TABLE 1.

List of H. pylori J99 genes and corresponding 26695 orthologs with putative functional assignments^a

Gene no. in:		Gene name	Function
J99	26695
Amino acid biosynthesis
General
206	0220		Aminotransferase
568	0624		Aminotransferase
632	0696		Hydantoin utilization
633	0695		Hydantoin utilization
673	0736		Aminotransferase
976	0405		Aminotransferase
Aromatic amino acid family
122	0134	aroF	Phospho-2-dehydro-3-deoxyheptonate aldolase
145	0157	aroK	Shikamate kinase I
268	0283	aroB	3-Dehydroquinate synthase
386	1038	aroD	3-Dehydroquinate dehydratase
608	0663	aroC	Chorismate synthase
980	0401	aroA	3-Phosphoshikimate 1-carboxyvinyl transferase
1170	1249	aroE	Shikimate 5-dehydrogenase
1198	1277	trpA	Tryptophan synthase alpha chain
1199	1278	trpB	Tryptophan synthase beta chain
1200	1279	trpC	Indole-3-glycerol phosphate synthase
1201	1280	trpD	Anthranilate phosphoribosyltransferase
1202	1281	trpG	Anthranilate synthase component II
1203	1282	trpE	Anthranilate synthase component I
1294	1380	tyrA	Prephenate dehydrogenase
Aspartate family
90	0098	thrC	Threonine synthase
98	0106	metB	Cystathionine gamma-synthase
198	0212	dapE	Succinyl-diaminopimelate desuccinylase
275	0290	lysA	Diaminopimelate decarboxylase
375	1050	thrB	Homoserine kinase
410	1013	dapA	Dihydrodipicolinate synthase
460	0510	dapB	Dihydrodipicolinate reductase
513	0566	dapF	Diaminopimelate epimerase
570	0626	dapD	2,3,4,5-Tetrahydropyridine-2-carboxylate-N-succinyltransferase
594	0649	aspA	Aspartate ammonia-lyase
615	0672	aspB	Aspartate aminotransferase
761	0822	hom	Homoserine dehydrogenase
1114	1189	asd	Aspartate-semialdehyde dehydrogenase
1150	1229	lysC	Aspartokinase 2 alpha and beta subunits
Glutamate family
461	0512	glnA	Glutamine synthetase
1001	0380	gdhA	Glutamate dehydrogenase
1085	1158	proC	Pyrroline-5-carboxylate reductase
Pyruvate family
313	0330	ilvC	Ketol-acid reductoisomerase
1361	1468	ilvE	Branched-chain amino acid aminotransferase
Serine family
99	0107	cysK	Cysteine synthase
171	0183	glyA	Serine hydroxymethyltransferase
597	0652	serB	Phosphoserine phosphatase
984	0397	serA	Phosphoglycerate dehydrogenase
1133	1210	cysE	Serine acetyltransferase
Biosynthesis of cofactors, prosthetic groups, and carriers
Biotin
25	0029	bioD	Dethiobiotin synthetase
545	0598	bioF	8-Amino-7-oxononanoate synthase
910	0976	bioA	Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
1068	1140		Biotin activation protein
1298	1406	bioB	Biotin synthetase
Folic acid
278	0293	pabB	p-Aminobenzoate synthetase
388	1036	folK	7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase
524	0577	folD	Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
862	0928	folE	GTP cyclohydrolase I
863	0928	folE	GTP cyclohydrolase I
1153	1232	folP	Dihydropteroate synthase
1403	1510	folB	Dihydroneopterin aldolase
1454	1545	folC	Folylpolyglutamate synthase
Heme and porphyrin
150	0163	hemB	δ-Aminolevulinic acid dehydratase
222	0237	hemC	Porphobilinogen deaminase
224	0239	hemA	Glutamyl-tRNA reductase
291	0306	hemL	Glutamate-1-semialdehyde-2,1-aminomutase
551	0604	hemE	Uroporphyrinogen decarboxylase
610	0665	hemN	Oxygen-independent coproporphyrinogen III oxidase
1000	0381	hemG	Protoporphyrinogen oxidase
1005	0376	hemH	Ferrochelatase
1145	1224	hemD	Uroporphyrinogen III synthase
1147	1226	hemN	Oxygen-independent coproporphyrinogen III oxidase
Menaquinone and ubiquinone
225	0240	ispB	Octaprenyl-diphosphate synthase
864	0929	ispA	Geranyltransferase
1278	1360	ubiA	4-Hydroxybenzoate octaprenyltransferase
1369	1476	ubiD	Octaprenyl-4-hydroxybenzoate carboxy-lyase
1376	1483	ubiE	Ubiquinone/menaquinone biosynthesis methyltransferase
Molybdopterin
158	0172	moeA	Molybdopterin biosynthesis protein
705	0768	moaA	Molybdopterin cofactor biosynthetic protein
706	0769	mobA	Molybdopterin-guanine dinucleotide biosynthesis protein A
734	0798	moaC	Molybdenum cofactor biosynthesis protein C
735	0799	mog	Molybdopterin biosynthesis protein
736	0800	moaE	Molybdopterin-converting factor, subunit 2
737	0801	moaD	Molybdopterin-converting factor, subunit 1
750	0814	moeB	Molybdopterin-synthase sulfurylase
Pantothenate
6	0006	panC	Pantoate-β-alanine ligase
30	0034	panD	Aspartate-1-decarboxylase
367	1058	panB	3-Methyl-2-oxobutanoate hydroxymethyltransferase
779	0841	dfp	Pantothenate metabolism flavoprotein
Pyridoxine
328	0354	dxs	1-Deoxyxylulose-5-phosphate synthase
1489	1582	pdxJ	Pyridoxal phosphate synthetase
1490	1583	pdxA	Pyridoxal phosphate biosynthetic protein A
Riboflavin
2	0002	ribE	Riboflavin synthase beta chain
338	1087	ribF	Riboflavin kinase
738	0802	ribA	GTP cyclohydrolase II
740	0804	ribBA	GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase
1398	1505	ribD	Riboflavin-specific deaminase
1482	1574	ribC	Riboflavin synthase alpha chain
Thioredoxin, glutaredoxin, and glutathione
763	0824	trxA	Thioredoxin
764	0825	trxB	Thioredoxin reductase
1046	1118	ggt	Gamma-glutamyl transpeptidase
1091	1164	trxB	Thioredoxin reductase
1351	1458		Thioredoxin
Thiamine
781	0843	thiE	Thiamine phosphate pyrophosphorylase
782	0844	thiD	Phosphomethylpyrimidine kinase
