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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 1. F. alocis AJCC 35896 — membrane fraction.

Spot Accessiona) Protein descriptiona) Mol. wt/Cal-
culated mol.
wt (kDa)		 PMF
Scoreb)/
(em PAI)		 Total
peptides
matchedc) 		PSORT
prediction
score and
categoryd) 		Domainse) HI
scoref) 		Nature of proteing)
1. HMPREF0389_01740 Hypothetical protein 104.4/104.3 35/0.09 5 0.243 CM SecA ATPase domain −0.56 Nonsecretory protein
2. HMPREF0389_00724 ATP-dependent chaperone protein (CIpB) 97.5/97.6 14.98/1.85 82 0.380 CM AAA domain (ATP associated with wide cellular activity) −0.85 Nonsecretory protein
3. HMPREF0389_01580 Leucotoxin translocation ATP-binding protein LktB 81/81.15 56/0.98 5 0.455 M Four TMMH Domain P-loop NTPase domain 0.78 Cleavage site with no N terminal signal sequence
4. HMPREF0389_00784 Copper amine oxidase N-domain protein 80/94.2 27/0.05 6 0.227C
0.112M		 No conserved domain −0.19 Nonsecretory protein
5. HMPREF0389_00575 Fibronectin-binding protein 68.3/68.3 22/0.11 12 0.421 CM N terminal fibronectin-binding domain with prokaryotes −0.56 Nonsecretory protein
6. HMPREF0389_00021 Hypothetical protein 70/69.2 76/0.63 8 2.356 C
0.114M		 DUF 2156 uncharacterized conserved domain −0.56 Nonsecretory protein
7. HMPREF0389_00233 TraG family protein 66.7/66.8 23/0.32 4 0.238 M Two TMMH domain 3.23 N terminal signal sequence Secretory protein
8. HMPREF0389_00426 Type IV pilus assembly protein (PilB) 61/61.51 25 7 0.274 C
0.111 CM		 Bacterial type II secretion system protein E signature domain −0.12 Nonsecretory protein
9. HMPREF0389_00804 Periplasmic Oligo peptide binding protein 60/60.3 106/0.31 14 0.640 CM ABC type transporter signal domain 2.26 N terminal cleavage site. Possible lipoprotein transporter
10. HMPREF0389_01305 Chaperonin GroL 57.7/60 2327/4.90 130 4.213 C
0.065 M		 Type-I chaperonin doman −0.19 Nonsecretory protein
11. HMPREF0389_00773 Amino acyl histidine dipeptidase 55/54.8 41/0.29 4 3.927 C
0.964 M		 M20 peptidase D domain 0.41 Nonsecretory protein
12. HMPREF0389_01130 Fe hydrogenase large subunit family protein 55.5/54.8 71/0.08 3 0.251C
0.284 M		 Iron hydrogenase domain 0.89 Nonsecretory protein
13. HMPREF0389_01643 Hypothetical protein 53/53.37 25/0.08 4 0.120 CM No conserved domains identified 1.85 N terminal signal peptide Secretory protein
14. HMPREF0389_01385 Mg chelate like protein-magnesium transporter 52.8/52.4 113/0.09 8 0.489 M Five TMMH domains Divalent cation transporter domain −0.19 Weak cleavage site with no N terminal signal peptide
15. HMPREF0389_00816 Signal recognition particle protein 49.7/49.8 22/0.07 27 0.483 CM SRP-Signal peptide binding domain −0.45 Nonsecretory protein
16. HMPREF0389_01719 Hypothetical protein 48.9/48.5 41/0.07 5 0.168 CM Bacterial trigger factor C terminus domain −0.11 Nonsecretory protein
17. HMPREF0389_01646 Trigger factor 48.5/48.6 41/0.09 5 0.168 CM Ribosome-associated trigger factor domain 0.23 Nonsecretory protein
18. HMPREF0389_00590 Caax amino protease family 47/47.15 75/0.16 6 0.579 CM Eight TMMH domains Caax protease—self-immunity domain −0.75 Cleavage site with no N terminal signal sequence
19. HMPREF0389_01716 Hypothetical protein 47.2 25/0.09 5 0.215 M Glutamate DH multi domain −0.78 Nonsecretory protein
20. HMPREF0389_01584 Arginine deaminase 46.6/46.5 247/0.54 27 2.31 C
0.193 M		 Amidotransferase domain 1.85 Nonsecretory protein
21. HMPREF0389_01173 Dehydrogenase/methenyl tetrahydrofolate cyclohydrolase 49/49.5 41/0.11 8 2.135C
0.129M		 Tetrahydrofolate catalytic domain 0.89 Nonsecretory protein
22. HMPREF0389_00745 Acetyl coA acetyl transferase 41/41.3 819/1.74 54 4.235 C
0.110M		 Thiolase domain −0.89 Nonsecretory protein
23. HMPREF0389_01570 Acetyl ornithine transaminase 43.9/44 550/1.22 52 0.203 C
0.432 CM		 AAT superfamily domain 0.89 Nonsecretory protein
24. HMPREF0389_00225 Transcriptional regulatory protein 48.3/47.9 64/0.09 5 0.128 CM No conserved domains −0.68 Nonsecretory protein
