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Table 2 Additional proteins identified using the SDS-PAGE approach after different treatments.

From: Identification of surface proteins in Enterococcus faecalis V583

     Peptide hitsd  
Gene Pfama Gene productsb Predicted localizationc Untreated 2 hours Trypsin 2 hours Beads 2 hours Coverage%
EF0517f   2-dehydropantoate 2-reductase Cytoplasmic    2 13.1
EF0968f   50S ribosomal protein L21 Cytoplasmic    2 35.3
EF2221   ABC transporter. substrate-binding protein Lipid anchor SP-II, LSA-CG    2 8.8
EF2224 Four DUF11 repeats Cell wall surface anchor family protein Cell wall, LPxTG, SP-I, MNA-FA    2 1.4
EF2633f   Chaperonin. GroEL Cytoplasmic    4 9.2
EF2713 Gram positive anchor Cell wall surface anchor family protein Cell wall, LPxTG, SP-I VWA-ED   2   9.4
EF2715f   Ribosomal protein L7/L12 Cytoplasmic    2 29.5
EF2857e   Penicillin-binding protein 2B N-terminal anchor    3 4.8
EF2903e   ABC transporter, substrate-binding protein Lipid anchor SP-II, LGA-CG   6 2 20.2
EF3106e   Peptide ABC transporter. peptide-binding protein Lipid anchor SP-II, LAA-CG   2   3.4
EF3257   Pyridine nucleotide-disulfide family oxidoreductase Multiple transmembrane proteins   2   7.3
EFA0052   Surface exclusion protein Sea1 Cell wall LPxTG SP-1, VQA-AE 2 2 2 6.3
  1. The gel approach yielded 25 unique proteins in total but only 12 of these were novel compared to the list of Table 1; see Additional file 2 for more details. Further details on the Sequest-based protein identification process are provided in the Materials and Methods section and in Table S6 (Additional file 5).
  2. aSignificant hits obtained after searches in Pfam [25] for putative and hypothetical proteins.
  3. bData extracted from the LocateP database [12].
  4. cPredicted localization and potential cleavage site. Localization is based on LocateP annotations, with seven exceptions (for Tables 1 and 2 in total) that are all explicitly mentioned in the text. See also Table 3.
  5. dNumber of peptide hits in each of the three treatments. Protein identifications were considered significant using the criteria described in Materials and Methods. Proteins were only considered a significant hit if at least two unique peptides were found.
  6. e Proteins that have been identified as being localised on the surface in a previous study of E. faecelis JH2-2 [13].
  7. fCytoplasmic proteins that have been identified in other studies of the surface proteomes of Gram-positive bacteria. See text for references.