783	0845	thiM	Hydroxyethylthiazole kinase
Pyridine nucleotides
312	0329	nadE	NH3-dependent NAD+ synthetase
1273	1355	nadC	Nicotinate-nucleotide pyrophosphorylase
1274	1356	nadA	Quinolinate synthetase
Cell envelope
Membranes and porins
7	0009		Outer membrane protein
21	0025		Outer membrane protein
73	0078		Outer membrane protein
	0079
117	0127		Outer membrane protein
195	0209		Outer membrane protein
212	0227		Outer membrane protein
214	0229	hopA	Outer membrane protein—porin
237	0252		Outer membrane protein
238	0253, 0254		Outer membrane protein
307	0324		Outer membrane protein
342	1083		Outer membrane protein
359	1066		Outer membrane protein
424	0472		Outer membrane protein
429	0477		Outer membrane protein
438	0486		Outer membrane protein
439	0487		Outer membrane protein
456	0506		Outer membrane protein
514	0567		Inner membrane protein
581	0638		Outer membrane protein
600	0655		Outer membrane protein
614	0671		Outer membrane protein
634	0694		Outer membrane protein
645	0706	hopE	Outer membrane protein—porin
649	0710		Outer membrane protein
659	0722		Outer membrane protein
662	0725		Outer membrane protein
663	0726		Outer membrane protein
719	0782		Outer membrane protein
725	0788		Outer membrane protein
732	0796		Outer membrane protein
777	0839		Outer membrane protein
810	0876	frpB	Iron-regulated outer membrane protein
833	1243	babB	Outer membrane protein—adhesin
848	0912	hopC	Outer membrane protein—porin
849	0913	hopB	Outer membrane protein—porin
850	0914		Outer membrane protein
851	0915, 0916	frpB	Iron-regulated outer membrane protein
857	0923		Outer membrane protein
870			Outer membrane protein
1008	0373		Outer membrane protein
1022	0358		Outer membrane protein
1034	1107		Outer membrane protein
1040	1113		Outer membrane protein
1054	1125		Outer membrane protein
1083	1156		Outer membrane protein
1084	1157		Outer membrane protein
1094	1167		Outer membrane protein
1103	1177		Outer membrane function
1138	1215, 1216	imp	Role in outer membrane permeability
1164	0896	babA	Outer membrane protein—adhesin
1261	1342		Outer membrane protein
1343	1450		Inner membrane protein
1346	1453		Outer membrane protein
1349	1456	lpp20	Conserved lipoprotein
1360	1467		Outer membrane protein
1362	1469		Outer membrane protein
1394	1501		Outer membrane protein
1405	1512	frpB	Iron-regulated outer membrane protein
1432	1395		Outer membrane protein
1472	1564		Outer membrane protein
1479	1571		Outer membrane protein
Murein sacculus and peptidoglycan
445	0493	mraY	Phospho-N-acetylmuramoyl-pentapeptide-transferase
446	0494	murD	UDP-N-acetylmuramoylalanine-d-glutamate ligase
496	0549	murI	Glutamate racemase
544	0597		Penicillin-binding protein
567	0623	murC	UDP-N-acetylmuramate-alanine ligase
590	0645		Lytic murein transglycosylase
593	0648	murA	UDP-N-acetylglucosamine enolpyruvyltransferase
675	0738	ddl	d-Alanine–d-alanine ligase
677	0740	murF	d-Alanyl–d-alanine-adding enzyme
709	0772	amiA	Probable N-acetylmuramoyl-l-alanine amidase
876	0941	alr	Alanine racemase, biosynthetic
1082	1155	murG	UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenoln-acetylglucosaminetransferase
1313	1418	murB	UDP-N-acetylenolpyruvoyl glucosamine reductase
1387	1494	murE	UDP-N-acetylmuramyl-tripeptide synthetase
1464	1556		Penicillin-binding protein
1473	1565		Penicillin-binding protein
Surface polysaccharides, lipopolysaccharides, and antigens
3	0003	kdsA	3-Deoxy-d-manno-octulosonic acid 8-phosphate synthase
37	0043	manA/manC	Phosphomannose isomerase/GDP-mannose pyrophosphorylase
38	0044	Gmd	GDP-d-mannose dehydratase
39	0045		Sugar nucleotide biosynthesis
70	0075	glmM	Phosphoglucosamine mutase
86	0093, 0094		α-(1,2)-Fucosyltransferase
147	0159		Lipopolysaccharide biosynthesis protein
166	0178	neuB	Sialic acid synthase
182	0196	lpxD	UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acetyltransferase
194	0208		Lipopolysaccharide biosynthesis protein
215	0230	kdsB	3-Deoxy-manno-octulosonate cytidylyltransferase
264	0279	waaC	Lipopolysaccharide heptosyltransferase-1
265	0280	waaM	Lipid A biosynthesis acyltransferase
309	0326	neuA	Acylneuraminate cytidylyltransferase
311	0328	lpxK	Tetraacyldisaccharide-1-p 4′-kinase
373	1052	lpxC	UDP-3-O-[3-hydroxymyristoyl]-N-acetylglucosamine deacetylase
562			Lipopolysaccharide biosynthesis protein
563	0619		Lipopolysaccharide biosynthesis protein
596	0651	fucT	α-(1,3)-Fucosyltransferase
620	0679		Lipopolysaccharide biosynthesis protein
741	0805		Lipopolysaccharide biosynthesis protein
765	0826		Lipopolysaccharide biosynthesis protein
778	0840		Sugar nucleotide biosynthesis protein
791	0857	gmhA	Phosphoheptose isomerase
792	0858	waaE	ADP-d-glycero-d-mannoheptose synthase
793	0859	gmhD	ADP-l-glycero-d-mannoheptose-6-epimerase
801	0867	lpxB	Lipid-A-disaccharide synthase
820			Lipopolysaccharide biosynthesis protein
891	0957	waaA	3-Deoxy-d-manno-octulosonic-acid transferase
963	0421		Polysaccharide biosynthesis protein
1002	0379	fucU	α-(1,3)-Fucosyltransferase
1015	0366		Sugar nucleotide biosynthesis
1020	0360	galE	UDP-glucose 4-epimerase
