SI tables Slater 2009

Supplementary tables for:

Slater, et al. (2009). Genome sequences of three Agrobacterium biovars elucidate the evolution of multichromosome genomes. J.Bacteriol (Submitted)

List of Supplementary Tables

Table S1. Genomes used for phylogenetic reconstruction among the Rhizobiaceae with outgroups in the Rhizobiales.

Table S2. Homology groups used to construct the species phylogeny. Each of these 423 groups contains a single gene in each of the 15 taxa under analysis and this gene is on the main chromosome within the Rhizobiaceae. Genbank protein accessions or genome-project protein identifiers are given for each genome identified by Genbank taxon ID (see Table S1). Rows correspond to gene families and columns correspond to genomes.

Table S3. Key gene clusters shared by chromosome II in several strains of Brucella (represented by B. suis 1330), chromosome II in Ochrobactrum anthropi, chromosome II in biovar 1 (C58) and 3 (S4) strains of Agrobacterium, 2651 kbp replicon in biovar 2 (K84) of Agrobacterium, plasmid p42e of Rhizobium etli (Ret), plasmid pRL11 of Rhizobium leguminosarum (Rleg), and plasmid pSymB of Sinorhizobium (Sino), most likely due to a shared repABC-type plasmid precursor (labeled IRT in the research article) that either entered an ancestral genome carrying these gene clusters and/or resulted from an ancestral intragenome gene transfer from chromosome I to the IRT plasmid early in the Rhizobiales lineage.

Table S4. Key gene clusters shared by chromosome I of Sinorhizobium meliloti (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Brucella strains (Brucella abortus biovar 1 strain 9-941 used as an example) and chromosome II of Ochrobactrum anthropi. These gene clusters are presumed to have moved from the ancestral chromosome I to the IRT plasmid-derived chromosome II prior to the divergence of the Brucella and Ochrobactrum clades.

Table S5. Key gene clusters shared by chromosome I of Sinorhizobium meliloti (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Brucella strains (Brucella abortus biovar 1 strain 9-941 used as an example), but not shared by chromosome II of Ochrobactrum anthropi. These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Brucella lineage after its divergence from the Ochrobactrum clade.

Table S6. First gene cluster: shared by chromosome II in Agrobacterium strains and by pSymB in Sinorhizobium meliloti. This gene cluster most likely moved from the ancestral chromosome I onto the pSymB precursor before the split of the Sinorhizobium lineage away from the rest of the Rhizobiaceae lineage. Remaining gene clusters: shared by chromosome I in Agrobacterium strains (extant examples of ancestral chromosome I) and by pSymB in Sinorhizobium meliloti. These gene clusters most likely moved from the ancestral chromosome I onto the pSymB precursor after the split of the Sinorhizobium lineage away from the rest of the Rhizobiaceae lineage.

Table S7. Key gene clusters shared by chromosome I in S. meliloti (extant examples of ancestral chromosome I), chromosome II in biovar 1 (C58) and 3 (S4) strains of Agrobacterium, the 2651 kbp replicon in biovar 2 (K84) of Agrobacterium, plasmid p42e of Rhizobium etli (Ret), and plasmid pRL11 of Rhizobium leguminosarum (Rleg), most likely due to an ancestral intragenome gene transfer from chromosome I to a repABC-type IRT plasmid in the Agrobacterium/Rhizobium lineage.

Table S8. Key gene clusters unique to chromosome II in biovar 1 and 3 strains of Agrobacterium (possible lateral gene transfers), or shared by chromosome I in S. meliloti or Agrobacterium bv. 2 (K84) (extant examples of ancestral chromosome I) and by chromosome II in biovar 1 (C58) and 3 (S4) strains of Agrobacterium, most likely due to an ancestral intragenome gene transfer from chromosome I to chromosome II in the lineage that includes biovars 1 and 3 after this lineage diverged from biovar 2.

Table S9. Key gene clusters shared by chromosome I in S. meliloti, Agrobacterium bv. 2 (K84), and Agrobacterium bv. 3 (extant examples of ancestral chromosome I) and by chromosome II in biovar 1 (C58), most likely due to an ancestral intragenome gene transfer from chromosome I to chromosome II in the biovar 1 lineage.

Table S10. Key gene clusters shared by chromosome I in Agrobacterium biovar 1 (extant example of ancestral chromosome) and by the 2651 kbp replicon in biovar 2 (K84) of Agrobacterium, plasmid p42e of Rhizobium etli (Ret), and plasmid pRL11 of Rhizobium leguminosarum (Rleg), most likely due to an ancestral intragenome gene transfer from chromosome I to a repABC-type IRT plasmid in the biovar 2 lineage after it diverged from the biovar 1/biovar 3 lineage.

Table S11. Key gene clusters shared by chromosome II of all sequenced Vibrio strains (Vibrio cholerae O1 biovar eltor strain N16961 used as an example) and chromosome II of Photobacterium profundum, but not by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I), indicative of the plasmid progenitor of chromosome II. This plasmid would have entered the common ancestor prior to the divergence of the Vibrio and Photobacterium clades.

Table S12. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Vibrio strains (Vibrio cholerae O1 biovar El Tor strain N16961 used as an example) and chromosome II of Photobacterium profundum. These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II prior to the divergence of the Vibrio and Photobacterium clades.

Table S13. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Vibrio strains (Vibrio cholerae O1 biovar El Tor strain N16961 used as an example), but not shared by chromosome II of Photobacterium profundum. These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Vibrio lineage after its divergence from the Photobacterium clade.

Table S14. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of Photobacterium profundum, but not shared by chromosome II of sequenced Vibrio strains (Vibrio cholerae O1 biovar El Tor strain N16961 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Photobacterium lineage after its divergence from the Vibrio clade.

Table S15. Key gene clusters shared by chromosome II of all sequenced Burkholderia strains (Burkholderia cenocepacia AU1054 used as an example) and chromosome II of all sequenced Ralstonia strains (Ralstonia eutropha JMP134 used as an example), but not by chromosome I of Bordetella bronchiseptica RB50 (extant representative of ancestral chromosome I), indicative of the plasmid progenitor of chromosome II. This plasmid would have entered the common ancestor prior to the divergence of the Burkholderia and Ralstonia clades.

Table S16. Key gene clusters shared by chromosome I of Bordetella bronchiseptica RB50 (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Burkholderia strains (Burkholderia cenocepacia AU1054 used as an example) and chromosome II of all sequenced Ralstonia strains (Ralstonia eutropha JMP134 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II prior to the divergence of the Burkholderia and Ralstonia clades.

Table S17. Key gene clusters shared by chromosome I of Bordetella bronchiseptica RB50 (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Burkholderia strains (Burkholderia cenocepacia AU1054 used as an example), but not shared by chromosome II of Ralstonia strains (Ralstonia eutropha JMP134 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Burkholderia lineage after its divergence from the Ralstonia clade.

Table S18. Key gene clusters shared by chromosome I of Bordetella bronchiseptica RB50 (extant representative of ancestral chromosome I) and by chromosome II of Ralstonia strains (Ralstonia eutropha JMP134 used as an example), but not shared by chromosome II of sequenced Burkholderia strains (Burkholderia cenocepacia AU1054 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Ralstonia lineage after its divergence from the Burkholderia clade.

Table S19. Key gene clusters shared by chromosome I or chromosome II of Burkholderia pseudomallei 1710b (extant representative of bichromosomal background) and by chromosome III of those sequenced Burkholderia strains with a chromosome III (Burkholderia cenocepacia AU1054 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I or from chromosome II to the plasmid-derived chromosome III in the Burkholderia sublineage that evolved a chromosome III.

Table S20. Composition of mountains for the Niche Map based on 625 sequenced prokaryotic genomes.

Table S21. The set of PFams that distinguish the members of the Rhizobiaceae from the rest of the prokaryotes on the Niche Finder map. PFam IDs and their associated annotations are shown.

Methods: All methods for the manuscript are reproduced here for the convenience of the reader.

Table S1. Genomes used for phylogenetic reconstruction among the Rhizobiaceae with outgroups in the Rhizobiales.

Genbank Taxon ID	Taxon Name
311402	Agrobacterium vitis S4
311403	Agrobacterium radiobacter K84
176299	Agrobacterium tumefaciens str. C58
347834	Rhizobium etli CFN 42
387	Rhizobium leguminosarum bv. viciae
266834	Sinorhizobium meliloti 1021
266835	Mesorhizobium loti MAFF303099
266779	Mesorhizobium sp. BNC1
262698	Brucella abortus biovar 1 str. 9-941
224914	Brucella melitensis 16M
283165	Bartonella quintana str. Toulouse
314269	Aurantimonas sp. SI85-9A1
224911	Bradyrhizobium japonicum USDA 110
316055	Rhodopseudomonas palustris BisA53
323097	Nitrobacter hamburgensis X14

