. 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 3. F. alocis AJCC 35896 — extracellular 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^,^h)
1.	HMPREF0389_01419	Conserved hypothetical protein	145.4	32/0.39	4	C-7.50 EC-0.73	DNA—ATP-binding domain	–	Nonsecretory
2.	HMPREF0389_01687	Pyruvate-flavodoxin oxidoreductase	130	24/0.07	2	C-7.50 EC-0.73	4 Fe-4S ferredoxin-type iron-sulfur binding domain	1.86	N terminal signal peptide
3.	HMPREF0389_01448	Calcium-binding acid repeat protein	103	34/0.42	6	Unknown	SLH domains —3 numbers	2.0	N terminal signal peptide
4.	HMPREF0389_01431	Conserved hypothetical protein	97.5	71/0.92	5	EC -2.92	Precursor signal domain	1.02	N terminal signal sequence
5.	HMPREF0389_00279	ATP-dependent protease La	87.9	22/0.12	4	C-9.97 EC-0.02	Serine protease La binding domain	–	Nonsecretory
6.	HMPREF0389_000638	Membrane protein	80.45	23/0.33	7	M	Membrane protein precursor signal	–	Nonsecretory
7.	HMPREF0389_01452	Conserved hypothetical protein	76.8	20/0.11	10	CM-9.8 EC-0.12	S-layer precursor signal domain	2.32	N terminal signal peptide
8.	HMPREF0389_01693	Conserved hypothetical protein	75.1	25/0.12	12	Unknown	GGDEF response regulatory domain	1.2	N terminal signal peptide
9.	HMPREF0389_01750	Hypothetical protein	71/69.8	30/0.05	8	3.10 C 1.05 M	Collagen binding protein B domain	–	Nonsecretory protein
10.	HMPREF0389_00315	Conserved hypothetical protein	70.7	28/0.07	6	C-7.50 EC-0.73	Secretory system-II pilus domain		Nonsecretory
11.	HMPREF0389_00575	Fibronectin-binding protein	68.1	34/0.32	7	C-7.50 EC-0.73	Protein A binding adherence fibronectin/fibrinogen domain	–	Nonsecretory
12.	HMPREF0389_00223	S layer Y containing domain	66.7	22/0.33	3	CW-9.2 EC-0.78	S layer homology domain	1.88	N terminal single peptide
13.	HMPREF0389_00803	Conserved hypothetical protein	63.8	24/0.07	3	Unknown	Histidine kinase domain	–	Nonsecretory
14.	HMPREF0389_01605	Formate tetra hydrofolate ligase	60.17	28/0.07	2	C-7.00 EC-0.73	FTH dignature domain	–	Nonsecretory
15.	HMPREF0389_00804	Oligopeptide-binding protein	60.25	32/0.11	4	EC-0.91	Lipid attachment domain at two positions	2.26	N terminal signal peptide
16.	HMPREF0389_00868	DAK 2 domain protein	58.8	22/0.07	2	C-7.50 EC-0.73	DhaL profile domain	–	Nonsecretory
17.	HMPREF038_00596	UDP-N –muramyl tripeptide synthetase	57.06	102/0.24	16	C-7.50	Cell wall tripeptide synthetase domain	–	Nonsecretory
18.	H22MPREF0389_00480	Amido transferase family protein	54.7	22/0.08	4	C-7.50 EC-0.73	GATB domain	–	Nonsecretory
19.	HMPREF0389_01130	Ferrous hydrogenase	54.3	51/0.16	12	C-7.5 EC-0.73	Ferrodoxin type Fe-S binding domain	1.88	N terminal signal peptide
20.	HMPREF0389_00225	Trancriptional regulatory protein	48	84/0.18	17	C-7.5 EC-0.73	No conserved domains	–	Nonsecretory
21.	HMPREF0389_01374	Conserved hypothetical protein	48.5	289/0.30	20	C-9.5 EC-0.2	YNIH-BH1805-YDJI domain		Nonsecretory
22.	HMPREF0389_00504	Peptidase U32 family protein	47.7	22/0.07	4	C-7.50 EC-0.73	Peptidase U 32 domain	–	Nonsecretory
23.	HMPREF0389_01584	Arginine deiminase	46.6	56/0.18	18	C-7.5 EC-0.73	Arginine deiminase domain	–	Nonsecretory
24.	HMPREF0389_01570	Acetyl ornithine transaminase	43.5	182/0.44	19	C-9.97 EC-0.02	AA transfer class 3 domain	–	Nonsecretory
25.	HMPREF0389_01465	Conserved hypothetical protein	41.5	55/0.16	8	C-7.5 EC-0.73	Hydrolase domain		Nonsecretory
26.	HMPREF0389_000744	Butryl coA dehydrogenase	41.25	64/0.16	12	C-7.50 EC-0.73	Acetyl coA DH1 and DH2 domain	–	Nonsecretory
27.	HMPREF0389_00745	Acetyl coA acetyl transfserase	40.9	78/0.15	32	C-7.2 EC-0.93	Thiolase 1,2,3 domain	–	Nonsecretory
