. 2014 Jun 25;9(6):e100349. doi: 10.1371/journal.pone.0100349

Table 1. Virulence genes in B. melitensis 16 M reported in the literature.

Gene id	Gene name	Gene function	COG	N.O.	Reference
BMEI0898	BMEI0898	Acyl-CoA transferase	C	104	[7]
BMEI0972	gor	Glutathione reductase	C	0	[8]
BMEI1749	glpD	Glycerol-3-phosphate dehydrogenase	C	173	[8]
BMEII0378	fdhA	Formate dehydrogenase alpha chain	C	209	[7]
BMEII0429	BMEII0429	Glycerol-3-phosphate dehydrogenase	C	271	[8]
BMEII0759	BMEII0759	Cytochrome D ubiquinol oxidase subunit II	C	419	[8]
BMEII0760	BMEII0760	Cytochrome D ubiquinol oxidase subunit I	C	449	[8]
BMEII0823	glcK	Glycerol kinase, partial	C	472	[7]
BMEII1001	norE	Heme-copper oxidase subunit III	C	52	[7]
BMEII0761	cydC	Transport ATP-binding protein	C/O	190	[8]
BMEII0762	cydD	Transport ATP-binding protein	C/O	222	[8]
BMEI0025	BMEI0025	L-sorbose dehydrogenase (FAD)	E	155	[8]
BMEI0433	dppA	Periplasmic dipeptide transport protein, partial	E	171	[7]
BMEI0933	cysK	Cysteine synthase A	E	212	[17]
BMEI1759	metH	B12-dependent methionine synthase	E	510	[17]
BMEII0040	gltB	Glutamate synthase [NADPH] large chain	E	566	[8]
BMEII0136	pheB	Homoprotocatechuate 2,3-dioxygenase	E	81	[7]
BMEII0626	BMEII0626	Membrane dipeptidase	E	269	[7]
BMEI1301	dapA	Dihydrodipicolinate synthase	E/M	728	[7]
BMEII0285	dppB	Peptide ABC transporter permease	E/P	105	[8]
BMEI1606	prlS	Sensory transduction histidine kinase	E/R	185	[17], [18]
BMEI0233	purH	Bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	F	665	[8]
BMEI0295	purK	Phosphoribosylaminoimidazole carboxylase atpase subunit	F	566	[8]
BMEI0296	purE	Phosphoribosylaminoimidazole carboxylase catalytic subunit	F	706	[8], [13]
BMEI1090	BMEI1090	Deoxyguanosinetriphosphate triphosphohydrolase-like protein	F	464	[20]
BMEI1123	purS	Phosphoribosylformylglycinamidine synthase subunit	F	336	[8]
BMEI1124	purQ	Phosphoribosylformylglycinamidine synthase I	F	694	[8]
BMEI1127	purL	Phosphoribosylformylglycinamidine synthase II	F	700	[8]
BMEI1240	purM	Phosphoribosylaminoimidazole synthetase	F	685	[8]
BMEI1488	BMEI1488	Amidophosphoribosyltransferase	F	688	[8]
BMEI1519	purD	Phosphoribosylamine-glycine ligase	F	706	[8]
BMEI1204	ppx	Exopolyphosphatase	F/P	216	[8], [24]
BMEI1396	pmm	Phosphomannomutase	G	5	[7]
BMEI1886	BMEI1886	Phosphoglucomutase	G	304	[8]
BMEI2031	ptsH	Phosphocarrier protein HPr	G	273	[8]
BMEII0485	galcD	D-galactarate dehydratase	G	185	[7]
BMEII0591	BMEII0591	Sugar transport system permease	G	119	[7]
BMEII0624	ugpA	SN-glycerol-3-phosphate transport system permease	G	136	[7]
BMEII0899	BMEII0899	Phosphomannomutase	G	32	[8]
BMEII0935	BMEII0935	Nickel resistance protein	G	184	[7]
BMEII1045	BMEII1045	HAD superfamily protein involved in N-acetyl-glucosamine catabolism	G	99	[7]
BMEII1095	sbgE	Aldolase	G	130	[8]
BMEI1415	rfbD	O-antigen export system permease protein	G/M	226	[8]
BMEI1416	rfbE	O-antigen export system ATP-binding protein RFBB	G/M	388	[8]
BMEI1427	capD	Capsular polysaccharide biosynthesis protein	G/M	390	[8]
BMEI0657	btuB	Metal chelate outer membrane receptor	H	290	[8]
BMEI1902	BMEI1902	Molybdopterin biosynthesis protein	H	97	[17]
BMEI0705	cobB	Cobyrinic acid A,C-diamide synthase	H	374	[7], [17]
BMEI0624	ilvC	Keto-acid reductoisomerase	H/E	633	[7]
BMEI1553	BMEI1553	Transporter	I	33	[8]
BMEI0983	rluA	Ribosomal large subunit pseudouridine synthase C	J	313	[8]
BMEI1057	cafA	Ribonucleases E/zinc metalloprotease	J	455	[8]
BMEI1775	rph	Ribonuclease PH	J	482	[8]