Homolog Group ID	Genbank Taxon ID
Homolog Group ID	311402	311403	176299	347834	387	266834	266835	266779	262698	224914	283165	314269	224911	316055	323097
10169	Avi4197	Arad4404	NP_533359	YP_471426	YP_770109	NP_387344	NP_105219	YP_675926	YP_222580	NP_539050	YP_032863	ZP_01229026	NP_767116	YP_779259	YP_578763
10173	Avi1441	Arad1586	NP_531726	YP_468914	YP_767109	NP_385170	NP_108005	YP_673507	YP_221404	NP_540214	YP_032102	ZP_01228762	NP_771706	YP_781944	YP_577508
10187	Avi0960	Arad1161	NP_531347	YP_468424	YP_766559	NP_384964	NP_107762	YP_673284	YP_221194	NP_540436	YP_032032	ZP_01228047	NP_774138	YP_783512	YP_578368
10223	Avi1739	Arad1870	NP_531978	YP_469149	YP_767323	NP_385392	NP_102953	YP_673602	YP_221564	NP_540057	YP_032235	ZP_01225736	NP_771517	YP_781462	YP_577449
10224	Avi0934	Arad1121	NP_531417	YP_468405	YP_766540	NP_384944	NP_107736	YP_673264	YP_221168	NP_540460	YP_032004	ZP_01228067	NP_767825	YP_783675	YP_575626
10233	Avi0907	Arad1083	NP_531390	YP_468374	YP_766505	NP_384908	NP_108389	YP_672998	YP_223007	NP_542016	YP_031952	ZP_01227885	NP_774134	YP_779865	YP_578365
10243	Avi2417	Arad2568	NP_532521	YP_469780	YP_768185	NP_385865	NP_101953	YP_673846	YP_221588	NP_540034	YP_032374	ZP_01228853	NP_772330	YP_780569	YP_577811
10245	Avi1731	Arad1867	NP_531975	YP_469146	YP_767320	NP_385387	NP_102957	YP_673599	YP_221559	NP_540060	YP_032234	ZP_01225740	NP_771542	YP_781456	YP_577457
10247	Avi2538	Arad2211	NP_532053	YP_469419	YP_767806	NP_385592	NP_102424	YP_673933	YP_221876	NP_539732	YP_032343	ZP_01227495	NP_771794	YP_782317	YP_577667
10265	Avi4198	Arad4405	NP_533360	YP_471427	YP_770110	NP_387345	NP_105218	YP_675927	YP_222579	NP_539051	YP_032862	ZP_01229027	NP_767117	YP_779260	YP_578764
10300	Avi2545	Arad2203	NP_532260	YP_469415	YP_767802	NP_385588	NP_102026	YP_674290	YP_221965	NP_539650	YP_032273	ZP_01227466	NP_772228	YP_781231	YP_577823
10305	Avi2160	Arad2413	NP_532184	YP_469665	YP_768056	NP_385705	NP_102217	YP_674145	YP_221714	NP_539902	YP_032258	ZP_01225595	NP_771154	YP_781786	YP_577265
10317	Avi1788	Arad1927	NP_532021	YP_469388	YP_767687	NP_385426	NP_102053	YP_674275	YP_221643	NP_539979	YP_032296	ZP_01225623	NP_770931	YP_781904	YP_577440
10328	Avi2511	Arad2234	NP_532076	YP_469438	YP_767827	NP_385613	NP_102399	YP_673954	YP_221855	NP_539752	YP_032327	ZP_01227514	NP_771487	YP_781484	YP_576983
10346	Avi1781	Arad1914	NP_532014	YP_469380	YP_767680	NP_385420	NP_102042	YP_674280	YP_221637	NP_539985	YP_032361	ZP_01225629	NP_771727	YP_782268	YP_577523
10348	Avi0031	Arad0063	NP_530760	YP_467609	YP_765655	NP_384164	NP_105744	YP_676026	YP_222716	NP_540965	YP_031905	ZP_01228888	NP_767286	YP_779311	YP_575481
10367	Avi0111	Arad0185	NP_530804	YP_467677	YP_765738	NP_384337	NP_106159	YP_676588	YP_220814	NP_540826	YP_031927	ZP_01227696	NP_774755	YP_783711	YP_575813
10374	Avi2208	Arad2475	NP_532431	YP_469708	YP_768114	NP_385527	NP_102620	YP_673567	YP_221783	NP_539828	YP_032215	ZP_01225706	NP_772163	YP_781267	YP_576933
10385	Avi2131	Arad2262	NP_532133	YP_469458	YP_767848	NP_385562	NP_102198	YP_674181	YP_221827	NP_539780	YP_032176	ZP_01227542	NP_771125	YP_781672	YP_577108
10386	Avi1856	Arad1992	NP_532611	YP_469212	YP_767393	NP_385477	NP_102135	YP_674223	YP_221922	NP_539689	YP_032431	ZP_01225663	NP_772025	YP_782481	YP_576842
10393	Avi1843	Arad1975	NP_532623	YP_469200	YP_767381	NP_385465	NP_102123	YP_674235	YP_221934	NP_539677	YP_032443	ZP_01225673	NP_772037	YP_782493	YP_576830
10394	Avi4110	Arad4310	NP_533290	YP_471346	YP_769980	NP_387143	NP_105026	YP_675752	YP_222460	NP_539166	YP_032755	ZP_01226749	NP_767083	YP_779222	YP_575883
10395	Avi2687	Arad2107	NP_532405	YP_469329	YP_767631	NP_385619	NP_102770	YP_674129	YP_221676	NP_539947	YP_032460	ZP_01227280	NP_771112	YP_781664	YP_577061
10412	Avi4156	Arad4370	NP_533328	YP_471388	YP_770073	NP_387196	NP_105062	YP_675900	YP_223149	NP_541397	YP_031869	ZP_01228989	NP_767180	YP_781627	YP_575992
10420	Avi0445	Arad0665	NP_531069	YP_467918	YP_765995	NP_384518	NP_106193	YP_676457	YP_222791	NP_540886	YP_031916	ZP_01228442	NP_767428	YP_779140	YP_575389
10428	Avi0206	Arad0441	NP_530962	YP_467812	YP_765874	NP_384390	NP_105787	YP_673239	YP_222753	NP_540924	YP_031801	ZP_01228366	NP_767347	YP_779436	YP_575436
10436	Avi1730	Arad1865	NP_531974	YP_469145	YP_767319	NP_385386	NP_102958	YP_673598	YP_221558	NP_540061	YP_032233	ZP_01225741	NP_771543	YP_781455	YP_577458
10456	Avi2170	Arad2356	NP_532470	YP_469601	YP_767971	NP_385763	NP_102555	YP_674329	YP_223413	NP_541662	YP_032393	ZP_01227572	NP_771248	YP_781702	YP_577058
10460	Avi1862	Arad1998	NP_532608	YP_469216	YP_767397	NP_385481	NP_102139	YP_674219	YP_221918	NP_539693	YP_032427	ZP_01225660	NP_772021	YP_782477	YP_576846
10472	Avi2445	Arad2387	NP_532365	YP_469624	YP_767993	NP_385688	NP_102476	YP_673963	YP_221803	NP_539803	YP_032407	ZP_01227562	NP_771333	YP_781683	YP_577040
10478	Avi0391	Arad0601	NP_531030	YP_467907	YP_765982	NP_384474	NP_106217	YP_672571	YP_220785	NP_540860	YP_031830	ZP_01228409	NP_767470	YP_778942	YP_575363
10479	Avi4288	Arad4870	NP_533450	YP_471532	YP_770238	NP_387261	NP_104992	YP_675997	YP_222505	NP_539119	YP_031848	ZP_01226337	NP_767060	YP_779495	YP_575864
10492	Avi1818	Arad1955	NP_532641	YP_469184	YP_767364	NP_385449	NP_102105	YP_674382	YP_221952	NP_539661	YP_032354	ZP_01225687	NP_772056	YP_782518	YP_576808
10493	Avi0368	Arad0561	NP_531020	YP_467879	YP_765952	NP_384451	NP_106025	YP_676594	YP_222340	NP_539275	YP_032702	ZP_01228402	NP_767398	YP_779405	YP_575413
10494	Avi0456	Arad0699	NP_531089	YP_467985	YP_766059	NP_384549	NP_105600	YP_672947	YP_223706	NP_541251	YP_032574	ZP_01227804	NP_774739	YP_779583	YP_578888
10513	Avi1724	Arad1858	NP_531969	YP_469140	YP_767314	NP_385381	NP_102963	YP_673593	YP_221553	NP_540066	YP_032228	ZP_01225746	NP_771548	YP_781450	YP_577463
10525	Avi0910	Arad1082	NP_531389	YP_468373	YP_766504	NP_384907	NP_108388	YP_672997	YP_223006	NP_542017	YP_031951	ZP_01227884	NP_774135	YP_779866	YP_578366
10537	Avi1902	Arad2577	NP_532525	YP_469788	YP_768192	NP_385880	NP_101945	YP_673840	YP_221580	NP_540041	YP_032378	ZP_01228846	NP_772363	YP_780539	YP_576914
10555	Avi2155	Arad2423	NP_532188	YP_469670	YP_768061	NP_385710	NP_102223	YP_674141	YP_221709	NP_539906	YP_032262	ZP_01225591	NP_771158	YP_781782	YP_577269
10561	Avi0992	Arad1193	NP_531436	YP_468449	YP_766582	NP_384985	NP_107787	YP_673301	YP_221215	NP_540414	YP_032041	ZP_01228037	NP_769289	YP_779998	YP_576116
10568	Avi3524	Arad3499	NP_533102	YP_470820	YP_769333	NP_386821	NP_104068	YP_674773	YP_222266	NP_539344	YP_032544	ZP_01226950	NP_773638	YP_779900	YP_576039
10570	Avi4130	Arad4339	NP_533305	YP_471365	YP_770010	NP_387163	NP_105212	YP_675930	YP_222576	NP_539054	YP_032860	ZP_01228933	NP_767097	YP_779240	YP_575896
10590	Avi1840	Arad1971	NP_532626	YP_469197	YP_767378	NP_385462	NP_102120	YP_674238	YP_221937	NP_539674	YP_032446	ZP_01225675	NP_772040	YP_782496	YP_576827
10625	Avi2188	Arad2763	NP_532207	YP_470207	YP_768755	NP_386018	NP_104436	YP_676535	YP_223797	NP_541152	YP_032583	ZP_01225776	NP_767574	YP_779127	YP_575967
10640	Avi1698	Arad1831	NP_531952	YP_469117	YP_767293	NP_385362	NP_108565	YP_673731	YP_221816	NP_539792	YP_032182	ZP_01227310	NP_771583	YP_781429	YP_577480
10645	Avi1742	Arad1876	NP_531982	YP_469153	YP_767327	NP_385395	NP_102580	YP_673816	YP_221567	NP_540054	YP_032390	ZP_01227475	NP_771506	YP_781468	YP_576969
10673	Avi2880	Arad2982	NP_532759	YP_470333	YP_768875	NP_386272	NP_103107	YP_674557	YP_222108	NP_539504	YP_032490	ZP_01226098	NP_773234	YP_781042	YP_576573
10679	Avi1102	Arad1288	NP_531503	YP_468541	YP_766696	NP_385038	NP_107826	YP_673337	YP_221273	NP_540353	YP_032058	ZP_01228001	NP_769178	YP_783309	YP_578694
10682	Avi2892	Arad2997	NP_532770	YP_470343	YP_768887	NP_386283	NP_103116	YP_674566	YP_222118	NP_539495	YP_032499	ZP_01226107	NP_773243	YP_781030	YP_576563
10687	Avi0103	Arad0195	NP_530809	YP_467684	YP_765745	NP_384329	NP_106153	YP_676618	YP_220819	NP_540821	YP_031930	ZP_01227690	NP_768062	YP_782678	YP_575727
10688	Avi4143	Arad4354	NP_533315	YP_471375	YP_770060	NP_387183	NP_105147	YP_675741	YP_222539	NP_539092	YP_031838	ZP_01228974	NP_767208	YP_779007	YP_575910
10690	Avi0464	Arad0695	NP_531086	YP_467977	YP_766052	NP_384545	NP_105609	YP_672949	YP_223707	NP_541250	YP_031787	ZP_01227714	NP_774741	YP_779585	YP_578886
10731	Avi0299	Arad0271	NP_530819	YP_467703	YP_765765	NP_384281	NP_104435	YP_676477	YP_220897	NP_540742	YP_031736	ZP_01228658	NP_774771	YP_783720	YP_575803
10738	Avi1867	Arad2005	NP_532603	YP_469221	YP_767402	NP_385486	NP_102144	YP_674214	YP_221913	NP_539698	YP_032422	ZP_01225655	NP_772016	YP_782472	YP_576851
10739	Avi3127	Arad3136	NP_532855	YP_470463	YP_769002	NP_385679	NP_103881	YP_674675	YP_222186	NP_539425	YP_032532	ZP_01225947	NP_77401		YP_782867
10778	Avi1465	Arad1613	NP_531753	YP_468936	YP_767132	NP_385213	NP_108036	YP_673524	YP_221424	NP_540194	YP_032116	ZP_01228780	NP_769201	YP_783290	YP_579145
10781	Avi2107	Arad2242	NP_532114	YP_469443	YP_767832	NP_385548	NP_102181	YP_674193	YP_221839	NP_539767	YP_032165	ZP_01227528	NP_771440	YP_781519	YP_577014
10785	Avi1795	Arad1933	NP_532030	YP_469172	YP_767346	NP_385435	NP_102060	YP_674269	YP_221650	NP_539973	YP_032242	ZP_01225617	NP_770946	YP_781895	YP_577097
10788	Avi2029	Arad2779	NP_532286	YP_469982	YP_768402	NP_386048	NP_102824	YP_673881	YP_221594	NP_540028	YP_032193	ZP_01226011	NP_770451	YP_780947	YP_576788
10798	Avi0899	Arad1090	NP_531395	YP_468382	YP_766514	NP_384916	NP_108401	YP_673007	YP_223015	NP_542007	YP_031957	ZP_01227896	NP_774155	YP_779816	YP_578373
10812	Avi4144	Arad4355	NP_533316	YP_471376	YP_770061	NP_387184	NP_105146	YP_675740	YP_222538	NP_539093	YP_032824	ZP_01228975	NP_767207	YP_779006	YP_575911
10817	Avi1927	Arad2602	NP_532540	YP_469819	YP_768208	NP_385893	NP_101930	YP_673831	YP_221570	NP_540050	YP_032266	ZP_01228838	NP_772346	YP_780560	YP_576922
10840	Avi2467	Arad2628	NP_532049	YP_469836	YP_768227	NP_385910	NP_102506	YP_673980	YP_221751	NP_539866	YP_032371	ZP_01228827	NP_772474	YP_780463	YP_576630
10865	Avi4203	Arad4410	NP_533362	YP_471429	YP_770112	NP_387346	NP_105262	YP_675877	YP_222482	NP_539143	YP_032818	ZP_01229029	NP_767121	YP_779266	YP_578767
10891	Avi4205	Arad4412	NP_533364	YP_471431	YP_770114	NP_387348	NP_105264	YP_675875	YP_222480	NP_539145	YP_032816	ZP_01229030	NP_767122	YP_779267	YP_578768
10917	Avi0406	Arad0622	NP_531040	YP_467951	YP_766027	NP_384489	NP_104357	YP_676202	YP_220925	NP_540708	YP_031744	ZP_01228470	NP_767361	YP_779367	YP_575538
10920	Avi1682	Arad1812	NP_531940	YP_469100	YP_767277	NP_385349	NP_108552	YP_673725	YP_221534	NP_540085	YP_032304	ZP_01225964	NP_771603	YP_781774	YP_577705
10959	Avi4378	Arad4933	NP_533411	YP_471583	YP_770290	NP_387434	NP_104799	YP_675950	YP_222402	NP_539220	YP_032711	ZP_01226843	NP_767953	YP_783037	YP_578930
10967	Avi1721	Arad1855	NP_531967	YP_469138	YP_767312	NP_385379	NP_102965	YP_673591	YP_221551	NP_540068	YP_032226	ZP_01225748	NP_771550	YP_781448	YP_577465
10981	Avi4242	Arad4454	NP_533420	YP_471448	YP_770132	NP_387293	NP_105165	YP_675776	YP_222548	NP_539083	YP_032771	ZP_01228958	NP_767243	YP_779346	YP_575449
11013	Avi0430	Arad0649	NP_531057	YP_467930	YP_766007	NP_384507	NP_106002	YP_676569	YP_220911	NP_540725	YP_032638	ZP_01228453	NP_767440	YP_779151	YP_575378
11039	Avi1833	Arad1966	NP_532631	YP_469192	YP_767373	NP_385457	NP_102115	YP_674243	YP_221942	NP_539669	YP_032451	ZP_01225680	NP_772045	YP_782501	YP_576822
11046	Avi1535	Arad1675	NP_531798	YP_468978	YP_767167	NP_385253	NP_108089	YP_674322	YP_221242	NP_540386	YP_032137	ZP_01227406	NP_770728	YP_782214	YP_577600
11047	Avi4391	Arad4944	NP_533498	YP_471594	YP_770302	NP_387445	NP_105346	YP_676010	YP_222701	NP_538921	YP_032872	ZP_01228903	NP_767275	YP_779321	YP_575469
11064	Avi1552	Arad1702	NP_531819	YP_469002	YP_767184	NP_385270	NP_108130	YP_674537	YP_221449	NP_540173	YP_032148	ZP_01227418	NP_770759	YP_782200	YP_577379
11075	Avi0454	Arad0704	NP_531091	YP_467987	YP_766061	NP_384551	NP_105596	YP_672944	YP_223704	NP_541253	YP_032572	ZP_01227801	NP_774737	YP_779581	YP_578890
11081	Avi2675	Arad2119	NP_532395	YP_469338	YP_767639	NP_385629	NP_102757	YP_674372	YP_221615	NP_540006	YP_032398	ZP_01227290	NP_771397	YP_781608	YP_577032
11122	Avi2513	Arad2232	NP_532074	YP_469436	YP_767825	NP_385611	NP_102401	YP_673952	YP_221857	NP_539750	YP_032329	ZP_01227512	NP_771489	YP_781482	YP_576981
11142	Avi4389	Arad4941	NP_533496	YP_471592	YP_770300	NP_387443	NP_105343	YP_676007	YP_222698	NP_538925	YP_032870	ZP_01228906	NP_767273	YP_779323	YP_575466
11169	Avi2929	Arad3030	NP_532799	YP_470368	YP_768912	NP_386307	NP_103156	YP_674591	YP_222141	NP_539470	YP_032509	ZP_01226145	NP_773325	YP_780963	YP_578139
11181	Avi0427	Arad0647	NP_531055	YP_467932	YP_766009	NP_384505	NP_106004	YP_676567	YP_220913	NP_540723	YP_032636	ZP_01228455	NP_767442	YP_779156	YP_575374
11200	Avi4208	Arad4416	NP_533366	YP_471433	YP_770116	NP_387350	NP_105193	YP_675980	YP_222561	NP_539067	YP_032801	ZP_01229033	NP_767126	YP_779269	YP_578770
11204	Avi0199	Arad0437	NP_530959	YP_467809	YP_765871	NP_384387	NP_105791	YP_673235	YP_222749	NP_540928	YP_031770	ZP_01228370	NP_767351	YP_779440	YP_575439
11221	Avi0401	Arad0616	NP_531036	YP_467956	YP_766032	NP_384485	NP_104353	YP_676198	YP_220930	NP_540703	YP_031746	ZP_01228474	NP_767365	YP_779371	YP_575532
11230	Avi3111	Arad3127	NP_532843	YP_470451	YP_768991	NP_386426	NP_103823	YP_674641	YP_222167	NP_539443	YP_032523	ZP_01225945	NP_774011	YP_779915	YP_578099
11241	Avi1841	Arad1973	NP_532625	YP_469198	YP_767379	NP_385463	NP_102121	YP_674237	YP_221936	NP_539675	YP_032445	ZP_01225674	NP_772039	YP_782495	YP_576828
11259	Avi1450	Arad1595	NP_531733	YP_468921	YP_767116	NP_385179	NP_108013	YP_673513	YP_221416	NP_540203	YP_032109	ZP_01228768	NP_771700	YP_781938	YP_577502
11264	Avi4387	Arad4940	NP_533495	YP_471591	YP_770299	NP_387442	NP_105342	YP_676006	YP_222697	NP_538926	YP_032869	ZP_01228907	NP_767272	YP_779324	YP_575465
11265	Avi0297	Arad0376	NP_530918	YP_467768	YP_765829	NP_384257	NP_106238	YP_676483	YP_222808	NP_540867	YP_031900	ZP_01227681	NP_768070	YP_782668	YP_575734
11290	Avi2286	Arad2184	NP_532485	YP_469400	YP_767700	NP_385824	NP_102024	YP_674292	YP_221967	NP_539648	YP_032275	ZP_01227452	NP_771050	YP_781835	YP_577398
11308	Avi1624	Arad1765	NP_531871	YP_469058	YP_767239	NP_385325	NP_108518	YP_673703	YP_221517	NP_540101	YP_032207	ZP_01227326	NP_771664	YP_781739	YP_576863
11323	Avi1865	Arad2003	NP_532605	YP_469219	YP_767400	NP_385484	NP_102142	YP_674216	YP_221915	NP_539696	YP_032424	ZP_01225657	NP_772018	YP_782474	YP_576849
11328	Avi1499	Arad1640	NP_531772	YP_468958	YP_767150	NP_385230	NP_108068	YP_673545	YP_221224	NP_540405	YP_032123	ZP_01227390	NP_770700	YP_782252	YP_577545
11405	Avi0007	Arad0006	NP_530721	YP_467567	YP_765610	NP_384112	NP_105386	YP_676019	YP_222709	NP_540972	YP_031817	ZP_01228895	NP_767281	YP_779315	YP_575477
11431	Avi0156	Arad0179	NP_530802	YP_467675	YP_765736	NP_384339	NP_106162	YP_676623	YP_220813	NP_540827	YP_031926	ZP_01227697	NP_774754	YP_783710	YP_575814
11447	Avi1069	Arad1256	NP_531481	YP_468504	YP_766646	NP_385023	NP_107811	YP_673318	YP_221254	NP_540371	YP_032047	ZP_01228014	NP_768132	YP_779651	YP_578739
11474	Avi2889	Arad2994	NP_532767	YP_470340	YP_768884	NP_386280	NP_103113	YP_674563	YP_222115	NP_539498	YP_032496	ZP_01226104	NP_773240	YP_781034	YP_576567
11498	Avi1537	Arad1676	NP_531800	YP_468979	YP_767168	NP_385255	NP_108091	YP_674321	YP_221437	NP_540184	YP_032138	ZP_01227407	NP_770742	YP_782210	YP_577597
11508	Avi4232	Arad4447	NP_533426	YP_471442	YP_770126	NP_387307	NP_105158	YP_675770	YP_222644	NP_538986	YP_032768	ZP_01228967	NP_767258	YP_779335	YP_575453
11530	Avi0118	Arad0426	NP_530947	YP_467798	YP_765860	NP_384375	NP_105383	YP_676607	YP_223720	NP_541237	YP_031789	ZP_01226764	NP_774790	YP_779763	YP_575788
11537	Avi1092	Arad1280	NP_531498	YP_468535	YP_766689	NP_385034	NP_107820	YP_673330	YP_221267	NP_540359	YP_032055	ZP_01228004	NP_769139	YP_783337	YP_578422
11549	Avi2085	Arad2684	NP_532297	YP_469884	YP_768279	NP_385960	NP_102306	YP_674022	YP_221728	NP_539889	YP_032317	ZP_01225841	NP_770397	YP_780913	YP_576764
11559	Avi2563	Arad2236	NP_532082	YP_469439	YP_767828	NP_385615	NP_102398	YP_674206	YP_221854	NP_539753	YP_032322	ZP_01227515	NP_771479	YP_781485	YP_576984
11561	Avi1556	Arad1711	NP_531825	YP_469008	YP_767190	NP_385276	NP_108126	YP_674534	YP_221453	NP_540169	YP_032149	ZP_01227421	NP_774111	YP_779861	YP_578341
11568	Avi1804	Arad1939	NP_532035	YP_469177	YP_767359	NP_385439	NP_102069	YP_674331	YP_221671	NP_539953	YP_032312	ZP_01225697	NP_772155	YP_781279	YP_576940
11573	Avi0312	Arad0208	NP_530783	YP_467692	YP_765752	NP_384295	NP_106214	YP_672574	YP_220788	NP_540857	YP_031932	ZP_01228412	NP_767405	YP_779182	YP_575407
11575	Avi0394	Arad0608	NP_531031	YP_467909	YP_765984	NP_384479	NP_105451	YP_676545	YP_220944	NP_540688	YP_031773	ZP_01228558	NP_767312	YP_779294	YP_575510
11584	Avi0399	Arad0614	NP_531035	YP_467914	YP_765989	NP_384484	NP_104375	YP_676551	YP_220940	NP_540694	YP_031776	ZP_01228554	NP_767316	YP_779290	YP_575514
11588	Avi1449	Arad1593	NP_531732	YP_468920	YP_767115	NP_385178	NP_108012	YP_673512	YP_221414	NP_540204	YP_032108	ZP_01228767	NP_771701	YP_781939	YP_577503
11593	Avi2271	Arad2156	NP_532292	YP_469368	YP_767667	NP_385833	NP_102644	YP_674016	YP_221981	NP_539636	YP_032270	ZP_01227073	NP_774810	YP_779035	YP_575782
11616	Avi3243	Arad3233	NP_532936	YP_470557	YP_769087	NP_386480	NP_104051	YP_674744	YP_222241	NP_539369	YP_032541	ZP_01226225	NP_769097	YP_780330	YP_578455
11622	Avi1507	Arad1643	NP_531774	YP_468960	YP_767152	NP_385232	NP_108070	YP_673547	YP_221227	NP_540403	YP_032125	ZP_01227392	NP_770702	YP_782250	YP_577543
11651	Avi2136	Arad2267	NP_532137	YP_469464	YP_767875	NP_385566	NP_102202	YP_674177	YP_221823	NP_539784	YP_032178	ZP_01227546	NP_771129	YP_781676	YP_577112
11656	Avi2524	Arad2222	NP_532066	YP_469428	YP_767817	NP_385603	NP_102410	YP_673944	YP_221866	NP_539742	YP_032336	ZP_01227504	NP_771499	YP_781473	YP_576972
11665	Avi1472	Arad1624	NP_531761	YP_468945	YP_767138	NP_385226	NP_108055	YP_673537	YP_221220	NP_540409	YP_032119	ZP_01227386	NP_770435	YP_780931	YP_576774
11678	Avi2433	Arad2542	NP_532506	YP_469762	YP_768168	NP_385843	NP_101906	YP_674342	YP_221663	NP_539961	YP_032247	ZP_01225606	NP_770975	YP_781887	YP_577582
11711	Avi4332	Arad4692	NP_533388	YP_471480	YP_770194	NP_387377	NP_104821	YP_675873	YP_222440	NP_539187	YP_032747	ZP_01228202	NP_767576	YP_779123	YP_575968
11722	Avi3159	Arad3162	NP_532874	YP_470507	YP_769038	NP_386438	NP_103950	YP_674695	YP_222197	NP_539413	YP_032026	ZP_01226180	NP_767540	YP_779172	YP_575593
11749	Avi1365	Arad1496	NP_531674	YP_468824	YP_767043	NP_385126	NP_107957	YP_673462	YP_221365	NP_540248	YP_032076	ZP_01227058	NP_769768	YP_780859	YP_576722
11775	Avi1015	Arad1213	NP_531454	YP_468473	YP_766618	NP_385007	NP_107773	YP_673295	YP_221207	NP_540423	YP_032037	ZP_01228032	NP_769271	YP_783489	YP_576111
11791	Avi1527	Arad1666	NP_531791	YP_468972	YP_767161	NP_385247	NP_108083	YP_674328	YP_221235	NP_540395	YP_032132	ZP_01227400	NP_770722	YP_782220	YP_577606
11795	Avi2159	Arad2416	NP_532185	YP_469666	YP_768057	NP_385706	NP_102218	YP_674144	YP_221713	NP_539903	YP_032259	ZP_01225594	NP_771155	YP_781785	YP_577266
11816	Avi0956	Arad1155	NP_531344	YP_468428	YP_766563	NP_384961	NP_107752	YP_673279	YP_221184	NP_540446	YP_032005	ZP_01228053	NP_769176	YP_783313	YP_578405
11859	Avi2280	Arad2163	NP_532272	YP_469397	YP_767697	NP_385827	NP_102625	YP_673552	YP_221970	NP_539645	YP_032303	ZP_01227080	NP_771017	YP_781851	YP_577559
11860	Avi1916	Arad2609	NP_532547	YP_469821	YP_768211	NP_385895	NP_101926	YP_673830	YP_221899	NP_539712	YP_032267	ZP_01228837	NP_772342	YP_780564	YP_576923
11863	Avi1372	Arad1502	NP_531679	YP_468828	YP_767047	NP_385130	NP_107961	YP_673466	YP_221369	NP_540244	YP_032080	ZP_01228736	NP_769773	YP_780868	YP_576730
11897	Avi4141	Arad4351	NP_533313	YP_471373	YP_770058	NP_387181	NP_105149	YP_675743	YP_222541	NP_539090	YP_032825	ZP_01228973	NP_767209	YP_779008	YP_575909
11899	Avi1302	Arad1476	NP_531617	YP_468782	YP_766986	NP_385106	NP_107922	YP_673440	YP_221335	NP_540276	YP_032061	ZP_01227018	NP_769709	YP_780798	YP_577867
11907	Avi4294	Arad4927	NP_533489	YP_471578	YP_770285	NP_387429	NP_105053	YP_675955	YP_222473	NP_539152	YP_032812	ZP_01228919	NP_767220	YP_778968	YP_575557
11947	Avi1373	Arad1503	NP_531680	YP_468829	YP_767049	NP_385131	NP_107962	YP_673467	YP_221371	NP_540242	YP_032083	ZP_01228737	NP_769780	YP_780875	YP_576731
11956	Avi0143	Arad0466	NP_530975	YP_467826	YP_765888	NP_384404	NP_107311	YP_672752	YP_223251	NP_541505	YP_032559	ZP_01227845	NP_774147	YP_783517	YP_578369
11970	Avi1582	Arad1729	NP_531842	YP_469022	YP_767204	NP_385294	NP_108317	YP_673681	YP_221495	NP_540121	YP_032386	ZP_01227436	NP_770761	YP_782193	YP_577371
11976	Avi0936	Arad1124	NP_531420	YP_468406	YP_766542	NP_384945	NP_107737	YP_673268	YP_221169	NP_540459	YP_032028	ZP_01228066	NP_769161	YP_783328	YP_578416
11985	Avi2855	Arad2967	NP_532745	YP_470322	YP_768865	NP_386263	NP_103100	YP_674552	YP_222104	NP_539508	YP_032487	ZP_01226082	NP_773229	YP_781047	YP_577986
12005	Avi2525	Arad2220	NP_532065	YP_469427	YP_767816	NP_385602	NP_102414	YP_673943	YP_221867	NP_539741	YP_032337	ZP_01227503	NP_771500	YP_781472	YP_576971
12007	Avi0006	Arad0004	NP_530720	YP_467566	YP_765609	NP_384111	NP_105353	YP_676018	YP_222708	NP_540973	YP_031735	ZP_01228896	NP_767280	YP_779316	YP_575476
12038	Avi2386	Arad2382	NP_532196	YP_469621	YP_767991	NP_385666	NP_102478	YP_673961	YP_221805	NP_539801	YP_032408	ZP_01227561	NP_771336	YP_781681	YP_577038
12063	Avi2894	Arad3000	NP_532772	YP_470345	YP_768889	NP_386285	NP_103118	YP_674568	YP_222120	NP_539493	YP_032501	ZP_01226109	NP_773245	YP_781028	YP_576561
12069	Avi2219	Arad2470	NP_532428	YP_469703	YP_768111	NP_385532	NP_102613	YP_673572	YP_221779	NP_539833	YP_032395	ZP_01225701	NP_772189	YP_781253	YP_576929
12136	Avi1794	Arad1932	NP_532029	YP_469171	YP_767345	NP_385434	NP_102059	YP_674271	YP_221648	NP_539974	YP_032241	ZP_01225618	NP_770945	YP_781896	YP_577096
12160	Avi2514	Arad2231	NP_532073	YP_469435	YP_767824	NP_385610	NP_102402	YP_673951	YP_221858	NP_539749	YP_032330	ZP_01227511	NP_771491	YP_781481	YP_576980
12168	Avi4108	Arad4308	NP_533289	YP_471345	YP_769979	NP_387142	NP_105025	YP_675753	YP_222459	NP_539167	YP_032754	ZP_01226748	NP_767082	YP_779221	YP_575882
12176	Avi2478	Arad2148	NP_532349	YP_469361	YP_767660	NP_385652	NP_102729	YP_674349	YP_221636	NP_539986	YP_032362	ZP_01227307	NP_771585	YP_781427	YP_577482
12190	Avi1866	Arad2004	NP_532604	YP_469220	YP_767401	NP_385485	NP_102143	YP_674215	YP_221914	NP_539697	YP_032423	ZP_01225656	NP_772017	YP_782473	YP_576850
12201	Avi0200	Arad0438	NP_530960	YP_467810	YP_765872	NP_384388	NP_105790	YP_673236	YP_222750	NP_540927	YP_031769	ZP_01228369	NP_767350	YP_779439	YP_575438
12223	Avi4385	Arad4938	NP_533493	YP_471589	YP_770297	NP_387440	NP_105340	YP_676004	YP_222695	NP_538928	YP_032867	ZP_01228909	NP_767270	YP_779326	YP_575463
12281	Avi1258	Arad1455	NP_531595	YP_468758	YP_766966	NP_385091	NP_107919	YP_673427	YP_221329	NP_540282	YP_032063	ZP_01226729	NP_767016	YP_780298	YP_578130
12282	Avi2683	Arad2111	NP_532403	YP_469331	YP_767633	NP_385622	NP_102766	YP_674132	YP_221680	NP_539944	YP_032457	ZP_01227283	NP_771115	YP_781667	YP_577102
12285	Avi0455	Arad0703	NP_531090	YP_467986	YP_766060	NP_384550	NP_105597	YP_672945	YP_223705	NP_541252	YP_032573	ZP_01227802	NP_774738	YP_779582	YP_578889
12292	Avi0048	Arad0041	NP_530745	YP_467592	YP_765636	NP_384146	NP_105813	YP_676109	YP_222731	NP_540948	YP_031778	ZP_01228485	NP_774788	YP_779761	YP_575789
12303	Avi1851	Arad1986	NP_532615	YP_469208	YP_767389	NP_385473	NP_102131	YP_674227	YP_221926	NP_539685	YP_032435	ZP_01225667	NP_772029	YP_782485	YP_576838
12327	Avi0586	Arad0791	NP_531189	YP_468085	YP_766181	NP_384655	NP_106297	YP_672664	YP_221098	NP_540528	YP_031980	ZP_01228324	NP_767780	YP_779658	YP_575905
12334	Avi2836	Arad2955	NP_532732	YP_470314	YP_768857	NP_386250	NP_103075	YP_674546	YP_222099	NP_539513	YP_032484	ZP_01227096	NP_773201	YP_781061	YP_577978
12371	Avi0173	Arad0169	NP_530793	YP_467664	YP_765725	NP_384349	NP_106202	YP_676466	YP_222798	NP_540879	YP_031908	ZP_01228427	NP_767420	YP_779133	YP_575396
12377	Avi1822	Arad1959	NP_532638	YP_469187	YP_767368	NP_385452	NP_102108	YP_674379	YP_221949	NP_539664	YP_032351	ZP_01225684	NP_772052	YP_782509	YP_576811
12378	Avi2808	Arad2901	NP_532715	YP_470289	YP_768830	NP_386224	NP_103034	YP_674302	YP_222078	NP_539533	YP_032473	ZP_01227118	NP_773144	YP_781110	YP_577962
12380	Avi1854	Arad1990	NP_532613	YP_469210	YP_767391	NP_385475	NP_102133	YP_674225	YP_221924	NP_539687	YP_032433	ZP_01225665	NP_772027	YP_782483	YP_576840
12396	Avi2666	Arad2129	NP_532388	YP_469345	YP_767646	NP_385637	NP_102750	YP_674363	YP_221622	NP_540000	YP_032154	ZP_01227295	NP_771389	YP_781615	YP_577064
12402	Avi1026	Arad1220	NP_531460	YP_468479	YP_766625	NP_385001	NP_107767	YP_673289	YP_221196	NP_540434	YP_032034	ZP_01228028	NP_769264	YP_783494	YP_576106
12418	Avi0437	Arad0656	NP_531062	YP_467925	YP_766002	NP_384511	NP_106183	YP_676451	YP_222784	NP_540893	YP_031923	ZP_01228449	NP_767435	YP_779146	YP_575383
12458	Avi1759	Arad1893	NP_531995	YP_469165	YP_767340	NP_385407	NP_102444	YP_673917	YP_223394	NP_541645	YP_032288	ZP_01225638	NP_771744	YP_782289	YP_577537
12459	Avi4296	Arad4929	NP_533491	YP_471580	YP_770287	NP_387431	NP_105051	YP_675953	YP_222471	NP_539154	YP_032814	ZP_01228917	NP_769090	YP_779832	YP_575597
12461	Avi0208	Arad0444	NP_530964	YP_467813	YP_765875	NP_384391	NP_105786	YP_673241	YP_222755	NP_540922	YP_031802	ZP_01228365	NP_767346	YP_779435	YP_575435
12495	Avi1846	Arad1979	NP_532620	YP_469203	YP_767384	NP_385468	NP_102126	YP_674232	YP_221931	NP_539680	YP_032440	ZP_01225671	NP_772034	YP_782490	YP_576833
12503	Avi0911	Arad1081	NP_531388	YP_468372	YP_766503	NP_384906	NP_108387	YP_672996	YP_223005	NP_542018	YP_031950	ZP_01227883	NP_774136	YP_779867	YP_578367
12560	Avi1628	Arad1770	NP_531874	YP_469061	YP_767242	NP_385328	NP_108521	YP_673706	YP_221520	NP_540098	YP_032209	ZP_01227329	NP_771661	YP_781742	YP_576866
12563	Avi0055	Arad0035	NP_530739	YP_467587	YP_765631	NP_384141	NP_105808	YP_676114	YP_222737	NP_540941	YP_031753	ZP_01228492	NP_767393	YP_779400	YP_575418
12566	Avi4134	Arad4342	NP_533307	YP_471367	YP_770013	NP_387175	NP_105173	YP_675780	YP_222550	NP_539080	YP_032796	ZP_01229060	NP_767155	YP_779453	YP_578807
12584	Avi2436	Arad2537	NP_532503	YP_469758	YP_768164	NP_385840	NP_101910	YP_674339	YP_221666	NP_539958	YP_032250	ZP_01225603	NP_770980	YP_781883	YP_577579
12590	Avi0009	Arad0009	NP_530723	YP_467569	YP_765612	NP_384114	NP_105388	YP_676021	YP_222711	NP_540970	YP_031819	ZP_01228893	NP_767282	YP_779314	YP_575478
12621	Avi1618	Arad1760	NP_531867	YP_469055	YP_767236	NP_385321	NP_108510	YP_673699	YP_221514	NP_540104	YP_032205	ZP_01227322	NP_771669	YP_781729	YP_577092
12635	Avi4106	Arad4306	NP_533287	YP_471343	YP_769977	NP_387140	NP_105023	YP_675755	YP_222457	NP_539169	YP_032752	ZP_01226746	NP_767080	YP_779219	YP_575879
12643	Avi0383	Arad0576	NP_531022	YP_467891	YP_765964	NP_384464	NP_104331	YP_676587	YP_223743	NP_541212	YP_031760	ZP_01228403	NP_767399	YP_779406	YP_575412
12656	Avi2153	Arad2425	NP_532190	YP_469672	YP_768063	NP_385712	NP_102225	YP_674139	YP_221707	NP_539908	YP_032264	ZP_01225589	NP_771161	YP_781779	YP_577271
12671	Avi2435	Arad2539	NP_532504	YP_469760	YP_768166	NP_385841	NP_1019082	YP_674340	YP_221665	NP_539959	YP_032249	ZP_01225604	NP_770979	YP_781885	YP_577580
12684	Avi0943	Arad1133	NP_531334	YP_468413	YP_766549	NP_384952	NP_107745	YP_673276	YP_221181	NP_540449	YP_032008	ZP_01228060	NP_769171	YP_783320	YP_578410
12693	Avi2037	Arad2773	NP_532280	YP_469977	YP_768397	NP_386043	NP_102828	YP_673876	YP_221590	NP_540032	YP_032189	ZP_01226015	NP_770447	YP_780942	YP_576784
12701	Avi2819	Arad2910	NP_532722	YP_470294	YP_768836	NP_386231	NP_103041	YP_674309	YP_222085	NP_539526	YP_032477	ZP_01227112	NP_773150	YP_781101	YP_577968
12715	Avi1038	Arad1226	NP_531466	YP_468489	YP_766631	NP_385009	NP_107794	YP_673305	YP_221244	NP_540384	YP_032043	ZP_01228025	NP_767809	YP_783649	YP_575614
12721	Avi0998	Arad1202	NP_531447	YP_468454	YP_766588	NP_384988	NP_107781	YP_673298	YP_221209	NP_540420	YP_032039	ZP_01228034	NP_769292	YP_780002	YP_576118
12740	Avi2087	Arad2682	NP_532296	YP_469882	YP_768277	NP_385959	NP_102547	YP_674023	YP_221729	NP_539888	YP_032316	ZP_01225838	NP_770418	YP_780915	YP_576765
12772	Avi1036	Arad1224	NP_531465	YP_468488	YP_766630	NP_384998	NP_107793	YP_673304	YP_221243	NP_540385	YP_032042	ZP_01228026	NP_767808	YP_783646	YP_575613
12782	Avi0405	Arad0620	NP_531039	YP_467952	YP_766028	NP_384488	NP_104356	YP_676201	YP_220926	NP_540707	YP_031745	ZP_01228471	NP_767362	YP_779368	YP_575537
12789	Avi1072	Arad1260	NP_531484	YP_468514	YP_766670	NP_385024	NP_107812	YP_673322	YP_221255	NP_540370	YP_032048	ZP_01228012	NP_768142	YP_779607	YP_578738
12792	Avi0311	Arad0209	NP_530782	YP_467693	YP_765753	NP_384294	NP_106215	YP_672573	YP_220787	NP_540858	YP_031832	ZP_01228411	NP_767467	YP_778944	YP_575365
12796	Avi1516	Arad1655	NP_531785	YP_468967	YP_767156	NP_385241	NP_108078	YP_674476	YP_221230	NP_540400	YP_032127	ZP_01227396	NP_770716	YP_782228	YP_577665
12811	Avi1633	Arad1774	NP_531877	YP_469064	YP_767245	NP_385331	NP_108524	YP_673709	YP_221523	NP_540095	YP_032212	ZP_01227332	NP_771658	YP_781745	YP_576869
12820	Avi4386	Arad4939	NP_533494	YP_471590	YP_770298	NP_387441	NP_105341	YP_676005	YP_222696	NP_538927	YP_032868	ZP_01228908	NP_767271	YP_779325	YP_575464
12825	Avi4136	Arad4346	NP_533309	YP_471369	YP_770015	NP_387177	NP_105176	YP_675782	YP_222552	NP_539078	YP_032798	ZP_01229035	NP_767153	YP_779450	YP_578805
12830	Avi2557	Arad2617	NP_532553	YP_469829	YP_768220	NP_385904	NP_101920	YP_673827	YP_221905	NP_539706	YP_032417	ZP_01228833	NP_772390	YP_780527	YP_576900
12833	Avi1452	Arad1597	NP_531736	YP_468924	YP_767119	NP_385194	NP_108015	YP_673514	YP_221417	NP_540202	YP_032110	ZP_01228769	NP_771698	YP_781935	YP_577500
12851	Avi0951	Arad1148	NP_531339	YP_468419	YP_766555	NP_384957	NP_107751	YP_673278	YP_221183	NP_540447	YP_032006	ZP_01228055	NP_769175	YP_783315	YP_578406
12857	Avi1595	Arad1740	NP_531855	YP_469029	YP_767213	NP_385305	NP_108473	YP_673685	YP_221500	NP_540117	YP_032383	ZP_01227439	NP_771697	YP_781934	YP_577499
12893	Avi2818	Arad2909	NP_532721	YP_470293	YP_768835	NP_386230	NP_103040	YP_674308	YP_222084	NP_539527	YP_032476	ZP_01227113	NP_773149	YP_781102	YP_577967
12901	Avi1820	Arad1958	NP_532639	YP_469186	YP_767366	NP_385451	NP_102107	YP_674380	YP_221950	NP_539663	YP_032352	ZP_01225685	NP_772054	YP_782516	YP_576810
12903	Avi2512	Arad2233	NP_532075	YP_469437	YP_767826	NP_385612	NP_102400	YP_673953	YP_221856	NP_539751	YP_032328	ZP_01227513	NP_771488	YP_781483	YP_576982
12930	Avi1384	Arad1510	NP_531685	YP_468834	YP_767055	NP_385137	NP_107967	YP_673471	YP_221375	NP_540238	YP_032085	ZP_01228743	NP_769163	YP_783326	YP_578414
12931	Avi1770	Arad1908	NP_532008	YP_469373	YP_767673	NP_385417	NP_102434	YP_673924	YP_223401	NP_541652	YP_032282	ZP_01225631	NP_771730	YP_782274	YP_577529
12951	Avi1720	Arad1854	NP_531966	YP_469137	YP_767311	NP_385378	NP_102966	YP_673590	YP_221550	NP_540069	YP_032225	ZP_01225749	NP_771551	YP_781447	YP_577466
12954	Avi0409	Arad0625	NP_531044	YP_467948	YP_766024	NP_384492	NP_104360	YP_676205	YP_220922	NP_540711	YP_031742	ZP_01228467	NP_767382	YP_779390	YP_575427
12976	Avi4122	Arad4332	NP_533301	YP_471361	YP_770005	NP_387159	NP_105204	YP_675934	YP_222570	NP_539058	YP_032856	ZP_01228938	NP_767092	YP_779236	YP_575892
12987	Avi0897	Arad1092	NP_531397	YP_468384	YP_766516	NP_384918	NP_108402	YP_673008	YP_223016	NP_542006	YP_031958	ZP_01227897	NP_774154	YP_779817	YP_578372
13005	Avi0423	Arad0639	NP_531051	YP_467937	YP_766013	NP_384501	NP_106014	YP_676563	YP_220916	NP_540718	YP_031815	ZP_01228459	NP_767564	YP_779185	YP_575963
13020	Avi0175	Arad0165	NP_530791	YP_467663	YP_765724	NP_384350	NP_106203	YP_676467	YP_222799	NP_540878	YP_031907	ZP_01228426	NP_767419	YP_779132	YP_575397
13036	Avi1768	Arad1906	NP_532006	YP_469371	YP_767671	NP_385415	NP_102437	YP_673922	YP_223399	NP_541650	YP_032283	ZP_01225633	NP_771734	YP_782280	YP_577531
13040	Avi0018	Arad0022	NP_530731	YP_467579	YP_765623	NP_384132	NP_105795	YP_673233	YP_222748	NP_540932	YP_031771	ZP_01228500	NP_767549	YP_779164	YP_575588
13046	Avi2778	Arad2866	NP_532695	YP_470241	YP_768785	NP_386174	NP_103001	YP_674057	YP_222068	NP_539541	YP_032470	ZP_01227129	NP_773137	YP_781117	YP_577959
13062	Avi2857	Arad2968	NP_532747	YP_470323	YP_768866	NP_386261	NP_103098	YP_674551	YP_222103	NP_539509	YP_032486	ZP_01226084	NP_773228	YP_781049	YP_577985
13065	Avi4176	Arad4383	NP_533343	YP_471408	YP_770093	NP_387324	NP_105240	YP_675885	YP_220860	NP_540779	YP_031777	ZP_01229010	NP_767098	YP_779241	YP_575897
13077	Avi2366	Arad2364	NP_532461	YP_469606	YP_767976	NP_385757	NP_102548	YP_674262	YP_223417	NP_541666	YP_032239	ZP_01227576	NP_771241	YP_781707	YP_577311
13118	Avi1857	Arad1994	NP_532610	YP_469213	YP_767394	NP_385478	NP_102136	YP_674222	YP_221921	NP_539690	YP_032430	ZP_01225662	NP_772024	YP_782480	YP_576843
