An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

Rivers, Adam R; Smith, Christa B; Moran, Mary Ann

doi:10.1186/1944-3277-9-11

Environmental Microbiome

Table 4 Updates and corrections to the genome sequence

From: An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3

Accession	Gene locus	CDS	Gene	Type of change
YP_166946	SPO1707a	Branched-chain amino acid ABC transporter, ATP-binding protein, putative		Locus name
YP_167418	SPO2192a	N-formylglutamate amidohydrolase	hutG	Locus name
YP_165298	SPO0025	Hydrolase, NUDIX family		ORF position
YP_165304	SPO0031	ErfK/YbiS/YcfS/YnhG family protein		ORF position
YP_165330	SPO0056	Hypothetical protein		ORF position
YP_165481	SPO0212	Hypothetical protein		ORF position
YP_165606	SPO0343	2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase	sucB	ORF position
YP_165666	SPO0403	Conserved domain protein		ORF position
YP_165678	SPO0415	D-isomer specific 2-hydroxyacid dehydrogenase family protein		ORF position
YP_165703	SPO0440	Thioesterase family protein		ORF position
YP_165709	SPO0446	ABC transporter, ATP-binding protein		ORF position
YP_165719	SPO0456	Hypothetical protein		ORF position
YP_165753	SPO0491	Hypothetical protein		ORF position
YP_165766	SPO0504	Hypothetical protein		ORF position
YP_165767	SPO0505	Ribosomal protein L15	rplO	ORF position
YP_165860	SPO0600	Carboxynorspermidine decarboxylase	nspC	ORF position
YP_165899	SPO0644	Hypothetical protein		ORF position
YP_165937	SPO0682	Monooxygenase family protein		ORF position
YP_165950	SPO0695	Hypothetical protein		ORF position
YP_008877643	SPO0876a	Hypothetical protein		ORF position
YP_166130	SPO0877	Conserved domain protein		ORF position
YP_166199	SPO0946	Phosphomannomutase/phosphoglucomutase	algC	ORF position
YP_166255	SPO1003	ATP-dependent Clp protease, proteolytic subunit ClpP	clpP	ORF position
YP_166256	SPO1004	ATP-dependent Clp protease, ATP-binding subunit ClpX	clpX	ORF position
YP_166357	SPO1106	Hypothetical protein		ORF position
YP_166419	SPO1172	FMN-dependent alpha-hydroxy acid dehydrogenase family protein		ORF position
YP_166421	SPO1174	DNA helicase II, putative		ORF position
YP_166518	SPO1273	Thymidylate synthase, flavin-dependent	thyX	ORF position
YP_166577	SPO1334	Hypothetical protein		ORF position
YP_166601	SPO1359	Pyruvate, phosphate dikinase	ppdK	ORF position
YP_166628	SPO1386	HIT family protein		ORF position
YP_166803	SPO1562	Glycine cleavage system T protein, putative		ORF position
YP_166874	SPO1633	Hypothetical protein		ORF position
YP_167013	SPO1776	Pyridine nucleotide-disulphide oxidoreductase family protein		ORF position
YP_167049	SPO1812	Adenylate kinase	adk-2	ORF position
YP_167155	SPO1920	Tellurite resistance protein	trgB	ORF position
YP_167190	SPO1955	Glutaryl-CoA dehydrogenase	gcdH	ORF position
YP_167207	SPO1972	Nodulation protein N		ORF position
YP_167208	SPO1973	3-dehydroquinte dehydratase, type II	aroQ	ORF position
YP_167281	SPO2051	DNA gyrase, A subunit	gyrA	ORF position
YP_167284	SPO2054	Cytochrome c oxidase assembly protein		ORF position
YP_167368	SPO2141	Pyridoxamine 5''-phosphate oxidase, putative		ORF position
YP_167443	SPO2217	Excinuclease		ORF position
YP_167514	SPO2290	Hypothetical protein		ORF position
