Skip to main content

Table 1 Proteins identified by LC-MS/MS analysis of tryptic fragments obtained after different treatments of intact E. faecalis V583.

From: Identification of surface proteins in Enterococcus faecalis V583

     Peptide hitsd  
Gene Pfama Gene productb Predicted localizationc Un-treated 1 hour Un-treated 2 hours Trypsin 1 hour Trypsin 2 hours Beads 1 hour Beads 2 hours Total cover-age%
EF_B0004e Bacterial extracellular solute-binding proteins, family 5 TraC protein Cell wall    2 2 (1) (1) 13.0
EF0071 Contains trehalase domain Putative lipoprotein Lipid anchor SP-II, VVS-CF    (3) 2    10.0
EF0123 Contains nine Clostridial hydro-phobic W domain Hypothetical protein Secreted SP-I, AYA-LE 5 2 9 7 (1) 4 23.2
EF0164   Putative lipoprotein Lipid anchor SP-II, FTS-CG 2 3 2 3   2 32.3
EF0176f Basic membrane protein Hypothetical protein Lipid anchor SP-II, LAA-CG    3 5   2 25.7
EF0177f Basic membrane protein Hypothetical protein Lipid anchor SP-II, LAA-CG    5 7 2   32.1
EF0195g   Phospho-glycerate mutase 1 Cytoplasmic    2 (1)    10.5
EF0199g   30S ribosomal protein S7 Cytoplasmic     2    30.1
EF0200g   Elongation factor G Cytoplasmic (1)   7 7    22.4
EF0201fg   Elongation factor Tu Cytoplasmic (1) 2 11 8 5 4 47.1
EF0205   30S ribosomal protein S10 Cytoplasmic    2    (1) 29.4
EF0206g   50S ribosomal protein L3 Cytoplasmic    2 5    23.4
EF0207g   50S ribosomal protein L4 Cytoplasmic    (1) 2    15.9
EF0211   50S ribosomal protein L22 Cytoplasmic (1) 2   2 (1) (1) 17.4
EF0218g   50S ribosomal protein L5 Cytoplasmic    (1) 3    21.2
EF0221g   50S ribosomal protein L6 Cytoplasmic    (1) 3    27.0
EF0223   50S ribosomal protein L18 Cytoplasmic    (1) 2    39.0
EF0226   50S ribosomal protein L15 Cytoplasmic (1) (2) 2 (1) (1) (1) 21.2
EF0228   Adenylate kinase Cytoplasmic    2 2    19.4
EF0234g   50S ribosomal protein L17 Cytoplasmic    2 (1)    26.0
EF0304 - Putative lipoprotein Lipid anchor SP-II, LSA-CS    (1) 2   2 20.5
EF0394 Cysteine-rich secretory protein family Secreted antigen, putative Secreted SP-I, ALA-DN 2     3 (1) 17.8
EF0417 - Hypothetical protein Secreted SP-I, VNA-LN 3 2 4 4   3 11.2
EF0502 - Hypothetical protein Multiple transmembrane proteins       2 7.9
EF0633   tyrosyl-tRNA synthetase Cytoplasmic     2    6.9
EF0685f   Rotamase family protein Lipid anchor SP-II, LAA-CS     2    10.8
EF0737   Amidase N-terminal anchor     2    6.8
EF0907f - Peptide ABC transporter peptide-binding protein Lipid anchor SP-II, LAA-CG     2    16.4
EF0916   50S ribosomal protein L20 Cytoplasmic (1) (1) 2     27.7
EF0970e   50S ribosomal protein L27 Cytoplasmic    2 2    34.7
EF0991   Penicillin-binding protein C N-terminal anchor    (1) 2    11.2
EF1033   Lipoamidase Cell wall anchored LPxTG SP-I, AQE-SI    2 2    4.7
EF1046g   Pyruvate kinase Cytoplasmic (2)   (2) 2    11.6
EF1167g   Fructose-bisphosphate aldolase Cytoplasmic (1) (2) 2 4 3 (1) 30.8
EF1264f   Sulfatase domain-containing protein Multiple trans-membrane proteins 2   10 11 (1) 5 29.8
EF1308fg   Dnak protein Cytoplasmic (1)   2 3    23.7