13127	Avi2033	Arad2776	NP_532283	YP_469980	YP_768400	NP_386046	NP_102825	YP_673880	YP_221593	NP_540029	YP_032192	ZP_01226012	NP_770449	YP_780945	YP_576786
13130	Avi1850	Arad1985	NP_532616	YP_469207	YP_767388	NP_385472	NP_102130	YP_674228	YP_221927	NP_539684	YP_032436	ZP_01225668	NP_772030	YP_782486	YP_576837
13136	Avi3229	Arad3220	NP_532926	YP_470546	YP_769079	NP_386471	NP_104004	YP_674736	YP_222233	NP_539377	YP_032537	ZP_01226215	NP_769105	YP_779876	YP_578446
13188	Avi2796	Arad2887	NP_532702	YP_470267	YP_768804	NP_386203	NP_103014	YP_674052	YP_222075	NP_539536	YP_032472	ZP_01227125	NP_773681	YP_779911	YP_576033
13199	Avi1443	Arad1588	NP_531727	YP_468915	YP_767110	NP_385171	NP_108006	YP_673508	YP_221405	NP_540213	YP_032103	ZP_01228763	NP_771705	YP_781943	YP_577507
13220	Avi0205	Arad0440	NP_530961	YP_467811	YP_765873	NP_384389	NP_105788	YP_673238	YP_222752	NP_540925	YP_031800	ZP_01228367	NP_767348	YP_779437	YP_575437
13234	Avi1785	Arad1920	NP_532018	YP_469384	YP_767684	NP_385423	NP_102049	YP_674278	YP_221640	NP_539982	YP_032359	ZP_01225626	NP_770925	YP_781912	YP_577085
13235	Avi0168	Arad0174	NP_530797	YP_467669	YP_765730	NP_384344	NP_106197	YP_676461	YP_222794	NP_540883	YP_031913	ZP_01228439	NP_767424	YP_779137	YP_575392
13283	Avi2211	Arad2472	NP_532429	YP_469704	YP_768112	NP_385531	NP_102615	YP_673569	YP_221780	NP_539832	YP_032213	ZP_01225703	NP_772177	YP_781257	YP_576946
13303	Avi0941	Arad1130	NP_531332	YP_468411	YP_766547	NP_384950	NP_107741	YP_673271	YP_221176	NP_540454	YP_032011	ZP_01228062	NP_769166	YP_783323	YP_578411
13312	Avi2537	Arad2212	NP_532054	YP_469420	YP_767807	NP_385593	NP_102423	YP_673934	YP_221875	NP_539733	YP_032342	ZP_01227496	NP_771793	YP_782316	YP_577666
13358	Avi0931	Arad1120	NP_531416	YP_468404	YP_766539	NP_384943	NP_107735	YP_673263	YP_221167	NP_540461	YP_032003	ZP_01228068	NP_767826	YP_783676	YP_575627
13365	Avi1462	Arad1609	NP_531750	YP_468934	YP_767129	NP_385210	NP_108032	YP_673521	YP_221420	NP_540199	YP_032114	ZP_01228775	NP_769194	YP_783294	YP_579148
13373	Avi0638	Arad4035	NP_531235	YP_468129	YP_766227	NP_384721	NP_106960	YP_672756	YP_221042	NP_540589	YP_032671	ZP_01228372	NP_767899	YP_783381	YP_575648
13408	Avi2890	Arad2995	NP_532768	YP_470341	YP_768885	NP_386281	NP_103114	YP_674564	YP_222116	NP_539497	YP_032497	ZP_01226105	NP_773241	YP_781032	YP_576565
13419	Avi4195	Arad4402	NP_533357	YP_471424	YP_770107	NP_387342	NP_105221	YP_675924	YP_222582	NP_539048	YP_032865	ZP_01229024	NP_767112	YP_779256	YP_575754
13437	Avi2114	Arad2247	NP_532120	YP_469447	YP_767836	NP_385552	NP_102189	YP_674189	YP_221834	NP_539772	YP_032170	ZP_01227534	NP_771422	YP_781532	YP_577025
13478	Avi1936	Arad2589	NP_532534	YP_469811	YP_768199	NP_385887	NP_101935	YP_673834	YP_221575	NP_540046	YP_032381	ZP_01228842	NP_772351	YP_780549	YP_576920
13484	Avi2128	Arad2259	NP_532131	YP_469456	YP_767846	NP_385560	NP_102196	YP_674183	YP_221829	NP_539777	YP_032174	ZP_01227540	NP_771118	YP_781670	YP_577106
13500	Avi3141	Arad3145	NP_532859	YP_470470	YP_769009	NP_385672	NP_103870	YP_674668	YP_222180	NP_539430	YP_032528	ZP_01225952	NP_774021	YP_782871	YP_578109
13546	Avi1434	Arad1583	NP_531722	YP_468912	YP_767107	NP_385166	NP_107999	YP_673504	YP_221400	NP_540217	YP_032100	ZP_01228758	NP_771710	YP_781947	YP_577512
13560	Avi0032	Arad0061	NP_530759	YP_467608	YP_765653	NP_384162	NP_105747	YP_676028	YP_222717	NP_540964	YP_031904	ZP_01228880	NP_767289	YP_779310	YP_575482
13563	Avi1558	Arad1712	NP_531826	YP_469009	YP_767191	NP_385277	NP_108125	YP_674533	YP_221454	NP_540168	YP_032150	ZP_01227422	NP_774110	YP_779860	YP_578342
13565	Avi1487	Arad1637	NP_531770	YP_468955	YP_767147	NP_385217	NP_108040	YP_673527	YP_221430	NP_540189	YP_032117	ZP_01228784	NP_770430	YP_780922	YP_576770
13571	Avi1359	Arad1491	NP_531669	YP_468819	YP_767038	NP_385121	NP_107952	YP_673457	YP_221360	NP_540253	YP_032072	ZP_01227053	NP_769762	YP_780853	YP_576716
13644	Avi0308	Arad0210	NP_530830	YP_467696	YP_765756	NP_384289	NP_105553	YP_673245	YP_222759	NP_540918	YP_031786	ZP_01228668	NP_767320	YP_779287	YP_575517
13654	Avi1826	Arad1962	NP_532636	YP_469189	YP_767370	NP_385454	NP_102110	YP_674377	YP_221947	NP_539666	YP_032349	ZP_01225682	NP_772050	YP_782507	YP_576813
13656	Avi0441	Arad0659	NP_531065	YP_467922	YP_765999	NP_384514	NP_106186	YP_676454	YP_222787	NP_540890	YP_031920	ZP_01228446	NP_767432	YP_779143	YP_575386
13674	Avi2261	Arad2520	NP_532161	YP_469743	YP_768151	NP_385495	NP_102152	YP_674208	YP_221716	NP_539900	YP_032415	ZP_01225648	NP_772006	YP_782457	YP_576856
13678	Avi0047	Arad0042	NP_530746	YP_467593	YP_765637	NP_384147	NP_105814	YP_676108	YP_222730	NP_540949	YP_031779	ZP_01228484	NP_774787	YP_779760	YP_575790
13702	Avi1853	Arad1988	NP_532614	YP_469209	YP_767390	NP_385474	NP_102132	YP_674226	YP_221925	NP_539686	YP_032434	ZP_01225666	NP_772028	YP_782484	YP_576839
13705	Avi0039	Arad0052	NP_530752	YP_467600	YP_765644	NP_384155	NP_105756	YP_676035	YP_222724	NP_540956	YP_031902	ZP_01228885	NP_767296	YP_779303	YP_575489
13706	Avi3233	Arad3224	NP_532930	YP_470549	YP_769082	NP_386474	NP_104007	YP_674739	YP_222236	NP_539374	YP_032540	ZP_01226218	NP_769102	YP_779873	YP_578449
13717	Avi0388	Arad0595	NP_531026	YP_467903	YP_765978	NP_384470	NP_104329	YP_676621	YP_223745	NP_541210	YP_031762	ZP_01228405	NP_767401	YP_779409	YP_575410
13725	Avi3216	Arad3207	NP_532917	YP_470537	YP_769071	NP_385928	NP_103994	YP_674728	YP_222224	NP_539387	YP_032535	ZP_01226209	NP_769124	YP_779883	YP_578437
13726	Avi4210	Arad4429	NP_533368	YP_471434	YP_770117	NP_387352	NP_105190	YP_675981	YP_222556	NP_539074	YP_032800	ZP_01229042	NP_767127	YP_779270	YP_578771
13742	Avi2381	Arad2377	NP_532202	YP_469618	YP_767988	NP_385663	NP_102491	YP_673957	YP_221812	NP_539795	YP_032410	ZP_01227558	NP_771342	YP_781807	YP_577338
13767	Avi0545	Arad0783	NP_531138	YP_468070	YP_766165	NP_384629	NP_106275	YP_672667	YP_221093	NP_540533	YP_031961	ZP_01226863	NP_767746	YP_783775	YP_575578
13781	Avi2657	Arad2138	NP_532249	YP_469353	YP_767654	NP_385646	NP_102740	YP_674354	YP_221630	NP_539992	YP_032159	ZP_01227303	NP_771373	YP_781822	YP_577075
13782	Avi1948	Arad2505	NP_532244	YP_469730	YP_768139	NP_385502	NP_102948	YP_673607	YP_223407	NP_541656	YP_032301	ZP_01227483	NP_771897	YP_782348	YP_577418
13783	Avi4292	Arad4926	NP_533488	YP_471577	YP_770284	NP_387428	NP_105054	YP_675956	YP_222474	NP_539151	YP_032811	ZP_01228920	NP_767221	YP_778967	YP_575556
13825	Avi0438	Arad0657	NP_531063	YP_467924	YP_766001	NP_384512	NP_106184	YP_676452	YP_222785	NP_540892	YP_031922	ZP_01228448	NP_767434	YP_779145	YP_575384
13836	Avi2270	Arad2154	NP_532293	YP_469367	YP_767666	NP_385834	NP_102645	YP_674015	YP_221982	NP_539635	YP_032271	ZP_01227072	NP_774813	YP_779044	YP_575781
13882	Avi2035	Arad2775	NP_532282	YP_469979	YP_768399	NP_386045	NP_102826	YP_673879	YP_221592	NP_540030	YP_032191	ZP_01226013	NP_770448	YP_780944	YP_576785
13887	Avi2884	Arad2988	NP_532762	YP_470336	YP_768878	NP_386275	NP_103110	YP_674560	YP_222112	NP_539501	YP_032493	ZP_01226101	NP_773237	YP_781039	YP_576570
13892	Avi2142	Arad2272	NP_532141	YP_469468	YP_767879	NP_385571	NP_102206	YP_674172	YP_221818	NP_539790	YP_032197	ZP_01227550	NP_771132	YP_781680	YP_577116
13905	Avi1819	Arad1957	NP_532640	YP_469185	YP_767365	NP_385450	NP_102106	YP_674381	YP_221951	NP_539662	YP_032353	ZP_01225686	NP_772055	YP_782517	YP_576809
13909	Avi1729	Arad1863	NP_531973	YP_469144	YP_767318	NP_385385	NP_102959	YP_673597	YP_221557	NP_540062	YP_032232	ZP_01225742	NP_771544	YP_781454	YP_577459
13960	Avi1532	Arad1672	NP_531796	YP_468976	YP_767165	NP_385251	NP_108087	YP_674324	YP_221240	NP_540388	YP_032136	ZP_01227404	NP_770726	YP_782216	YP_577602
13967	Avi0478	Arad0778	NP_531134	YP_468064	YP_766161	NP_384625	NP_106271	YP_672577	YP_221090	NP_540536	YP_031820	ZP_01226856	NP_767740	YP_783781	YP_575584
13972	Avi4261	Arad4658	NP_533381	YP_471502	YP_770173	NP_387355	NP_104881	YP_675940	YP_222417	NP_539205	YP_032737	ZP_01226261	NP_770605	YP_781311	YP_577794
14036	Avi2893	Arad2998	NP_532771	YP_470344	YP_768888	NP_386284	NP_103117	YP_674567	YP_222119	NP_539494	YP_032500	ZP_01226108	NP_773244	YP_781029	YP_576562
14038	Avi4207	Arad4414	NP_533365	YP_471432	YP_770115	NP_387349	NP_105194	YP_675979	YP_222562	NP_539066	YP_032802	ZP_01229032	NP_767123	YP_779268	YP_578769
14067	Avi3122	Arad3135	NP_532851	YP_470460	YP_768999	NP_385682	NP_103843	YP_674652	YP_222171	NP_539439	YP_032525	ZP_01225946	NP_774017	YP_782866	YP_578103
14085	Avi0398	Arad0612	NP_531034	YP_467913	YP_765988	NP_384483	NP_105447	YP_676549	YP_220941	NP_540693	YP_031775	ZP_01228555	NP_767315	YP_779291	YP_575513
14093	Avi0171	Arad0171	NP_530794	YP_467666	YP_765727	NP_384347	NP_106200	YP_676464	YP_222797	NP_540880	YP_031910	ZP_01228436	NP_767421	YP_779134	YP_575395
14113	Avi4135	Arad4345	NP_533308	YP_471368	YP_770014	NP_387176	NP_105175	YP_675781	YP_222551	NP_539079	YP_032797	ZP_01229034	NP_767154	YP_779451	YP_578806
14136	Avi1834	Arad1967	NP_532630	YP_469193	YP_767374	NP_385458	NP_102116	YP_674242	YP_221941	NP_539670	YP_032450	ZP_01225679	NP_772044	YP_782500	YP_576823
14162	Avi1575	Arad1725	NP_531838	YP_469018	YP_767200	NP_385290	NP_108163	YP_674524	YP_221465	NP_540157	YP_032367	ZP_01227431	NP_770765	YP_782197	YP_577375
14177	Avi0440	Arad0658	NP_531064	YP_467923	YP_766000	NP_384513	NP_106185	YP_676453	YP_222786	NP_540891	YP_031921	ZP_01228447	NP_767433	YP_779144	YP_575385
14202	Avi1763	Arad1899	NP_532000	YP_469169	YP_767344	NP_385411	NP_102440	YP_673921	YP_223398	NP_541649	YP_032284	ZP_01225634	NP_771737	YP_780145	YP_577533
14206	Avi4189	Arad4396	NP_533352	YP_471419	YP_770103	NP_387337	NP_105229	YP_675895	YP_220869	NP_540769	YP_031826	ZP_01229020	NP_767108	YP_779251	YP_575761
14228	Avi0353	Arad0545	NP_531009	YP_467869	YP_765942	NP_384443	NP_105456	YP_676542	YP_220946	NP_540686	YP_032568	ZP_01228561	NP_767309	YP_779297	YP_575507
14254	Avi0013	Arad0014	NP_530727	YP_467573	YP_765616	NP_384118	NP_105894	YP_676137	YP_220899	NP_540740	YP_031763	ZP_01228395	NP_767463	YP_778946	YP_575366
14292	Avi3536	Arad3512	NP_533115	YP_470831	YP_769344	NP_386831	NP_104781	YP_675683	YP_222320	NP_539294	YP_031974	ZP_01226901	NP_773976	YP_779753	YP_578087
14297	Avi1588	Arad1732	NP_531848	YP_469025	YP_767207	NP_385297	NP_108468	YP_673682	YP_221496	NP_540120	YP_032385	ZP_01227437	NP_770775	YP_782191	YP_577369
14326	Avi1614	Arad1755	NP_531865	YP_469041	YP_767226	NP_385317	NP_108509	YP_673698	YP_221513	NP_540105	YP_032204	ZP_01227321	NP_771670	YP_781728	YP_577091
14335	Avi4188	Arad4395	NP_533351	YP_471417	YP_770102	NP_387336	NP_105230	YP_675894	YP_220868	NP_540770	YP_031827	ZP_01229019	NP_767107	YP_779250	YP_575760
14371	Avi1592	Arad1734	NP_531850	YP_469027	YP_767209	NP_385300	NP_108471	YP_673683	YP_221497	NP_540119	YP_032384	ZP_01227438	NP_770783	YP_782189	YP_577368
14393	Avi0169	Arad0173	NP_530796	YP_467668	YP_765729	NP_384345	NP_106198	YP_676462	YP_222795	NP_540882	YP_031912	ZP_01228438	NP_767423	YP_779136	YP_575393
14432	Avi1835	Arad1968	NP_532629	YP_469194	YP_767375	NP_385459	NP_102117	YP_674241	YP_221940	NP_539671	YP_032449	ZP_01225678	NP_772043	YP_782499	YP_576824
14433	Avi0022	Arad0030	NP_530735	YP_467583	YP_765627	NP_384136	NP_105800	YP_673228	YP_222742	NP_540937	YP_031759	ZP_01228496	NP_767387	YP_779395	YP_575422
14474	Avi4196	Arad4403	NP_533358	YP_471425	YP_770108	NP_387343	NP_105220	YP_675925	YP_222581	NP_539049	YP_032864	ZP_01229025	NP_767113	YP_779257	YP_575753
14505	Avi0056	Arad0034	NP_530738	YP_467586	YP_765630	NP_384140	NP_105807	YP_676115	YP_222738	NP_540940	YP_031752	ZP_01228493	NP_767392	YP_779399	YP_575419
14513	Avi0473	Arad0685	NP_531077	YP_467967	YP_766044	NP_384539	NP_105624	YP_672956	YP_223710	NP_541247	YP_031790	ZP_01227702	NP_774744	YP_779589	YP_578884
14531	Avi2081	Arad2687	NP_532299	YP_469887	YP_768283	NP_385962	NP_102308	YP_674020	YP_221726	NP_539891	YP_032319	ZP_01225843	NP_770395	YP_780911	YP_576762
14565	Avi1620	Arad1762	NP_531868	YP_469056	YP_767237	NP_385322	NP_108511	YP_673700	YP_221515	NP_540103	YP_032206	ZP_01227323	NP_771668	YP_781730	YP_577093
14566	Avi4168	Arad4378	NP_533338	YP_471402	YP_770087	NP_387320	NP_105248	YP_675400	YP_220856	NP_540784	YP_031748	ZP_01229006	NP_767165	YP_778979	YP_578814
14596	Avi1723	Arad1857	NP_531968	YP_469139	YP_767313	NP_385380	NP_102964	YP_673592	YP_221552	NP_540067	YP_032227	ZP_01225747	NP_771549	YP_781449	YP_577464
14607	Avi1855	Arad1991	NP_532612	YP_469211	YP_767392	NP_385476	NP_102134	YP_674224	YP_221923	NP_539688	YP_032432	ZP_01225664	NP_772026	YP_782482	YP_576841
14619	Avi3527	Arad3503	NP_533106	YP_470824	YP_769337	NP_386824	NP_104064	YP_674770	YP_222272	NP_539340	YP_032546	ZP_01226947	NP_768840	YP_783175	YP_578561
14623	Avi1497	Arad1639	NP_531771	YP_468957	YP_767149	NP_385229	NP_108067	YP_673543	YP_221223	NP_540406	YP_032122	ZP_01227389	NP_770699	YP_782253	YP_576964
14765	Avi3185	Arad3189	NP_532900	YP_470519	YP_769051	NP_386460	NP_103973	YP_674714	YP_222213	NP_539398	YP_032016	ZP_01226196	NP_774081	YP_780367	YP_578300
14781	Avi2099	Arad2754	NP_532678	YP_470064	YP_768542	NP_386007	NP_103929	YP_674689	YP_222193	NP_539418	YP_032534	ZP_01226172	NP_774071	YP_783096	YP_578150
14786	Avi0369	Arad0562	NP_531021	YP_467880	YP_765953	NP_384452	NP_106033	YP_676591	YP_223742	NP_541213	YP_031750	ZP_01226738	NP_770685	YP_781962	YP_576957
14796	Avi3194	Arad3195	NP_532906	YP_470525	YP_769059	NP_386463	NP_103975	YP_674716	YP_222215	NP_539396	YP_032013	ZP_01226198	NP_774079	YP_780369	YP_578298
14820	Avi2165	Arad2343	NP_532476	YP_469590	YP_767960	NP_385778	NP_102294	YP_674255	YP_223424	NP_541673	YP_032257	ZP_01227583	NP_771225	YP_781715	YP_577304
14831	Avi1470	Arad1620	NP_531759	YP_468940	YP_767136	NP_385228	NP_108059	YP_673541	YP_221222	NP_540407	YP_032121	ZP_01227388	NP_770437	YP_780933	YP_576776
14848	Avi0902	Arad1088	NP_531394	YP_468380	YP_766512	NP_384914	NP_108398	YP_673004	YP_223012	NP_542010	YP_031955	ZP_01227893	NP_774158	YP_779814	YP_578376
14859	Avi1906	Arad2573	NP_532523	YP_469785	YP_768190	NP_385878	NP_101947	YP_673842	YP_221582	NP_540039	YP_032376	ZP_01228848	NP_772369	YP_780536	YP_576912
14860	Avi0395	Arad0609	NP_531032	YP_467910	YP_765985	NP_384480	NP_105450	YP_676546	YP_220943	NP_540689	YP_031774	ZP_01228557	NP_767313	YP_779293	YP_575511
14886	Avi2233	Arad2457	NP_532304	YP_469692	YP_768095	NP_385546	NP_102377	YP_674194	YP_221840	NP_539766	YP_032164	ZP_01227526	NP_771445	YP_781513	YP_577013
14892	Avi4154	Arad4366	NP_533326	YP_471386	YP_770071	NP_387193	NP_105069	YP_675767	YP_222633	NP_538994	YP_031868	ZP_01228993	NP_767188	YP_778985	YP_575959
14898	Avi0352	Arad0543	NP_531008	YP_467868	YP_765941	NP_384442	NP_105455	YP_676543	YP_220945	NP_540687	YP_032569	ZP_01228560	NP_767310	YP_779296	YP_575508
14931	Avi3190	Arad3192	NP_532903	YP_470522	YP_769054	NP_386461	NP_103974	YP_674715	YP_222214	NP_539397	YP_032015	ZP_01226197	NP_774080	YP_780368	YP_578299
14936	Avi1845	Arad1978	NP_532621	YP_469202	YP_767383	NP_385467	NP_102125	YP_674233	YP_221932	NP_539679	YP_032441	ZP_01225672	NP_772035	YP_782491	YP_576832
14949	Avi2900	Arad3006	NP_532777	YP_470350	YP_768894	NP_386290	NP_103123	YP_674573	YP_222125	NP_539488	YP_032506	ZP_01226114	NP_773250	YP_781023	YP_576556
15003	Avi2137	Arad2268	NP_532138	YP_469465	YP_767876	NP_385567	NP_102203	YP_674176	YP_221822	NP_539785	YP_032179	ZP_01227547	NP_771130	YP_781677	YP_577113
15009	Avi1915	Arad2610	NP_532548	YP_469822	YP_768212	NP_385896	NP_101925	YP_673829	YP_221900	NP_539711	YP_032268	ZP_01228836	NP_772386	YP_780532	YP_576903
15061	Avi0005	Arad0003	NP_530719	YP_467565	YP_765608	NP_384110	NP_105352	YP_676017	YP_222707	NP_540974	YP_031734	ZP_01228897	NP_767279	YP_779317	YP_575475
15101	Avi3226	Arad3216	NP_532923	YP_470543	YP_769076	NP_386468	NP_104001	YP_674733	YP_222230	NP_539380	YP_032536	ZP_01226212	NP_769109	YP_779880	YP_578442
15132	Avi3529	Arad3506	NP_533110	YP_470826	YP_769339	NP_386826	NP_104062	YP_674768	YP_222271	NP_539341	YP_032547	ZP_01226945	NP_768831	YP_783189	YP_578567
15154	Avi0602	Arad0808	NP_531201	YP_468099	YP_766196	NP_384643	NP_106248	YP_672596	YP_223199	NP_541443	YP_032561	ZP_01226622	NP_767794	YP_779653	YP_575605
15157	Avi2876	Arad2980	NP_532757	YP_470330	YP_768872	NP_386270	NP_103104	YP_674555	YP_222106	NP_539506	YP_032488	ZP_01226095	NP_773231	YP_781045	YP_576575
15192	Avi1580	Arad1728	NP_531841	YP_469021	YP_767203	NP_385293	NP_108316	YP_673680	YP_221494	NP_540122	YP_032387	ZP_01227435	NP_770762	YP_782194	YP_577372
15210	Avi1761	Arad1896	NP_531997	YP_469167	YP_767342	NP_385409	NP_102442	YP_673919	YP_223396	NP_541647	YP_032286	ZP_01225636	NP_771740	YP_782286	YP_577535
15212	Avi2521	Arad2223	NP_532067	YP_469429	YP_767818	NP_385604	NP_102409	YP_673945	YP_221865	NP_539743	YP_032335	ZP_01227505	NP_771498	YP_781474	YP_576973
15258	Avi2656	Arad2139	NP_532248	YP_469354	YP_767655	NP_385647	NP_102739	YP_674353	YP_221631	NP_539991	YP_032160	ZP_01227304	NP_771372	YP_781821	YP_577076
15293	Avi4280	Arad4878	NP_533444	YP_471539	YP_770245	NP_387267	NP_104986	YP_675992	YP_222498	NP_539126	YP_031860	ZP_01226342	NP_767069	YP_779205	YP_575870
15337	Avi2561	Arad2240	NP_532085	YP_469441	YP_767830	NP_385716	NP_102395	YP_674202	YP_221850	NP_539757	YP_032265	ZP_01227518	NP_771466	YP_781489	YP_577004
15343	Avi0110	Arad0186	NP_530805	YP_467678	YP_765739	NP_384336	NP_106158	YP_676589	YP_220815	NP_540825	YP_031928	ZP_01227695	NP_774756	YP_783712	YP_575812
15358	Avi0050	Arad0038	NP_530742	YP_467590	YP_765634	NP_384144	NP_105811	YP_676111	YP_222734	NP_540944	YP_031755	ZP_01228488	NP_767397	YP_779404	YP_575414
15400	Avi4191	Arad4397	NP_533353	YP_471420	YP_770104	NP_387338	NP_108446	YP_675896	YP_220870	NP_540768	YP_031825	ZP_01229021	NP_767109	YP_779252	YP_575762
15488	Avi0292	Arad0372	NP_530921	YP_467764	YP_765827	NP_384255	NP_106236	YP_676485	YP_222810	NP_540865	YP_031901	ZP_01227680	NP_768071	YP_782667	YP_575735
15500	Avi4390	Arad4943	NP_533497	YP_471593	YP_770301	NP_387444	NP_105344	YP_676008	YP_222699	NP_538924	YP_032871	ZP_01228905	NP_767274	YP_779322	YP_575467
15582	Avi1681	Arad1810	NP_531939	YP_469099	YP_767276	NP_385348	NP_108551	YP_673724	YP_221533	NP_540086	YP_032305	ZP_01225965	NP_771602	YP_781775	YP_577704
15593	Avi3173	Arad3179	NP_532888	YP_470514	YP_769045	NP_386451	NP_103964	YP_674709	YP_222208	NP_539403	YP_032018	ZP_01226191	NP_774086	YP_780363	YP_578290
15595	Avi4380	Arad4934	NP_533412	YP_471585	YP_770293	NP_387436	NP_105035	YP_675745	YP_222466	NP_539159	YP_032760	ZP_01228912	NP_767263	YP_779331	YP_575457
15603	Avi0209	Arad0445	NP_530965	YP_467814	YP_765876	NP_384392	NP_105784	YP_673242	YP_222756	NP_540921	YP_031803	ZP_01228364	NP_767345	YP_779432	YP_575434
15606	Avi2665	Arad2130	NP_532387	YP_469346	YP_767647	NP_385638	NP_102749	YP_674362	YP_221623	NP_539999	YP_032155	ZP_01227296	NP_771388	YP_781617	YP_577065
15609	Avi1799	Arad1938	NP_532032	YP_469174	YP_767348	NP_385437	NP_102062	YP_674267	YP_221652	NP_539971	YP_032244	ZP_01225615	NP_770948	YP_781893	YP_577099
15618	Avi1941	Arad2585	NP_532530	YP_469793	YP_768196	NP_385885	NP_101938	YP_673838	YP_221577	NP_540044	YP_032379	ZP_01228843	NP_772359	YP_780542	YP_576915
15649	Avi1863	Arad2000	NP_532607	YP_469217	YP_767398	NP_385482	NP_102140	YP_674218	YP_221917	NP_539694	YP_032426	ZP_01225659	NP_772020	YP_782476	YP_576847
15654	Avi4137	Arad4348	NP_533310	YP_471370	YP_770016	NP_387178	NP_105177	YP_675783	YP_222553	NP_539077	YP_032799	ZP_01229036	NP_767152	YP_779449	YP_578804
15666	Avi0051	Arad0037	NP_530741	YP_467589	YP_765633	NP_384143	NP_105810	YP_676112	YP_222735	NP_540943	YP_031754	ZP_01228489	NP_767396	YP_779403	YP_575415
15689	Avi1717	Arad1848	NP_531964	YP_469134	YP_767308	NP_385375	NP_102969	YP_673588	YP_221548	NP_540071	YP_032223	ZP_01225751	NP_771554	YP_781443	YP_577468
15724	Avi0341	Arad0530	NP_530999	YP_467858	YP_765933	NP_384433	NP_105458	YP_676133	YP_223724	NP_541233	YP_032575	ZP_01228643	NP_767355	YP_779442	YP_575546
15737	Avi0895	Arad1095	NP_531399	YP_468386	YP_766522	NP_384922	NP_108408	YP_673010	YP_223018	NP_542004	YP_031960	ZP_01227898	NP_774133	YP_780352	YP_578364
15744	Avi1859	Arad1995	NP_532609	YP_469214	YP_767395	NP_385479	NP_102137	YP_674221	YP_221920	NP_539691	YP_032429	ZP_01225661	NP_772023	YP_782479	YP_576844
15770	Avi2891	Arad2996	NP_532769	YP_470342	YP_768886	NP_386282	NP_103115	YP_674565	YP_222117	NP_539496	YP_032498	ZP_01226106	NP_773242	YP_781031	YP_576564
15790	Avi2163	Arad2341	NP_532477	YP_469475	YP_767886	NP_385779	NP_102298	YP_674256	YP_223423	NP_541672	YP_032256	ZP_01227582	NP_771226	YP_781714	YP_577305
15801	Avi0976	Arad1174	NP_531424	YP_468437	YP_766572	NP_384974	NP_107756	YP_673280	YP_221185	NP_540445	YP_032029	ZP_01228051	NP_769210	YP_783284	YP_579138
15805	Avi2659	Arad2136	NP_532251	YP_469351	YP_767652	NP_385644	NP_102742	YP_674356	YP_221628	NP_539994	YP_032158	ZP_01227301	NP_771376	YP_781825	YP_577072
15825	Avi1847	Arad1980	NP_532619	YP_469204	YP_767385	NP_385469	NP_102127	YP_674231	YP_221930	NP_539681	YP_032439	ZP_01225670	NP_772033	YP_782489	YP_576834
15838	Avi1756	Arad1891	NP_531994	YP_469164	YP_767339	NP_385406	NP_102557	YP_673915	YP_223392	NP_541644	YP_032289	ZP_01225639	NP_771751	YP_782291	YP_577687
15841	Avi0942	Arad1132	NP_531333	YP_468412	YP_766548	NP_384951	NP_107749	YP_673277	YP_221182	NP_540448	YP_032007	ZP_01228061	NP_769165	YP_783324	YP_578412
15868	Avi1810	Arad1946	NP_532670	YP_469180	YP_767360	NP_385444	NP_102094	YP_673646	YP_221956	NP_539658	YP_032357	ZP_01225693	NP_772139	YP_782592	YP_577752
15893	Avi4279	Arad4880	NP_533443	YP_471540	YP_770246	NP_387268	NP_104985	YP_675991	YP_222497	NP_539127	YP_031861	ZP_01226343	NP_767070	YP_779206	YP_575871
15910	Avi4384	Arad4937	NP_533415	YP_471588	YP_770296	NP_387439	NP_105338	YP_675853	YP_222694	NP_538929	YP_032834	ZP_01228910	NP_767269	YP_779327	YP_575461
15917	Avi1546	Arad1688	NP_531808	YP_468987	YP_767176	NP_385262	NP_108098	YP_674314	YP_221445	NP_540177	YP_032144	ZP_01227414	NP_770749	YP_782203	YP_577590
15942	Avi2896	Arad3002	NP_532774	YP_470347	YP_768891	NP_386287	NP_103120	YP_674570	YP_222122	NP_539491	YP_032503	ZP_01226111	NP_773247	YP_781026	YP_576559
16016	Avi4107	Arad4307	NP_533288	YP_471344	YP_769978	NP_387141	NP_105024	YP_675754	YP_222458	NP_539168	YP_032753	ZP_01226747	NP_767081	YP_779220	YP_575881
16043	Avi0170	Arad0172	NP_530795	YP_467667	YP_765728	NP_384346	NP_106199	YP_676463	YP_222796	NP_540881	YP_031911	ZP_01228437	NP_767422	YP_779135	YP_575394
16073	Avi4352	Arad4671	NP_533430	YP_471496	YP_770179	NP_387363	NP_104870	YP_675915	YP_222429	NP_539196	YP_032744	ZP_01228183	NP_766796	YP_779065	YP_575857
16095	Avi2879	Arad2981	NP_532758	YP_470332	YP_768874	NP_386271	NP_103105	YP_674556	YP_222107	NP_539505	YP_032489	ZP_01226097	NP_773233	YP_781043	YP_576574
16097	Avi0997	Arad1198	NP_531445	YP_468451	YP_766585	NP_384986	NP_107784	YP_673300	YP_221214	NP_540415	YP_032040	ZP_01228035	NP_769291	YP_780001	YP_576117
16141	Avi2558	Arad2618	NP_532554	YP_469830	YP_768221	NP_385905	NP_101919	YP_673824	YP_221906	NP_539704	YP_032418	ZP_01228832	NP_772395	YP_780523	YP_576895
16180	Avi0540	Arad0680	NP_531074	YP_467964	YP_766041	NP_384527	NP_105630	YP_672960	YP_223714	NP_541243	YP_031792	ZP_01227707	NP_774747	YP_779592	YP_578881
16227	Avi0180	Arad0159	NP_530858	YP_467660	YP_765721	NP_384353	NP_106207	YP_676470	YP_222801	NP_540874	YP_031840	ZP_01228420	NP_767410	YP_779195	YP_575402
16302	Avi4227	Arad4444	NP_533428	YP_471440	YP_770124	NP_387309	NP_105156	YP_675960	YP_222646	NP_538984	YP_032826	ZP_01228970	NP_767260	YP_779333	YP_575455
16344	Avi1869	Arad2007	NP_532602	YP_469222	YP_767403	NP_385487	NP_102145	YP_674213	YP_221912	NP_539699	YP_032421	ZP_01225654	NP_772015	YP_782471	YP_576852
16404	Avi0903	Arad1087	NP_531393	YP_468379	YP_766511	NP_384913	NP_108397	YP_673003	YP_223011	NP_542011	YP_031954	ZP_01227892	NP_774159	YP_779813	YP_578377
16492	Avi1886	Arad2551	NP_532510	YP_469769	YP_768175	NP_385847	NP_101898	YP_674346	YP_221658	NP_539966	YP_032245	ZP_01225612	NP_770964	YP_781891	YP_577586
16542	Avi0889	Arad1002	NP_531320	YP_468327	YP_766454	NP_384862	NP_108462	YP_673039	YP_223321	NP_541575	YP_031857	ZP_01227937	NP_770610	YP_782185	YP_577791
16634	Avi1500	Arad1642	NP_531773	YP_468959	YP_767151	NP_385231	NP_108069	YP_673546	YP_221226	NP_540404	YP_032124	ZP_01227391	NP_770701	YP_782251	YP_577544
16680	Avi0336	Arad0523	NP_530995	YP_467854	YP_765929	NP_384429	NP_107346	YP_673033	YP_223578	NP_541868	YP_031879	ZP_01226594	NP_770625	YP_782177	YP_577785
16695	Avi0166	Arad0176	NP_530798	YP_467670	YP_765731	NP_384343	NP_106196	YP_676460	YP_222793	NP_540884	YP_031914	ZP_01228440	NP_767425	YP_779138	YP_575391
16709	Avi1848	Arad1982	NP_532618	YP_469205	YP_767386	NP_385470	NP_102128	YP_674230	YP_221929	NP_539682	YP_032438	ZP_01225669	NP_772032	YP_782488	YP_576835
16729	Avi3530	Arad3507	NP_533111	YP_470827	YP_769340	NP_386827	NP_104061	YP_674767	YP_222269	NP_539342	YP_032548	ZP_01226944	NP_768829	YP_783192	YP_578570
16755	Avi4112	Arad4315	NP_533292	YP_471348	YP_769982	NP_387145	NP_105030	YP_675750	YP_222462	NP_539164	YP_032756	ZP_01226752	NP_767085	YP_779225	YP_575885
16757	Avi2120	Arad2251	NP_532124	YP_469451	YP_767840	NP_385556	NP_102193	YP_674186	YP_221832	NP_539774	YP_032172	ZP_01227537	NP_771418	YP_781536	YP_577027
16784	Avi1762	Arad1897	NP_531998	YP_469168	YP_767343	NP_385410	NP_102441	YP_673920	YP_223397	NP_541648	YP_032285	ZP_01225635	NP_771739	YP_782285	YP_577534
16800	Avi1670	Arad1800	NP_531935	YP_469094	YP_767270	NP_385345	NP_108545	YP_673721	YP_221530	NP_540089	YP_032199	ZP_01225971	NP_771608	YP_781766	YP_577710
16811	Avi4282	Arad4875	NP_533446	YP_471537	YP_770243	NP_387265	NP_104988	YP_675994	YP_222500	NP_539124	YP_031858	ZP_01226340	NP_767065	YP_779489	YP_575867
16823	Avi2109	Arad2243	NP_532116	YP_469444	YP_767833	NP_385549	NP_102184	YP_674192	YP_221838	NP_539768	YP_032166	ZP_01227529	NP_771434	YP_781525	YP_577018
16922	Avi1371	Arad1500	NP_531677	YP_468827	YP_767046	NP_385129	NP_107960	YP_673465	YP_221368	NP_540245	YP_032079	ZP_01228735	NP_769772	YP_780867	YP_576729
16929	Avi3171	Arad3177	NP_532886	YP_470512	YP_769043	NP_386449	NP_103962	YP_674707	YP_222206	NP_539405	YP_032020	ZP_01226189	NP_774084	YP_780365	YP_578292
16934	Avi0164	Arad0177	NP_530799	YP_467671	YP_765732	NP_384342	NP_106195	YP_676459	YP_222792	NP_540885	YP_031915	ZP_01228441	NP_767426	YP_779139	YP_575390
16941	Avi2881	Arad2984	NP_532760	YP_470334	YP_768876	NP_386273	NP_103108	YP_674558	YP_222110	NP_539503	YP_032491	ZP_01226099	NP_773235	YP_781041	YP_576572
16944	Avi0045	Arad0045	NP_530748	YP_467595	YP_765639	NP_384149	NP_105816	YP_676106	YP_222727	NP_540952	YP_031781	ZP_01228482	NP_774785	YP_779758	YP_575792
16962	Avi0578	Arad0785	NP_531182	YP_468078	YP_766174	NP_384630	NP_106260	YP_672585	YP_221082	NP_540544	YP_031764	ZP_01226609	NP_767772	YP_779674	YP_575562
16964	Avi2194	Arad2491	NP_532194	YP_469719	YP_768125	NP_385517	NP_102426	YP_673932	YP_221878	NP_539731	YP_032344	ZP_01227493	NP_771796	YP_782319	YP_577670
16979	Avi1823	Arad1960	NP_532637	YP_469188	YP_767369	NP_385453	NP_102109	YP_674378	YP_221948	NP_539665	YP_032350	ZP_01225683	NP_772051	YP_782508	YP_576812
17028	Avi0327	Arad0510	NP_530987	YP_467846	YP_765921	NP_384420	NP_107351	YP_673063	YP_223575	NP_541865	YP_031880	ZP_01226598	NP_770629	YP_782176	YP_577784
17067	Avi1773	Arad1909	NP_532009	YP_469374	YP_767674	NP_385418	NP_102432	YP_673926	YP_223402	NP_541653	YP_032281	ZP_01225630	NP_771729	YP_782270	YP_577527
17144	Avi4295	Arad4928	NP_533490	YP_471579	YP_770286	NP_387430	NP_105052	YP_675954	YP_222472	NP_539153	YP_032813	ZP_01228918	NP_767219	YP_778969	YP_575558
17166	Avi2363	Arad2361	NP_532463	YP_469604	YP_767974	NP_385759	NP_102550	YP_674264	YP_223415	NP_541664	YP_032391	ZP_01227575	NP_771243	YP_781705	YP_577313
17191	Avi2858	Arad2971	NP_532748	YP_470324	YP_768867	NP_386260	NP_103097	YP_674550	YP_222102	NP_539510	YP_032485	ZP_01226086	NP_767771	YP_779676	YP_575570
17198	Avi2484	Arad2026	NP_532594	YP_469230	YP_767411	NP_385491	NP_102147	YP_674210	YP_221910	NP_539701	YP_032419	ZP_01225651	NP_772007	YP_782466	YP_576854
17201	Avi4114	Arad4319	NP_533293	YP_471352	YP_769996	NP_387152	NP_105195	YP_675939	YP_222563	NP_539065	YP_032804	ZP_01228944	NP_767086	YP_779226	YP_575886
17222	Avi0929	Arad1117	NP_531414	YP_468402	YP_766537	NP_384941	NP_107733	YP_673261	YP_221165	NP_540463	YP_032001	ZP_01228069	NP_767828	YP_783678	YP_575629
17226	Avi1471	Arad1622	NP_531760	YP_468941	YP_767137	NP_385227	NP_108058	YP_673540	YP_221221	NP_540408	YP_032120	ZP_01227387	NP_770436	YP_780932	YP_576775
17284	Avi1827	Arad1963	NP_532635	YP_469190	YP_767371	NP_385455	NP_102111	YP_674376	YP_221946	NP_539667	YP_032348	ZP_01225681	NP_772049	YP_782506	YP_576814
17314	Avi1520	Arad1658	NP_531788	YP_468970	YP_767159	NP_385244	NP_108080	YP_674474	YP_221233	NP_540397	YP_032130	ZP_01227399	NP_770719	YP_782222	YP_577607
17404	Avi3166	Arad3170	NP_532880	YP_470503	YP_769033	NP_386444	NP_103955	YP_674702	YP_222202	NP_539409	YP_032024	ZP_01226184	NP_774102	YP_780357	YP_578332
17467	Avi4193	Arad4399	NP_533355	YP_471422	YP_770105	NP_387340	NP_105227	YP_675898	YP_220872	NP_540766	YP_031823	ZP_01229022	NP_767111	YP_779254	YP_575764
17486	Avi1749	Arad1884	NP_531986	YP_469158	YP_767333	NP_385399	NP_102572	YP_673908	YP_223385	NP_541637	YP_032306	ZP_01227477	NP_771764	YP_782298	YP_577693
17498	Avi3104	Arad3117	NP_532840	YP_470444	YP_768982	NP_386420	NP_103805	YP_674026	YP_222163	NP_539449	YP_032518	ZP_01225939	NP_773989	YP_779989	YP_578094
18059	Avi3139	Arad3143	NP_532858	YP_470469	YP_769008	NP_385673	NP_103871	YP_674669	YP_222181	NP_539429	YP_032529	ZP_01225951	NP_774020	YP_782870	YP_578108
18446	Avi1362	Arad1493	NP_531671	YP_468821	YP_767040	NP_385123	NP_107954	YP_673459	YP_221362	NP_540251	YP_032073	ZP_01227055	NP_769765	YP_780856	YP_576719
18452	Avi2906	Arad3010	NP_532787	YP_470355	YP_768899	NP_386294	NP_103126	YP_674576	YP_222130	NP_539482	YP_032579	ZP_01226121	NP_773251	YP_781022	YP_576555
18459	Avi4347	Arad4675	NP_533418	YP_471493	YP_770182	NP_387366	NP_104867	YP_675912	YP_222433	NP_539193	YP_032742	ZP_01228199	NP_766799	YP_779068	YP_575854
18462	Avi4148	Arad4359	NP_533321	YP_471380	YP_770065	NP_387188	NP_105142	YP_675736	YP_222534	NP_539097	YP_032822	ZP_01228979	NP_767204	YP_779003	YP_575915
18479	Avi2040	Arad2676	NP_532342	YP_469878	YP_768273	NP_385952	NP_102540	YP_674024	YP_221731	NP_539886	YP_032315	ZP_01225834	NP_770420	YP_780917	YP_576767
18678	Avi2980	Arad3099	NP_532835	YP_470429	YP_768962	NP_386413	NP_103761	YP_674631	YP_222159	NP_539453	YP_032517	ZP_01225935	NP_767119	YP_779262	YP_578766
18807	Avi0945	Arad1134	NP_531336	YP_468415	YP_766551	NP_384954	NP_107744	YP_673274	YP_221179	NP_540451	YP_032009	ZP_01228059	NP_769173	YP_783318	YP_578409
18940	Avi1542	Arad1682	NP_531804	YP_468983	YP_767172	NP_385259	NP_108095	YP_674317	YP_221441	NP_540180	YP_032142	ZP_01227411	NP_770746	YP_782206	YP_577593
19008	Avi2794	Arad2885	NP_532700	YP_470265	YP_768802	NP_386192	NP_103012	YP_674054	YP_222073	NP_539538	YP_032471	ZP_01227127	NP_771704	YP_781942	YP_577506
19042	Avi2202	Arad2480	NP_532436	YP_469713	YP_768119	NP_385522	NP_102039	YP_674282	YP_221958	NP_539656	YP_032358	ZP_01225711	NP_772192	YP_781250	YP_576926
19072	Avi0425	Arad0643	NP_531053	YP_467935	YP_766011	NP_384503	NP_106007	YP_676566	YP_220914	NP_540722	YP_032635	ZP_01228456	NP_772556	YP_780387	YP_576591
19122	Avi2895	Arad3001	NP_532773	YP_470346	YP_768890	NP_386286	NP_103119	YP_674569	YP_222121	NP_539492	YP_032502	ZP_01226110	NP_773246	YP_781027	YP_576560
19324	Avi2885	Arad2989	NP_532763	YP_470337	YP_768879	NP_386276	NP_103111	YP_674561	YP_222113	NP_539500	YP_032494	ZP_01226102	NP_773238	YP_781038	YP_576569
19347	Avi2519	Arad2225	NP_532069	YP_469431	YP_767820	NP_385606	NP_102407	YP_673947	YP_221863	NP_539745	YP_032334	ZP_01227507	NP_771496	YP_781476	YP_576975
19367	Avi2438	Arad2536	NP_532502	YP_469757	YP_768163	NP_385839	NP_101911	YP_674338	YP_221667	NP_539957	YP_032251	ZP_01225602	NP_770981	YP_781882	YP_577578
19382	Avi1539	Arad1679	NP_531802	YP_468981	YP_767170	NP_385257	NP_108093	YP_674319	YP_221439	NP_540182	YP_032140	ZP_01227409	NP_770744	YP_782208	YP_577595
19397	Avi0797	Arad0943	NP_531300	YP_468246	YP_766362	NP_384809	NP_107008	YP_672728	YP_223237	NP_541490	YP_031984	ZP_01227820	NP_773401	YP_782620	YP_578466
19484	Avi0433	Arad0652	NP_531059	YP_467928	YP_766005	NP_384509	NP_106181	YP_676449	YP_222782	NP_540895	YP_031924	ZP_01228451	NP_767438	YP_779149	YP_575381
19546	Avi1322	Arad1485	NP_531624	YP_468792	YP_766998	NP_385115	NP_107930	YP_673447	YP_221342	NP_540269	YP_032068	ZP_01227026	NP_769741	YP_780807	YP_576684
19550	Avi1627	Arad1768	NP_531873	YP_469060	YP_767241	NP_385327	NP_108520	YP_673705	YP_221519	NP_540099	YP_032208	ZP_01227328	NP_771662	YP_781741	YP_576865
19553	Avi2565	Arad2435	NP_532370	YP_469682	YP_768076	NP_385765	NP_102382	YP_674197	YP_221845	NP_539762	YP_032161	ZP_01227523	NP_771448	YP_781510	YP_577010
19586	Avi3106	Arad3123	NP_532841	YP_470448	YP_768988	NP_386424	NP_103806	YP_674025	YP_222164	NP_539447	YP_032519	ZP_01225940	NP_773990	YP_779990	YP_578095
19605	Avi0534	Arad0744	NP_531109	YP_468025	YP_766113	NP_384589	NP_106081	YP_672640	YP_221072	NP_540553	YP_031847	ZP_01227904	NP_773398	YP_782617	YP_578463