YP_167549	SPO2326	Hypothetical protein		ORF position
YP_167562	SPO2339	Enoyl-CoA hydratase/isomerase family protein		ORF position
YP_167570	SPO2347	Hypothetical protein		ORF position
YP_167571	SPO2348	Sarcosine oxidase, beta subunit family		ORF position
YP_167714	SPO2499	Hypothetical protein		ORF position
YP_167808	SPO2595	Hypothetical protein		ORF position
YP_167819	SPO2608	Aldehyde dehydrogenase, putative		ORF position
YP_167822	SPO2612	DNA-binding protein HU, putative		ORF position
YP_008877659	SPO2723a	Hypothetical protein		ORF position
YP_167934	SPO2724	Hypothetical protein		ORF position
YP_167992	SPO2785	NADH dehydrogense I, B subunit	nuoB	ORF position
YP_168024	SPO2816	Peptide/nickel/opine uptake family ABC transporter, permease protein		ORF position
YP_168061	SPO2853	Cobalt chelatase, CobS subunit		ORF position
YP_168080	SPO2872	Cobyrinic acid a,c-diamide synthase	cobB	ORF position
YP_168096	SPO2888	Membrane protein, putative		ORF position
YP_168125	SPO2917	Glutathione S-transferase family protein		ORF position
YP_168133	SPO2925	Sporulation related		ORF position
YP_168143	SPO2936	Hypothetical protein		ORF position
YP_168150	SPO2942	Hypothetical protein		ORF position
YP_168197	SPO2991	Nitroreductase family protein		ORF position
YP_168209	SPO3003	AMP-binding enzyme		ORF position
YP_168292	SPO3089	ATPase, putative		ORF position
YP_168317	SPO3114	Hypothetical protein		ORF position
YP_168354	SPO3151	HAD-superfamily subfamily IIA hydrolase, TIGR01459		ORF position
YP_168406	SPO3203	Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase, putative		ORF position
YP_168423	SPO3220	Aminotransferase, classes I and II		ORF position
YP_168448	SPO3245	Nicotinate-nucleotide pyrophosphorylase	nadC	ORF position
YP_168475	SPO3278	Orotidine 5'-phosphate decarboxylase	pyrF	ORF position
YP_168540	SPO3344	Cys/Met metabolism PLP-dependent enzyme family protein		ORF position
YP_168563	SPO3367	Deoxyribose-phosphate aldolase	deoC	ORF position
YP_168618	SPO3422	ATP-dependent protease La domain protein		ORF position
YP_168712	SPO3517	Preprotein translocase, SecE subunit	secE	ORF position
YP_168722	SPO3527	Universal stress protein family protein		ORF position
YP_168735	SPO3540	Hypothetical protein		ORF position
YP_168802	SPO3607	Hypothetical protein		ORF position
YP_168911	SPO3717	Cytosol aminopeptidase family protein		ORF position
YP_168940	SPO3746	Adenine deaminse	ade	ORF position
YP_169017	SPO3829	S-formylglutathione hydrolase, putative		ORF position
YP_169021	SPO3833	ATP-dependent RNA helicase, DEAD/DEAH box family		ORF position
YP_164889	SPOA0058	Glycine cleavage system protein H	gcvH-2	ORF position
YP_165979	SPO0725	Bacterial SH3 domain family protein		ORF position, Function
YP_167233	SPO1999	Collagen domain protein		ORF position, Function
YP_008877641	SPO0561	ABC transporter		Sequence
YP_008877654	SPO2024	Aminotransferase		Sequence
YP_008877662	SPO3316a	Stress protein		Sequence
YP_008877661	SPO3904	Heat shock protein		Sequence
YP_167141	SPO1905	Fumarate hydratase, class II	fumC	Sequence, ORF position
YP_165491	SPO0222	Alanine dehydrogenase	ald	Function
YP_165503	SPO0234	Lysine dehydrogenase	lysdh	Function
YP_165504	SPO0235	α-aminoadipic-δ-semialdehyde dehydrogenase	aasadh	Function
