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Table 1 Identified proteins of E. faecalis V583 whose abundance is affected by the presence of 1% bovine bile—the three columns to the right show the results for cells harvested at three different time points (20, 60 and 120 minutes)

From: Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile

Spot no. Functional class a Putative function a ORF Mass (kDa) pI b Coverage c No. of peptides matched Fold ratio d
T(20) T(60) T(120)
1 e Fatty acid and phospholipid metabolsim Enoyl-(acyl carrier protein) reductase EF0282 26.9 5.29 42 14 1.01 0.67 0.3
2 e   Acetyl_coA carboxylase, biotin carboxyl carrier protein EF2879 17.6 4.23 40 8 0.92 0.39 0.28
3 e   (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase EF0284 16.4 5.73 22 5 1.09 0.71 0.49
4 e   3-oxoacyl-(acyl-carrier-protein) synthase II EF0283 43.5 5.11 40 12 0.51 0.87 0.41
5 e   3-ketoacyl-(acyl-carrier-protein) reductase EF2881 26.1 5.92 35 10 1.70 0.37 0.55
6 Transport and binding protein Phosphocarrier protein HPr EF0709 9.3 4.92 13 11 0.99 0.70 0.52
7 e   PTS system, mannose-specific IIAB components EF0020 35.5 5.11 50 22 1.62 3.06 0.90
8   peptide ABC transporter, ATP-binding protein EF0912 35.9 5.97 20 7 1.10 1,00 0.46
9 e Amino acid biosynthesis Ornithine carbamoyltransferase EF0105 38.1 5.02 18 5 1.03 0.64 3.48
10 e   Decarboxylase, putative EF0634 71.96 5.14 47 29 0.52 1.21 1.86
11 Other cellular processes Glutathione reductase EF3270 49.6 5.23 21 10 2.42 0.96 0.87
12   Dps family protein EF3233 17.9 4.56 46 6 0.51 0.81 1.23
13   General stress protein, putative EF1744 20.5 4.61 31 6 0.88 0.66 0.52
14   Cell division protein DivIVA EF1002 26.6 4.53 62 16 0.61 1.21 3.5
15 e Energy metabolism Deoxyribose-phosphate aldolase EF0174 23.3 4.65 48 10 1.39 1.28 0.47
16 f   Formate acetyltransferase EF1613 84.5 5.31 11 8 1.00 0.95 2.87
17 e   Fumarate reductase flavoprotein subunit EF2556 53.8 5.26 10 6 0.86 1.57 2.26
18   Phosphoglycerate mutase 1 EF0195 26.0 5.09 41 11 0.87 1.13 0.36
19 f   Formate acetyltransferase EF1613 84.7 5.31 14 11 0.94 1.21 2.09
20 e   V-type ATP synthase subunit B EF1499 51.3 5.03 18 8 0.59 2.02 1.29
21   Pyruvate kinase EF1046 62.6 4.99 41 25 2.99 3.61 1.09
22   Enolase EF1961 46.5 4.56 54 22 1.46 0.98 0.45
23   Thioredoxin EF1405 11.7 4.35 66 9 1.49 0.40 0.60
24 e Cell wall/membrane biogenesis D-fructose-6-phosphate amidotransferase EF2151 65.7 4.93 24 12 1.93 1.13 2.12
25 Coenzyme transport and metabolism Naphthoate synthase EF0445 30.0 5.24 39 10 0.89 1.46 0.43
26 e   2-dehydropantoate 2-reductase EF2445 34.7 5.08 3 1 (39)g 1.32 1.40 0.46
27 e Transcription and translation Transcriptional regulator, AraC family EF0432 34.6 6.76 25 7 0.91 2.64 0.18
28   Cold-shock domain-contain protein EF2925 7.3 4.35 60 5 0.97 0.33 0.37
29   Peptide deformylase EF3066 21.0 5.08 48 6 1.15 0.77 0.5
30   30S ribosomal protein S2 EF2398 29.5 5 24 8 2.82 1.87 0.81
