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. Author manuscript; available in PMC: 2015 Jul 24.
Published in final edited form as: Proteomics. 2012 Nov;12(22):3343–3364. doi: 10.1002/pmic.201200211

Table 4. F. alocis D-62D— extracellular fraction.

Spot Accessiona) Protein descriptiona) Mol. wt/Cal-
culated mol.
wt (kDa)		 PMF
scoreb)/
(emPAl)		 Total
peptides
matchedc) 		PSORT
prediction
score and
categoryd) 		Domainse) HI
scoref) 		Nature of proteing)
1. HMPREF0389_01110 Cell wall associated serine proteinase 262 29/0.01 32 CM-9.39
EC-0.61		 Membrane lipid attachment domain 1.61 N terminal signal peptide
2. HMPREF0389_01728 Conserved hypothetical protein 246.5 25/0.04 4 EC-4.32
CW-5.69		 Peptidoglycan anchor domain 1.37 N terminal signal peptide
3. HMPREF0389_01692 Hypothetical protein 223 98/0.16 4 C-7.50
EC-0.73		 Hemolysin III type calcium-binding signature domain Inorganic pyrophosphate domain – Nonsecretory
4. HMPREF0389_01419 Conserved hypothetical protein 145.2 43/0.11 7 C-7.5
EC-0.73		 DNA-binding domain – Nonsecretory
5. HMPREF0389_01687 Pyruvate-flavodoxin oxidoreductase 130 156/0.29 45 C-7.50
EC-0.73		 4 Fe-4S ferredoxin-type iron–sulfur binding domain 1.86 N terminal signal peptide
6. HMPREF0389_01448 Calcium-binding acid repeat protein 103 25/020 16 Unknown SLH domains-3 numbers 2.0 N terminal signal peptide
7. HMPREF0389_00724 ATP-dependent chaperone protein 97.5 902/0.68 45 C-9.97
EC-0.02		 Chaperonin cIpA/B signature domain – Nonsecretory
8. HMPREF0389_01431 Conserved hypothetical protein 97.5 21/0.07 4 EC-2.92 Precursor signal domain 1.02 N terminal signal sequence
9. HMPREF0389_00122 Protease 88.5 32/0.10 7 EC-0.73 Peptidase collagenase family domain – Nonsecretory
10. HMPREF0389_00279 ATP-dependent protease La 87.9 26/0.07 5 C-9.97
EC-0.02		 Serine protease La binding domain – Nonsecretory
11. HMPREF0389_000638 Membrane protein 80.45 18/0.11 6 M Membrane protein precursor signal –
12. HMPREF0389_01580 Leucotoxin translocation ATP-binding protein 81.1 59/0.09 8 CM-10 Peptidase C-39, ABC transporter 2 domains – Nonsecretory
13. HMPREF0389_01452 Conserved hypothetical protein 76.8 12/0.05 3 CM-9.87
EC-0.03		 S-layer precursor signal domain 2.32 N terminal signal peptide
14. HMPREF0389_01452 Conserved hypothetical protein 76.8 16/0.07 3 CM-9.8
EC-0.12		 S-layer precursor signal domain 2.32 N terminal signal peptide
15. HMPREF0389_01750 Hypothetical protein 71/69.8 22/0.05 8 3.10C
1.05 M		 Collagen-binding protein B domain 0.12 Nonsecretory protein
16. HMPREF0389_00315 Conserved hypothetical protein 70.7 138/0.08 6 C-7.5
EC-0.75		 Secretory system-2 pilus domain – Nonsecretory
17. HMPREF0389_00315 Conserved hypothetical protein 70.7 35/0.11 4 C-7.50
EC-0.73		 Secretory system-2 pilus domain – Nonsecretory
18. HMPREF0389_00575 Fibronectin-binding protein 68.1 102/0.25 12 C-7.50
EC-0.73		 Protein A binding adherence fibronectin/fibrinogen domain – Nonsecretory
19. HMPREF0389_00223 S layer Y containing domain 66.7 651/0.69 22 CW-9.2
EC-0.78		 S layer homology domain 1.88 N terminal single peptide
