List of Orthologous Open Reading Frames in 26 Geobacteraceae Operons
Operon	G. sulfurreducens					G.metallireducens				D.vulgaris
	ORF	PID	Function	Start	End	ORF	Blastp E-value	Start	End	ORF	Blastp E-value	Start	End
17	ORF00043	39981898	tolB protein, putative	1427	132
17	ORF00045	39981899	TonB-dependent receptor, putative	2107	1430	GMET_S071_013	1.2×10-36	300	626
188	ORF00374	39982091	cytochrome c oxidase, subunit I	300	1922	GMET_S039_022	2.0×10-160	1981	878	dvul_1047	0	2306	723
188	ORF00376	39982092	cytochrome c oxidase, subunit III	1922	2521	GMET_S039_021	6.4×10-58	833	300	dvul_1046	1.2×10-52	712	101
264	ORF00519	39982179	hydrogenase assembly chaperone hypC/hupF	9	236	GMET_S038_009	1.5×10-22	300	455
264	ORF00520	39982180	hydrogenase expression/formation protein HypD	329	1327	GMET_S038_010	1.0×10-166	458	1546
334	ORF00675	39982281	flagellar M-ring protein FliF	27	1607	GMET_S007_051	0	3788	2244	dvul_2738	1.0×10-85	3378	1771
334	ORF00677	39982282	flagellar motor switch protein FliG	1622	2611	GMET_S007_049	2.0×10-146	2079	1201	dvul_2737	4.5×10-61	1736	786
334	ORF00679	39982283	flagellar assembly protein fliH, putative	2601	3479	GMET_S007_048	1.9×10-85	1043	300	dvul_2736	1.2×10-9	754	47
485	ORF01009	39982475	thiamine biosynthesis protein ThiC	1607	300	GMET_S043_012	0	1556	300
485	ORF01010	39982476	phosphomethylpyrimidine kinase	3129	1660	GMET_S043_013	1.0×10-175	3152	1851
498	ORF01040	39982497	GDP-mannose 4,6-dehydratase	300	1346	GMET_S005_002	9.0×10-158	1256	300
498	ORF01042	39982498	GDP-fucose synthetase	1342	2283
502	ORF01053	39982505	glycosyl transferase, group 1 family protein	7	1200					dvul_1034	1.0×10-3	2129	300
502	ORF01054		membrane protein, putative	1233	1862
674	ORF01410	39982706	nucleoside diphosphate kinase regulator protein, putative	464	60
674	ORF01411	39982707	response regulator	941	534	GMET_S009_030	3.4×10-11	300	707
681	ORF01424	39982717	rubredoxin	359	204
681	ORF01425	39982718	ferredoxin family protein, putative	659	441	GMET_S010_022	2.9×10-21	153	299
681	gene 3			901	656
765	ORF01592	39982812	cystathionine beta-lyase	300	1430	GMET_S001_077	2.2×10-66	851	300
765	ORF01594	39982813	cystathionine beta-lyase	1449	2582
849	ORF01772	39982911	MutT/nudix family protein	59	1174
849	ORF01774	39982912	conserved hypothetical protein	1240	1677
849	ORF01776	39982913	conserved hypothetical protein	1694	2575	GMET_S001_058	5.5×10-82	1019	300	dvul_1675	5.5×10-23	998	153
893	ORF01865	39982964	phosphate ABC transporter, permease protein	976	59	GMET_S006_071	1.7×10-32	994	158	dvul_1605	1.1×10-37	927	1988
893	ORF01866	39982965	phosphate ABC transporter, permease protein	1953	979	GMET_S006_072	3.2×10-22	1953	997	dvul_1604	6.4×10-54	79	972
991	ORF02056	39983194	conserved hypothetical protein	1073	99	GMET_S008_058	6.0×10-109	300	977
991	ORF02059	39983195	conserved hypothetical protein	2453	1140
991	gene 3			3063	2545
1256	ORF02671	39983563	adenosylmethionine--8-amino-7-oxononanoate aminotransferase	1400	42	GMET_S009_009	0	300	1595	dvul_1680	4.0×10-134	300	2078
1256	ORF02672	39983564	dethiobiotin synthase	2115	1396
1294	ORF02760	39983621	cytochrome d ubiquinol oxidase, subunit I	146	1495	GMET_S011_021	0	1604	300	dvul_2344	9.0×10-143	2620	1331
1294	ORF02761	39983622	cytochrome d ubiquinol oxidase, subunit II	1500	2525					dvul_2343	1.6×10-85	1240	260
1410	ORF02986	39983778	ATP-dependent Clp protease, ATP-binding subunit ClpX	1267	17	GMET_S078_001	0	1463	300	dvul_643	5.0×10-151	2345	3655
1410	ORF02988	39983779	ATP-dependent Clp protease, proteolytic subunit ClpP	1863	1267	GMET_S078_002	1.2×10-56	1888	1529	dvul_642	1.5×10-66	1786	2391