1031	1105		Lipopolysaccharide biosynthesis protein
1032			Lipopolysaccharide biosynthesis protein
1116	1191	waaF	ADP-heptose-lipopolysaccharide heptosyltransferase II
1196	1275	manB	Phosphomannomutase
1289	1375	lpxA	UDP-N-acetylglucosamine acyltransferase
1311	1416		Lipopolysaccharide biosynthesis protein
1368	1475	kdtB	Lipopolysaccharide core biosynthesis protein
1488	1581	wecA	Undecaprenyl-phosphate-α-N-acetylglucosaminyltransferase
Surface structures
107	0115	flaB	Flagellin B
159	0173	fliR	Flagellar biosynthesis protein
217	0232		Motility protein
231	0246	flgI	Flagellar P-ring protein
280	0295	flgL	Flagellar hook-associated protein 3 (hap3)
308	0325	flgH	Flagellar L-ring protein precursor (basal body L-ring protein)
310	0327	flaG	Flagellar biosynthesis protein
325	0351	fliF	Flagellar M-ring protein
326	0352	fliG	Flagellar motor switch protein
327	0353	fliH	Flagellar export apparatus
333	1092	flgG	Flagellar basal-body rod protein
383	1041	flhA	Flagellar biosynthesis protein
389	1035	flhF	Flagellar biosynthesis protein
393	1031	fliM	Flagellar motor switch protein
394	1030		Flagellar motor switch protein
444	0492		Paralogue of hpaA
531	0584	fliN	Flagellar motor switch protein
548	0601	flaA	Flagellin A
625	0684, 0685	fliP	Flagellar biosynthesis protein
688	0751		Flagellin protein
689	0752	fliD	Flagellar hook-associated protein 2 (hap2)
690	0753	fliS	Flagellar protein
707	0770	flhB	Flagellar biosynthesis protein
733	0797	hpaA	Neuraminyllactose-binding hemagglutinin precursor
745	0809	fliL	Flagellar biosynthesis protein
751	0815	motA	Chemotaxis protein (motility protein a)
752	0816	motB	Flagellar motor protein
804	0870	flgE	Flagellar hook protein
843	0907		Flagellar biosynthesis protein
844	0908		Flagellar basal-body/rod/hook protein
971	0410		Paralogue of hpaA
1047	1119	flgK	Flagellar hook-associated protein 1 (Hap1)
1117	1192		Motility protein
1195	1274	pflA	Flagellar functional protein
1314	1419	fliQ	Flagellar biosynthesis protein
1315	1420	fliI	Flagellum-specific ATP synthase
1355	1462		Motility protein
1465	1557	fliE	Flagellar hook–basal-body complex protein
1466	1558	flgC	Flagellar basal-body rod protein
1467	1559	flgB	Flagellar basal-body rod protein
1483	1575	flhB	Flagellar biosynthesis protein
1492	1585	flgG	Flagellar basal-body rod protein (distal rod protein)
Cellular processes
General
4	0004	icfA	Carbonic anhydrase
161	0175		Peptidyl-prolyl cis-trans isomerase
183	0197	metK	S-Adenosylmethionine synthetase
228	0243	napA	Neutrophil-activating protein A
466	0517	era	GTP-binding protein
678	0741		HIT family protein
865	0930	surE	Stationary-phase protein
977	0404		HIT family protein
1112	1186		Carbonic anhydrase
Cell division
314	0331	minD	Cell division inhibitor
315	0332	minE	Cell division topological specificity factor
335	1090	ftsK	Septum formation protein
680	0743	rodA	Rod shape-determining protein
912	0978	ftsA	Septum formation protein
913	0979	ftsZ	GTPase in circumferential ring formation
1086	1159	fic	cAMP-induced cell filamentation protein
1287	1373	mreB	Rod shape-determining protein
1468	1560	rodA	Rod shape-determining protein
Cell killing
274	0289		Vacuolating cytotoxin (VacA) paralogue
339	1086	hlyA	Hemolysin
556	0609, 0610		Vacuolating cytotoxin (VacA) paralogue
819	0887	vacA	Vacuolating cytotoxin
856	0922		Vacuolating cytotoxin (VacA) paralog
Cag island proteins and transposable elements
15	0017	virB4a	DNA transfer protein
36	0041, 0042	virB10	DNA transfer protein
469	0520	orf6	Cag island protein
470	0521	orf7	Cag island protein
471	0522	orf8	Cag island protein
472	0523	orf9	Cag island protein
473	0524	virD4	Cag island protein, DNA transfer protein
474	0525	virB11a	Cag island protein, DNA transfer protein
475	0526	orf12	Cag island protein
476	0527	orf13/14	Cag island protein
477	0528	orf15	Cag island protein
478	0529	orf16	Cag island protein
479	0530	orf17	Cag island protein
480	0531	orf18	Cag island protein
481	0532	cagT	Cag island protein
482	0534	cagS	Cag island protein
483	0535	cagQ	Cag island protein
484	0536	cagP	Cag island protein
485	0537	cagM	Cag island protein
486	0538	cagN	Cag island protein
487	0539	cagL	Cag island protein
488	0540	cagI	Cag island protein
489	0541	cagH	Cag island protein
490	0542	cagG	Cag island protein
491	0543	cagF	Cag island protein
492	0544	cagE	DNA transfer protein (Agrobacterium VirB4 homologue)
493	0545	cagD	Cag island protein
494	0546	cagC	Cag island protein
495	0547	cagA	Cag island protein, cytotoxicity-associated immunodominant antigen
826		tnpB	IS606 transposase
827		tnpA	IS606 transposase
917		virB4b	DNA transfer protein
918		virB4c	DNA transfer protein
1279	1361	comEC	DNA transfer protein
1316	1421	virB11b	DNA transfer protein
Chaperones
8	0010	groEL	60-kDa chaperone
9	0011	groES	10-kDa chaperone
101	0109	dnaK	70-kDa chaperone
102	0110	grpE	24-kDa chaperone
196	0210	htpG	90-kDa chaperone
400	1024	dnaJ2	Cochaperone with DnaK
861	0927	htpX	Stress protein
1252	1332	dnaJ1	Cochaperone with DnaK
Detoxification
809	0875	katA	Catalase
991	0390	tpx	Thiol peroxidase
992	0389	sodF	Iron-dependent superoxide dismutase