EF1319 - Hypothetical protein N-terminal anchor    (1) 3    23.3
EF1379   Alanyl-tRNA synthetase Cytoplasmic      2   3.3
EF1420 - Hypothetical protein Lipid anchor SP-II, MTA-CS    2 (1)    15.6
EF1523e - Hypothetical protein Cytoplasmic    (1) 3    6.4
EF1613fg   Formate acetyltransferase Cytoplasmic    3 (2)    13.4
EF1818f   Coccolysin Secreted SP-I, VAA-EE 8 3 8 5 (1) 2 45.1
EF1898   50S ribosomal protein L19 Cytoplasmic    (1) 2    30.4
EF1961fg   Enolase Cytoplasmic    2 4 (1)   25.7
EF1964fg   Glycer-aldehyde-3-phosphate dehydrogenase (GAPDH) Cytoplasmic    3 8    36.0
EF2144 - Putative lipoprotein Lipid anchor SP-II LTA-CS (1) 2 (1) 2    22.4
EF2174 Glycosyl hydrolases family 25 Hypothetical protein Secreted SP-I, ASG-EE     3    4.5
EF2398g   30S ribosomal protein S2 Cytoplasmic (1)   2 4 2 (1) 19.2
EF2556f   Fumarate reductase flavoprotein subunit Lipid anchor SP-II, ATG-CT 40 39 40 41 22 37 79.2
EF2718ge   50S ribosomal protein L1 Cytoplasmic    2 2    24.0
EF2746   DltD protein N-terminal anchor (1) 2 2 3 (1) 2 10.4
EF2860f   YkuD putative, peptido-glycan binding domain Cell wall, SP-I VYF-QS, 2 6 5 9 (1) 7 36.3
EF2864 - Hypothetical protein Lipid anchor SP-II, LTA-CR 2 2 3 4 2 2 25.7
EF2925g   Cold-shock domain-contain protein Cytoplasmic (1) 2    (1) 2 45.5
EF3041f   Pheromone binding protein Lipid anchor SP-II, LAA-CG 2 3 2 7   2 24.3
EF3256f   Pheromone cAD1 precursor lipoprotein Lipid anchor SP-II, LAA-CG    (1) 2    19.4
EFA0003   TraC protein Lipid anchor SP-II, LGA-CN     2    9.4
  1. Further details on the Sequest-based protein identification process are provided in the Materials and Methods section and in Table S5 (Additional file 4).
  2. aSignificant hits (or absence thereof, indicated by -) obtained after searches in Pfam [25] for putative and hypothetical proteins.
  3. bAll data extracted from the LocateP database [12] with two exceptions: EF1033 (annotated as 6-aminohexanoate-cyclic-dimer hydrolase; annotated as putative, in LocateP) and EF2860 annotated as ErfK/YbiS/YcfS/YnhG family protein; annotated as putative, in LocateP).
  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. dThe column shows the number of peptide hits from four biological replicates. Protein identifications were considered significant using the criteria described in Materials and Methods. One criterium was the detection of at least two different peptides; another the detection of peptides in at least two independent parallels; these criteria are met for all listed proteins. Putative, non-significant additional identifications of these proteins (based on just one peptide and/or on just one parallel) are indicated in parentheses.
  6. eSecretomeP value >0.5; this means that the protein is predicted to be secreted via a "non-classical" pathway.
  7. fProteins that have been identified as being localised on the surface in a previous study of E. faecelis JH2-2 [13].
  8. gCytoplasmic proteins that have been identified in other studies of the surface proteomes of Gram-positive bacteria. See text for references.