28A.	HMPREF0389_01567	N acetyl gamma glutamyl phosphate reductase	38.7	212/0.56	20	Unknown	NAC gama glutamyl phosphate domain	–	Nonsecretory
28B.	HMPREF0389_00567	Glyceraldehyde 3 phosphate dehydrogenase	37.9/39.5	39/0.06	5	0.351 C	Nil	–	Nonsecretory
29.	HMPREF0389_01445	O-Sialoglycoprotein endopeptidase	36.6/36.2	248/0.65	24	1.806 C 1.17M	Metal-dependent protease—molecular chaperone domain	–0.45	Potent cleavage site without N terminal signal sequence
30.	HMPREF0389_00607	Conserved hypothetical protein	36.2	22/0.09	5	Unknown	Precursor signal domain	1.71	N terminal signal peptide
31.	HMPREF0389_00704	TRAP transporter solute receptor protein	35.9	35/0.12	6	Unknown	Lipoportein lipid attachment domain	1.12	N terminal signal peptide
32.	HMPREF0389_01401	Conserved hypothetical protein	34.9	32/0.09	7	EC-0.73	Precursor signal YQFA trans membrane domain	3.67	Strong N terminal signal peptide
33.	HMPREF0389_00901	Cobalt import ATP-binding protein	33.9-5.2		9	CM-8.73 EC-0.09	CBIO-ATP binding domain	–	Nonsecretory
34.	HMPREF0389_01489	Conserved hypothetical protein	32.3	67/0.25	7	Unknown	No conserved domains	2.21	Signal peptide at the N terminal
35.	HMPREF0389_01569	Acetyl glutamate kinase	31.03	42/0.08	7	EC-0.73	Arginine amino acid kinase		Nonsecretory
36.	HMPREF0389_01545	Copper amine oxidase N-domain protein	30.5	43/0.13	6	Unknown	Precursor signal domain	1.96	N terminal signal sequence
37.	HMPREF0389_01471	Glutaconyl coA decarboxylase	29.4	313/0.18	16	CM	Acetyl CoA CT- N and C terminal domains	–	Nonsecretory
38.	HMPREF0389_	Glutamate racemase	29.4	42/0.12	6	EC-0.75 C-3.45	Aspartate glutamate racemase signature	–	Nonsecretory
39.	HMPREF0389_00100	Septum site determining protein	28.9	306/0.84	17	CM	Septum site determining cell division inhibitor domain	28.9	N terminal signal peptide
40.	HMPREF0389_01597	Electron transfer flavoprotein beta	28.2	14/0.07	2	EC-0.73 C-6.32	ET-Flavoprotein beta domain	–	Nonsecretory
41.	HMPREF0389_01177	Conserved hypothetical protein	27.1	45/0.14	6	Unknown	No conserved domains	–
42.	HMPREF0389_01259	Histidinol phosphatase	25.2-6.36	32/0.11	4	C-7.50 EC-0.73	PHP-C terminal domain	–	Nonsecretory
43.	HMPREF0389_01071	Tetracyclin resistant protein	20.8-6.35	59/0.13	11	C-7.50 EC-0.73	No conserved domain	–	Nonsecretory
44.	HMPREF0389_01503	Conserved hypothetical protein	15.7-9.1	43/0.11	10	Unknown	No conserved domain	–	Nonsecretory
45.	HMPREF0389_01654	Neutrophil-activating factor protein A	14/16.2	33/0.12	8	2.310 C 0.099 M	DPS domain	0.32	Nonsecretory
46.	HMPREF0389_01741	Conserved hypothetical protein	8.7-9.4	12/0.04	2	Unknown	No conserved domain	–	Nonsecretory
47.	HMPREF0389_01594	GTP pyrophosphokinase	25.1/26.8	28/0.07	2	0.244 C	GTP kinase domain	–0.84	Nonsecretory
48.	HMPREF0389_ 01239	Hypothetical protein	23/27.3	69/0.10	2	0.094 C	None	1.833	Signal peptide Lipoprotein cleavage signal
49.	HMPREF0389_01176	N-acetylmuramoyl-L-alanine amidase	27	16/0.09	4	Multiple localization	Autolysin precursor signal domain		Nonsecretory
50.	HMPREF0389_00927	Hypothetical protein	23.9	11/0.03	2	C-7.5 EC-0.73	Unknown	–	Nonsecretory
51.	HMPREF0389_01268	3H domain protein	20.5	22/0.07	2	C-7.5 EC-0.73	Biotin 3H domain	–	Nonsecretory
52.	HMPREF0389_00921	Thioredoxin family protein	33.2	12/0.07	2	Multiple localization	Reductase peptide methionine		Nonsecretory
53.	HMPREF0389_00877	Radical SAM domain containing protein	36	11/0.06	4	C-7.5 EC-0.73	Oxidoreductase SAM 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.

^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 non-secretory,

^h)

Nonclassical secretory protein in silico prediction through “Secretome.”