YP_165716	SPO0453	DMSP lyase	dddW	Function
YP_165850	SPO0590	LacI family transcriptional regulator	hpsR	Function
YP_165851	SPO0591	Dihydroxypropanesulfonate (DHPS) TRAP transporter	hpsK	Function
YP_165852	SPO0592	Dihydroxypropanesulfonate (DHPS) TRAP transporter	hpsL	Function
YP_165853	SPO0593	Dihydroxypropanesulfonate (DHPS) TRAP transporter	hpsM	Function
YP_165854	SPO0594	Dihydroxypropanesulfonate-3-dehydrogenase	hpsN	Function
YP_165855	SPO0595	R or S-dihydroxypropanesulfonate-2-dehydrogenase	hpsO	Function
YP_165856	SPO0596	S or R-dihydroxypropanesulfonate-2-dehydrogenase	hpsP	Function
YP_165857	SPO0597	UspA stress protein	hpsQ	Function
YP_165858	SPO0598	Membrane-bound sulfolactate dehydrogenase	slcD	Function
YP_165912	SPO0657	Metallochaperone, putative	naaT	Function
YP_165913	SPO0658	N-acetyltaurine amidohydrolase	naaS	Function
YP_165914	SPO0659	LysR family transcriptional regulator	naaR	Function
YP_165915	SPO0660	N-acetyltaurine ABC transporter, periplasmic binding protein	naaA	Function
YP_165916	SPO0661	N-acetyltaurine ABC transporter, permease protein	naaB	Function
YP_165917	SPO0662	N-acetyltaurine ABC transporter, permease protein	naaB'	Function
YP_165918	SPO0663	N-acetyltaurine ABC transporter, ATP-binding protein	naaC	Function
YP_165919	SPO0664	N-acetyltaurine ABC transporter, ATP-binding protein	naaC'	Function
YP_165928	SPO0673	Taurine-pyruvate aminotransferase	tpa	Function
YP_165929	SPO0674	Taurine ABC transporter, periplasmic taurine-binding protein	tauA	Function
YP_165930	SPO0675	Taurine ABC transporter, ATP-binding protein	tauB	Function
YP_165931	SPO0676	Taurine ABC transporter, permease protein	tauC	Function
YP_166034	SPO0781	Phosphonate ABC transporter substrate-binding protein	phnD	Function
YP_166387	SPO1136	Diaminobutyric acid transaminase	doeD	Function
YP_166388	SPO1137	Aspartate-semialdehyde dehydrogenase	doeC	Function
YP_166389	SPO1138	AsnC/Lrp-like DNA-binding protein, transcriptional regulator	doeX	Function
YP_166390	SPO1139	Nα-acetyl-L-2,4-diaminobutyric acid deacetylase	doeB	Function
YP_166391	SPO1140	Ectoine hydrolase	doeA	Function
YP_166392	SPO1141	Ectoine utilization protein EutC	eutC	Function
YP_166394	SPO1143	Ectoine utilization protein EutA	eutA	Function
YP_166396	SPO1145	Ectoine/5-hydroxyectoine TRAP transporter, periplasmic binding protein	uehC	Function
YP_166397	SPO1146	Ectoine/5-hydroxyectoine TRAP transporter, small integral membrane protein	uehB	Function
YP_166398	SPO1147	Ectoine/5-hydroxyectoine TRAP transporter, large integral membrane protein	uehA	Function
YP_166399	SPO1148	Transcriptional regulator, GntR family	gntR	Function
YP_166792	SPO1551	Trimethylamine (TMA) monooxygenase	tmm	Function
YP_166837	SPO1596	DMSP lyase	dddQ	Function
YP_166942	SPO1703	DMSP lyase	dddD	Function
YP_167149	SPO1914	NADPH-dependent acrylyl-CoA reductase	acuI	Function
YP_167183	SPO1948	Phosphate ABC transporter substrate-binding protein	pstS	Function
YP_167275	SPO2045	3-methylmercaptopropionyl-CoA ligase	dmdB	Function
YP_167522	SPO2299	DMSP lyase	dddP	Function
YP_167578	SPO2355	Isethionate dissimilation regulator	iseR	Function
YP_167579	SPO2356	Isethionate TRAP transporter	iseM	Function