Table S3. Key gene clusters shared by chromosome II in several strains of Brucella (represented by B. suis 1330), chromosome II in Ochrobactrum anthropi, chromosome II in biovar 1 (C58) and 3 (S4) strains of Agrobacterium, 2651 kbp replicon in biovar 2 (K84) of Agrobacterium, plasmid p42e of Rhizobium etli (R.etli), plasmid pRL11 of Rhizobium leguminosarum (R.legum), and plasmid pSymB of Sinorhizobium (S.mel), most likely due to a shared repABC-type plasmid precursor (labeled IRT in the research article) that either entered an ancestral genome carrying these gene clusters and/or resulted from an ancestral intragenome gene transfer from chromosome I to the IRT plasmid early in the Rhizobiales lineage.

Product	*Gene number*
	*B. suis*	*O.anthropi*	*C58*	S4	*K84*	*R. etli*	*R. legum*	*S. mel*
RepC1 replication protein C^a	BRA0001	Oant_4454	Atu3922	Avi5002	Arad7003	RHE_PE00459	pRL110003	SM_b20044
RepB1 replication protein B^a	BRA1203	Oant_4455	Atu3923	Avi5001	Arad7001	RHE_PE00458	pRL110002	SM_b20045
RepA1 replication protein A^a	BRA1202	Oant_4456	Atu3924	Avi5000	Arad7000	RHE_PE00457	pRL110001	SM_b20046