1471	1563	tsaA	Peroxidase
Protein and peptide secretion
69	0074	lspA	Lipoprotein signal peptidase
168	0180	lnt	Apolipoprotein N-acyltransferase
329	0355	lepA	GTP-binding protein
523	0576	lepB	Signal peptidase I
700	0763	ftsY	Functional homolog of srp receptor
723	0786	secA	Preprotein translocase subunit
731	0795	tig	Trigger factor
889	0955	lgt	Prolipoprotein diacylglyceryl transferase
1079	1152	ffh	Signal recognition particle protein
1126A	1203A	secE	Preprotein translocase subunit
1176	1255	secG	Protein export membrane protein
1220	1300	secY	Preprotein translocase subunit
1449	1550	secD	Protein export membrane protein
1450	1549	secF	Protein export membrane protein
Phosphorus compounds
413	1010	ppk	Polyphosphate kinase
564	0620	ppa	Inorganic pyrophosphatase
Polyamine biosynthesis
18	0020	nspC	Carboxynorspermidine decarboxylase
771	0832	speE	Spermidine synthase
962	0422	speA	Arginine decarboxylase
Urea
62	0067	ureH	Urease accessory protein
63	0068	ureG	Urease accessory protein
64	0069	ureF	Urease accessory protein
65	0070	ureE	Urease accessory protein
67	0072	ureB	Urease beta subunit
68	0073	ureA	Urease alpha subunit
DNA replication
10	0012	dnaG	DNA primase
108	0116	topA	DNA topoisomerase I
199	0213	gidA	Glucose-inhibited division protein A
362	1063	gidB	Glucose-inhibited division protein B
452	0500	dnaN	DNA polymerase III, beta chain
453	0501	gyrB	DNA gyrase subunit B
558	0615	lig	DNA ligase
641	0701	gyrA	DNA gyrase subunit A
655	0717	dnaX	DNA polymerase III subunits gamma and tau
847	0911		ATP-dependent helicase
919		topA	Topoisomerase I
931		topA	Topoisomerase I
994	0387	priA	Primosomal protein n′ (replication factor y)
1152	1231	holB	DNA polymerase III subunit delta′
1166	1245	ssb	Single-strand binding protein
1280	1362	dnaB	Replicative DNA helicase
1353	1460	dnaE	DNA polymerase III, alpha chain
1363	1470	polA	DNA polymerase I
1371	1478	rep	ATP-dependent DNA helicase
1412	1523	recG	ATP-dependent DNA helicase
1417	1529	dnaA	Chromosomal replication initiator protein
1438	1387		DNA polymerase III
1446	1553	pcrA	ATP-dependent helicase
DNA restriction, modification, recombination, and repair
43	0050		Type II DNA modification enzyme (methyltransferase)
44			Type II DNA modification enzyme (methyltransferase)
45			Type II DNA modification enzyme (methyltransferase)
46			Type II restriction enzyme
84	0091		Type II restriction enzyme
85	0092		Type II DNA modification enzyme (methyltransferase)
130	0142	mutY	A/G-specific adenine glycosylase
141	0153	recA	Recombination protein
164			Restriction enzyme
209	0223	radA	DNA repair protein
243	0259	xseA	Exodeoxyribonuclease large subunit
244	0260		Type II DNA modification enzyme (methyltransferase)
248	0263		Type II DNA modification enzyme (methyltransferase)
306	0323		Endonuclease
322	0348	recJ	Single-stranded-DNA-specific exonuclease
366	1059	ruvB	Holliday junction DNA helicase
414		hsdS1	Type I restriction enzyme (specificity subunit)
415	0463	hsdM1	Type I restriction enzyme (modification subunit)
416	0464	hsdR1	Type I restriction enzyme (restriction subunit)
430	0478		Type II DNA modification enzyme (methyltransferase)
433	0481		Type II DNA modification enzyme (methyltransferase)
435	0483		Type II DNA modification enzyme (methyltransferase)
532	0585	nth	Endonuclease III
549	0602		Endonuclease III
565	0621	mutS	DNA mismatch repair protein
606	0661	rnhA	RNase HI
617	0675		Integrase-recombinase protein (xerCD family)
618	0676	ogt	Methylated-DNA–protein-cysteine methyltransferase
629			Type II DNA modification enzyme (methyltransferase)
630			Type II restriction enzyme
644	0705	uvrA	Excinuclease ABC subunit A
726		hsdS	Type I restriction enzyme (specificity subunit)
756			Type II DNA modification enzyme (methyltransferase)
760	0821	uvrC	Excinuclease ABC subunit C
784	0846	hsdR2	Type I restriction enzyme (restriction subunit)
785	0848, 0849	hsdS2	Type I restriction enzyme (specificity subunit)
786	0850	hsdM2	Type I restriction enzyme (modification subunit)
811	0877	ruvC	Crossover junction endodeoxyribonuclease
815	0883	ruvA	Holliday junction DNA helicase
846	0910		Type II DNA modification enzyme (methyltransferase)
859	0925	recR	Recombination protein
941	0995		Integrase/recombinase (xerCD family)
951			Integrase/recombinase (xerCD family)
1012	0369		Type II DNA modification enzyme (methyltransferase)
1041	1114	uvrB	Excinuclease ABC subunit B
1050	1121		Type II DNA modification enzyme (methyltransferase)
1131	1208	M.HpyI	Type II DNA modification enzyme (methyltransferase)
1149	1228	mutT	dGTP pyrophosphohydrolase
1243	1323	rnhB	RNase HII
1266	1347	ung	Uracil-DNA glycosylase
1271	1352		Type II DNA modification enzyme (methyltransferase)
1284			Type II DNA modification enzyme (methyltransferase)
1295	1382		Endonuclease
1296		mod1	Type III DNA modification enzyme (methyltransferase)
1297		res1	Type III restriction enzyme
1364	1471		Type II restriction enzyme
1365	1472		Type II DNA modification enzyme (methyltransferase)
1409			Type II DNA modification enzyme (methyltransferase)