BMEI0357	BMEI0357	AsnC family transcriptional regulator	K	64	[7]
BMEI0371	virF	Regulatory factor (rpoE)	K	430	[8]
BMEI0378	rpoH2	RNA polymerase factor sigma 32	K	320	[14]
BMEI0430	nolR	Nodulation protein NOLR	K	124	[16]
BMEI0508	greA	Transcription elongation factor	K	651	[8]
BMEI0513	lysR	LysR family transcriptional regulator	K	86	[8]
BMEI0781	rpoA	DNA-directed RNA polymerase subunit alpha	K	700	[7]
BMEI0808	merR	MerR family transcriptional regulator	K	121	[8]
BMEI1178	merR	MerR family transcriptional regulator	K	181	[8]
BMEI1297	rpoZ	DNA-directed RNA polymerase subunit omega	K	256	[8]
BMEI1364	mucR	Transcriptional regulator protein	K	81	[8]
BMEI1776	hrcA	Heat-inducible transcription repressor	K	462	[8]
BMEII0116	gntR10	Gntr family transcriptional regulator	K	218	[16]
BMEII1066	BMEII1066	Pyruvate dehydrogenase complex repressor	K	209	[7]
BMEII1116	vjbR	Transcriptional activator LuxR familily	K	23	[8], [21]
BMEI0040	xerD	Site-specific tyrosine recombinase	L	609	[8]
BMEI0334	ruvB	Holliday junction DNA helicase	L	688	[8]
BMEI1307	xerC	Integrase	L	94	[8]
BMEI2023	uvrD/rep	ATP-dependent nuclease subunit a	L	371	[8], [24]
BMEII0527	xseA	Exodeoxyribonuclease VII large subunit	L	612	[7]
BMEI0275	mgpS	ATP-dependent DNA helicase	L/K/J	78	[17]
BMEI0271	mgtA	Monofunctional biosynthetic peptidoglycan transglycosylase	M	209	[17]
BMEI0359	macA	Periplasmic protein of efflux system	M	327	[7]
BMEI0921	galE	UDP-glucose 4 epimerase	M	383	[20]
BMEI0997	wbdA	Mannosyltransferase	M	5	[8], [12]
BMEI0998	wboA	Glycosyltransferase	M	1	[22]
BMEI1249	omp25	25 kda outer-membrane immunogenic protein precursor	M	14	[10]
BMEI1302	mltE	Soluble lytic murein transglycosylase	M	166	[8]
BMEI1326	BMEI1326	Hypothetical protein	M	12	[8], [24]
BMEI1393	BMEI1393	Mannosyltransferase	M	221	[8]
BMEI1413	gmd	GDP-mannose 4,6-dehydratase	M	341	[8]
BMEI1414	perA	Perosamine synthetase	M	385	[8]
BMEI1426	BMEI1426	Undecaprenyl-phosphate alpha-N acetylglucosaminyltransferase	M	89	[8]
BMEII0260	lepA	GTP-binding protein	M	698	[8]
BMEII0380	acrA	Acriflavin resistance protein A	M	148	[8]
BMEII0472	mtrC	Membrane fusion protein	M	89	[8]
BMEII0150	fliC	Flagellin	N	135	[9]
BMEII0154	motB	Flagellar motor protein	N	176	[9]
BMEII0159	flgE	Flagellar hook protein	N	285	[9]
BMEII0161	flgL	Flagellar hook-associated protein	N	30	[9]
BMEII1107	flgF	Flagellar basal-body rod protein, partial	N	32	[24]
BMEII0035	virB11	ATPase VIRB11-like protein	N/U	419	[8]
BMEII0151	fliF	Flagellar M-ring protein, partial	N/U	340	[7], [9]
BMEII0152	fliF2	Flagellar M-ring protein	N/U	134	[9]
BMEII0166	flhA1	Flagellar biosynthetic protein	N/U	367	[9]
BMEII0167	flhA2	Flagellar, biosynthesis protein partial	N/U	372	[9]
BMEI0193	BMEI0193	Hypothetical protein	NC	1	[8]
BMEI0540	BMEI0540	Hypothetical protein	NC	1	[8]
BMEI1229	BMEI1229	Exonuclease	NC	7	[7]
BMEI1339	BMEI1339	Hypothetical protein	NC	3	[7]
BMEI1361	BMEI1361	Hypothetical protein	NC	33	[7]
BMEI1433	BMEI1433	Hypothetical protein	NC	56	[7]
BMEI1807	BMEI1807	Hypothetical protein	NC	53	[8]
BMEI1844	BMEI1844	Hypothetical protein	NC	17	[7]
BMEI1879	BMEI1879	Hypothetical protein	NC	4	[7]
BMEI0514	BMEI0514	Hypothetical protein	NC	1	[8]
BMEII0428	BMEII0428	D-erythrulose 4 phosphate dehydrogenase	NC	13	[8]
BMEI0455	BMEI0455	Glutathione S-transferase	O	198	[17]
BMEI0816	clpA	ATP-dependent Clp protease ATP-binding subunit	O	295	[8]
BMEI1049	bcp	Bacterioferritin comigratory protein	O	577	[24]
BMEI1069	tig	Trigger factor	O	660	[7]
BMEI1513	dnaJ	Molecular chaperone	O	113	[17]