PcaB 3-carboxy-cis,cis-muconate Cycloisomerase^b	BRA0647	Oant_3729	Atu4538	Avi6130	Arad9505	RHE_PE00055	pRL110085	SM_b20575
PcaG protocatechuate 3,4-dioxygenase alpha chain^b	BRA0646	Oant_3728	Atu4539	Avi6129	Arad9504	RHE_PE00056	pRL110086	SM_b20576
PcaH protocatechuate 3,4-dioxygenase beta chain^b	BRA0645	Oant_3727	Atu4540	Avi6128	Arad9503	RHE_PE00057	pRL110087	SM_b20577
PcaC gamma carboxymuconolactone decarboxylase^b	BRA0644	Oant_3726	Atu4541	Avi6127	Arad9502	RHE_PE00058	pRL110088	SM_b20578
PcaD beta-ketoadipate enol-lactone hydrolase^b	BRA0643	Oant_3725	Atu4542	Avi6126	Arad9500	RHE_PE00059	pRL110089	SM_b20579
PcaQ transcriptional activator^b	BRA0642	Oant_3724	Atu4543	Avi6124	Arad9499	RHE_PE00060	pRL110090	SM_b20580
4-hydroxybenzoate hydroxylase^b	BRA0641	Oant_3723	Atu4544	Avi6123	Arad9498	RHE_CH03444	RL3905	SM_b20583
Transcriptional regulator, AraC family^b	BRA0640	Oant_3722	Atu4545	Avi6122	Arad9497	RHE_CH03443	RL3904
IclR family transcriptional regulator^b	BRA0639	Oant_3721	Atu4546	Avi6121	Arad9496	RHE_PE00200	pRL110286	SM_b20586
CoA-transferase subunit A^b	BRA0648	Oant_3720	Atu4547	Avi6120	Arad9494	RHE_PE00201	pRL110287	SM_b20587
3-oxoadipate CoA-transferase subunitB^b	BRA0637	Oant_3719	Atu4548	Avi6118	Arad9491	RHE_PE00202	pRL110288	SM_b20588
PcaF beta-ketoadipyl CoA thiolase^b	BRA0636	Oant_3718	Atu4549	Avi6117	Arad9490	RHE_PE00203	pRL110289	SM_b20589

HutU urocanase^a	BRA0932	Oant_1433^c	Atu3931	Avi5956	Arad4562^d	RHE_PE00070	pRL110203	SM_b21163
HutG formiminoglutamase^a	BRA0931	Oant_1434^c	Atu3932	Avi5957		RHE_PE00071	pRL110204	SM_b21164
HutH1 histidine ammonia-lyase^a	BRA0930	Oant_1435^c	Atu3933	Avi5958	Arad4563^d	RHE_PE00072	pRL110205	SM_b21165
HutI imidazolonepropionase^a	BRA0929	Oant_1436^c	Atu3934	Avi5959	Arad4564^d	RHE_PE00073	pRL110206	SM_b21166
N-formimino-L-glutamate deiminase^a	BRA0928	Oant_1437^c	Atu3935	Avi5960	Arad4565^d	RHE_PE00074	pRL110207	SMc00673
Transcriptional regulator, GntR family^a	BRA0927	Oant_1438^c	Atu3936	Avi5963	Arad4566^d	RHE_PE00075	pRL110208	SM_b20048

MinE cell division inhibitor^a	BRA0323	Oant_2972	Atu3247	Avi3506^e	Arad8858	RHE_PE00407	pRL110544	SM_b21522
MinD cell division inhibitor^a	BRA0322	Oant_2971	Atu3248	Avi3507^e	Arad8857	RHE_PE00408	pRL110545	SM_b21523
MinC cell division inhibitor^a	BRA0321	Oant_2970	Atu3249	Avi3508^e	Arad8856	RHE_PE00409	pRL110546	SM_b21524

^a These genes are absent from the unichromosome genome of Azorhizobium caulidans, also of the Rhizobiales, in support of IRT plasmid origin.

^b These genes are present in the unichromosome genome of Azorhizobium caulidans, also of the Rhizobiales (supports intragenome transfer to IRT plasmid).

^c These genes are on chromosome I in Ochrobacter anthropi, most likely due to a intragenome transfer in the opposite direction from IRT to chromosome I. The presence of a larger syntenic cluster that houses the hut gene cluster on ChrII of all Brucella species and ChrI of O. anthropi supports a retrotransfer after the split of these two lineages from their most recent common ancestor.

^d These genes are on chromosome I in Agrobacterium radiobacter, most likely due to a intragenome transfer in the opposite direction from IRT to chromosome I. The presence of a larger syntenic cluster that houses the hut gene cluster on ChrII of Rhizobium etli and R. leguminosarum but on ChrI of A. radiobacter supports a retrotransfer after the divergence of the biovar II lineage from the biovar I/III lineage.

^e These genes are on chromosome I in Agrobacterium vitis, most likely due to a intragenome transfer in the opposite direction from IRT to chromosome I. There is no larger syntenic support for this explanation, but is it is the simplest explanation given that the minCDE operon is found rarely in the alpha-Proteobacteria outside of the Rhizobiales and it is only found on second chromosomes or megareplicons in all other members of the Rhizobiales except A. vitis. This retrotransfer occurred after the divergence of the biovar III and biovar I lineages.

Product	Gene ID
	*S. meliloti*	*B. abortus*	*O. anthropi*
response regulator	SMc04044	BruAb2_0043	Oant_4284
hypothetical formiminoglutamase	SMc04043	BruAb2_0044	Oant_4283
inositol monophosphatase family protein	SMc04042	BruAb2_0045	Oant_4282
hypothetical lysophospholipase L2	SMc04041	BruAb2_0046	Oant_4281
hypothetical threonine aldolase, low-specificity	SMc04029	BruAb2_0052	Oant_4278
GltB glutamate synthase, large subunit	SMc04028	BruAb2_0054	Oant_4277
conserved hypothetical protein	SMc04025	BruAb2_0057	Oant_4274
hypothetical transglycosylase	SMc04024	BruAb2_0070	Oant_4273
GalU UTP--glucose-1-phosphate uridylyltransferase	SMc04023	BruAb2_0071	Oant_4272
KpsF/GutQ sugar isomerase	SMc02268	BruAb2_0073	Oant_4269
conserved hypothetical protein	SMc04021	BruAb2_0074	Oant_4268
SPFH domain/Band 7 family protein	SMc04020	BruAb2_0075	Oant_4267
Omp10 lipoprotein	SMc04017	BruAb2_0077	Oant_4265
homospermidine synthase	SMc04016	BruAb2_0078	Oant_4263
para-aminobenzoate synthase, component I	SMc04014	BruAb2_0079	Oant_4262
para-aminobenzoate synthase, component I	SMc04013	BruAb2_0080	Oant_4261
PepF oligoendopeptidase F	SMc04012	BruAb2_0081	Oant_4260
conserved hypothetical protein	SMc04010	BruAb2_0083	Oant_4258

high-affinity nickel-transporter	SMc02986	BruAb2_0095	Oant_4249
hypothetical protein	SMc02985	BruAb2_0096	Oant_4248
LysR family transcriptional regulator	SMc02984	BruAb2_0097	Oant_4247

spermidine/putrescine ABC transporter, ATP-binding protein	SMc01608	BruAb2_0110	Oant_4232
spermidine/putrescine ABC transporter permease	SMc01607	BruAb2_0111	Oant_4231
spermidine/putrescine ABC transporter permease	SMc01606	BruAb2_0112	Oant_4230
BC transporter, periplasmic substrate-binding protein	SMc01605	BruAb2_0113	Oant_4228

conserved hypothetical protein	SMc03017	BruAb2_0118	Oant_4223
flagellar biosynthetic protein FlhB	SMc03018	BruAb2_0119	Oant_4222
chemotaxis motA protein	SMc03022	BruAb2_0124	Oant_4217
conserved hypothetical protein	SMc03023	BruAb2_0125	Oant_4216
FlgF flagellar basal-body rod protein FlgF	SMc03024	BruAb2_0126	Oant_4215
flagellum-specific ATP synthase FliI	SMc03025	BruAb2_0127	Oant_4214
conserved hypothetical protein	SMc03926	BruAb2_0128	Oant_4213
FlgB flagellar basal-body rod protein	SMc03027	BruAb2_0147	Oant_4212
FlgC flagellar basal-body rod rotein FlgC	SMc03928	BruAb2_0148	Oant_4211
FliE flagellar hook-basal body complex protein	SMc03029	BruAb2_0149	Oant_4210
flagellar basal-body rod protein FlgG	SMc03030	BruAb2_0150	Oant_4209
FlgA flagellar basal-body P-ring formation protein	SMc03031	BruAb2_0151	Oant_4208
conserved hypothetical protein	SMc03033	BruAb2_0153	Oant_4206
FlgH flagellar L-ring protein	SMc03034	BruAb2_0154	Oant_4205
FliP flagellar biosynthetic protein	SMc03036	BruAb2_0156	Oant_4203

ErfK/YbiS/YcfS/YnhG family protein	SMc00924	BruAb2_0179	Oant_3014
DNA-3-methyladenine glycosidase I	SMc00923	BruAb2_0180	Oant_3015
HisS histidyl-tRNA synthetase	SMc00919	BruAb2_0182	Oant_3017
conserved hypothetical protein	SMc00918	BruAb2_0183	Oant_3018
hypothetical ATP phosphoribosyltransferase	SMc00917	BruAb2_0184	Oant_3019
GroEL 60 kDa chaperonin	SMc01758	BruAb2_0190	Oant_3026
GroES chaperonin, 10 kDa	SMc00912	BruAb2_0191	Oant_3027
hydrolase, haloacid dehalogenase-like family	SMc00910	BruAb2_0194	Oant_3029
RibF riboflavin biosynthesis protein	SMc00909	BruAb2_0196	Oant_3030
IleS isoleucyl-tRNA synthetase	SMc00908	BruAb2_0197	Oant_3032
conserved hypothetical protein	SMc00907	BruAb2_0198	Oant_3033
conserved hypothetical protein	SMc00902	BruAb2_0202	^a
conserved hypothetical protein	SMc01003	BruAb2_0205	^a
hypothetical glutathione-regulated potassium-efflux system protein	SMc00898	BruAb2_0206	Oant_3041
PmbA protein	SMc00897	BruAb2_0207	Oant_3042
inositol monophosphatase family protein	SMc00896	BruAb2_0208	Oant_3043
conserved hypothetical protein	SMc00895	BruAb2_0209	Oant_3044
conserved hypothetical protein	SMc00933	BruAb2_0213	Oant_3048
MutL DNA mismatch repair protein	SMc00932	BruAb2_0214	Oant_3049

conserved hypothetical protein	SMc03800	BruAb2_0338	Oant_3283
Trx-2 thioredoxin	SMc03801	BruAb2_0339	Oant_3284
hypothetical ATP-dependent protease La	SMc03802	BruAb2_0340	Oant_3285
conserved hypothetical protein	SMc03803	BruAb2_0341	Oant_3286

MarR family transcriptional regulator	SMc00098	BruAb2_0346	Oant_3291
Ohr organic hydroperoxide resistance protein	SMc00040	BruAb2_0347	Oant_3292

hypothetical protein	SMc02149	BruAb2_0401	Oant_4047
2-nitropropane dioxygenase family protein	SMc02150	BruAb2_0402	Oant_4046

ATP-dependent RNA helicase, DEAD/DEAH box family	SMc02237	BruAb2_0406	Oant_4042
conserved hypothetical protein	SMc02236	BruAb2_0407	Oant_4041
conserved hypothetical protein	SMc02234	BruAb2_0408	Oant_4040
hypothetical membrane protein	SMc02232	BruAb2_0409	Oant_4039
acyl-CoA dehydrogenase family protein	SMc02229	BruAb2_0437	Oant_4033
hypothetical fatty oxidation complex, beta subunit	SMc02228	BruAb2_0438	Oant_4032
FadB, fatty oxidation complex, alpha subunit	SMc02227	BruAb2_0439	Oant_4031
peptidase, S24 family	SMc02223	BruAb2_0440	Oant_4030
conserved hypothetical protein	SMc02222	BruAb2_0441	Oant_4029

AzlC family protein	SMc00559	BruAb2_0458	Oant_3946
branched-chain amino acid transport	SMc00560	BruAb2_0457	Oant_3947

glutamate--putrescine ligase	SMc00762	BruAb2_0464	Oant_3936
FAD dependent oxidoreductase	SMc00761	BruAb2_0462	Oant_3937
Pgl 6-phosphogluconolactonase	SMc03069	BruAb2_0453	Oant_3957
Zwf glucose-6-phosphate 1-dehydrogenase	SMc03070	BruAb2_0454	Oant_3956

GcvT glycine cleavage system T protein	SMc02047	BruAb2_0504	Oant_3862
GcvH glycine cleavage system H protein	SMc02048	BruAb2_0505	Oant_3863
GcvP glycine cleavage system P protein	SMc02049	BruAb2_0506	Oant_3864

IolD, TPP-requiring enzyme	SMc01166	BruAb2_0515	Oant_3838
IolE protein	SMc00433	BruAb2_0516	Oant_3839

hypothetical ribosomal RNA large subunit methyltransferase J	SMc00811	BruAb2_0543	Oant_3812
phosphatase, Ppx/GppA family	SMc00810	BruAb2_0544	Oant_3811

conserved hypothetical protein	SMc01372	BruAb2_0612	Oant_3679
DivK polar differentiation response regulator	SMc01371	BruAb2_0613	Oant_3678
response regulator/GGDEF domain protein	SMc01370	BruAb2_0614	Oant_3677
RpmG ribosomal protein L33	SMc01369	BruAb2_0615	Oant_3676
major facilitator family transporter	SMc01368	BruAb2_0616	Oant_3675
conserved hypothetical protein	SMc01366	BruAb2_0618	Oant_3673
exoribonuclease, VacB/RNase II family	SMc01365	BruAb2_0619	Oant_3672
TopA DNA topoisomerase I	SMc01364	BruAb2_0620	Oant_3671
hypothetical membrane protein	SMc01362	BruAb2_0623	Oant_3668
PyrC-2 dihydroorotase, multifunctional complex type	SMc01361	BruAb2_0624	Oant_3667
PyrB aspartate carbamoyltransferase	SMc01360	BruAb2_0625	Oant_3666
acyl-CoA dehydrogenase family protein	SMc01359	BruAb2_0626	Oant_3665
conserved hypothetical protein TIGR00250	SMc01355	BruAb2_0627	Oant_3664
metallo-beta-lactamase family protein	SMc01354	BruAb2_0628	Oant_3663
GatC glutamyl-tRNA(Gln) amidotransferase, C subunit	SMc01353	BruAb2_0629	Oant_3662
GatA glutamyl-tRNA(Gln) amidotransferase, A subunit	SMc01352	BruAb2_0630	Oant_3660

GlmU UDP-N-acetylglucosamine pyrophosphorylase	SMc00232	BruAb2_0641	Oant_3644
GlmS glucosamine--fructose-6-phosphate aminotransferase	SMc00231	BruAb2_0642	Oant_3643
RecG ATP-dependent DNA helicase	SMc00228	BruAb2_0643	Oant_3642
conserved hypothetical protein	SMc00227	BruAb2_0644	Oant_3641
transcription-repair coupling factor	SMc04450	BruAb2_0645	Oant_3640
oxidoreductase	SMc00952	BruAb2_0647	Oant_3639
extracellular solute-binding protein	SMc00951	BruAb2_0648	Oant_3638
invasion associated locus B family protein	SMc00950	BruAb2_0649	Oant_3637
hemimethylated DNA binding protein	SMc00949	BruAb2_0650	Oant_3636

2-octaprenyl-6-methoxyphenyl hydroxylase	SMc00316	BruAb2_0651	Oant_3635
Pcs phosphatidylcholine synthase	SMc00247	BruAb2_0652	Oant_3634
ABC transporter, ATP-binding protein	SMc00245	BruAb2_0654	Oant_3632
ABC transporter, permease protein	SMc00243	BruAb2_0655	Oant_3631
ABC transporter, permease protein	SMc00244	BruAb2_0656	Oant_3630

Bfr bacterioferritin	SMc03786	BruAb2_0659	Oant_3626
conserved hypothetical protein	SMc03787	BruAb2_0660	Oant_3625

branched-chain alpha-keto acid dehydrogenase subunit E2	SMc03203	BruAb2_0698	Oant_3553
2-oxoisovalerate dehydrogenase beta subunit	SMc03202	BruAb2_0699	Oant_3552
2-oxoisovalerate dehydrogenase alpha subunit	SMc03201	BruAb2_0700	Oant_3551

putative oxidoreductase protein	SMc04138	BruAb2_0703	Oant_3549
ABC transporter permease	SMc04137	BruAb2_0704	Oant_3548
ABC transporter permease	SMc04136	BruAb2_0705	Oant_3547
putative periplasmic binding (signal peptide) ABC transporter protein	SMc04135	BruAb2_0707	Oant_3546
hypothetical protein	SMc02875	BruAb2_0708	Oant_3545
putative transcription regulator protein	SMc02876	BruAb2_0709	Oant_3544

putative quinol oxidase subunit II transmembrane protein	SMc02254	BruAb2_0711	Oant_3542
putative quinol oxidase subunit I transmembrane protein	SMc02255	BruAb2_0712	Oant_3541

monovalent cation/proton antiporter, MnhG/PhaG subunit	SMc03184	BruAb2_0717	Oant_3536
monovalent cation/proton antiporter, MnhF/PhaF subunit	SMc03183	BruAb2_0718	Oant_3535
monovalent cation/proton antiporter, MnhE/PhaE subunit	SMc03182	BruAb2_0719	Oant_3534
monovalent cation/proton antiporter, MnhD/PhaD subunit	SMc03181	BruAb2_0720	Oant_3533
monovalent cation/proton antiporter, MnhC/PhaC subunit	SMc03180	BruAb2_0721	Oant_3532

EmrB/QacA family drug resistance transporter	SMc00563	BruAb2_0751	Oant_4227
HlyD family secretion protein	SMc00564	BruAb2_0750	Oant_4226

GuaA GMP synthase	SMc00394	BruAb2_0821	Oant_3058
MTA/SAH nucleosidase family protein	SMc00395	BruAb2_0822	Oant_3057
conserved hypothetical protein	SMc00396	BruAb2_0823	Oant_3056

KatA catalase	SMc00819	BruAb2_0827	Oant_3054
transcriptional regulator OxyR	SMc00818	BruAb2_0828	Oant_3053

ZnuA, zinc ABC transporter, periplasmic zinc-bnding protein	SMc04245	BruAb2_1059	Oant_4176
ZnuC, zinc ABC transporter, ATP binding protein	SMc04244	BruAb2_1060	Oant_4177
ZnuB, zinc ABC transporter, permease protein	SMc04243	BruAb2_1061	Oant_4178
transcriptional regulator, Fur family	SMc04242	BruAb2_1062	Oant_4179

conserved hypothetical protein	SMc03057	BruAb2_1064	Oant_4181
conserved hypothetical protein	SMc03072	BruAb2_1065	Oant_4182
conserved hypothetical protein	SMc03071	BruAb2_1066	Oant_4183
hypothetical FliR, flagellar biosynthesis protein	SMc03055	BruAb2_1068	Oant_4185
FlhA flagellar biosynthesis protein	SMc03054	BruAb2_1069	Oant_4186
FliQ flagellar biosynthesis protein	SMc03953	BruAb2_1070	Oant_4187
hypothetical FlgD basal-body rod modification protein	SMc03952	BruAb2_1071	Oant_4188
hypothetical FlbT, flagellar protein	SMc03951	BruAb2_1072	Oant_4189
hypothetical FlaF	SMc03050	BruAb2_1073	Oant_4190
FlgE flagellar hook protein	SMc03047	BruAb2_1076	Oant_4193
transcriptional regulator	SMc03046	BruAb2_1077	Oant_4194
conserved hypothetical protein	SMc03045	BruAb2_1078	Oant_4195

^a These genes appear to have been lost from the genome.

Product	*Gene ID*
	*S. meliloti*	*B. abortus*
putative sulfite oxidase subunit YedZ	SMc01281	BruAb2_0243
putative sulfite oxidase subunit YedY	SMc01282	BruAb2_0244

WD repeat-containing protein	SMc02979	BruAb2_0246
cobalamin synthesis protein/P47K family protein	SMc02978	BruAb2_0247
creatinine amidohydrolase	SMc02977	BruAb2_0248

conserved hypothetical protein	SMc03941	BruAb2_0259
PntA, NAD(P) transhydrogenase, alpha subunit	SMc03950	BruAb2_0260
PntAB, NAD(P) transhydrogenase, alpha2 subunit	SMc03939	BruAb2_0261
PntB, NAD(P) transhydrogenase, beta subunit	SMc03938	BruAb2_0262

ABC transporter, permease protein	SMc03158	BruAb2_0271
ABC transporter, ATP-binding protein	SMc03159	BruAb2_0272
lipoprotein, YaeC family	SMc03157	BruAb2_0273
oxidoreductase, GMC family	SMc03116	BruAb2_0275
branched-chain amino acid ABC transporter, permease protein	SMc03117	BruAb2_0276
branched-chain amino acid ABC transporter, permease protein	SMc03118	BruAb2_0277
branched-chain amino acid ABC transporter, ATP-binding protein	SMc03119	BruAb2_0278
branched-chain amino acid ABC transporter, ATP-binding protein	SMc03120	BruAb2_0279
branched-chain amino acid ABC transporter, periplasmic binding protein	SMc03121	BruAb2_0280
transcriptional regulator, LysR family	SMc03122	BruAb2_0281

DgoK, 2-dehydro-3-deoxygalactonokinase	SMc00881	BruAb2_0294
2-dehydro-3-deoxyphosphogalactonate aldolase, hypothetical	SMc00882	BruAb2_0295

conserved hypothetical protein	SMc00667	BruAb2_0300
HutH, histidine ammonia-lyase	SMc00669	BruAb2_0303
Atz/Trz family protein	SMc00673	BruAb2_0305
HutC histidine utilization repressor	SMc00674	BruAb2_0306

omega-amino acid--pyruvate aminotransferase	SMc04388	BruAb2_0307
transcriptional regulator, hypothetical	SMc04387	BruAb2_0308
aldehyde dehydrogenase family protein	SMc04385	BruAb2_0325
conserved hypothetical protein	SMc04383	BruAb2_0326
LysR family transcriptional regulator	SMc04882	BruAb2_0327

ArsR family transcriptional regulator	SMc01226	BruAb2_0330
oxidoreductase, FMN-binding	SMc01227	BruAb2_0331

transcriptional regulator, AsnC family	SMc03092	BruAb2_0332
RocF, arginase	SMc03091	BruAb2_0333

D-amino acid oxidase family protein	SMc00761	BruAb2_0462
glutamine synthetase family protein	SMc00762	BruAb2_0464
transcriptional regulator, LysR family	SMc00820	BruAb2_0467

alcohol dehydrogenase, iron-containing	SMc01582	BruAb2_0498
glutamine synthetase family protein	SMc01594	BruAb2_0499
conserved hypothetical protein	SMc01600	BruAb2_0500
iron compound ABC transporter, ATP-binding protein, hypothetical	SMc01608	BruAb2_0529
RibH-2, riboflavin synthase, beta subunit	SMc01609	BruAb2_0535

Ade, adenine deaminase	SMc01533	BruAb2_0573
renal dipeptidase family protein	SMc01524	BruAb2_0572

hypothetical FrnE	SMc00952	BruAb2_0647
peptide ABC transporter, periplasmic peptide-binding protein	SMc00951	BruAb2_0648
conserved hypothetical protein	SMc00950	BruAb2_0649
conserved hypothetical protein	SMc00949	BruAb2_0650

oxidoreductase, Gfo/Idh/MocA family	SMc02870	BruAb2_0703
sugar ABC transporter, permease protein	SMc02871	BruAb2_0704
sugar ABC transporter, permease protein	SMc02872	BruAb2_0705
conserved hypothetical protein	SMc02875	BruAb2_0708
transcriptional regulator, GntR family	SMc02876	BruAb2_0709
NagB glucosamine-fructose-6-phosphate aminotransferase	SMc02877	BruAb2_0321
NagA N-acetylglucosamine-6-phosphate deacetylase	SMc02878	BruAb2_0322

hypothetical glyoxalase	SMc04054	BruAb2_0742
transcriptional regulator, MarR family	SMc04052	BruAb2_0743

50S ribosomal protein L34	SMc04434	BruAb2_0961
RnpA, ribonuclease P, protein component	SMc01720	BruAb2_0962
inner-membrane protein, 60 kDa	SMc01721	BruAb2_0963
hypothetical GTP-binding protein	SMc01722	BruAb2_0964
hydrolase, haloacid dehalogenase-like family	SMc01730	BruAb2_0966
conserved hypothetical protein TIGR00730, hypothetical	SMc01731	BruAb2_0967

DapE, succinyl-diaminopimelate desuccinylase	SMc01096	BruAb2_0971
TruA, tRNA pseudouridine synthase A	SMc01099	BruAb2_0973
Fmt, methionyl-tRNA formyltransferase	SMc01100	BruAb2_0974
Def-2, polypeptide deformylase	SMc01101	BruAb2_0975
conserved hypothetical protein	SMc01102	BruAb2_0976

glutathione S-transferase family protein	SMc00407	BruAb2_0984
hypothetical iron-sulfur cluster-binding protein	SMc00406	BruAb2_0985
conserved hypothetical protein	SMc00405	BruAb2_0986

MepA, penicillin-insensitive murein endopeptidase	SMc02833	BruAb2_0987
MgsA, methylglyoxal synthase	SMc02834	BruAb2_0988
Glk, glucokinase	SMc02835	BruAb2_0989
ABC transporter, ATP-binding/permease protein	SMc02836	BruAb2_0990
DapB, dihydrodipicolinate reductase	SMc02837	BruAb2_0991
Gpm, phosphoglycerate mutase	SMc02838	BruAb2_0992

ubiquinone biosynthesis protein UbiB	SMc01156	BruAb2_1005
ubiquinone/menaquinone biosynthesis methlytransferase UbiE	SMc01155	BruAb2_1006

Product	Gene ID
	C58	S4	K84	*S. meliloti*
transcriptional regulator, AraC family	atu4659	avi5122	arad9546	SM_b21649
alpha-galactosidase	atu4660	avi5121	arad9545	SM_b21648
ABC transporter	atu4661	avi5120	arad9544	SM_b21647
ABC transporter	atu4662	avi5118	arad9543	SMb21646
ABC transporter	atu4663	avi5117	arad9540	SM_b21645
ABC transporter	atu4664	avi5116	arad9539	SM_b21644
alpha-galactosidase	atu4665	avi5115	arad9538	SM_b21643


transcriptional regulator	Atu0235	Avi2977	Arad4508	SM_b20039
hypothetical transmembrane protein	Atu0234	Avi2978	Arad4509	SM_b20040

transcriptional regulator, GntR or ArsR family	Atu0182	Avi0266	Arad0293	SM_b20758
C-P (carbon-phosphorus lyase component	Atu0181	Avi0267	Arad0292	SM_b20759
PhnH C-P (carbon-phosphorus) lyase component	Atu0180	Avi0269	Arad0291	SM_b20760
PhnI C-P (carbon-phosphorus) lyase component	Atu0179	Avi0270	Arad0289	SM_b20761
PhnJ C-P (carbon-phosphorus) lyase component	Atu0178	Avi0273	Arad0288	SM_b20762
PhnK phosphonate ABC transporter, ATP-binding subunit	Atu0177	Avi0274	Arad0287	SM_b20763
PhnL phosphonate ABC transporter, ATP-binding subunit	Atu0176	Avi0275	Arad0285	SM_b20764
acetyltransferase	Atu0175	Avi0277	Arad0283	SM_b20765

conserved hypothetical protein	Atu2267	^a	Arad4851	SM_b20532
ECF family sigma factor	Atu2268	^a	Arad4853	SM_b20531

^a These genes appear to have been lost from the genome.

