. 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 2. F. alocis D-62 D—membrane fraction.

Spot	Accession^a)	Protein description^a)	Mol. wt/Cal- culated mol. wt (kDa)	PMF score^b)/ (emPAl)	Total peptides matched^c)	PSORT prediction score and category^d)	Domains^e)	HI score^f)	Nature of protein^g)
1.	HMPREF0389_01532	Calcium-binding acid repeat proteins	205/209	21/19.8	2	4.23 C 0.112 M	Lipase domain	1.785	N terminal signal sequence
2.	HMPREF0389_01139	S-layery domain containing protein	140/147	89/89.2	17	0.300 M	SLH domain	1.167	Signal peptide Cleavage protein
3.	HMPREF0389_00555	Peptidoglycan biosynthesis transpeptidase	107/107.7	41/0.39	5	2.104 M	Pencillin-binding protein transpeptidase domain	3.25	Uncleavable N terminal signal peptide sequence
4.	HMPREF0389_01225	Copper amine oxidase N domain protein	80.2/80.3	25/0.06	6	3.00 CW/M	N terminal copper amine oxidase domain	2.75	Cleavable N terminal signal sequence Secretory protein
5.	HMPREF0389_01580	Leucotoxin translocation ATP-binding protein LktB	81/81.15	71/0.91	5	0.455 M	Four TMMH domain P loop NTPase domain	0.78	Cleavage site with no N terminal signal sequence
6.	HMPREF0389_01693	Hypothetical protein	75/75.1	25/0.12	4	0.232C	Two TMMH domains	2.35	Uncleavable N terminal signal sequence Secretory protein
7.	HMPREF0389_01750	Hypothetical protein	71/69.8	30/0.05	8	3.10 C	Collagen binding protein B domain	0.12	Nonsecretory protein
8.	HMPREF0389_00575	Fibronectin-binding protein	68.3/68.3	20/0.11	10	0.421 CM	N terminal fibronectin-binding domain with prokaryotes	−0.56	Nonsecretory protein
9.	HMPREF0389_00239	Peptidase M23/M37 family	69.8/69.9	23/0.33	5	2.37 M	NlpC/P60 family Lipoprotein domain	−0.63	Non classical secretory protein^h)
10.	HMPREF0389_00416	Type IV pilus assembly protein	65/64.8	24/0.07	2	3.65 C 1.230 M	Tfp pilus assembly protein domain		Nonsecretory protein
11.	HMPREF0389_00926	Oligo endo peptidase F	65.7/65.9	22/0.56	2	4.37 C 0.128 M	Peptidase family M3B domain	0.23	Nonsecretory protein
12.	HMPREF0389_00804	Periplasmic oligo peptide binding protein	60.3/60.1	106/0.31	14	0.640 CM	ABC type transporter signal domain	2.26	N terminal cleavage site. Possible lipoprotein transporter
13.	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
14.	HMPREF0389_01064	Amino acid carrier protein	50.8/50.2	125/0.09	18	4.789 M	Nine TMMH domainsSodium: alanine symporter family domain	−0.98	Nonsecretory protein
15.	HMPREF0389_01173	Dehydrogenase/methenyl tetrahydrofolate cyclohydrolase Bifunctional protein GlmU	49/49.5	42/0.10	9	2.135 C 0.129M	Tetrahydrofolate catalytic domain	−0.75	Nonsecretory protein
16.	HMPREF0389_01385	Mg chelate like protein-magnesium transporter	52.8/53	124/0.12	9	0.489 M	Five TMMH domains Divalent cation transporter domain	−0.19	Weak cleavage site with no IM terminal signal peptide
17.	HMPREF0389_00590	Caax amino protease family	47/47.15	127/0.07	15	0.579 CM	Eight TMMH domains Caax protease-self-immunity domain	−0.75	Cleavage site with no N terminal signal sequence
18.	HMPREF0389_01276	Iron permease FTR1 family	47.4/47	52/7.4	6	4.286 M	Six TMMH domainsFTR1 domain	2.29	Cleavable N terminal signal sequence Secretory protein
19.	HMPREF0389_01538	Xaa pro dipeptidase	42/39.8	75/0.16	6	4.491 C 0.477 M	Metallopeptidase family M24 (play roles in regulation of biological processes rather than general protein degradation)	0.12	Nonsecretory protein
20.	HMPREF0389_00799	Signal peptidase (amino peptidase l family)	42.6/42.2	39/0.32	6	4.673 M	Eight TMMH domains	−0.84	Nonsecretory protein
21.	HMPREF0389_01222	Hypothetical protein	44/43.5	27/0.23	17	4.302 C 0.470 M	Metal-dependent hydrolase domain	−0.12	Nonsecretory protein
22.	HMPREF0389_01570	Acetyl ornithine transaminase	43.9/44	208/0.59	15	0.203C 0.432CM	AAT superfamily domain	0.89	Nonsecretory protein
23.	HMPREF0389_00112	ATP-dependent RIP metalloprotease	38.3/38.1	85/7.3	8	4.501 M	Three TMMH domains PDZ metalloprotease domain	2.96	Cleavable N terminal signal sequence Secretory protein
24.	HMPREF0389_00090	Heat inducible transcr858iptional repressor protein	39.7/39.76	21/0.11	3	3.59 C 1.35 M	HrcA protein C domain (negatively regulate the transcription of heat shock qenes)	−0.56	Nonsecretory protein
25.	HMPREF0389_00672	Hypothetical protein	38.7/38.5	21/0.84	4	4.375 M	Five TMMH domain	0.74	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_01104	Hypothetical protein	38.3/38.4	21/0.32	6	2.39 C 1.36 M	DHH family domain	−0.36	Nonsecretory