20. HMPREF0389_01573 V-type ATP synthetase alpha chain 66.4 21/0.09 3 C-9.97 ATP-binding V type domain – Nonsecretory
21. HMPREF0389_00803 Conserved hypothetical protein 63.8 30/0.05 4 Unknown Histidine kinase domain – Nonsecretory
22. HMPREF0389_00261 Conserved hypothetical protein 62.9 17/0.07 4 Unknown EF-hand calcium-binding domain – Nonsecretory
23. HMPREF0389_00804 Oligopeptide-binding protein 60.25 27/0.07 7 EC-0.91 Lipid attachment domain at two positions 2.26 N terminal signal peptide
24. HMPREF0389_01605 Formate tetra hydrofolate ligase 60.17 16/0.07 3 C-7.0
EC-0.73		 FTH dignature domain – Nonsecretory
25. HMPREF0389_00868 DAK 2 domain protein 58.8 11/0.06 2 C-7.50
EC-0.73		 DhaL profile domain – Nonsecretory
26. HMPREF0389_00596 UDP-N-muramyl tripeptide synthetase 57.06 145/0.13 16 C-7.50
EC-0.73		 Cell wall tripeptide synthetase domain – Nonsecretory
27. HMPREF0389_00480 Amido transferase family protein 54.7 345/0.54 34 C-7.5
EC-0.73		 GATB domain – Nonsecretory
28. HMPREF0389_01130 Ferrous hydrogenase 54.3 32/0.07 3 C-7.5
EC-0.73		 Ferrodoxin type Fe-S binding domain 1.88 N terminal signal peptide
29. HMPREF0389_01374 Conserved hypothetical protein 48.5 52/0.07 6 C-9.5
EC-0.2		 YNIH -BH1805-YDJI domain – Nonsecretory
30. HMPREF0389_00504 Peptidase U32 family protein 47.7 22/0.09 7 C-7.50
EC-0.73		 Peptidase U 32 domain – Nonsecretory
31. HMPREF0389_01584 Arginine deiminase 46.6 23/0.07 12 C-7.5
EC-0.73		 Arginine deiminase domain Nonsecretory
32. HMPREF0389_01344 NLP/P60 domain protein 45.4 26/0.07 8 EC-9.60
C-0.15		 G5 domain – Nonsecretory
33. HMPREF0389_01570 Acetyl ornithine transaminase 43.5 195/0.44 16 C-9.97
EC0.02		 AA transfer class 3 domain – Nonsecretory protein
34. HMPREF0389_00538 Processive diacylglycerol glucosyl transferase 42.2 11/0.05 2 Unknown MGDG domain – Nonsecretory
35. HMPREF0389_01465 Conserved hypothetical protein 41.5 29/0.13 4 C-7.5
EC-0.73		 Hydrolase domain – Nonsecretory
36. HMPREF0389_00744 Butryl coA dehydrogenase 41.25 11/0.07 2 C-7.5
EC-0.73		 Acetyl coA DH1 and DH2 domain – Nonsecretory
37. HMPREF0389_00745 Acetyl coA acetyl transfserase 40.9 51/0.07 9 C-7.2
EC-0.93		 Thiolase 1,2,3 domain – Nonsecretory
38. HMPREF0389_01008 Membrane lipoprotein 39.54 39/0.06 5 Unknown N terminal lipoprotein lipid attachment domain 2.31 N terminal signal peptide
39. HMPREF0389_01567 N acetyl gamma glutamyl phosphate reductase 38.7 79/0.34 13 Unknown NAC gama glutamyl phosphate domain –
40. HMPREF0389_01445 O-Sialoglycoprotein endo peptidase. 36.6/36.2 22/0.55 5 1.806 C
1.17M
1.17M		 Metal-dependent protease-molecular chaperone domain –0.45 Potent cleavage site without N terminal signal sequence
41. HMPREF0389_00940 Phosphate acetyl transferase 36.0 26/0.11 2 C-7.5
EC-0.73		 Acetyl transferase metal binding domain – Nonsecretory
42. HMPREF0389_00704 TRAP transporter solute receptor protein 35.9 344/0.30 16 Unknown Membrane lipoprotein lipid attachment domain 1.12 N terminal signal peptide
43. HMPR45EF0389_01401 Conserved hypothetical protein 34.9 30/0.09 6 EC-0.73 Precursor signal YQFA trans membrane domain 3.67 Strong N terminal signal peptide