Product	Gene ID
	*S. meliloti*	C58	S4	K84	*R. etli*	*R. legum*
ABC transporter [sugar]
ATPase subunit	SMc01980	Atu3171	^a	Arad9098	RHE_PE00248	pRL110367
permease subunit	SMc01979	Atu3172	^a	Arad9096	RHE_PE00247	pRL110366
permease subunit	SMc01978	Atu3173	^a	Arad9095	RHE_PE00246	pRL110365
periplasmic substrate-binding subunit	SMc01977	Atu3174	^a	Arad9093	RHE_PE00245	pRL110364
methionine gamma-lyase	SMc01976	Atu3175	Avi5346	Arad9092	RHE_PE00244	pRL110363
GntR-type transcriptional regulator	SMc01975	Atu3176	Avi5347	Arad9091	RHE_PE00243	pRL110362

sarcosine oxidase alpha subunit	SMc02606	Atu4222	Avi5744	Arad8356	RHE_PE00426	pRL110562
sarcosine oxidase delta subunit	SMc02607	Atu4223	Avi5745	Arad8357	RHE_PE00425	pRL110561
sarcosine oxidase beta subunit	SMc02608	Atu4224	Avi5746	Arad8358	RHE_PE00424	pRL110560
AraC-type transcriptional regulator (glxA)	SMc02609	Atu4225	Avi5747	Arad8359	RHE_PE00423	pRL110559
transcriptional regulator	SMc02620	Atu4226	Avi5748	Arad8360	RHE_PE00422	pRL110558
amidophosphoribosyltransferase (glxB)	SMc02610	Atu4227	Avi5749	Arad8362	RHE_PE00421	pRL110557
formyl-methanofuran dehydrogenase (glxC)	SMc02611	Atu4228	Avi5750	Arad8364	RHE_PE00420	pRL110556
glutamate synthase large subunit (glxD)	SMc02612	Atu4229	Avi5751	Arad8365	RHE_PE00419	pRL110555
glutamine synthetase III	SMc02613	Atu4230	Avi5752	Arad8357	RHE_PE00418	pRL110554

^a These genes appear to have been lost from the genome.

Table S8. Key gene cluster shared by chromosome II in biovar 1 and 3 strains of Agrobacterium and by chromosome I in S. meliloti and Agrobacterium bv. 2 (K84), most likely due to an ancestral intragenome gene transfer from chromosome I to chromosome II in the lineage that includes biovars 1 and 3 after this lineage diverged away from biovar 2.

Product	Gene ID
	C58 (bv 1)	S4 (bv 3)	K84 (bv 2)	*S. meliloti*
ABC transporter, ATPase subunit	Atu3111	Avi5585	Arad4630	SMc04140
Oxidoreductase	Atu3966	Avi5584	Arad4629	SMc04139
Oxidoreductase	Atu3965	Avi5583	Arad4627	SMc04138
ABC transporter, permease subunit	Atu3112	Avi5582	Arad4625	SMc04137
ABC transporter, permease subunit	Atu3113	Avi5581	Arad4624	SMc04136
ABC transporter, periplasmic substrate-binding subunit	Atu3114	Avi5580	Arad4622	SMc04135
Transcriptional regulator, TetR family	Atu3115	Avi6229	Arad4621	SMc04134
Oxidoreductase	Atu3116	^a	Arad4620	SMc04133
Conserved hypothetical	Atu3117	^a	Arad8627	SMc04132
Conserved hypothetical	Atu3118	^a	Arad8628	SMc04130
Conserved hypothetical	Atu3119	Avi5579	Arad4618	SMc04129

^a These genes appear to have been lost from the genome.

Table S9. Key gene clusters shared by chromosome I in S. meliloti or Agrobacterium bv. 2 (K84) or Agrobacterium bv. 3 (S4) (extant examples of ancestral chromosome I) and by chromosome II in biovar 1 (C58), most likely due to an ancestral intragenome gene transfer from chromosome I to chromosome II in the biovar 1 lineage after it diverged from biovar 3 lineage.

Product	Gene ID
	C58 (bv 1)	S4 (bv 3)	K84 (bv 2)	*S. meliloti*
ABC transporter, membrane protein (sorbitol/mannitol)	Atu3168^a	Avi3568	Arad4016	SMc01497
ABC transporter, membrane protein (sorbitol/mannitol)	Atu3169^a	Avi3569	Arad4014	SMc01498
ABC transporter, nucleotide binding/ATPase protein	Atu3170^a	Avi3570	Arad4012	SMc01499

Transcriptional regulator, luxR family	Atu3318^d	^e	Arad7628	SMc03150
hypothetical protein	Atu3319
Fibrinogen binding protein	Atu3320^d	^e	^e	SMc03149
Hypothetical protein	Atu3321^d	^e	^e	SMc03148
ABC transporter, nucleotide binding/ATPase protein	Atu3322^d	^e	^e	SMc03147
secretion protein, HlyD family	Atu3323^d	^e	^e	SMc03146
Hypothetical protein	Atu3324^d	^e	^e	SMc03145

hypothetical protein	Atu3347	Avi2407	Arad2648	SMc04253
hypothetical protein	Atu3348	Avi2406	Arad2649	SMc04254
ABC transporter, nucleotide binding/ATPase protein	Atu3349	Avi2404	Arad2652	SMc04256
ABC transporter, membrane spanning protein	Atu3350	Avi2402	Arad2653	SMc04257
ABC transporter, membrane spanning protein (sugar)	Atu3351	Avi2400	Arad2655	SMc04258
ABC transporter, substrate binding protein (sugar)	Atu3352	Avi2399	Arad2656	SMc04259

secretion protein, HlyD family	Atu3382	Avi1113	Arad4713	SMc04208
rhizobicin secretion	Atu3383	Avi1114	Arad4714	SMc04207
conserved hypothetical protein	Atu3384	^e	^e	SMc04206
heme receptor	Atu3385	^e	^e	SMc04205

branched-chain alpha-keto acid dehydrogenase subunit E2	Atu3471^d	^e	^e	SMc03203
2-oxoisovalerate dehydrogenase beta subunit	Atu3472^d	^e	^e	SMc03202
2-oxoisovalerate dehydrogenase alpha subunit	Atu3473^d	^e	^e	SMc03201

pantoate--beta-alanine ligase	Atu3482	Avi2846	Arad2962	SMc01880
3-methyl-2-oxobutanoate hydroxymethyltransferase	Atu3483	Avi2847	Arad2963	SMc01881

3-demethylubiquinone-9 3-methyltransferase	Atu3508^b	Avi3965	Arad4133	SMc02440
hypothetical protein	Atu3509^b	Avi3967	Arad4135	SMc02441
amidohydrolase	Atu3510^b	Avi3968	Arad4137	SMc02442
glutaredoxin	Atu3511^b	Avi3969	Arad4139	SMc02443
competence protein F	Atu3512^b	Avi3970	Arad4141	SMc02444
methyltransferase	Atu3513^b	Avi3971	Arad4146	SMc02445
hypothetical protein	Atu3515^b	Avi3974	Arad4150	SMc02447
NTP pyrophosphohydrolase, MutT family	Atu3516^b	Avi3976	Arad4152	SMc02448
acetyltransferase	Atu3517^b	Avi3977	Arad4153	SMc02449
ornithine acetyltransferase/N-acetylglutamate synthase	Atu3518^b	Avi3979	Arad4154	SMc02450
peptidyl-prolyl cis-trans isomerase	Atu3519^b	Avi3981	Arad4155	SMc02451
preprotein translocase SecA subunit	Atu3520^b	Avi3982	Arad4157	SMc04458

glutamyl-Q tRNA(Asp) synthetase	Atu3589 ^b	Avi4004	Arad4184	SMc00735
transporter	Atu3590^b	Avi4005	Arad4186	SMc00734
short chain dehydrogenase	Atu3591 ^b	Avi4006	Arad4187	SMc00733
hypothetical protein	Atu3593^b	Avi4008	Arad4189	SMc00731
hypothetical protein	Atu3594^b	^e	^e	SMc00730
electron transfer flavoprotein beta subunit	Atu3595^b	Avi4010	Arad4191	SMc00729
electron transfer flavoprotein alpha subunit	Atu3596^b	Avi4012	Arad4193	SMc00728
3-hydroxybutyryl-CoA dehydrogenase	Atu3597^b	Avi4015	Arad4195	SMc00727
thiol:disulfide interchange protein	Atu3599^b	Avi4017	Arad4197	SMc00725
argininosuccinate lyase	Atu3598^b	Avi4016	Arad4196	SMc00726
hypothetical protein	Atu3600^b	Avi4018	Arad4198	SMc00724
diaminopimelate decarboxylase	Atu3601^b	Avi4020	Arad4200	SMc00723
hypothetical protein	Atu3602^b	Avi4021	Arad4202	SMc00722
two component response regulator	Atu3603^b	Avi4023	Arad4317	SMc00720
hypoxanthine phosphoribosyltransferase	Atu3604^b	Avi4024	Arad4205	SMc00719
hypothetical protein	Atu3605^b	Avi4026	Arad4206	^e
cell division ATP-binding protein	Atu3606^b	Avi4027	Arad4207	SMc00717
cell division protein	Atu3607^b	Avi4028	Arad4208	SMc00716
hypothetical protein	Atu3608^b	Avi4029	Arad4209	SMc00715
1-acyl-sn-glycerol-3-phosphate acyltransferase	Atu3609^b	Avi4030	Arad4211	SMc00714
transporter	Atu3610^b	Avi4031	Arad4212	SMc00713
cyclohexadienyl dehydrogenase	Atu3611^b	Avi4033	Arad4216	SMc00711
histidinol-phosphate aminotransferase	Atu3612^b	Avi4034	Arad4217	SMc00710
hypothetical protein	Atu3613^b	Avi4035	Arad4218	SMc00709
glyoxalase II	Atu3614^b	Avi4036	Arad4219	SMc00708
hypothetical protein	Atu3615^b	Avi4037	Arad4220	SMc00707
hypothetical protein	Atu3616^b	Avi4040	Arad4223	SMc00705
50S ribosomal protein L28	Atu3617^b	Avi4041	Arad4224	SMc00704
hypothetical protein	Atu3618^b	Avi4043	Arad4225	SMc00703
hypothetical protein	Atu3620^b	Avi4044	Arad4227	SMc00702
cobyrinic acid synthase	Atu3621^b	Avi4045	Arad4228	SMc00701
cobalamin biosynthesis protein	Atu3622^b	Avi4046	Arad4229	SMc00700
molecular chaperone, DnaJ family	Atu3623^b	Avi4048	Arad4231	SMc00699
stress induced morphogen	Atu3624 ^b	Avi4050	Arad4232	SMc00698
3-dehydroquinate synthase	Atu3625^b	Avi4051	Arad4234	SMc00696
shikimate kinase	Atu3626^b	Avi4053	Arad4236	SMc00695
hypothetical protein	Atu3628^b	Avi4054	Arad4237	SMc00692
site-specific tyrosine recombinase XerD	Atu3629^b	Avi4056	Arad4238	SMc00691
acetyl-CoA carboxylase carboxyltransferase subunit alpha	Atu3630^b	Avi4057	Arad4239	SMc00690
hypothetical protein	Atu3631^b	Avi4058	Arad4240	SMc00689
hypothetical protein	Atu3632^b	Avi4059	Arad4242	SMc00688
hypothetical protein	Atu3633^b	Avi4060	Arad4243	SMc00684
penicillin-binding protein dacf precursor	Atu3634^b	Avi4061	Arad4244	SMc00682
amidohydrolase	Atu3635^b	Avi4062	Arad4246	SMc00683

D-3-phosphoglycerate dehydrogenase	Atu3706^c	Avi3595	Arad3664	SMc00641
phosphoserine aminotransferase	Atu3707^c	Avi3596	Arad3666	SMc00640
outer surface protein	Atu3708^c	Avi3602	Arad3670	SMc00638
phosphoglucomutase/phosphomannomutase	Atu3709^c	Avi3629	Arad3674	SMc00637
metalloprotease	Atu3710^c	Avi3627	Arad3675	SMc04459
conserved hypothetical protein	Atu3711^c	Avi3626	Arad3676	SMc02940
hypothetical protein	Atu3712^c	Avi3624	Arad3677	SMc02941
omp16 protein	Atu3713^c	Avi3622	Arad3678	SMc02942
TolB protein	Atu3714^c	Avi3621	Arad3679	SMc04461
hypothetical protein	Atu3715^c	Avi3620	Arad3681	SMc03956
tolR protein	Atu3716^c	Avi3619	Arad3682	SMc03957
tolQ Protein	Atu3717^c	Avi3618	Arad3684	SMc03958
hypothetical protein	Atu3718^c	Avi3616	Arad3685	SMc03960
MutT/nudix family protein	Atu3719^c	Avi3611	Arad3693	SMc02448
conserved hypothetical protein	Atu3720^c	Avi3614	Arad3692	^e
hypothetical protein	Atu3721
Holliday junction DNA helicase B	Atu3722^c	Avi3609	Arad3695	SMc03965
Holliday junction DNA helicase motor protein	Atu3723^c	Avi3605	Arad3697	SMc03966
Holliday junction resolvase	Atu3724^c	Avi3604	Arad3699	SMc03967
methyl-accepting chemotaxis protein	Atu3725
flavin dependant oxidoreductase	Atu3726^c	Avi3603	Arad3701	SMc03968
hypothetical protein	Atu3727^c	Avi3631	Arad3703	SMc03969
conserved hypothetical protein	Atu3728^c	Avi3632	^e	^e
hypothetical protein	Atu3729^c	Avi3633	Arad3704	SMc03970
hypothetical protein	Atu3730^c	Avi3650	Arad3706	SMc03973
5-formyltetrahydrofolate cyclo-ligase	Atu3731^c	Avi3649	Arad3708	SMc03974
hemolysin	Atu3732^c	Avi1919	Arad2040	SMc00240
hypothetical protein	Atu3733
conserved hypothetical protein	Atu8191^c	Avi3642	Arad3724	SMc03976
conserved hypothetical protein	Atu8192^c	Avi3640	Arad3726	SMc03977
transketolase	Atu3736^c	Avi3638	Arad3727	SMc03978
Glyceraldehyde 3-Phosphate Dehydrogenase	Atu3737^c	Avi3637	Arad3729	SMc03979
Na+/H+ antiporter	Atu3738^c	Avi3634	Arad3731	^e
phosphoglycerate kinase	Atu3739^c	Avi3651	Arad3732	SMc03981
fructose bisphosphate aldolase	Atu3740^c	Avi3652	Arad3734	SMc03983
MFS permease	Atu3741^c	Avi3661	Arad3741	SMc03987
hypothetical protein	Atu3742^c	Avi3663	Arad3745	SMc03989
50S ribosomal protein L31	Atu3743^c	Avi3665	Arad3749	SMc03990
ABC transporter, nucleotide binding/ATPase protein	Atu3744^c	Avi3667	Arad3750	SMc03991
conserved hypothetical	Atu3745^c	Avi3668	Arad9600	^e
hypothetical protein	Atu3746^c	Avi3670	Arad3755	SMc03992
hypothetical protein	Atu3747^c	Avi3671	Arad3757	SMc03993
extragenic suppressor protein SuhB	Atu3748^c	Avi3672	Arad3759	SMc03994
enhanced entry protein	Atu3749^c	Avi3674	Arad3763	SMc03995
thiamine-phosphate pyrophosphorylase	Atu3750^c	Avi3675	Arad3764	SMc03996
hypothetical protein	Atu3751^c	Avi3677	^e	SMc03997
conserved hypothetical protein	Atu3752
hypothetical protein	Atu3753^c	Avi3681	Arad3768	SMc04000
phosphoribosylaminoimidazole carboxylase catalytic subunit	Atu3754^c	Avi3683	Arad3770	SMc04001
phosphoribosylaminoimidazole carboxylase ATPase subunit	Atu3755^c	Avi3684	Arad3771	SMc04002
hypothetical protein	Atu8067^c	Avi3686	Arad3772	SMc04003
hypothetical protein	Atu3757^c	Avi3687	Arad3773	SMc04004
hypothetical protein	Atu3758^c	Avi3695	Arad3789	SMc04009
hypothetical protein	Atu3759^c	Avi3693	Arad3787	SMc04008
hypothetical protein	Atu3760^c	Avi3692	Arad3786	SMc04007
hypothetical protein	Atu3761^c	Avi3691	Arad3784	SMc04006
pyruvate kinase	Atu3762^c	Avi3690	Arad3783	SMc04005
hypothetical protein	Atu3763^c	Avi3698	Arad3804	SMc04010
sigma 54 dependent transcriptional activator	Atu3764^c	Avi3699	Arad3805	SMc04011
oligoendopeptidase F	Atu3765^c	Avi3702	Arad3807	SMc04012
hypothetical protein	Atu3766^c	Avi3704	Arad3809	SMc04014
GGDEF family protein	Atu3767^c	^e	^e	SMc04015
homospermidine synthase	Atu3768^c	Avi3707	Arad3814	SMc04016
outer membrane lipoprotein	Atu3769^c	Avi3710	Arad3816	SMc04017
5'-nucleotidase	Atu3770^c	Avi3711	Arad3820	SMc04018
ferrochelatase	Atu3771^c	Avi3712	Arad3821	SMc04019
hypothetical protein	Atu3772^c	Avi3720	Arad3825	SMc04020
hypothetical protein	Atu3773^c	Avi3721	Arad3826	SMc04021
capsule expression protein	Atu3774^c	Avi3722	Arad3827	SMc02268
Conserved hypothetical protein	Atu3775
hypothetical protein	Atu3776
hypothetical protein	Atu3777^c	Avi3723	Arad3828	SMc04022
UTP-glucose-1-phosphate uridylyltransferase	Atu3778^c	Avi3724	Arad3829	SMc04023
lytic murein transglycosylase	Atu3779^c	Avi3727	Arad0178	SMc04024
hypothetical protein	Atu3780^c	Avi3728	Arad3831	SMc04025
two component response regulator	Atu3781
two component sensor kinase	Atu3782
glutamate synthase subunit beta	Atu3783^c	Avi3730	Arad3834	SMc04026
glutamate synthase large subunit	Atu3784^c	Avi3734	Arad3836	SMc04028
threonine aldolase	Atu3785^c	Avi3736	Arad3838	SMc04029

chemotaxis response regulator	Atu3883^d	Avi3746	Arad3856	SMc04044
hypothetical protein	Atu3884^d	Avi3744	Arad3854	SMc04043
inositol monophosphatase family protein	Atu3885^d	Avi3743	Arad3852	SMc04042
lysophospholipase	Atu3886^d	Avi3740	Arad3851	SMc04041
small heat shock protein	Atu3887^d	Avi3739	Arad3843	SMc04040
hypothetical protein	Atu3888^d	Avi5029	Arad3842	SMc04030
transcriptional regulator, LysR family	Atu3889^d	^e	Arad3841	^e

hypothetical protein	Atu3891^d	Avi0100	Arad4610	SMc02514
hypothetical protein	Atu3892^d	Avi0099	Arad4609	SMc02515
ABC transporter, membrane spanning protein (sugarl)	Atu3893^d	Avi0098	Arad4608	SMc02516
ABC transporter, membrane spanning protein (sugar)	Atu3894^d	Avi0097	Arad4608	SMc02517
ABC transporter, nucleotide binding/ATPase protein (sugar)	Atu3895^d	Avi0096	Arad4605	SMc02518
ABC transporter, nucleotide binding/ATPase protein (sugar)	Atu3896^d	Avi0095	Arad4604	SMc02519
glycerol-3-phosphate dehydrogenase	Atu3897^d	Avi0094	Arad4294	SMc02520
transcriptional regulator, DeoR family	Atu3898^d	Avi0092	Arad4293	SMc02521

O-linked GlcNAc transferase	Atu4063^c	Avi3772	Arad3887	SMc03935
30S ribosomal protein S21	Atu4064^c	Avi3775	Arad3885	SMc03934
hypothetical protein	Atu4065
sarcosine oxidase beta subunit	Atu4066^c	Avi3774	Arad3882	SMc03933
conserved hypothetical protein	Atu4067^c	^e	Arad3881	^e
sarcosine oxidase delta subunit	Atu4068^c	Avi3776	Arad3879	SMc03932
sarcosine oxidase alpha subunit	Atu4069^c	Avi3777	Arad3878	SMc03931
sarcosine oxidase gamma subunit	Atu4070^c	Avi3778	Arad3877	SMc03930
hypothetical protein	Atu4071^c	Avi3766	^e	SMc03928
nodulation protein N	Atu4072^c	Avi3765	Arad3875	SMc03927
glycogen debranching enzyme	Atu4073^c	Avi3764	Arad3874	SMc03926
phosphoglucomutase	Atu4074^c	Avi3763	Arad3873	SMc03925
glycogen synthase	Atu4075^c	Avi3762	Arad3872	SMc03924
glucose-1-phosphate adenylyltransferase	Atu4076^c	Avi3761	Arad3871	SMc03923
glycogen branching enzyme	Atu4077^c	Avi3760	Arad3869	SMc03922
glycogen phosphorylase	Atu4078^c	Avi3758	Arad3868	SMc04460

cytidylate kinase	Atu4103	Avi0193	Arad0143	SMc00334
30S ribosomal protein S1	Atu4104	Avi0194	Arad0142	SMc00335
hypothetical protein	Atu4105	Avi0130	Arad0141	^e