25. HMPREF0389_00021 Hypothetical protein 37.3/37.2 41/0.11 5 0.425C
0.056CM		 DUF 2156 domain −0.23 Nonsecretory protein
26. HMPREF0389_00599 Hypothetical protein 39.5/39.2 24/0.24 4 3.872 M Five TMMH domains 1.74 N terminal signal sequence Secretory protein
27. HMPREF0389_01692 Hypothetical protein 44/44.2 908/1.75 53 0.298 C
0.123 CM		 Translation elongation factor domain −0.56 Nonsecretory
28. HMPREF0389_01658 Acetate kinase 43.7/43 80/0.16 6 0.106 C
0.056 M		 Acetate kinase domain −0.35 No signal sequence
29. HMPREF0389_01707 Hypothetical protein 42.5/42.3 80/0.16 6 1.12 C
0.89 M		 Acetate kinase domain 0.12 Nonsecretory protein
30. HMPREF0389_01733 Hypothetical protein 44/43.98 201/0.24 16 3.21 C
0.11 M		 Translation elongation factor domain −0.19 Nonsecretory protein
31. HMPREF0389_01077 Dihydrodipicolinate reductase 37/38.01 21/0.11 3 2.31 C
0.239 M		 Dehyrogenase domain 0.78 Nonsecretory protein
32. HMPREF0389_00704 TRAP transporter solute receptor—TAXI family 36/35.9 47/0.31 9 0.119M One TMMH domain 0.36 N terminal signal peptide Secretory protein
33. HMPREF0389_00145 TIM —barrel protein 36.2/36.15 38/0.09 5 3.564 C
0.117 M		 Phosphate-binding domain −0.56 Nonsecretory protein
34. HMPREF0389_00742 Electron transfer flavoprotein alpha subunit protein 35/35.1 246/0.43 15 0.160 M ETF electron acceptor domain −0.56 Nonsecretory protein
35. HMPREF0389_01141 Hypothetical protein 30/30 24/0.11 9 4.65 C
0.362 M		 No conserved domain − Nonsecretory protein
36. HMPREF0389_01354 NG, NG dimethyl arginine, dimethyl amino hydrolase 29/29.2 48/0.11 5 2.568 C
0.116 M		 Amidotransferase domain −0.36 Nonsecretory protein
37. HMPREF0389_00553 Septum site determining protein MinD 29/29.5 55/0.11 3 0.126 M Membrane-associated ATPase domain −0.56 Nonsecretory protein
38. HMPREF0389_01240 3-Oxy acyl carrier protein Amino acid carrier protein 27.5/28 341/1.23 19 0.747 M Eight TMMH domains 0.45 Uncleavable N terminal signal sequence
39. HMPREF0389_00128 GTP sensing transcriptional pleotropic repressor CodY 28/28.4 72/0.40 7 0.374 C
0.089 M		 GAF-like domain (found to repress the dipeptide transport operon) 0.36 Nonsecretory protein
40. HMPREF0389_01469 Glutaconate coA transferase 29.5/30 1385/7.46 191 0.110C
0.056 M		 CoA tranferase domain −0.51 Nonsecretory protein
41. HMPREF0389_01209 Ruberythrin 21.4/21.6 48/0.34 10 4.84 C
0.213 M		 Ferritin-like di iron binding domain −0.65 Nonsecretory protein
42. HMPREF0389_01167 CRISPR-associated protein 18./20.1 22/3.9 16 3.56 C
0.251 M		 CRISPR domain (clustered regularly interspaced short palindromic repeats) −0.36 Nonsecretory protein
43. HMPREF0389_01230 Hypothetical protein 22/22.02 123/1.06 13 0.447 CM No conserved domain 0.11 Nonsecretory protein
44. HMPREF0389_00682 CBS domain protein 23.5/23.7 38/0.40 6 3.61 C
0.197 M		 CBS-Bateman domain 0.12 Nonsecretory protein
45. HMPREF0389_00796 Superoxide reductase 12.5 53/0.56 3 4.235 C
1.89 M		 SOR-like domain −0.45 Nonsecretory protein
46. HMPREF0389_00708 Alkaline shock protein 14/14.02 80/0.24 3 0.175 C
0.052 M		 DUF322 domain 0.36 Nonsecretory protein
47. HMPREF0389_00532 D-Alanine–D-alanine ligase 40/40.3 45/0.330 10 3.21 C
0.112 M		 Substrate binding LTTR domain 0.89 Nonsecretory protein
48. HMPREF0389_00019 Membrane protein 37.8/36.2 32/0.31 7 0.703 CM TMMH domain −0.78 Nonsecretory protein
49. HMPREF0389_00429 Serine-glucine-hydroxymethyl transferase 47/46.9 24/0.09 7 2.123 C
0.075 M		 SHMT domain −0.48 Nonsecretory protein
50. HMPREF0389_00639 ATP/GTP-binding protein 28/32.2 120/0.09 10 0.348 CM Protein transfer/ATP-GTP binding domain 1.85 Nonsecretory protein
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)

Psort prediction score classifying protein as C, cytoplasmic; CM, cytoplasmic membrane; M, membrane; CW, cell wall; PP, periplasm; Ex, extra cellular.

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 nonsecretory.

g)

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