1410	1521	res2	Type III restriction enzyme
1411	1522	mod2	Type III DNA modification enzyme (methyltransferase)
1415	1526	exoA	Exodeoxyribonuclease
1422		hsdS3	Type I restriction enzyme (specificity subunit)
1423	1403	hsdM3	Type I restriction enzyme (modification subunit)
1424	1402	hsdR3	Type I restriction enzyme (restriction subunit)
1434	1393	recN	DNA repair protein
1442	1366		Type II restriction enzyme
Energy metabolism
Amino acids and amines
120	0132	sdaB	l-Serine/l-Threonine deaminase
279	0294	aimE	Aliphatic amidase
585			3-Hydroxyacid dehydrogenase
661	0723	ansB	l-Asparaginase II
1159	1238		Aliphatic amidase
1427	1399	rocF	Arginase
1428	1398	ald	l-Alanine dehydrogenase
ATP-proton motive force interconversion
767	0828	atpB	ATP synthase F0, subunit a
1059	1131	atpC	ATP synthase F1, subunit epsilon
1060	1132	atpD	ATP synthase F1, subunit beta
1061	1133	atpG	ATP synthase F1, subunit gamma
1062	1134	atpA	ATP synthase F1, subunit alpha
1063	1135	atpH	ATP synthase F1, subunit delta
1064	1136	atpF	ATP synthase F0, subunit b
1065	1137	atpX	ATP synthase B′
1135	1212	atpE	ATP synthase F0, subunit c
Electron transport
40	0047	hypE	Hydrogenase expression/formation protein
48	0056	putA	Proline/pyrroline-5-carboxylate dehydrogenase
132	0144	fixN	Cytochrome oxidase (CBB3-TYPE)
133	0145	fixO	Cytochrome oxidase (CBB3-TYPE)
134	0146	fixQ	Cytochrome oxidase (CBB3-TYPE)
135	0147	fixP	Cytochrome oxidase (CBB3-TYPE)
177	0191	frdB	Fumarate reductase
178	0192	frdA	Fumarate reductase
179	0193	frdC	Fumarate reductase
250	0265	ccdA	Cytochrome c biogenesis protein
262	0277		Ferredoxin
459	0509	glcD	Glycolate oxidase
574	0631	hyaA	Hydrogenase, small subunit
575	0632	hyaB	Hydrogenase, large subunit
576	0633	hyaC	Hydrogenase, cytochrome subunit
577	0634	hyaD	Hydrogenase expression/formation protein
611	0666	glpC	Glycerol-3-phosphate dehydrogenase
803	0869	hypA	Hydrogenase expression/formation protein
835	0898	hypD	Hydrogenase expression/formation protein
836	0899	hypC	Hydrogenase expression/formation protein
837	0900	hypB	Hydrogenase expression/formation protein
878	0943	dadA	d-Amino acid dehydrogenase
895	0961	gpsA	Glycerol-3-phosphate dehydrogenase (NAD+)
974	0407		S/N-oxide reductase
1003	0378		Cytochrome c biogenesis protein
1035	1108	porG	Pyruvate ferrodoxin oxidoreductase
1036	1109	porD	Pyruvate ferrodoxin oxidoreductase
1037	1110	porA	Pyruvate ferrodoxin oxidoreductase
1038	1111	porB	Pyruvate ferrodoxin oxidoreductase
1088	1161	fldA	Flavodoxin
1090	1163	fixS	Component of cation transport for cbb3-type oxidase
1143	1222	dld	d-Lactate dehydrogenase
1148	1227		Periplasmic cytochrome c-553
1181	1260	nuoA	NADH oxidoreductase I
1182	1261	nuoB	NADH oxidoreductase I
1183	1262	nuoC	NADH oxidoreductase I
1184	1263	nuoD	NADH oxidoreductase I
1185	1264	nuoE	NADH oxidoreductase I
1186	1265	nuoF	NADH oxidoreductase I
1187	1266	nuoG	NADH oxidoreductase I
1188	1267	nuoH	NADH oxidoreductase I
1189	1268	nuoI	NADH oxidoreductase I
1190	1269	nuoJ	NADH oxidoreductase I
1191	1270	nuoK	NADH oxidoreductase I
1192	1271	nuoL	NADH oxidoreductase I
1193	1272	nuoM	NADH oxidoreductase I
1194	1273	nuoN	NADH oxidoreductase I
1354	1461		Cytochrome c peroxidase
1401	1508	fixG	Component of cation transport for cbb3-type oxidase
1459	1540	petA	Ubiquinol cytochrome c oxidoreductase, 2Fe-2S subunit
1460	1539	petB	Ubiquinol cytochrome c oxidoreductase, cytochrome b subunit
1461	1538	petC	Ubiquinol cytochrome c oxidoreductase, cytochrome c1 subunit
Entner-Doudoroff pathway
1025	1099	eda	2-Keto-3-deoxy-6-phosphogluconate aldolase
1026	1100	edd	Phosphogluconate dehydratase
Fermentation
840	0903	ackA	Acetate kinase
841	0904, 0905	pta	Phosphotransacetylase
1030	1104		Zinc-dependent alcohol dehydrogenase
1429			Zinc-dependent alcohol dehydrogenase
Gluconeogenesis
111	0121	ppsA	Phosphoenolpyruvate synthase
142	0154	eno	Enolase
162	0176	fba	Fructose-bisphosphate aldolase
180	0194	tpi	Triose-phosphate isomerase
855	0921	gap	Glyceraldehyde-3-phosphate dehydrogenase
908	0974	pgm	2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
1093	1166	pgi	Glucose-6-phosphate isomerase
1264	1345	pgk	Phosphoglycerate kinase
1265	1346	gap	Glyceraldehyde 3-phosphate dehydrogenase
1440	1385	fbp	Fructose-1,6-bisphosphatase
Phosphopentose pathway
337	1088	tktA	Transketolase
521	0574	rpi	Ribose 5-phosphate isomerase
1027	1101	zwf	Glucose-6-phosphate-1-dehydrogenase
1388	1495	tal	Transaldolase
1439	1386	rpe	Ribulose-phosphate-3-epimerase
Sugars
1029	1103	glk	Glucokinase
Tricarboxylic acid cycle
22	0026	gltA	Citrate synthase
23	0027	icd	Isocitrate dehydrogenase
536	0588	oorD	Subunit of 2-oxoglutarate oxidoreductase
537	0589	oorA	Subunit of 2-oxoglutarate oxidoreductase
538	0590	oorB	Subunit of 2-oxoglutarate oxidoreductase
539	0591	oorC	Subunit of 2-oxoglutarate oxidoreductase
716	0779	acnB	Aconitate hydratase
1245	1325	fumC	Fumarase
Other
88	0096		Keto-acid dehydrogenase
586	0642		Oxidoreductase
888	0954		Aldehyde dehydrogenase
1023	0357		Oxidoreductase
1028	1102		Dehydrogenase
1345	1452	thdF	Thiophene/furan oxidation protein
