Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions

Mandel, Mark J; Stabb, Eric V; Ruby, Edward G

doi:10.1186/1471-2164-9-138

Table 1 V. fischeri ES114 loci modified due to sequence changes.

From: Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions

Locus tag	Gene	Description	Correction	s/m	Effect on ORFs	Locus tag deaccessioned	Target
VF_0040	yidZ	transcriptional regulator, LysR family	fs	s	fusion	VF0039	101
VF_0044	rmuC	predicted recombination limiting protein	fs	s	fusion	VF0045	102
VF_0056	rhlB	ATP-dependent RNA helicase	fs	s	fusion	VF0055	103
VF_0093	add	adenosine deaminase	dl	m	fusion	VF0092	104
VF_0124	slmA	division inhibitor	fs	s	fusion	VF0123	105
VF_0157	wbfB	WbfB protein	fs, ms, n	m	fusion	VF0156	106
VF_0160	wbfD	WbfD protein	fs	s	fusion	VF0159	107
VF_0214	prkB	phosphoribulokinase	fs	s	fusion	VF0213	109
VF_0220	kefB	potassium:proton antiporter	fs, ns	m	fusion	VF0221	110
VF_0235	rplC	50S ribosomal subunit protein L3	fs	s	fusion	VF0236	111
VF_0246	rplN	50S ribosomal subunit protein L14	fs	s	fusion	VF0247	112
VF_0256	rplO	50S ribosomal subunit protein L15	fs	s	3' extension		168
VF_0281	yjjP	predicted inner membrane protein	fs	s	fusion	VF0282	113
VF_0300		putative salt-induced outer membrane protein	fs	s	fusion	VF0299	114
VF_0397	yrbC	predicted ABC-type organic solvent transporter	fs	s	fusion	VF0398	116
VF_0418	dgkA	diacylglycerol kinase	fs	m	3' extension		169
VF_0420	mltC	membrane-bound lytic murein transglycosylase C	fs, ms	m	fusion	VF0419	117
VF_0481	glmM	phosphoglucosamine mutase	fs	m	fusion	VF0482	118
VF_0651		amino-acid abc transporter binding protein	fs	s	3' extension		170
VF_0657		succinylglutamate desuccinylase/aspartoacylase family protein	n	s	ambiguous residue clarified		179
VF_0729	nqrE	sodium-translocating NADH:quinone oxidoreductase, subunit E	fs	s	fusion	VF0730	119
VF_0762	ychF	predicted GTP-binding protein	fs, ms	m	fusion	VF0761	120
VF_0960	tolA	membrane anchored protein in TolA-TolQ-TolR complex	dl	m	fusion	VF0961	171
VF_0993	icmF	secretion protein IcmF	dl	m	fusion	VF0992	182
VF_1031	trpG	anthranilate phosphoribosyltransferase	fs	s	fusion	VF1030	122
VF_1214	thrS	threonyl-tRNA synthetase	fs	s	fusion	VF1215	123
VF_1304		copper-exporting ATPase	fs	s	fusion	VF1305	125
VF_1308	fnr	transcriptional regulatory protein Fnr, global regulator of anaerobic growth	ms, ns	m	fusion	VF1309	183
VF_1358	fdnI	formate dehydrogenase N, gamma subunit	fs	m	fusion	VF1357	126
VF_1515		GGDEF domain protein	fs	s	3' extension		185
VF_1669	menB	dihydroxynaphthoic acid synthetase	fs	s	fusion	VF1668	127
VF_1771	prkA	serine kinase PrkA	dl	m	fusion	VF1772	128
VF_2633		lipoprotein, putative	dl	m	none		172
VF_1828		C-terminal CheW domain, putative chemotaxis coupling protein	fs	s	fusion, 3' extension	VF1827	129
None		Intergenic: VF_1856 – VF_1858	dl	m	deletion	VF1857	130
VF_1895	ptsI	PEP-protein phosphotransferase of PTS system (enzyme I)	fs	s	fusion	VF1896	184
VF_1932	fadE	acyl coenzyme A dehydrogenase	fs	s	fusion	VF1933	131