UDP-glucuronic acid epimerase	Atu4148	Avi3924	Arad3521	SMc02640
UDP-glucose 6-dehydrogenase	Atu4149	Avi1502	Arad3519	SMc02641

aspartate kinase	Atu4172^b	Avi3957	Arad4131	SMc02438
phosphoenolpyruvate-protein phosphotransferase	Atu4173^b	Avi3956	Arad4130	SMc02437
peptide chain release factor 1	Atu4174^b	Avi3955	Arad4128	SMc02436
protoporphyrinogen oxidase	Atu4175^b	Avi3954	Arad4127	SMc02435
hypothetical protein	Atu4176^b	Avi3953	Arad4126	SMc02434
ATP-dependent Clp protease, ATP-binding subunit	Atu4177^b	Avi3951	Arad4124	SMc02433
conserved hypothetical protein	Atu4178^b	Avi3949	Arad4121	SMc02432

hypothetical protein	Atu4446^a	Avi3563	Arad4019	SMc01495
ABC transporter, substrate binding protein (sorbitol)	Atu4447^a	Avi3567	Arad4017	SMc01496
ABC transporter, membrane spanning protein	Atu4448^a	Avi3568	Arad4016	SMc01497
ABC transporter, membrane spanning protein	Atu4449^a	Avi3569	Arad4014	SMc01498
ABC transporter, nucleotide binding/ATPase protein (sugar)	Atu4450^a	Avi3570	Arad4012	SMc01499
mannitol 2-dehydrogenase	Atu4451^a	Avi3572	Arad4011	SMc01501
hypothetical protein	Atu4452^a	Avi3573	Arad4010	SMc01502
ribitol kinase	Atu4453^a	Avi3574	Arad4009	SMc01503
transcriptional regulator, RpiR family	Atu4454^a	^e	Arad4008	^e
conserved hypothetical protein	Atu4456^a	Avi3841	Arad4006	SMc02882
endonuclease III	Atu4457^a	Avi3842	Arad4005	SMc02843
hypothetical protein	Atu4458^a	Avi3844	Arad4004	SMc02842
6-O-methylguanine-DNA methyltransferase	Atu4459^a	Avi3845	Arad4003	SMc02841

hypothetical protein	Atu4472	Avi3855	Arad3963	SMc03174
lysyl-tRNA synthetase	Atu4473^c	Avi3856	Arad3954	SMc03173
glutamyl-tRNA synthetase	Atu4474^c	Avi3858	Arad3953	SMc03172
transporter	Atu4475^c	Avi3860	^e	SMc04179
hypothetical protein	Atu4476^c	Avi3839	Arad3947	SMc03171
transcriptional regulator, TetR family	Atu4477^c	Avi3838	Arad3945	SMc03169
multidrug resistance efflux pump	Atu4478^c	Avi3837	Arad3944	SMc03168
MFS permease	Atu4479^c	Avi3836	Arad3942	SMc03167
conserved hypothetical protein	Atu4480
transcriptional regulator, LacI family	Atu4481^c	Avi3834	Arad3940	SMc03165
xylulokinase	Atu4482^c	Avi3833	Arad3939	SMc03164
xylose isomerase	Atu4483^c	Avi3832	Arad3938	SMc03163
hypothetical protein	Atu4484
beta-glucosidase	Atu4485^c	Avi3827	Arad3925	SMc03160
nitroreductase	Atu4486^c	Avi1179^f	^e	^e
ABC transporter, nucleotide binding/ATPase protein	Atu4487^c	Avi7230	Arad3603	SMc03159
ABC transporter, membrane spanning protein	Atu4488^c	Avi7231	Arad3604	SMc03158
outer membrane lipoprotein	Atu4489^c	Avi7233	Arad3600	SMc03157
GGDEF family protein	Atu4490^c	Avi5602	Arad3923	^e
hypothetical protein	Atu4491^c	Avi3823	Arad3921	SMc03156
hypothetical protein	Atu4492^c	Avi3820	Arad3920	SMc03155
hypothetical protein	Atu4493^c	Avi3819	Arad3919	SMc03154
keto-hydroxyglutarateketo-deoxy-phosphogluconate aldolase	Atu4494^c	Avi3816	Arad3917	SMc03153
hypothetical protein	Atu4495^c	Avi3814	Arad3925	SMc03152
acetyltransferase	Atu4496^c	Avi3813	Arad3390	SMc03151
hypothetical protein	Atu4497^c	Avi3812	Arad3915	SMc02989
hypothetical protein	Atu4498^c	Avi3811	Arad3914	SMc02986
hypothetical protein	Atu4499^c	Avi3809	Arad3913	SMc02985
hypothetical protein	Atu4501^c	Avi3798	Arad3905	SMc02979
cobalamin synthesis protein	Atu4502^c	Avi3796	Arad3903	SMc02978
transcriptional regulator, MarR family	Atu4504^c	Avi3793	Arad3901	SMc02976
creatinine amidohydrolase	Atu4503^c	Avi3547	Arad3523	SMc02977
transcriptional regulator, LacI family	Atu4505^c	Avi3792	Arad3900	SMc02975

hypothetical protein	Atu4509	Avi0080	Arad1555	SMc00432
hypothetical protein	Atu4510	Avi0078	Arad1557	SMc00433
acetolactate synthase	Atu4511	Avi0077	Arad1558	SMc01166
myo-inositol catabolism IolC protein	Atu4512	Avi0076	Arad1559	SMc01165

transcriptional regulator, LysR family	Atu4705^d	Avi4101	Arad4288	SMc02523
formate dehydrogenase subunit gamma	Atu4706^d	Avi4099	Arad4287	SMc02524
NADH ubiquinone oxidoreductase chain F	Atu4707^d	Avi4098	Arad4286	SMc02525
formate dehydrogenase alpha subunit	Atu4708^d	Avi4097	Arad4285	SMc04444
formate dehydrogenase delta subunit	Atu4709^d	Avi4095	Arad4282	SMc03086
MFS permease	Atu4710^d	Avi4093	Arad4281	^e

^a part of a ~38 kbp transfer from chromosome I (positions 2603823 to 2635533 on S. meliloti chromosome I)

^b part of a ~219 kbp transfer from chromosome I (positions 2699551 to 2918883 on S. meliloti chromosome I)

^c part of a ~201 kbp transfer from chromosome I (positions 2935226 to 3136047 on S. meliloti chromosome I)

^d part of a ~124 kbp transfer from chromosome I (positions 3163235 to 3287471 on S. meliloti chromosome I)

^e appears to have been lost from the genome

^f appears to have moved again to another component of the genome

Table S10. Key gene cluster shared by chromosome I in Agrobacterium biovar 1 (extant example of ancestral chromosome) and by the 2651 kbp replicon in biovar 2 (K84) of Agrobacterium, plasmid p42e of Rhizobium etli (Ret), and plasmid pRL11 of Rhizobium leguminosarum (Rleg), most likely due to an ancestral intragenome gene transfer from chromosome I to the repABC-type IRT plasmid in the biovar 2 lineage after it diverged from the biovar 1/biovar 3 lineage.

Product	Gene ID
	K84 (bv 2)	*R. etli*	*R. legume*	C58 (bv 1)
precorrin-4 C11-methyltransferase protein	Arad9589	RHE_PE00449	pRL110625	Atu2796
precorrin-6Y C5,15-methyltransferase (decarboxylating) protein	Arad9591	RHE_PE00450	pRL110626	Atu2798
precorrin 6x reductase protein	Arad9592	RHE_PE00451	pRL110627	Atu2799
precorrin-3B C17-methyltransferase protein	Arad9593	RHE_PE00452	pRL110628	Atu2800
precorrin-2 c20-methyltransferase protein	Arad9594	RHE_PE00453	pRL110629	Atu2801
precorrin-8x Methylmutase protein	Arad9595	RHE_PE00454	pRL110630	Atu2802

Product	Gene ID
	*V. cholerae*	*P. profundum*
conserved hypothetical protein	VC_A_43	PRPRB_820
putative membrane protein	VC_A_40	PRPRB_747
hypothetical protein	VC_A_39	PRPRB_746

hypothetical protein	VC_A_4	PRPPB_1769
hypothetical protein	VC_A_3	PRPRB_792
RctB replication protein	VC_A_2	PRPRB_1
ParB family protein	VC_A_1114	PRPRB_2024

hypothetical protein	VC_A_922	PRPRB_376
lipoprotein	VC_A_920	PRPRB_1176
TetR family transcription factor	VC_A_917	PRPRB_1177

CreA protein	VC_A_800	PRPRB _517
hypothetical protein	VC_A_799	PRPRB_787

hypothetical protein	VC_A_571	PRPRB _930
hypothetical protein	VC_A_579	PRPRB _663

Molybdenum ABC transport periplasmid binding protein	VC_A_726	PRPRB _1349
Cobyric acid synthase	VC_A_727	PRPRB _991

conserved hypothetical protein	VC_A_208	PRPRB _912
ammonia-dependent NAD(+) synthetase	VC_A_207	PRPRB _911

Table S12. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Vibrio strains (Vibrio cholerae O1 biovar eltor strain N16961 used as an example) and chromosome II of Photobacterium profundum. These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II prior to the divergence of the Vibrio and Photobacterium clades.

Product	Gene ID
	*A. hydrophila*	*V. cholerae*	*P. profundum*
NrdD anaerobic ribonucleoside-triphosphate reductase	AHA_1231	VC_A_511	PRPRB_442
NrdG anaerobic ribonucleoside-triphosphate reductase activating protein	AHA_1232	VC_A_512	PRPRB_443

maltose-binding periplasmic protein	AHA_1667	VC_A_945	PRPRB_421
MalF maltose transport system permease protein	AHA_1668	VC_A_944	PRPRB_422
MalG maltose transport system permease protein	AHA_1669	VC_A_943	PRPPB_423
MalK maltose/maltodextrin import ATP-binding protein	AHA_1670	VC_A_946	PRPRB_420

HlyD family secretion protein	AHA_2700	VC_A_1080	PRPRB_584
toxin secretion ATP-binding protein	AHA_2701	VC_A_1084	PRPRB_579

UhpA transcriptional regulatory protein	AHA_2796	VC_A_682	PRPRB_378
UhpC regulatory protein	AHA_2798	VC_A_684	PRPRB_376

MarR family transcriptional regulator	AHA_3609	VC_A_1005	PRPRB_1176
organic hydroperoxide reductase	AHA_3610	VC_A_1006	PRPRB_1177

PntB NAD(P) transhydrogenase, beta subunit	AHA_4079	VC_A_564	PRPRB _903
PntA NAD(P) transhydrogenase, alpha subunit	AHA_4080	VC_A_563	PRPRB_902

Table S13. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of all sequenced Vibrio strains (Vibrio cholerae O1 biovar eltor strain N16961 used as an example), but not shared by chromosome II of Photobacterium profundum. These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Vibrio lineage after its divergence from the Photobacterium clade.

Product	Gene ID
	*A. hydrophila*	*V. cholerae*
conserved hypothetical protein	AHA_1099	VC_A_55
PhrB deoxyribodipyrimidine photolyase	AHA_1101	VC_A_57

GGDEF domain protein	AHA_1796	VC_A_190
response regulator	AHA_1797	VC_A_189

FruA PTS system fructose-specific IIBC component	AHA_2346	VC_A_516
1-phosphofructokinase	AHA_2347	VC_A_517
multiphosphoryl transfer protein	AHA_2348	VC_A_518
FruR fructose repressor	AHA_2349	VC_A_519

YiaW inner membrane protein	AHA_2621	VC_A_48
trans-2-enoyl-CoA reductase	AHA_2629	VC_A_47
conserved hypothetical protein	AHA_1099	VC_A_55

MoxR protein	AHA_3136	VC_A_175
uridine phosphorylase	AHA_3168	VC_A_134
cAMP-binding protein	AHA_3169	VC_A_135

ABC transporter ATP-binding protein	AHA_3488	VC_A_782
acyl-CoA thioesterase I	AHA_3489	VC_A_783

Kbl 2-amino-3-ketobutyrate coenzyme A ligase	AHA_4234	VC_A_886
Tdh L-threonine 3-dehydrogenase	AHA_4235	VC_A_885

Table S14. Key gene clusters shared by chromosome I of Aeromonas hydrophila (extant representative of ancestral chromosome I) and by chromosome II of Photobacterium profundum, but not shared by chromosome II of sequenced Vibrio strains (Vibrio cholerae O1 biovar eltor strain N16961 used as an example). These gene clusters are presumed to have moved from the ancestral chromosome I to the plasmid-derived chromosome II in the Photobacterium lineage after its divergence from the Vibrio clade.

Product	Gene ID
	*A. hydrophila*	*P. profundum*
sensor histidine kinase	AHA_0066	PRPRB_1913
response regulator receiver domain	AHA_0067	PRPRB_1914
YhjX inner membrane protein	AHA_0068	PRPRB_1915

endoribonuclease L-PSP	AHA_0132	PRPRB_1933
ABC-type sugar transport system, periplasmic component	AHA_0135	PRPRB_1906
signal transduction histidine kinase	AHA_0136	PRPRB_1907
GltR transcriptional regulator	AHA_0137	PRPRB_1908

YeiG esterase	AHA_0213	PRPRB_1568
LysR-type transcriptional regulator	AHA_0215	PRPRB_1569

KefB glutathione-regulated potassium-efflux system protein	AHA_0342	PRPRB_550
modulator of glutathione-dependent potassium efflux system	AHA_0343	PRPRB_548

HlyD family secretion protein	AHA_0355	PRPRB_1862
LysR-type transcriptional regulator	AHA_0356	PRPRB_1860

class II aldolase, tagatose bisphosphate family	AHA_0805	PRPRB_1043
NagA-1 N-acetylglucosamine-6-phosphate deacetylase	AHA_0806	PRPRB_1042
N-acetyl-galactosamine ???	AHA_0807	PRPRB_1041
N-acetylgalactosamine permease IID component	AHA_0808	PRPRB_1040
N-acetylgalactosamine permease IIC component 1	AHA_0809	PRPRB_1039
N-acetylgalactosamine phosphotransferase enzyme IIB component2	AHA_0810	PRPRB_1038
D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit	AHA_0812	PRPRB_1037
glucitol operon repressor	AHA_0813	PRPRB_1035

YhaO inner membrane transport protein	AHA_1617	PRPRB_242
conserved hypothetical protein	AHA_1619	PRPRB_240

periplasmic binding protein	AHA_1964	PRPRB_1817
ABC iron chelate uptake transporter, ATP-binding protein	AHA_1666	PRPRB_1814
ABC iron chelate uptake transporter permease protein	AHA_1967	PRPRB_1815
ABC iron chelate uptake transporter permease protein	AHA_1968	PRPRB_1816
TonB-dependent siderophore receptor	AHA_1969	PRPRB_1825

electron transfer flavoprotein beta-subunit	AHA_1976	PRPRB_1098
electron transfer flavoprotein alpha-subunit	AHA_1977	PRPRB_1097

MerR-type transcriptional regulator	AHA_2073	PRPRB_1113
hydroxymethylglutaryl-CoA lyase	AHA_2074	PRPRB_1119
enoyl-CoA hydratase/isomerase family protein	AHA_2076	PRPRB_1118
methylcrotonoyl-CoA carboxylase beta chain	AHA_2077	PRPRB_1115
isovaleryl-CoA dehydrogenase 2	AHA_2078	PRPRB_1114
MmsA-2 methylmalonate-semialdehyde dehydrogenase	AHA_2079	PRPRB_1111
acyl-CoA dehydrogenase family member	AHA_2080	PRPRB_1110
3-hydroxybutyryl-CoA dehydratase	AHA_2081	PRPRB_1109
MmsB 3-hydroxyisobutyrate dehydrogenase	AHA_2083	PRPRB_1107
3-oxoacyl-[acyl-carrier-protein] reductase	AHA_2084	PRPRB_1106

PrpB methylisocitrate lyase	AHA_2265	PRPRB_235
2-methylcitrate synthase	AHA_2266	PRPRB_236
PrpD 2-methylcitrate dehydratase	AHA_2267	PRPRB_237

dimodular nonribosomal peptide synthetase	AHA_2473	PRPRB_1818
nonribosomal peptide synthetase	AHA_2474	PRPRB_1819
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase	AHA_2475	PRPRB_1820
nonribosomal peptide synthetase	AHA_2476	PRPRB_1821
isochorismatase	AHA_2477	PRPRB_1822
2,3-dihydroxybenzoate-AMP ligase	AHA_2478	PRPRB_1823
isochorismate synthases	AHA_2479	PRPRB_1824

conserved hypothetical protein	AHA_2544	PRPRB_1033
conserved hypothetical protein	AHA_2545	PRPRB_1027
hypothetical membrane protein	AHA_2546	PRPRB_1032
amine oxidase, flavin-containing superfamily	AHA_2547	PRPRB_1031
conserved hypothetical protein	AHA_2548	PRPRB_1030
conserved hypothetical protein	AHA_2549	PRPRB_1029

MaiA maleylacetoacetate isomerase	AHA_2660	PRPRB_1167
fumarylacetoacetate hydrolase family protein	AHA_2661	PRPRB_1166
HmgA homogentisate 1,2-dioxygenase	AHA_2662	PRPRB_1165
HppD 4-hydroxyphenylpyruvate dioxygenase	AHA_2663	PRPRB_1180

pyruvate dehydrogenase, dihydrolipoamide acyltransferase component	AHA_2865	PRPRB_1096
pyruvate dehydrogenase E1 component, beta subunit	AHA_2866	PRPRB_1095
pyruvate dehydrogenase E1 component, alpha subunit	AHA_2867	PRPRB_1094

ViuB vibriobactin utilization protein	AHA_2992	PRPRB_1812
phospho-2-dehydro-3-deoxyheptonate aldolase	AHA_2993	PRPRB_1813

LysR-type transcriptional regulator	AHA_3112	PRPRB_1787
PurA adenylosuccinate synthetase	AHA_3113	PRPRB_1785

TtrA	AHA_3285	PRPRB_3
tetrathionate reductase, subunit B	AHA_3287	PRPRB_6
two component system histidine kinase	AHA_3288	PRPRB_7
FixJ transcriptional regulator	AHA_3289	PRPRB_8

glycine betaine/L-proline ABC transporter, permease protein	AHA_3375	PRPRB_1789
glycine betaine/L-proline ABC transporter, ATP binding protein	AHA_3376	PRPRB_1788

3-oxoacyl-[acyl-carrier-protein] synthase II	AHA_3382	PRPRB_104
4-hydroxybenzoyl-CoA thioesterase domain protein	AHA_3389	PRPRB_111
phenylalanine and histidine ammonia-lyase	AHA_3390	PRPRB_112
glycosyl transferase, group 2 family protein	AHA_3391	PRPRB_113
3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratase	AHA_3392	PRPRB_114
acyl carrier protein	AHA_3395	PRPRB_117
putative acyl carrier protein	AHA_3396	PRPRB_118
conserved hypothetical protein	AHA_3399	PRPRB_121
SAM-dependent methyltransferase	AHA_3400	PRPRB_122

TolR	AHA_3435	PRPRB_1219
TonB system transport protein ExbB2	AHA_3436	PRPRB_1220
biopolymer transport exbD2 protein	AHA_3437	PRPRB_1218

ABC-type multidrug transport system, permease component	AHA_3506	PRPRB_516
ABC-type multidrug transport system, permease component	AHA_3507	PRPRB_515
membrane-fusion protein	AHA_3508	PRPRB_514
outer membrane efflux protein	AHA_3509	PRPRB_513

LysR-type transcriptional regulator	AHA_3731	PRPRB_1802
transporter, drug/metabolite exporter family	AHA_3732	PRPRB_1803

paraquat-inducible protein B	AHA_3795	PRPRB_1160
paraquat-inducible protein A	AHA_3796	PRPRB_1161

ABC transporter substrate-binding protein	AHA_3983	PRPRB_175
conserved hypothetical protein	AHA_3984	PRPRB_176
ABC transporter permease protein	AHA_3985	PRPRB_177
ABC transporter permease protein	AHA_3986	PRPRB_178

DhaM dihydroxyacetone kinase, phosphotransferase subunit	AHA_4006	PRPRB_217
dihydroxyacetone kinase, L subunit	AHA_4007	PRPRB_218
DhaK dihydroxyacetone kinase, DhaK subunit	AHA_4008	PRPRB_219

two-component system, regulatory protein	AHA_4052	PRPRB_844
conserved hypothetical protein	AHA_4053	PRPRB_845

TonB-2 outer membrane receptor-mediated transport energizer protein	AHA_4248	PRPRB_1217
ExbD2 biopolymer transport protein	AHA_4249	PRPRB_1218
TonB system biopolymer transport component	AHA_4250	PRPRB_1219
TonB system biopolymer transport component	AHA_4251	PRPRB_1219

AtpC ATP synthase F1, epsilon subunit	AHA_4261	PRPRB_137
AtpD ATP synthase F1, beta subunit	AHA_4262	PRPRB_136
AtpG ATP synthase F1, gamma subunit	AHA_4263	PRPRB_135
AtpA ATP synthase F1, alpha subunit	AHA_4264	PRPRB_134
AtpH ATP synthase F1, delta subunit	AHA_4265	PRPRB_133
AtpF ATP synthase F0, B subunit	AHA_4266	PRPRB_132
AtpE ATP synthase F0, C subunit	AHA_4267	PRPRB_131
AtpB ATP synthase F0, A subunit	AHA_4268	PRPRB_130

Product	Gene ID
	*B. cenocepacia*	*R. eutropha*
Major facilitator superfamily member	Bcen_3861	Reut_B4859
NirD nitrite reductase NADPH oxidoreductase subunit	Bcen_3864	Reut_B4861

OsmC family protein	Bcen_4500	Reut_B5559
MarR family transcription factor	Bcen_4499	Reut_B5560
transglutaminase	Bcen_4253	Reut_B5565
integrase/recombinase	Bcen_5161	Reut_B5594

Product	Gene ID
	*B. bronchiseptica*	*B. cenocepacia*	*R. eutropha*
putative multidrug-efflux system protein	BB0436	Bcen_3015	Reut_B4334
HlyD family secretion protein	BB0437	Bcen_3014	Reut_B4335
LysR family regulatory protein	BB0438	Bcen_3012	Reut_B4337

conserved hypothetical protein	BB1129	Bcen_4707	Reut_B3904
probable outer membrane protein	BB1130	Bcen_4708	Reut_B3905

CioA cytochrome oxidase subunit I	BB1238	Bcen_5383	Reut_B4101
CioB cytochrome oxidase subunit II	BB1239	Bcen_5382	Reut_B4100

GabD succinate-semialdehyde dehydrogenase [NADP+]	BB1806	Bcen_3004	Reut_B5660
GoaG 4-aminobutyrate aminotransferase	BB1807	Bcen_3006	Reut_B5663

MetR transcriptional regulatory protein	BB2078	Bcen_3080	Reut_B4244
MetE 5-methyltetrahydropteroyltriglutamate homocysteine methyltransferase	BB2079	Bcen_3081	Reut_B4245

probable acyl-CoA dehydrogenase	BB2630	Bcen_3404	Reut_B4257
MmsB 3-hydroxyisobutyrate dehydrogenase	BB2632	Bcen_3407	Reut_B4259

MxcB iron utilization protein	BB2831	Bcen_5142	Reut_B4272
conserved hypothetical protein	BB2832	Bcen_5141	Reut_B4273

probable aldehyde reductase	BB2942	Bcen_5450	Reut_B5116
LysR-family transcriptional regulator	BB2944	Bcen_5454	Reut_B5117

GlnQ glutamine transport ATP-binding protein	BB2974	Bcen_4282	Reut_B3697
GlnP glutamine transport system permease protein	BB2975	Bcen_4283	Reut_B3698
GlnH glutamine-binding periplasmic protein precursor	BB2976	Bcen_4284	Reut_B3699
conserved hypothetical protein	BB2977	Bcen_4281	Reut_B3696

putative ABC-transporter ATP-binding protein	BB3366	Bcen_3195	Reut_B4811
putative binding-protein-dependent transport protein	BB3367	Bcen_3196	Reut_B4810

AccB carboxyltransferase subunit of acetyl-CoA carboxylase	BB4948	Bcen_3128	Reut_B4463
AccA biotin carboxylase subunit of acetyl-CoA carboxylase	BB4949	Bcen_3130	Reut_B4460

Product	Gene ID
	*B. bronchiseptica*	*B. cenocepacia*
HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase	BB0736	Bcen_4133
HpaD homoprotocatechuate 2,3-dioxygenase	BB0737	Bcen_4132

LeuB 3-isopropylmalate dehydrogenase	BB1014	Bcen_4415
LeuD 3-isopropylmalate dehydratase small subunit	BB1015	Bcen_4416
LeuC 3-isopropylmalate dehydratase large subunit	BB1016	Bcen_4418

FabI enoyl-[acyl-carrier-protein] reductase [NADH]	BB1383	Bcen_3497
AckA acetate kinase	BB1384	Bcen_3495
phosphate acetyl/butaryl transferase	BB1385	Bcen_3494

putative iron-sulfur protein	BB1906	Bcen_4489
XseB exodeoxyribonuclease VII small subunit	BB1910	Bcen_4488
probable geranyltranstransferase	BB1911	Bcen_4487
Dxs 1-deoxy-D-xylulose 5-phosphate synthase	BB1912	Bcen_4486
conserved hypothetical protein	BB1913	Bcen_4485

LeuC 3-isopropylmalate dehydratase large subunit	BB2130	Bcen_4418
LeuD 3-isopropylmalate dehydratase small subunit	BB2131	Bcen_4416
LeuB 3-isopropylmalate dehydrogenase	BB2132	Bcen_4415
Asd aspartate-semialdehyde dehydrogenase	BB2133	Bcen_4414
TruA tRNA pseudouridine synthase A	BB2135	Bcen_4411
TrpF N-(5-phosphoribosyl)anthranilate isomerase	BB2139	Bcen_4410

putative GntR-family transcriptional regulator	BB2428	Bcen_3850
putative GNAT-family acetyltransferase	BB2429	Bcen_3849

FolC bifunctional folylpolyglutamate synthase/dihydrofolate synthase	BB2597	Bcen_4405
PurF amidophosphoribosyltransferase	BB2600	Bcen_4402

RpoD RNA polymerase sigma factor 70	BB3161	Bcen_4480
DnaG primase	BB3162	Bcen_4481
RpsU 30S ribosomal protein S21	BB3163	Bcen_4482

putative carboxymethylenebutenolidase	BB3237	Bcen_4491
PolA DNA polymerase I	BB3239	Bcen_4493
putative exported protein	BB3240	Bcen_4494

GltA citrate synthase	BB3677	Bcen_4428
SdhB succinate dehydrogenase iron-sulfur protein	BB3679	Bcen_4430
SdhA succinate dehydrogenase flavoprotein subunit	BB3680	Bcen_4431
SdhD succinate dehydrogenase membrane anchor protein	BB3681	Bcen_4432
SdhC succinate dehydrogenase cytochrome B subunit	BB3682	Bcen_4433
GntR-family transcriptional regulator	BB3683	Bcen_4434
Mdh malate dehydrogenase	BB3684	Bcen_4435
PrpB methylisocitrate lyase	BB3685	Bcen_5344
PrpC 2-methylcitrate synthase	BB3686	Bcen_5345
AcnA aconitate hydratase	BB3687	Bcen_5346
conserved hypothetical protein	BB3688	Bcen_5347

AccD acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	BB3772	Bcen_4406
TrpA tryptophan synthase alpha chain	BB3773	Bcen_4407
TrpB tryptophan synthase beta chain	BB3774	Bcen_4409

BhuS putative hemin transport protein	BB4656	Bcen_4430
BhuT putative hemin binding protein	BB4657	Bcen_4429
BhuU putative hemin permease	BB4658	Bcen_4428
BhuV putative ATP-binding component of hemin transport system	BB4659	Bcen_4427

Product	Gene ID
	*B. bronchiseptica*	*R.eutropha*
peptidoglycan binding protein	BB0019	Reut_B4942
two-component response regulator	BB0020	Reut_B4943

conserved hypothetical protein	BB0764	Reut_B3511
putative thiolase	BB0765	Reut_B3512

putative exported protein	BB1095	Reut_B5438
LysR-family transcriptional regulator	BB1096	Reut_B5436
probable acyl-CoA dehydrogenase	BB1098	Reut_B5437
putative exported protein	BB1099	Reut_B5438

conserved hypothetical protein	BB1217	Reut_B5243
enoyl-CoA dehydratase	BB1218	Reut_B5245
LysR-family transcriptional regulator	BB1219	Reut_B5246

conserved hypothetical protein	BB1272	Reut_B3559
putative exported protein	BB1273	Reut_B3558

CyoA ubiquinol oxidase polypeptide II	BB1283	Reut_B4579
CyoB ubiquinol oxidase polypeptide I	BB1284	Reut_B4578
CyoC cytochrome O ubiquinol oxidase	BB1285	Reut_B4577

cytochrome ubiquinol oxidase subunit IV	BB1307	Reut_B4893
cytochrome ubiquinol oxidase subunit III	BB1308	Reut_B4892
cytochrome ubiquinol oxidase subunit I	BB1309	Reut_B4891
putative ubiquinol oxidase subunit II	BB1310	Reut_B4890
putative membrane transport protein	BB1311	Reut_B4889

putative membrane protein	BB1825	Reut_B5408
Type II secretion system protein	BB1826	Reut_B5409
Type II secretion system protein	BB1828	Reut_B5411
putative membrane protein	BB1829	Reut_B5412
putative lipoprotein	BB1831	Reut_B5414
putative exported protein	BB1832	Reut_B5415
transcriptional regulator	BB1898	Reut_B5518
putative ABC transport permease	BB1900	Reut_B5524

conserved hypothetical protein	BB2262	Reut_B3511
putative thiolase	BB2263	Reut_B3512