Fatty acid and phospholipid metabolism
83	0090	fabD	Malonyl-CoA-ACP transacylase
176	0190		Cardiolipin synthase
181	0195	fabI	Enoyl-ACP reductase
187	0201	plsX	Fatty acid/phospholipid synthesis protein
188	0202	fabH	β-Ketoacyl-ACP synthase III
201	0215	cdsA	CDP-diacylglycerol synthase
354	1071	pssA	Phosphatidylserine synthase
407	1016	pgsA	Phosphatidylglycerophosphate synthase
409	1014		Short-chain dehydrogenase
451	0499	pldA	Phospholipase A1
504	0557	accA	Acetyl-CoAa carboxylase subunit A
505	0558	fabB	β-Ketoacyl-ACP synthase I
506	0559	acpP	ACP
508	0561	fabG	Acetyl-CoA carboxylase subunit A
636	0692	scoB	3-Oxoacid CoA-transferase, subunit B
637	0691	scoA	3-Oxoacid CoA-transferase, subunit A
638	0690	thl	Acetyl-CoA acetyltransferase
640	0700	dgkA	Diacylglycerol kinase
674	0737	pgpA	Phosphatidylglycerophosphatase A
744	0808	acpS	Holo-ACP synthase
805	0871	cdh	CDP-diacylglycerol pyrophosphatase
884	0950	accD	Acetyl-CoA carboxylase subunit B
968	0416	cfa	Cyclopocyclopropane fatty acid synthase
1010	0371	accB	Biotin carboxyl carrier protein
1011	0370	accC	Biotin carboxylase
1267	1348	plsC	1-Acyl-SN-glycerol-3-phosphate acyltransferase
1275	1357	psd	Phosphatidylserine decarboxylase
1290	1376	fabZ	Hydroxymyristoyl-ACP dehydratase
Purines, pyrimidines, nucleosides and nucleotides
2′-Deoxyribonucleotide metabolism
621	0680	nrdA	Ribonucleoside-diphosphate reductase 1 alpha chain
799	0865	dut	Deoxyuridine 5′-triphosphate nucleotidohydrolase
1009	0372	dcd	Deoxycytidine triphosphate deaminase
1016	0364	nrdB	Ribonucleoside-diphosphate reductase 1 beta chain
Purine ribonucleotide biosynthesis
1039	1112	purB	Adenylosuccinate lyase
1140	1218	purD	Glycinamide ribonucleotide synthetase
1327	1434	purU	Formyltetrahydrofolate hydrolase
Pyrimidine ribonucleotide biosynthesis
5	0005	pyrF	Orotidine 5′-phosphate decarboxylase
184	0198	ndk	Nucleoside diphosphate kinase
251	0266	pyrC1	Dihydroorotase
323	0349	pyrG	CTP synthase
341	1084	pyrB	Aspartate carbamoyltransferase catalytic chain
412	1011	pyrD	Dihydroorotate dehydrogenase
528	0581	pyrC2	Dihydroorotase
714	0777	pyrH	Uridylate kinase
853	0919	pyrA1	Carbamoyl-phosphate synthase large chain
1158	1237	pyrA2	Carbamoyl-phosphate synthase small chain
1178	1257	pyrE	Orotate phosphoribosyltransferase
Salvage and interconversion of nucleosides and nucleotides
96	0104	cpdB	2′,3′-Cyclic nucleotide 2′-phosphodiesterase
239	0255	purA	Adenylosuccinate synthetase
304	0321	gmk	Guanylate kinase
519	0572	apt	Adenine phosphoribosyltransferase
561	0618	adk	Adenylate kinase
672	0735	gpt	Xanthine-guanine phosphoribosyltransferase
679	0742	prsA	Phosphoribosyl pyrophosphate synthetase
768	0829	guaB	Inosine-5′-monophosphate dehydrogenase
790	0854	guaC	GMP reductase
972	0409	guaA	GMP synthetase
1104	1178	deoD	Purine nucleoside phosphorylase
1105	1179	deoB	Phosphopentomutase
1367	1474	tmk	Thymidylate kinase
Sugar-nucleotide biosynthesis and conversions
591	0646	galU	UTP-glucose-1-phosphate uridylyltransferase
624	0683	glmU	UDP-N-acetylglucosamine pyrophosphorylase
1420	1532	glmS	Glutamine fructose-6-phosphate minotransferase
Regulatory functions
General
41	0048		Transcriptional regulator
81	0088	rpoD	RNA polymerase sigma 70 factor
151	0164, 0165		Histidine kinase sensor protein
152	0166		Transcriptional regulator
229	0244		Histidine kinase sensor protein
263	0278	gppA	Guanosine-5′-triphosphate,3′-diphosphate pyrophosphatase
381	1043		Transcriptional regulator
392	1032	fliA	RNA polymerase sigma 28 factor
397	1027	fur	Ferric uptake regulation protein
399	1025		Transcriptional regulator
403	1021		Transcriptional regulator
643	0703		Transcriptional regulator
652	0714	rpoN	RNA polymerase sigma-54 factor
664	0727		Transcriptional regulator
712	0775	spoT	Guanosine-3′,5′-bis(diphosphate)-3′-pyrophosphohydrolase
981	0400	lytB	Lysis tolerance protein
1207	1287		Transcriptional regulator
1282	1364		Histidine kinase sensor protein
1283	1365		Transcriptional regulator
1335	1442	csrA	Carbon storage regulator
1443	1365		Transcriptional regulator
1480	1572	dniR	Regulatory protein
Chemotaxis and motility
17	0019	cheV1	Chemotaxis protein
75	0082		MCP
91	0099		MCP
95	0103		MCP
358	1067	cheY	Response regulator
546	0599		MCP
559	0616	cheV2	Chemotaxis protein
988	0393	cheV3	Chemotaxis protein
989	0392	cheA	Histidine kinase
990	0391	cheW	Histidine kinase-MCP coupling protein
Transcription
Degradation of RNA
1136	1213	pnp	Polyribonucleotide nucleotidyltransferase
1169	1248	vacB	RNase II family protein
1299	1407	rbn	RNase N
DNA-dependent RNA polymerase
1121	1198	rpoB	DNA-directed RNA polymerase, beta subunit
1213	1293	rpoA	DNA-directed RNA polymerase, alpha subunit
1458	1541	mfd	Transcription-repair coupling factor
Transcription factors
1	0001	nusB	Transcription termination
497	0550	rho	Transcription termination factor
800	0866	greA	Transcription elongation factor (transcript cleavage factor)
1126	1203	nusG	Transcription antitermination protein
1407	1514	nusA	N utilization substance protein A
RNA processing
583	0640	pcnB	Polynucleotide adenylyltransferase