44. HMPREF0389_00901 Cobalt import ATP-binding protein 33.92 22/0.08 8 CM-8.79
EC-0.09		 CBIO and ATP transporter domain – Nonsecretory
45. HMPREF0389_01198 L-aminopeptidase 33.3 12/0.09 4 C-7.50
EC-0.73		 Peptidase DMPA hydrolase domain – Nonsecretory
46. HMPREF0389_01569 Acetyl glutamate kinase 31.03 741/2.34 59 EC-0.73 Arginine amino acid kinase –
47. HMPREF0389_01545 Copper amine oxidase N-domain protein 30.5 22/0.09 6 Unknown Precursor signal domain 1.96 N terminal signal sequence
48. HMPREF0389_01619 Iron-sulfur cluster-binding protein 29.1 24/0.51 2 C-7.5
EC-0.73		 4Fe-4S-ferredoxin type iron-sulfur binding domain – Nonsecretory
49. HMPREF0389J582 Phosphoglycerate mutase 29.1 45/0.56 7 C-6.23 PGAM domain – Nonsecretory
50. HMPREF0389_00100 Glutamate racemase 29.4 47/0.06 10 EC-0.75 C-3.45 Aspartate glutamate racemase signature –
51. HMPREF0389_01471 Glutaconyl coA decarboxylase 29.4 383/0.22 18 CM Acetyl CoA CT- N and C terminal domains –
52. HMPREF0389_00119 Pyrroline-5-carboxylate reductase 28.8 10/0.07 2 C-9.95 P5CR domain – Nonsecretory
53. HMPREF0389_00743 Electron transfer flavoprotein beta 28.2 26/0.12 3 EC-0.73
C-6.32		 ET-Flavoprotein beta domain –
54. HMPREF0389_01259 Histidinol phosophatase 25.2 36/0.10 3 C-7.50
EC-0.73		 PHP-C terminal domain – Nonsecretory
55. HMPREF0389_00321 Conserved hypothetical protein 23.9 21/0.10 4 Unknown No conserved domain 2.01 N terminal signal peptide
56. HMPREF0389_00975 TetR family transcriptional regulator 22.8 65/0.12 6 C-7.50
EC-0.73		 HTH-TETR-2 domain – Nonsecretory
57. HMPREF0389_01744 Conserved hypothetical protein 22.7 11/0.09 2 C-7.5
EC-0.73		 Uncharacterized domain – Nonsecretory
58.h) HMPREF0389_01071 Tetracyclin resistant protein 20.8 34/0.11 4 C-7.50
EC-0.73		 No conserved domain – Nonsecretory
59.h) HMPREF0389_01503 Conserved hypothetical protein 15.7 11/0.07 2 Unknown No conserved domain – Nonsecretory
60.h) HMPREF0389_01654 Neutrophil-activating factor protein A 14/16.2 12/0.07 2 2.310 C
0.099 M		 DPS domain 0.32 Nonsecretory
61.h) HMPREF0389_01741 Conserved hypothetical protein 8.7 32/0.07 2 Unknown No conserved domain – Nonsecretory
a)

Accession numbers and protein descriptions are from the NCBI F alocis genome project (http://www.ncbi.nlm.nih.gov/genomeprj/46625).

b)

Peptide mass fingerprinting score from Mascot.

c)

Number of matched peptides derived from Mascot.

d)

Psortb prediction score classifying protein as: C, cytoplasmic; CM, cytoplasmic membrane; M, membrane; CW, cell wall; PP, periplasm; Ex, extra cellular. Non classical secretory protein in silico prediction through “Secretome.”

e)

Conserved domain prediction using the NCBI-Conserved domain database search.

f)

Hydropathy index (HI) score from the iPsort predictions on the nature of protein, high positive score indicate presence of a signal sequence negative scores predict proteins as non secretory.

g)

iPsort prediction showing protein to contain signal sequence, cleavage site and classification of protein to be secretory or nonsecretory.

h)

Low molecular weight protein spots not clearly seen in Fig. 6 but confirmed by MS analysis.