28.	HMPREF0389_00019	Membrane protein	37.8/36.2	28/0.25	5	1.102 M 2.838 Ex	TMMH domain	−0.78	Nonsecretory protein
29.	HMPREF0389_00858	Pyridoxine biosynthesis protein	30/30.27	22/0.14	4	4.836 C 0.148 M	No conserved domain	−0.63	Nonsecretory protein
30.	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
31.	HMPREF0389_01172	Hypothetical protein	27.52/27.3	38/0.24	4	4.251 M	Six TMMH domains membrane transporter domain protein	−0.74	Nonsecretory protein
32.	HMPREF0389_00639	ATP/GTP-binding protein	28/32.2	26/0.62	3	0.348 CM	Protein transfer/ATP-GTP binding domain	−1.09	Nonsecretory
33.	HMPREF0389_01587	Aspartate racimase	26.3/26.4	25/0.13	4	3.018 C 1.706 M	Aspartate racemase multidomain	−0.12	Nonsecretory protein
34.	HMPREF0389_00107	UMP kinase	25.6/25.1	24/0.13	6	4.580 C 0.365 M	UMPK domain	−0.56	Nonsecretory protein
35.	HMPREF0389_01594	GTP pyrophospokinase	27.1/27.3			4.535 C 0.428 M	Nucleotidyl transferase (NT) domain	−	Nonsecretory protein
36.	HMPREF0389_00415	Fimbrial assembly protein PilN	25.9/26.1	32/0.71	5	3.37 C 1.15M	Fimbrial assembly protein domain	0.12	Nonsecretory protein
37.	HMPREF0389_01157	Hypothetical protein	19/19.4	27/0.23	3	4.667 C 0.115M	DUF 1877 domain	−0.56	Nonsecretory protein
38.	HMPREF0389_01657	Membrane protein	37.5/36.8	22	2	0.442 CM	Six TMMH domains and precursor signal inner protein domain	1.366	N terminal cleavage signal
39.	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
40.	HMPREF0389_00637	NLP/P60 family protein	27/36.1	22/0.45	4	3.860 CM	Lipoprotein domain	2.35	N terminal signal sequence Secretory protein
41.	HMPREF0389_00816	Signal recognition particle protein	49.7/49.8	21/0.25	25	0.483 CM	SRP signal peptide binding domain	−0.45	Nonsecretory protein
42.	HMPREF0389_01566	Oligo peptide/dipeptide ABC transporter substrate/ATP binding protein	31.3/31	78/7.42	16	2.175 M	Copper amine oxidase N terminal domain	2.87	A gram positive N terminal signal peptide sequence Secretory protein
43.	HMPREF0389_00768	Peroxiredoxin	20/19.9	26/0.36	6	4.129 C 0.490 M	Thiol specific antioxidant domain	−0.65	Nonsecretory protein
44.	HMPREF0389_01476	Hypothetical protein	20.1/20	48/0.42	4	1.973 M	DUF 1836 uncharacterized domain	−0.78	Nonsecretory
45.	HMPREF0389_00295	Ribose ABC transporter, periplasmic ribose binding protein	32/32.4	65/0.56	6	0.300 M	Periplasmic binding fold domain	2.84	N terminal signal peptide sequence
46.	HMPREF0389_01217	Hypothetical protein	37.3/37	21/0.09	4	3.837 C 1.038 M	ParB-like nuclease domain	−0.68	Nonsecretory protein
47.	HMPREF0389_01478	Protein export membrane protein	35/35.3	21/0.09	4	4.754 M	Nine TMMH domains SecD and SecF domain	3.23	N terminal signal peptide sequence
48.	HMPREF0389_01477	Hemolysin III type calcium-binding protein.	31/31.1	32/1.01	6	4.807 M	Six TMMH Domains-Hemolysin –III domain	−0.23	Nonsecretory
49.	HMPREF0389_00894	Zinc ABC transporter periplasmic zinc binding protein	34.1/34.3	54/5.2	7	4.811 C 0.105 M	Periplasmic solute binding protein domain	2.84	Cleavable N terminal signal sequence Secretory protein
50.	HMPREF0389_00243	Toxin antitoxin component, ribbon —helix-helix fold protein	10.6/10.5	45/1.03	5	3.913 C 0.509 PP	RelB antitoxin domain	0.11	Nonsecretory
51.	HMPREF0389_01445	O-Sialoglycoprotein endopeptidase.	36.6/36.2	22/0.55	5	1.806 C 1.17 M	Metal-dependent protease–molecular chaperone domain	−0.45	Potent cleavage site without IM terminal signal sequence
52.	HMPREF0389_01654	Neutrophil-activating factor protein A	14/16.2	29/0.56	2	2.310 C 0.099 M	DPS domain	0.32	Nonsecretory
53.	HMPREF0389_01030	Hypothetical protein	15.6/15.9	24/0.22	4	4.662 C 0.103 M	No conserved domain	−0.41	Nonsecretory
54.	HMPREF0389_00964	Ferric uptake regulatory protein	17/17.2	21/0.32	4	3.74 C 0.820 M	Iron-dependent DNA binding reporessor/activator domain	−0.88	Nonsecretory protein
55.	HMPREF0389_ 01266	Cation transporting ATPase	99.7/99.76	49/0.72	6	2.781 M	C terminus cation transporting ATPase domain	−0.41	Nonsecretory protein
56.	HMPREF0389_01748	Hypothetical protein	52/52.1	26/0.32	4	2.489 M	Anion permease transmembrane domain	2.67	Potent cleavage site without IM terminal signal sequence

^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 non-secretory,

^h)

Nonclassical secretory protein in silico prediction through “Secretome.”