607	0662	rnc	RNase III
Translation
Aminoacyl-tRNA synthetases
113	0123	thrS	Threonyl-tRNA synthetase
170	0182	lysS	Lysyl-tRNA synthetase
223	0238	proS	Prolyl-tRNA synthetase
302	0319	argS	Arginyl-tRNA synthetase
428	0476	gltX	Glutamyl-tRNA synthetase
560	0617	aspS	Aspartyl-tRNA synthetase
588	0643	gltX	Glutamyl-tRNA synthetase
711	0774	tyrS	Tyrosyl-tRNA synthetase
818	0886	cysS	Cysteinyl-tRNA synthetase
894	0960	glyQ	Glycyl-tRNA synthetase alpha chain
906	0972	glyS	Glycyl-tRNA synthetase beta chain
967	0417	metG	Methionyl-tRNA synthetase
978	0403	pheS	Phenylalanyl-tRNA synthetase alpha chain
979	0402	pheT	Phenylalanyl-tRNA synthetase beta chain
1080	1153	valS	Valyl-tRNA synthetase
1115	1190	hisS	Histidyl-tRNA synthetase
1162	1241	alaS	Alanyl-tRNA synthetase
1174	1253	trpS	Tryptophanyl-tRNA synthetase
1317	1422	ileS	Isoleucyl-tRNA synthetase
1373	1480	serS	Seryl-tRNA synthetase
1452	1547	leuS	Leucyl-tRNA synthetase
Degradation of proteins, peptides and glycopeptides
29	0033	clpA	ATP-dependent protease, ATP-binding subunit
155	0169		Protease
249	0264	clpB	Heat shock protein
271	0286	ftsH	ATP-dependent Zn metallopeptidase
356	1069	ftsH	ATP-dependent Zn metallopeptidase
387	1037	pepQ	Proline peptidase
405	1019	htrA	Protease DO
411	1012		Zn protease
422	0470	pepF	Oligopeptidase
464	0515	hslV	Heat shock protein
465	0516	hslU	Heat shock protein
517	0570	pepA	Aminopeptidase
602	0657		Processing protease
603	0658	gatB	Glu-tRNA amidotransferase, subunit B
730	0794	clpP	ATP-dependent protease, proteolytic subunit
769	0830	gatA	Glu-tRNA amidotransferase, subunit A
909	0975	gatC	Glu-tRNA amidotransferase, subunit C
999	0382		Zn-metallo protease
1269	1350	prc	Carboxyl-terminal protease
1288	1374	clpX	ATP-dependent protease, ATP-binding subunit
1293	1379	lon	ATP-dependent protease 1a
1328	1435	sppA	Protease
1491	1584	ydiE	O-Sialoglycoprotein endopeptidase
Nucleoproteins
774	0835		DNA-binding protein HU
1052	1123	slyD	FKBP-type peptidyl-prolyl cis-trans isomerase
Protein modification
210	0224		Peptide methionine sulfoxide reductase
729	0793	def	Polypeptide deformylase
1017	0363	pcm	Protein-l-isoaspartate O-methyltransferase
1219	1299	map	Methionine aminopeptidase
1334	1441	ppiA	Peptidyl-prolyl cis-trans isomerase
Ribosomal proteins, synthesis and modification
71	0076	rpsT	30S ribosomal protein S20
76	0083	rpsI	30S ribosomal protein S9
77	0084	rplM	50S ribosomal protein L13
115	0125	rpmI	50S ribosomal protein L35
116	0126	rplT	50S ribosomal protein L20
186	0200	rpmF	50S ribosomal protein L32
281	0296	rplU	50S ribosomal protein L21
282	0297	rpmA	50S ribosomal protein L27
357	1068	prmA	Ribosomal protein L11 methyltransferase
378	1047	rbfA	Ribosome-binding factor A
384	1040	rpsO	30S ribosomal protein S15
443	0491	rpmB	50S ribosomal protein L28
463	0514	rplI	50S ribosomal protein L9
498	0551	rpmE	50S ribosomal protein L31
509	0562	rpsU	30S ribosomal protein S21
982	0399	rpsA	30S ribosomal protein S1
1074	1147	rplS	50S ribosomal protein L19
1078	1151	rpsP	30S ribosomal protein S16
1119	1196	rpsG	30S ribosomal protein S7
1120	1197	rpsL	30S ribosomal protein S12
1122	1199	rplL	50S ribosomal protein L7/L12
1123	1200	rplJ	50S ribosomal protein L10
1124	1201	rplA	50S ribosomal protein L1
1125	1202	rplK	50S ribosomal protein L11
1127	1204	rpmG	50S ribosomal protein L33
1165	1244	rpsR	30S ribosomal protein S18
1167	1246	rpsF	30S ribosomal protein S6
1212	1292	rplQ	50S ribosomal protein L17
1214	1294	rpsD	30S ribosomal protein S4
1215	1295	rpsK	30S ribosomal protein S11
1217	1296	rpsM	30S ribosomal protein S13
1217	1297	rpmJ	50S ribosomal protein L36
1221	1301	rplO	50S ribosomal protein L15
1222	1302	rpsE	30S ribosomal protein S5
1223	1303	rplR	50S ribosomal protein L18
1224	1304	rplF	50S ribosomal protein L6
1225	1305	rpsH	30S ribosomal protein S8
1226	1306	rpsN	30S ribosomal protein S14
1227	1307	rplE	50S ribosomal protein L5
1228	1308	rplX	50S ribosomal protein L24
1229	1309	rplN	50S ribosomal protein L14
1230	1310	rpsQ	30S ribosomal protein S17
1231	1311	rpmC	50S ribosomal protein L29
1232	1312	rplP	50S ribosomal protein L16
1233	1313	rpsC	30S ribosomal protein S3
1234	1314	rplV	50S ribosomal protein L22
1235	1315	rpsS	30S ribosomal protein S19
1236	1316	rplB	50S ribosomal protein L2
1237	1317	rplW	50S ribosomal protein L23
1238	1318	rplD	50S ribosomal protein L4
1239	1319	rplC	50S ribosomal protein L3
1240	1320	rpsJ	30S ribosomal protein S10
1340	1447	rpmH	50S ribosomal protein L34
1389	1496	rplY	50S ribosomal protein L25
1445	1554	rpsB	30S ribosomal protein S2
tRNA modification
266	0281	tgt	Queuine-tRNA-ribosyltransferase
363	1062	queA	S-Adenosylmethionine tRNA ribosyltransferase-isomerase
1019	0361	truA	Pseudouridylate synthase I
1069	1141	fmt	Methionyl-tRNA formyltransferase
1075	1148	trmD	tRNA (guanine-n1)-methyltransferase
1254	1335	trmU	tRNA(5-methylaminomethyl-2-thiouridylate)-methyltransferase
1310	1415	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase
1341	1448	rnpA	RNase protein component
1390	1497	pth	Peptidyl-tRNA hydrolase
1406	1513	selA	l-Seryl-tRNA selenium transferase