YP_167580	SPO2357	Isethionate TRAP transporter	iseL	Function
YP_167581	SPO2358	Isethionate TRAP transporter	iseK	Function
YP_167582	SPO2359	Isethionate dehydrogenase	iseJ	Function
YP_167694	SPO2477	Manganese uptake regulator	mur	Function
YP_168390	SPO3187	(2R)-3-sulfolactate dehydrogenase	comC	Function
YP_168503	SPO3307	Lysine-ketoglutarate reductase	lkr	Function
YP_168559	SPO3363	Manganese ABC transporter, permease protein	sitD	Function
YP_168560	SPO3364	Manganese ABC transporter, permease protein	sitC	Function
YP_168561	SPO3365	Manganese ABC transporter, ATP-binding protein	sitB	Function
YP_168562	SPO3366	Manganese ABC transporter, periplasmic protein	sitA	Function
YP_168752	SPO3557	Sulfite dehydrogenase subunit SoeC; transmembrane sulfate transporter	soeC	Function
YP_168753	SPO3558	Sulfite dehydrogenase iron-sulfur cluster-binding subunit SoeB; cytosolic protein	soeB	Function
YP_168754	SPO3559	Sulfite dehydrogenase molybdopterin cofactor-binding subunit SoeA; cytosolic protein	soeA	Function
YP_168755	SPO3560	Phosphate acetyltransferase	pta	Function
YP_168757	SPO3562	Taurine transcriptional regulator	tauR	Function
YP_168992	SPO3804	3-methylmercaptopropionyl-CoA dehydrogenase	dmdC	Function
YP_168993	SPO3805	Methylthioacryloyl-CoA hydratase	dmdD	Function
YP_164988	SPOA0157	Sulfite exporter	cuyZ	Function
YP_164989	SPOA0158	L-cysteate sulfo-lyase	cuyA	Function
YP_164990	SPOA0159	Transcriptional regulator cuyR	cuyR	Function
YP_165136	SPOA0309	Sulphoacetaldehyde acetyltransferase		Function
YP_008877636	SPO0344a	Hypothetical protein		New ORF
YP_008877637	SPO0346a	Hypothetical protein		New ORF
YP_008877638	SPO0360a	Hypothetical protein		New ORF
YP_008877639	SPO0491a	Hypothetical protein		New ORF
YP_008877640	SPO0504a	Hypothetical protein		New ORF
YP_008877642	SPO0628a	Hypothetical protein		New ORF
YP_008877644	SPO1044a	Hypothetical protein		New ORF
YP_008877645	SPO1094a	Hypothetical protein		New ORF
YP_008877646	SPO1226a	Hypothetical protein		New ORF
YP_008877647	SPO1252a	Transcriptional regulator		New ORF
YP_008877648	SPO1310a	Hypothetical protein		New ORF
YP_008877649	SPO1337a	Hypothetical protein		New ORF
YP_008877650	SPO1352a	Hypothetical protein		New ORF
YP_008877651	SPO1356a	Signal transduction		New ORF
YP_008877652	SPO1364a	Hypothetical protein		New ORF
YP_008877653	SPO1412a	Hypothetical protein		New ORF
YP_008877655	SPO2213a	Hypothetical protein		New ORF
YP_008877656	SPO2341a	Hypothetical protein		New ORF
YP_008877657	SPO2478	RNA helicase		New ORF
YP_008877658	SPO2652a	Polyketide cyclase		New ORF
YP_008877660	SPO2973a	Hypothetical protein		New ORF
YP_008877663	SPO3452a	Hypothetical protein		New ORF
YP_008877664	SPO3498a	Hypothetical protein		New ORF
YP_008877665	SPO3673a	Hypothetical protein		New ORF
AHC32567	SPOA0087a	Esterase-lipase		New ORF
AHC32568	SPOA0272a	Hypothetical protein		New ORF
YP_165305	-	Hypothetical protein		Removed ORF
YP_165605	-	Hypothetical protein		Removed ORF
YP_166669	-	Hypothetical protein		Removed ORF
YP_168865	-	Hypothetical protein		Removed ORF
YP_165238	-	Hypothetical protein		Removed ORF

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ISSN: 2524-6372

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