31 e   Ribosomal protein L31 EF1171 10.1 5.57 95 10 1.65 0.36 0.29
32   Elongation factor G EF0200 76.6 4.8 23 19 0.93 0.87 1.97
33   30S ribosomal protein S3 EF0212 24.4 9.8 12 3 0.86 2.19 0.68
34   Phenylalanyl-tRNA synthetase subunit beta EF1116 88.8 4.76 12 11 0.87 0.97 2.18
35   Methionyl-tRNA formyltransferase EF3123 34.3 6.06 3 1 (48)g 0.96 1.29 0.41
36 Hypothetical protein Hypothetical protein EF1967 EF1967 20.7 5.98 20 5 0.51 0.86 0.25
37   Hypothetical protein EF2909 EF2909 12.1 4.33 52 7 0.99 0.47 0.69
38   Hypothetical protein EF2763 EF2763 12.1 4.7 43 5 1.25 0.43 0.66
39   Hypothetical protein EF2888 EF2888 8.9 4.54 42 6 1.07 0.32 0.43
40 e   Hypothetical protein EF3184 EF3184 26.4 4.86 28 7 0.80 0.31 0.38
41 e   Hypothetical protein EF3186 EF3186 25.7 4.91 28 8 1.44 1.80 0.44
42   Hypothetical protein EF0123 EF0123 85.5 7.23 4 3 1.89 2.11 0.43
43   Hypothetical protein EF0352 EF0352 29.3 6.91 4 1 (61)g 1.44 2.18 0.48
44   Hypothetical protein EF2174 EF2174 99.6 8.68 36 33 1.54 1.41 0.32
45   Hypothetical protein EF 2104 EF2104 43.6 4.88 18 6 0.82 2.36 1.17
46 Protein fate Glutamyl-aminopeptidase EF3037 39.4 5.68 22 8 0.87 1.90 1.01
47 e   DnaK protein EF1308 65.5 4.59 56 31 1.11 1.20 2.21
48 e   Heat shock protein GrpE EF1307 20.1 4.5 26 8 1.10 0.30 0.30
49 f Nucleotid metabolism Ribose-phosphate pyrophosphokinase EF3163 35.4 6.16 22 9 1.21 2.5 0.47
50   Inositol-5-monophosphate dehydrogenase EF3293 52.8 5.7 50 84 1.24 2.0 1.05
51 f   Ribose-phosphate pyrophosphokinase EF3163 35.5 6.16 15 7 0.95 1.21 0.38
52 Unknown function DNAbinding response regulator VicR EF1193 26.9 5.17 15 6 0.87 1.20 0.51
53   Glyoxalase family protein EF2591 31.7 4.85 50 15 1.04 0.99 0.30
54   PhnA protein EF1374 12.4 5.01 66 6 0.9 0.55 0.47
55   Oxidoreductase, aldo/keto reductase family EF1138 31.0 5.28 18 5 0.97 1.22 0.44
  1. a The putative function is based on the JCVI Comprehensive Microbial Resource database http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi.
  2. bThe pI values are theoretical values calculated from the protein sequences
  3. c The coverage shows the percentage of the protein that is covered by the identified peptides.
  4. d Proteins with values over 1 are up-regulated in response to bile, proteins with values below 1 are down-regulated. Values representing a change larger than 1.9-fold are printed in bold face.
  5. e Proteins that also were shown to be regulated in a transcriptome study of bile responses in E. faecalis V583 [15]; see text for details.
  6. f Note that proteins EF3163 (spots 49 & 51) and EF1613 (spots 16 & 19) were identified twice.
  7. gThe value in parenthesis shows the probability-based Mowse score for proteins that were identified by only one peptide (in all cases using the LC-LTQ Orbitrap). The Mowse score equals -10*Log (P), where P is the probability that the observed match is a random event; Mowse scores greater than 38 indicate identity or extensive homology (p < 0.05).