VF_1938		hydroxyacylglutathione hydrolase	ms, n	m	amino acid substitutions		121
VF_1945	tilS	tRNA(Ile)-lysidine synthetase	dl	m	fusion	VF1944	132
VF_2049	malZ	maltodextrin glucosidase	fs, ns	m	fusion	VF2050	133
VF_2078	mazG	nucleoside triphosphate pyrophosphohydrolase	fs	s	fusion	VF2077	134
VF_2152	amtB	ammonium transporter	fs	s	3' extension		173
VF_2166	pcnB	poly(A) polymerase I	fs, ms, ns	m	fusion	VF2167	135
VF_2181	aceE	pyruvate dehydrogenase, decarboxylase component E1, thiamin-binding	dl	m	fusion	VF2180	136
VF_2199	ftsQ	cell division protein FtsQ	fs	m	fusion	VF2198	137
VF_2220		ubiquinol-cytochrome c reductase iron-sulfur subunit	fs	s	fusion	VF2219	138
VF_2252	dnaG	DNA primase	fs, ms, ns	m	fusion	VF2253	139
VF_2347	cysE	serine acetyltransferase	fs, ms	m	fusion	VF2346	140
VF_2366	znuA2	high-affinity zinc uptake system protein ZnuA2	fs	s	fusion	VF2365	141
VF_2370	yeiR	predicted enzyme	fs	s	fusion	VF2371	142
VF_2377		hypothetical protein	dl	m	fusion	VF2378	143
VF_2383	acs	acetyl-CoA synthetase	fs	m	fusion	VF2384	144
VF_2389	dusB	tRNA-dihydrouridine synthase B	fs, ms	m	fusion	VF2390	145
VF_2412	rpoC	RNA polymerase, beta prime subunit	fs	m	fusion	VF2411	146
VF_2414	rpoB	RNA polymerase, beta subunit	fs	m	fusion, 5' extension	VF2413	147–148
VF_2418	rplA	50S ribosomal subunit protein L1	fs	m	fusion	VF2417	149
VF_2421	nusG	transcription termination factor NusG	fs	m	fusion	VF2420	150
VF_2450	rpoH	RNA polymerase, sigma-32 (sigma-H) factor	fs, ms, n	m	fusion	VF2449	151
VF_2463	nudE	ADP-ribose diphosphatase	fs	s	5' extension		174
VF_2528	ilvC	ketol-acid reductoisomerase, NAD(P)-binding	dl	m	fusion	VF2526, VF2527	152
VF_A0046		acriflavin resistance plasma membrane protein	fs	m	fusion	VFA0047	153
VF_A0244		GGDEF/EAL domains protein	fs, dl	m	fusion	VFA0242, VFA0243	154–155
VF_A0251	fdhF	formate dehydrogenase-H	fs	m	fusion	VFA0252	156
VF_A0304		hypothetical protein	fs	s	5' extension		176
VF_A0338		putative glucosyl hydrolase precursor	fs	m	fusion	VFA0337	158
VF_A0353	galT	galactose-1-phosphate uridylyltransferase	fs	m	fusion	VFA0354	159
VF_A0432	mukB	fused chromosome partitioning protein: predicted nucleotide hydrolase	fs, ms	m	fusion	VFA0433	160
VF_A0460	mfd	transcription-repair coupling factor	fs	s	fusion	VFA0459	161
None		Intergenic: VF_A0655-VF_A0666	fs, ms, n	m			178
VF_A0832	putA	proline dehydrogenase	dl	m	fusion	VFA0831	162
VF_A0856		hypothetical protein	dl	m	fusion	VFA0855	163
VF_A1008		hypothetical protein	fs, ms	m	fusion	VFA1009	165
VF_A1152	acrA	multidrug efflux system	fs	m	fusion	VFA1151, VFA1150	166
VF_A1156		ATP-dependent DEXH-box helicase	dl	m	fusion	VFA1157	167

Correction types: dl, large deletion; fs, frameshift; ms, missense; ns, nonsense; n, ambiguous nucleotide. s/m indicates whether (s)ingle or (m)ultiple nucleotides were affected by the sequence change.

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ISSN: 1471-2164

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