall anchored.<p><b>Copyright information:</b></p><p>Taken from "LocateP: Genome-scale subcellular-location predictor for bacterial proteins"</p><p>http://www.biomedcentral.com/1471-2105/9/173</p><p>BMC Bioinformatics 2008;9():173-173.</p><p>Published online 27 Mar 2008</p><p>PMCID:PMC2375117.</p><p></p