BMEI1804	glnD	P II urydyl-transferase	O	315	[8]
BMEII0932	nrdH	Glutaredoxin	O	94	[8]
BMEI1327	glnE	Glutamine-synthetase adenylyltransferase	O/T	328	[8]
BMEI1766	cysL	Sulfite reductase (ferredoxin)	P	341	[17]
BMEII0056	mgtB	Magnesium ABC transporter ATPase	P	489	[17]
BMEI1167	BMEI1167	Hypothetical protein	Q	62	[7]
BMEI1143	mbl	Metal dependent hydrolase	R	500	[8]
BMEI1282	gcvT	Glycine cleavage system protein T	R	162	[8]
BMEI1443	BMEI1443	2-haloalkanoic acid dehalogenase	R	92	[17]
BMEI1487	colV	Colicin V production protein	R	174	[8]
BMEI1499	pirA	Pirin	R	326	[8]
BMEI1531	BMEI1531	Hypothetical protein	R	131	[7]
BMEI1867	nifB/elp3	Florfenicol resistance protein	R	604	[8]
BMEII0701	rbsC	Ribose ABC transporter permease	R	304	[17]
BMEII0039	gltD	Glutamate synthase subunit beta	R/E	0	[8]
BMEI0186	BMEI0186	Hypothetical protein	S	101	[8]
BMEI0330	opgC	Uncharacterized protein	S	68	[7]
BMEI0331	BMEI0331	Hypothetical protein	S	50	[7]
BMEI0490	BMEI0490	Hypothetical protein	S	70	[8]
BMEI0603	BMEI0603	Hypothetical protein	S	91	[8]
BMEI0732	BMEI0732	Hypothetical protein	S	183	[8]
BMEI1298	BMEI1298	Hypothetical protein	S	117	[8]
BMEI1809	BMEI1809	Hypothetical protein	S	66	[7]
BMEI1894	grsT	Gramicidin S biosynthesis protein	S	53	[8]
BMEII0128	BMEII0128	Hypothetical protein	S	54	[17]
BMEI1336	phoQ	Sensor protein	T	154	[7]
BMEI1448	BMEI1448	C-di-GMP phosphodiesterase A-related protein	T	28	[7], [19]
BMEI1453	bpdA	Diguanylate cyclase/phosphodiesterase	T	174	[19]
BMEII0011	hydG	Transcriptional regulator protein	T	55	[8]
BMEII0986	nnrA	CRP family transcriptional regulator	T	365	[15]
BMEI0066	ompR	Two component response regulator	T/K	81	[8], [23]
BMEI1296	BMEI1296	Guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphohydrolase	T/K	635	[8]
BMEI1607	prlR	Glycerol metabolism activator	T/K	166	[18]
BMEII0025	virB1	Attachment mediating protein VIRB1-like protein	U	44	[8]
BMEII0026	virB2	Virb2	U	10	[8]
BMEII0027	virB3	Virb3	U	18	[8]
BMEII0028	virB4	ATPase VIRB4-like protein	U	129	[8], [20]
BMEII0029	virB5	Virb5	U	27	[8]
BMEII0030	virB6	Channel protein VIRB6-like protein	U	20	[8], [24]
BMEII0031	virB7	Virb7	U	2	[8]
BMEII0032	virB8	Virb8	U	67	[8], [24]
BMEII0033	virB9	Channel protein VIRB9-like protein	U	80	[8]
BMEII0034	virB10	Channel protein VIRB10-like protein	U	124	[8]
BMEI0926	emrA	Multidrug resistance protein A	V	1	[8]
BMEII0318	BMEII0318	6-aminohexanoate-dimer hydrolase, partial	V	62	[7]

Abbreviations: N.O.: number of orthologs in 789 non-redundant bacterial and archaeal genomes, COG: cluster of orthologous groups, A: RNA processing and modification, B: chromatin structure and dynamics, C: energy production and conversion, D: cell cycle control, cell division, chromosome partitioning, E: amino acid transport and metabolism, F: nucleotide transport and metabolism, G: carbohydrate transport and metabolism, H: coenzyme transport and metabolism, I: lipid transport and metabolism, J: translation, ribosomal structure and biogenesis, K: transcription, L: replication, recombination and repair, M: cell wall/membrane/envelope biogenesis, N: cell motility, NC: not in COG, O: posttranslational modifications, protein turnover, chaperones, P: inorganic ion transport and metabolism, Q: secondary metabolites biosynthesis, transport and catabolism, R: general function prediction only, S: function unknown, T: signal transduction mechanisms, U: intracellular trafficking, secretion and vesicular transport, V: defense mechanisms, W: extracellular structures.