1410	ORF02990	39983780	trigger factor	3180	1888	GMET_S078_003	3.0×10-141	3271	2153	dvul_641	3.2×10-47	298	1599
1483	ORF03122	39983867	phosphoe0lpyruvate-protein phosphotransferase	1870	107	GMET_S051_015	0	271	2034	dvul_181	2.0×10-128	1894	122
1483	ORF03123	39983868	phosphocarrier protein HPr	2117	1854
1538	ORF03244	39983949	glycosyl transferase, group 2 family protein	902	18					dvul_2521	1.9×10-23	300	1355
1538	ORF03246	39983950	glycosyl transferase, group 2 family protein	1874	939
1581	ORF03373	39984029	sigma-54 dependent DNA-binding response regulator	1664	300
1581	ORF03376	39984030	sensor histidine kinase	3275	1704	GMET_S003_042	3.8×10-94	1208	300
1581	ORF00506	39982172	sigma-54 dependent DNA-binding response regulator, interruption-N
1816	ORF03920	39984364	N-(5'phosphoribosyl)anthranilate isomerase	908	300	GMET_S044_020	2.0×10-54	1792	2103
1816	ORF03923	39984365	tryptophan synthase, beta subunit	2268	916	GMET_S044_019	0	300	1505
1856	ORF03993	39984405	nickel-dependent hydrogenase, large subunit	300	1718	GMET_S013_018	0	1718	300
1856	ORF03995	39984406	ferredoxin family protein	1721	1969					dvul_195	2.8×10-6	300	803
1900	ORF04091	39984467	potassium-transporting ATPase, A subunit	46	1821	GMET_S004_043	0	4551	2794	dvul_2397	4×10-125	4494	2794
1900	ORF04094	39984468	potassium-transporting ATPase, B subunit	1889	3955	GMET_S004_042	0	2739	721	dvul_2396	0	2615	741
1900	ORF04096	39984469	potassium-transporting ATPase, C subunit	4004	4570	GMET_S004_041	1.6×10-77	679	137	dvul_2395	1.2×10-29	701	174
2029	ORF04375	39984622	alpha-amylase family protein	1925	75	GMET_S012_041	0	1875	97
2029	ORF04377	39984623	alcohol dehydrogenase, zinc-containing	2996	2013	GMET_S012_042	1.0×10-160	2957	2013	dvul_1850	5.0×10-19	1057	191
2029	ORF03886	39984348	alpha amylase family protein
2097	ORF04513	39984705	NAD-reducing hydrogenase, delta subunit	595	11
2097	ORF04515	39984706	NAD-reducing hydrogenase, gamma subunit	1308	595					dvul_1005	1.2×10-26	2108	252
2207	ORF04724	39984890	ribosomal protein S19	303	25					dvul_620	1.3× 10-38	2596	2877
2207	ORF04726	39984891	ribosomal protein L2	1155	334	GMET_S001_121	3.0×10-106	929	300	dvul_619	7.0×10-106	1756	2586
2207	ORF04727	39984892	ribosomal protein L23	1464	1183					dvul_618	3.7×10-5	1588	1752
2207	ORF04728	39984893	ribosomal protein L4/L1 family	2084	1464					dvul_617	6.5×10-11	1140	1448
2207	ORF04731	39984894	ribosomal protein L3	2741	2112					dvul_616	1.3×10-57	180	809
2449	ORF05304	39985224	ferredoxin family protein	133	321
2449	ORF05303	39985225	rubredoxin	391	546					dvul_2255	1.7×10-18	16	174
Note:
Shown are predicted open reading frames in 26 conserved operons.
Operons were predicted by the public version of program FGENESB (Solovyev and Salamov, unpublished).
For each open reading frame in G. sulfurreducens, its orthologs are listed in G. metallireducens and D. vulgaris.
Locations of each ORF are provided within DNA sequences posted on this supplementary Web site.
The upstream, intergenic, and downstream regions of the operons within 300 bp from each ORF were used as input for AlignACE
(Roth, F. P., Hughes, J. D., Estep, P. W., Church, G. M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clusted by whole-genome mRNA quantitation. Nature Biotechnol. 16, 939-945).
PID, GenBank GI identification number.
Shown in italic are open reading frames that predicted to be a part of the operon by FGENESB, but no orthologs for such ORFs were identified in G. metallireducens or D. vulgaris.