Translation factors
72	0077	prfA	Peptide chain release factor 1
114	0124	infC	Translation initiation factor IF-3
157	0171	prfB	Peptide chain release factor 2 (RF-2)
163	0177	efp	Elongation factor P (EF-P)
232	0247	deaD	ATP-dependent RNA helicase dead
377	1048	infB	Translation initiation factor IF-2
1118	1195	fusA	Elongation factor G (EF-G)
1128	1205	tufA	Elongation factor TU (EF-TU)
1177	1256	frr	Ribosome recycling factor (ribosome-releasing factor [RRF])
1218	1298	infA	Translation initiation factor IF-1
1322	1431	ksgA	Dimethyladenosine transferase
1444	1555	tfs	Elongation factor TS (EF-TS)
Transport and binding proteins
General
66	0071	ureI	Urea transporter
167	0179		ABC transporter, ATP-binding protein
200	0214		Transporter
235	0250		ABC transporter, ATP-binding protein
236	0251		ABC transporter, permease
300	0613		ABC transporter, ATP-binding protein
343	1082	msbA	Multidrug resistance protein
449	0497		Transporter
450	0498		Transporter
547	0600		Secretion/efflux ABC transporter, ATP-binding protein
553	0606		Efflux transporter
554	0607		Efflux transporter
653	0715		ABC transporter, ATP-binding protein
685	0748		ABC transporter, ATP-binding protein
754	0818		Osmoprotection binding protein
757	0818		Osmoprotection binding protein
758	0819		Osmoprotection ATP-binding protein
789	0853		ABC transporter, ATP-binding protein
806	0872	phnA	Alkylphosphonate uptake protein
871	0936	proP	Proline/betaine transporter
1055	1126	tolB	tonB-independent protein-uptake protein
1057	1129	exbD1	Biopolymer transport protein
1058	1130	exbB1	Biopolymer transport protein
1107	1181		Transporter
1129	1206		ABC transporter, ATP-binding protein
1141	1220		ABC transporter, ATP-binding protein
1320	1427		Histidine-rich metal-binding protein
1321	1432		Histidine- and glutamine-rich metal-binding protein
1338	1445	exbB3	Biopolymer transport protein
1339	1446	exbD3	Biopolymer transport protein
1484	1576		ABC transporter, ATP-binding protein
1485	1577		ABC transporter, permease
Amino acids, peptides, and amines
47	0055	putP	Sodium/proline symporter
121	0133	sdaC	l-Serine transporter
283	0298	dppA	Periplasmic dipeptide transport substrate-binding protein
284	0299	dppB	Dipeptide transport system permease protein
285	0300	dppC	Dipeptide transport system permease protein
286	0301	dppD	Dipeptide transport system ATP-binding protein
287	0302	dppF	Dipeptide transport system ATP-binding protein
406	1017		Amino acid permease
874	0939		Amino acid ABC transporter, permease protein
875	0940		Amino acid ABC transporter, binding protein precursor
877	0942		Sodium/alanine symporter
1096	1169		Amino acid ABC transporter, permease protein
1097	1170		Amino acid ABC transporter, permease protein
1098	1171		Amino acid ABC transporter, ATP-binding protein
1099	1172		Amino acid ABC transporter, binding protein precursor
1172	1251		Peptide ABC transporter, ATP-binding protein
1358	1465		Amino acid ABC transporter, ATP-binding protein
1399	1506	gltS	Sodium/glutamate symporter
Anions
425	0473	modA	Molybdenum ABC transporter, periplasmic binding protein
426	0474	modB	Molybdenum ABC transporter, permease
427	0475	modC	Molybdenum ABC transporter, ATP-binding protein
1384	1491		Phosphate permease
Carbohydrates, organic alcohols, and acids
128	0140	lldP	l-Lactate permease
129	0141	lldP	l-Lactate permease
334	1091	kgtP	α-Ketoglutarate permease
635	0693	atoE	Short-chain fatty acids transporter
660	0724	dcuA	Anaerobic C4-dicarboxylate membrane transporter
1101	1174	gluP	Glucose/galactose transporter
Cations
124	0136	bcp	Bacterioferritin comigratory protein
348	1077	nixA	High-affinity nickel transport protein
352	1073	copP	Copper-associated protein
353	1072	copA	Copper-transporting P-type ATPase
423	0471	kefB	Glutathione-regulated potassium efflux system protein
442	0490		Putative potassium channel protein
529	0582	tonB1	Siderophore-mediated iron transport protein
598	0653	pfr	Nonheme iron-containing ferritin
626	0686	fecA1	Iron(III) dicitrate transport protein
627	0687	feoB	Ferrous iron transport protein B
727	0791	hmcT	Heavy-metal cation-transporting P-type ATPase
743	0807	fecA2	Iron(III) dicitrate transport protein
821	0888	fecE	Iron(III) dicitrate transport system ATP-binding protein
822	0889	fecD	Iron(III) dicitrate transport system permease protein
903	0969	czcA1	Cation efflux system protein
904	0970	czcB1	Cation efflux system protein
1109	1183		Na+/H+ antiporter
1248	1328	czcB2	Cation efflux system protein
1249	1329	czcA2	Cation efflux system protein
1258	1339	exbB2	Biopolymer transport protein
1259	1340	exbD2	Biopolymer transport protein
1260	1341	tonB2	Siderophore-mediated iron transport protein
1263	1344	corA	Magnesium and cobalt transport protein
1396	1503	fixI	Component of cation transport for cbb3-type oxidase
1426	1400	fecA3	Iron(III) dicitrate transport protein
1447	1552	nhaA	Na+/H+ antiporter I
Nucleosides, purines, and pyrimidines
1106	1180		Nucleoside transporter
1210	1290	pnuC	Nicotinamide mononucleotide transporter

^aGene numbers correspond to those in Fig. 1.