FliA RNA polymerase sigma factor for flagellar operon	BB2540	Reut_B5619
FlhB flagellar transcriptional activator	BB2541	Reut_B5604
FlhC flagellar transcriptional activator	BB2542	Reut_B5605
MotA chemotaxis protein	BB2543	Reut_B5606
MotB chemotaxis protein	BB2544	Reut_B5607
CheA chemotaxis protein	BB2546	Reut_B5608
CheW chemotaxis protein	BB2547	Reut_B5609
CheR chemotaxis protein methyltransferase	BB2549	Reut_B5610
Protein-glutamate methylesterase	BB2550	Reut_B5612
CheY chemotaxis protein	BB2551	Reut_B5613
CheZ chemotaxis protein	BB2552	Reut_B5614
FlhB flagellar biosynthetic protein	BB2553	Reut_B5615
FlhF flagellar biosynthesis protein	BB2555	Reut_B5617
FlgA flagella basal body P-ring formation protein	BB2558	Reut_B5624
FlgB flagellar basal-body rod protein	BB2559	Reut_B5625
FlgC flagellar basal-body rod protein	BB2560	Reut_B5626
FlgD basal-body rod modification protein	BB2561	Reut_B5627
FlgE flagellar hook protein	BB2562	Reut_B5628
FlgF flagellar basal-body rod protein	BB2563	Reut_B5629
FlgG flagellar basal-body rod protein	BB2564	Reut_B5630
FlgH flagellar L-ring protein precursor	BB2565	Reut_B5631
FlgI flagellar P-ring protein precursor	BB2566	Reut_B5632
FlgJ peptidoglycan hydrolase	BB2567	Reut_B5633
FlgK flagellar hook-associated protein 1	BB2568	Reut_B5634

FliR flagellar biosynthetic protein	BB2576	Reut_B5879
FliO flagellar protein	BB2579	Reut_B5882
FliN flagellar motor switch protein	BB2580	Reut_B5883
FliM flagellar motor switch protein	BB2581	Reut_B5884
FliL flagellar protein	BB2582	Reut_B5885

FliJ flagellar protein FliJ	BB2584	Reut_B5101
FliH flagellar assembly protein FliH	BB2586	Reut_B5099
FliG flagellar motor switch protein FliG	BB2587	Reut_B5098
FliF flagellar M-ring protein	BB2588	Reut_B5097
FliE flagellar hook-basal body complex protein FliE	BB2589	Reut_B5096
putative flagellar protein	BB2591	Reut_B5095
FliS flagellar protein FliS	BB2594	Reut_B5092
FlaG putative flagellar protein	BB2596	Reut_B5090

ATP-binding component of ABC transporter protein	BB2758	Reut_B3782
TetR-family transcriptional regulator	BB2760	Reut_B3781
NapE component of of periplasmic nitrate reductase system	BB2798	Reut_B4761
NapA periplasmic nitrate reductase precursor	BB2800	Reut_B4763
NapB diheme cytochrome C precursor	BB2801	Reut_B4764
NapC cytochrome C-type protein	BB2802	Reut_B4765
CcmA Putative heme export protein	BB2803	Reut_B4766
CcmC Putative heme export protein	BB2805	Reut_B4768
CcmE cytochrome C-type biogenesis protein	BB2807	Reut_B4769
CcmF cytochrome C-type biogenesis protein	BB2808	Reut_B4770
CcmG cytochrome C-type biogenesis protein	BB2809	Reut_B4771
CcmH cytochrome C-type biogenesis protein	BB2810	Reut_B4772
putative exported protein	BB2885	Reut_B4879
putative exported protein	BB2886	Reut_B4878

pyridine nucleotide-disulfide oxidoreductase	BB3010	Reut_B4451
glutaredoxin	BB3011	Reut_B4452

putative membrane protein	BB3082	Reut_B4097
HlyD family secretion protein	BB3083	Reut_B4096

conserved hypothetical protein	BB3086	Reut_B4525
DNA polymerase III alpha chain	BB3088	Reut_B4523

hypothetical protein	BB3205	Reut_B5399
conserved hypothetical protein	BB3206	Reut_B5398
LysR-family transcriptional regulator	BB3207	Reut_B5397

putative membrane protein	BB3279	Reut_B5215
putative exported protein	BB3280	Reut_B5214
putative exported protein	BB3281	Reut_B5213
ApbE thiamine biosynthesis protein	BB3282	Reut_B5212
probable oxidoreductase	BB3283	Reut_B5211

putative 3-isopropylmalate dehydratase large subunit	BB4085	Reut_B4843
putative 3-isopropylmalate dehydratase small subunit	BB4086	Reut_B4842

conserved hypothetical protein	BB4341	Reut_B3555
conserved hypothetical protein	BB4342	Reut_B3554
conserved hypothetical protein	BB4343	Reut_B3553

probable dioxygenase	BB4476	Reut_B4145
putative exported protein	BB4481	Reut_B4142

putative exported protein	BB4540	Reut_B3795
putative exported protein	BB4541	Reut_B3796
CDP-6-deoxy-delta-3,4-glucoseen reductase	BB4641	Reut_B3765
conserved hypothetical protein	BB4642	Reut_B3764
aldehyde dehydrogenase	BB4643	Reut_B3763
conserved hypothetical protein	BB4644	Reut_B3762
putative membrane protein	BB4645	Reut_B3760
GntR-family transcription regulator	BB4647	Reut_B3766
ornithine cyclodeaminase	BB4648	Reut_B3761
putative ferredoxin	BB4649	Reut_B3757
hypothetical protein	BB4650	Reut_B3758
ferredoxin	BB4651	Reut_B3759
serine--glyoxylate aminotransferase	BB4671	Reut_B5140
GntR-family transcriptional regulator	BB4672	Reut_B5139

putative membrane protein	BB4816	Reut_B3665
CtaD cytochrome c oxidase polypeptide I	BB4830	Reut_B3633
putative exported protein	BB4843	Reut_B3614

AraC family regulatory protein	BB4904	Reut_B5332
PrfC peptide chain release factor 3	BB4916	Reut_B5334

Product	Gene ID
	*B. pseudomallei* chrI	*B. pseudomallei* chrII	*B. cenocepacia*
ExbD/TolR biopolymer transport protein	BURPS1710b_A3729		Bcen_5877
MotA/TolQ/ExbB proton channel	BURPS1710b_A3730		Bcen_5878

aldehyde dehydrogenase	BURPS1710b_A0279		Bcen_6479
porin, Gram-negative type	BURPS1710b_A0272		Bcen_6482

glycosyl transferase, family 2		BURPS1710b_B1538	Bcen_5508
GtrA-like protein		BURPS1710b_B1536	Bcen_5509

porin, Gram-negative type		BURPS1710b_B2774	Bcen_5613
YadA-like		BURPS1710b_B2793	Bcen_5619

Table S20. Composition of mountains for the Niche Map based on 625 sequenced prokaryotic genomes.

Mount	Species	Represented Genus and Species	Taxonomic Group
NM1	18	Bartonella (A-4), Candidatus (A-1), Helicobacter (E-2), Rickettsia (A-10), Wolbachia (A-1)	Alphaproteobacteria (A), Epsilonproteobacteria (E)
NM2	21	Acidobacteria (H-1), Anaeromyxobacter (D-2), Azoarcus (B-1), Candidatus (D-1), Desulfovibrio (D-3), Geobacter (D-3), Halorhodospira (G-1), Magnetococcus (1), Myxococcus (D-1), Pelobacter (D-2), Solibacter (H-1), Syntrophobacter (D-1), Syntrophus (D-1), Thiobacillus (B-1), Thiomicrospira (G-1)	Acidobacteria (H), Betaproteobacteria (B), Deltaproteobacteria (D), Gammaproteobacteria (G)
NM3	22	Bacillus (F-17), Clostridium (F-2), Geobacillus (F-2), Oceanobacillus (F-1)	Firmicutes (F)
NM4	22	Listeria (F-4), Staphylococcus (F-18)	Firmicutes (F)
NM5	28	Alcanivorax (G-1), Colwellia (G-1), Hahella (G-1), Idiomarina (G-1), Marinobacter (G-1), Marinomonas (G-1), Pseudoalteromonas (G-2), Pseudomonas (G-1), Psychrobacter (G-1), Psychromonas (G-1), Saccharophagus (G-1), Shewanella (G-15), Vibrio (G-1)	Gammaproteobacteria (G)
NM6	31	Aquifex (Q-1), Arcobacter (E-1), Campylobacter (E-9), Candidatus (G-2), Chlorobium (O-2), Dehalococcoides (L-2), Desulfotalea (D-1), Helicobacter (E-2), Lawsonia (D-1), Leptospira (S-4), Nitratiruptor (E-1), Pirellula (P-1), Sulfurovum (E-1), Thiomicrospira (E-1), Wolinella (E-1), Zymomonas (A-1)	Alphaproteobacteria (A), Aquificae (Q), Bacteroidetes/Chlorobi (O), Chloroflexi (L), Deltaproteobacteria (D), Epsilonproteobacteria (E), Gammaproteobacteria (G), Planctomycetes (P), Spirochaetes (S)
NM7	31	Alkaliphilus (F-2), Caldicellulosiruptor (F-1), Carboxydothermus (F-1), Clostridium (F-13), Desulfitobacterium (F-1), Desulfotomaculum (F-1), Fervidobacterium (T-1), Fusobacterium (K-1), Moorella (F-1), Pelotomaculum (F-1), Petrotoga (T-1), Symbiobacterium (I-1), Syntrophomonas (F-1), Thermoanaerobacter (F-1), Thermosipho (T-1), Thermotoga (T-3)	Actinobacteria (I), Firmicutes (F), Fusobacteria (K), Thermotogae (T)
NM8	33	Acaryochloris (Y-1), Anabaena (Y-1), Chlorobium (O-1), Cyanobacteria (Y-2), Gloeobacter (Y-1), Nostoc (Y-1), Pelodictyon (O-1), Prochlorococcus (Y-12), Prosthecochloris (O-1), Synechococcus (Y-8), Synechocystis (Y-1), Thermosynechococcus (Y-1), Thermus (J-1), Trichodesmium (Y-1)	Bacteroidetes/Chlorobi (O), Cyanobacteria (Y), Deinococcus-Thermus (J)
NM9	45	Enterococcus (F-1), Lactobacillus (F-12), Lactococcus (F-3), Leuconostoc (F-1), Oenococcus (F-1), Pediococcus (F-1), Streptococcus (F-26)	Firmicutes (F)
NM10	47	Alkalilimnicola (G-1), Bacteroides (O-4), Bdellovibrio (D-1), Coxiella (G-3), Cytophaga (O-1), Dichelobacter (G-1), Flavobacterium (O-2), Francisella (G-7), Gramella (O-1), Haemophilus (G-6), Legionella (G-4), Methylococcus (G-1), Neisseria (B-5), Nitrosococcus (G-1), Nitrosomonas (B-2), Nitrosospira (B-1), Parabacteroides (O-1), Psychrobacter (G-2), Salinibacter (O-1), Xylella (G-2)	Bacteroidetes/Chlorobi (O), Betaproteobacteria (B), Deltaproteobacteria (D), Gammaproteobacteria (G)
NM11	49	Aeropyrum (C-1), Archaeoglobus (U-1), Caldivirga (C-1), Candidatus (U-1), Haloarcula (U-1), Halobacterium (U-1), Haloquadratum (U-1), Hyperthermus (C-1), Ignicoccus (C-1), Metallosphaera (C-1), Methanobacterium (U-1), Methanobrevibacter (U-1), Methanococcoides (U-1), Methanococcus (U-7), Methanocorpusculum (U-1), Methanoculleus (U-1), Methanopyrus (U-1), Methanosaeta (U-1), Methanosarcina (U-3), Methanosphaera (U-1), Methanospirillum (U-1), Nanoarchaeum (N-1), Natronomonas (U-1), Nitrosopumilus (C-1), Picrophilus (U-1), Pyrobaculum (C-4), Pyrococcus (U-3), Staphylothermus (C-1), Sulfolobus (C-3), Thermococcus (U-1), Thermofilum (C-1), Thermoplasma (U-2)	Crenarchaeota (C), Euryarchaeota (U), Nanoarchaeota (N)
NM12	53	Acidothermus (I-1), Arthrobacter (I-2), Bifidobacterium (I-2), Chloroflexus (L-1), Clavibacter (I-1), Corynebacterium (I-6), Deinococcus (J-2), Frankia (I-3), Herpetosiphon (L-1), Kineococcus (I-1), Leifsonia (I-1), Mycobacterium (I-16), Nocardia (I-1), Nocardioides (I-1), Propionibacterium (I-1), Renibacterium (I-1), Rhodococcus (I-1), Roseiflexus (L-2), Rubrobacter (I-1), Saccharopolyspora (I-1), Salinispora (I-2), Sorangium (D-1), Streptomyces (I-2), Thermobifida (I-1), Thermus (J-1)	Actinobacteria (I), Chloroflexi (L), Deinococcus-Thermus (J), Deltaproteobacteria (D)
NM13	53	Acidiphilium (A-1), Agrobacterium (A-3), Azorhizobium (A-1), Bradyrhizobium (A-3), Brucella (A-7), Caulobacter (A-1), Dinoroseobacter (A-1), Erythrobacter (A-1), Gluconacetobacter (A-1), Gluconobacter (A-1), Granulobacter (A-1), Hyphomonas (A-1), Jannaschia (A-1), Magnetospirillum (A-1), Maricaulis (A-1), Mesorhizobium (A-2), Methylobacterium (A-1), Nitrobacter (A-2), Novosphingobium (A-1), Ochrobactrum (A-1), Paracoccus (A-1), Parvibaculum (A-1), Rhizobium (A-2), Rhodobacter (A-3), Rhodopseudomonas (A-5), Rhodospirillum (A-1), Roseobacter (A-1), Silicibacter (A-2), Sinorhizobium (A-2), Sphingomonas (A-1), Sphingopyxis (A-1), Xanthobacter (A-1)	Alphaproteobacteria (A)
NM14	54	Actinobacillus (G-2), Aeromonas (G-2), Citrobacter (G-1), Enterobacter (G-2), Erwinia (G-1), Escherichia (G-10), Klebsiella (G-1), Mannheimia (G-1), Pasteurella (G-1), Photobacterium (G-1), Photorhabdus (G-1), Salmonella (G-7), Serratia (G-1), Shigella (G-6), Sodalis (G-1), Vibrio (G-6), Yersinia (G-10)	Gammaproteobacteria (G)
NM15	57	Anaplasma (A-2), Aster (F-1), Baumannia (G-1), Borrelia (S-3), Buchnera (G-4), Candidatus (O-4), Chlamydia (V-3), Chlamydophila (V-7), Dehalococcoides (L-1), Ehrlichia (A-4), Helicobacter (E-1), Mesoplasma (F-1), Mycoplasma (F-13), Neorickettsia (A-1), Onion (F-1), Orientia (A-1), Parachlamydia (V-1), Porphyromonas (O-1), Treponema (S-2), Tropheryma (I-2), Ureaplasma (F-1), Wigglesworthia (G-1), Wolbachia (A-1)	Actinobacteria (I), Alphaproteobacteria (A), Bacteroidetes/Chlorobi (O), Chlamydiae (V), Chloroflexi (L), Epsilonproteobacteria (E), Firmicutes (F), Gammaproteobacteria (G), Spirochaetes (S)
NM16	60	Acidovorax (B-2), Acinetobacter (G-2), Azoarcus (B-1), Bordetella (B-4), Burkholderia (B-16), Chromobacterium (B-1), Chromohalobacter (G-1), Dechloromonas (B-1), Delftia (B-1), Herminiimonas (-1), Janthinobacterium (B-1), Methylibium (B-1), Methylobacillus (B-1), Polaromonas (B-2), Polynucleobacter (B-1), Pseudomonas (G-12), Ralstonia (B-4), Rhodoferax (B-1), Verminephrobacter (B-1), Xanthomonas (G-6)	Betaproteobacteria (B), Gammaproteobacteria (G)

Table S21. The set of PFams that distinguish the members of the Rhizobiaceae from the rest of the prokaryotes on the Niche Finder map. PFam IDs and their associated annotations are shown.

PF ID	Annotation
PF00274	Glycolytic, Fructose-bisphosphate aldolase class-I
PF00445	Ribonuclease_T2, Ribonuclease T2 family
PF00722	Glyco_hydro_16, Glycosyl hydrolases family 16
PF00728	Glyco_hydro_20, Glycosyl hydrolase family 20, catalytic domain
PF00765	Autoind_synth, Autoinducer synthetase
PF00775	Dioxygenase_C, Dioxygenase
PF01322	Cytochrom_C_2, Cytochrome C'
PF01745	IPT, Isopentenyl transferase
PF01935	DUF87, Domain of unknown function DUF87
PF02056	Glyco_hydro_4, Family 4 glycosyl hydrolase
PF02073	Peptidase_M29, Thermophilic metalloprotease (M29)
PF02104	SURF1, SURF1 family
PF02469	Fasciclin, Fasciclin domain
PF02530	Porin_2, Porin subfamily
PF02538	Hydantoinase_B, Hydantoinase B/oxoprolinase
PF02615	Ldh_2, Malate/L-lactate dehydrogenase
PF03030	H_PPase, Inorganic H+ pyrophosphatase
PF03050	Transposase_25, Transposase IS66 family
PF03135	CagE_TrbE_VirB, CagE, TrbE, VirB family, component of type IV transporter system
PF03389	MobA_MobL, MobA/MobL family
PF03401	Bug, Bordetella uptake gene (bug) product
PF03411	Peptidase_M74, Penicillin-insensitive murein endopeptidase
PF03428	RP-C, Replication protein C
PF03472	Autoind_bind, Autoinducer binding domain
PF03524	CagX, Conjugal transfer protein
PF03552	Cellulose_synt, Cellulose synthase
PF03576	Peptidase_S58, Peptidase family S58
PF03743	TrbI, Bacterial conjugation TrbI-like protein
PF03786	UxuA, D-mannonate dehydratase (UxuA)
PF04115	Ureidogly_hydro, Ureidoglycolate hydrolase
PF04168	DUF403, Bacterial domain of unknown function (DUF403)
PF04227	Indigoidine_A, Indigoidine synthase A like protein
PF04267	SoxD, Sarcosine oxidase, delta subunit family
PF04268	SoxG, Sarcosine oxidase, gamma subunit family
PF04273	DUF442, Protein of unknown function (DUF442)
PF04295	GD_AH_C, D-galactarate dehydratase / Altronate hydrolase, C terminus
PF04305	DUF455, Protein of unknown function (DUF455)
PF04311	DUF459, Protein of unknown function (DUF459)
PF04317	DUF463, YcjX-like family, DUF463
PF04330	DUF471, Family of unknown function (DUF471)
PF04332	DUF475, Protein of unknown function (DUF475)
PF04335	VirB8, VirB8 protein
PF04391	DUF533, Protein of unknown function (DUF533)
PF04430	DUF498, Protein of unknown function (DUF498/DUF598)
PF04442	CtaG_Cox11, Cytochrome c oxidase assembly protein CtaG / Cox11
PF04610	TrbL, TrbL/VirB6 plasmid conjugal transfer protein
PF04654	DUF599, Protein of unknown function, DUF599
PF04655	APH_6_hur, Aminoglycoside/hydroxyurea antibiotic resistance kinase
PF04752	ChaC, ChaC-like protein
PF04800	ETC_C1_NDUFA4, ETC complex I subunit conserved region
PF04964	Flp_Fap, Flp/Fap pilin component
PF04982	HPP, HPP family
PF05035	DGOK, 2-keto-3-deoxy-galactonokinase
PF05071	NDUFA12, NADH ubiquinone oxidoreductase subunit NDUFA12
PF05128	DUF697, Family of unknown function (DUF697)
PF05161	MOFRL, MOFRL family
PF05163	DinB, DinB family
PF05169	Seleno_W_rel, Selenoprotein W-related family
PF05233	PHB_acc, PHB accumulation regulatory domain
PF05284	DUF736, Protein of unknown function (DUF736)
PF05443	ROS_MUCR, ROS/MUCR transcriptional regulator protein
PF05544	Pro_racemase, Proline racemase
PF05717	Transposase_34, IS66 Orf2 like protein
PF05845	PhnH, Bacterial phosphonate metabolism protein (PhnH)
PF05861	PhnI, Bacterial phosphonate metabolism protein (PhnI)
PF05899	Cupin_3, Protein of unknown function (DUF861)
PF05951	Peptidase_M15_2, Bacterial protein of unknown function (DUF882)
PF05990	DUF900, Alpha/beta hydrolase of unknown function (DUF900)
PF06007	PhnJ, Phosphonate metabolism protein PhnJ
PF06035	DUF920, Bacterial protein of unknown function (DUF920)
PF06037	DUF922, Bacterial protein of unknown function (DUF922)
PF06055	ExoD, Exopolysaccharide synthesis, ExoD
PF06057	VirJ, Bacterial virulence protein (VirJ)
PF06059	DUF930, Domain of Unknown Function (DUF930)
PF06073	DUF934, Bacterial protein of unknown function (DUF934)
PF06089	Asparaginase_II, L-asparaginase II
PF06108	DUF952, Protein of unknown function (DUF952)
PF06155	DUF971, Protein of unknown function (DUF971)
PF06165	Glyco_transf_36, Glycosyltransferase family 36
PF06169	DUF982, Protein of unknown function (DUF982)
PF06170	DUF983, Protein of unknown function (DUF983)
PF06172	Cupin_5, Cupin superfamily (DUF985)
PF06181	DUF989, Protein of unknown function (DUF989)
PF06186	DUF992, Protein of unknown function (DUF992)
PF06204	CBM_X, Putative carbohydrate binding domain
PF06205	GT36_AF, Glycosyltransferase 36 associated family
PF06210	DUF1003, Protein of unknown function (DUF1003)
PF06224	DUF1006, Protein of unknown function (DUF1006)
PF06226	DUF1007, Protein of unknown function (DUF1007)
PF06230	DUF1009, Protein of unknown function (DUF1009)
PF06233	Usg, Usg-like family
PF06282	DUF1036, Protein of unknown function (DUF1036)
PF06283	DUF1037, Protein of unknown function (DUF1037)
PF06299	DUF1045, Protein of unknown function (DUF1045)
PF06319	DUF1052, Protein of unknown function (DUF1052)
PF06408	Homo_sperm_syn, Homospermidine synthase
PF06412	TraD, Conjugal transfer protein TraD
PF06426	SATase_N, Serine acetyltransferase, N-terminal
PF06481	COX_ARM, COX Aromatic Rich Motif
PF06537	DUF1111, Protein of unknown function (DUF1111)
PF06559	DCD, 2'-deoxycytidine 5'-triphosphate deaminase (DCD)
PF06568	DUF1127, Domain of unknown function (DUF1127)
PF06577	DUF1134, Protein of unknown function (DUF1134)
PF06604	OMP_19, Bacterial outer membrane lipoprotein omp19
PF06620	DUF1150, Protein of unknown function (DUF1150)
PF06627	DUF1153, Protein of unknown function (DUF1153)
PF06629	MipA, MltA-interacting protein MipA
PF06676	DUF1178, Protein of unknown function (DUF1178)
PF06684	DUF1185, Protein of unknown function (DUF1185)
PF06718	DUF1203, Protein of unknown function (DUF1203)
PF06719	AraC_N, AraC-type transcriptional regulator N-terminus
PF06742	DUF1214, Protein of unknown function (DUF1214)
PF06748	DUF1217, Protein of unknown function (DUF1217)
PF06754	PhnG, Phosphonate metabolism protein PhnG
PF06764	DUF1223, Protein of unknown function (DUF1223)
PF06776	IalB, Invasion associated locus B (IalB) protein
PF06793	UPF0262, Uncharacterised protein family (UPF0262)
PF06821	DUF1234, Alpha/Beta hydrolase family of unknown function (DUF1234)
PF06823	DUF1236, Protein of unknown function (DUF1236)
PF06829	DUF1238, Protein of unknown function (DUF1238)
PF06832	BiPBP_C, Penicillin-Binding Protein C-terminus Family
PF06845	IolB, Myo-inositol catabolism protein IolB
PF06850	PHB_depo_C, PHB de-polymerase C-terminus
PF06904	Extensin-like_C, Extensin-like protein C-terminus
PF06921	VIRB2, VIRB2 type IV secretion protein
PF06964	Alpha-L-AF_C, Alpha-L-arabinofuranosidase C-terminus
PF07007	DUF1311, Protein of unknown function (DUF1311)
PF07045	DUF1330, Protein of unknown function (DUF1330)
PF07049	DUF1332, Protein of unknown function (DUF1332)
PF07077	DUF1345, Protein of unknown function (DUF1345)
PF07090	DUF1355, Protein of unknown function (DUF1355)
PF07164	HAP3, Putative flagellar hook-associated protein 3 (HAP3)
PF07167	PhaC_N, Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus
PF07171	MlrC_C, MlrC C-terminus
PF07182	DUF1402, Protein of unknown function (DUF1402)
PF07221	GlcNAc_2-epim, N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
PF07298	NnrU, NnrU protein
PF07309	FlaF, Flagellar protein FlaF
PF07323	DUF1465, Protein of unknown function (DUF1465)
PF07330	DUF1467, Protein of unknown function (DUF1467)
PF07364	DUF1485, Protein of unknown function (DUF1485)
PF07370	DUF1489, Protein of unknown function (DUF1489)
PF07372	DUF1491, Protein of unknown function (DUF1491)
PF07378	FlbT, Flagellar protein FlbT
PF07433	DUF1513, Protein of unknown function (DUF1513)
PF07446	GumN, GumN protein
PF07506	RepB, RepB plasmid partitioning protein
PF07536	HWE_HK, HWE histidine kinase
PF07542	ATP12, ATP12 chaperone protein
PF07582	AP_endonuc_2_N, AP endonuclease family 2 C terminus
PF07695	7TMR-DISM_7TM, 7TM diverse intracellular signalling
PF07696	7TMR-DISMED2, 7TMR-DISM extracellular 2
PF07756	DUF1612, Protein of unknown function (DUF1612)
PF07786	DUF1624, Protein of unknown function (DUF1624)
PF07820	TraC, TraC-like protein
PF07835	COX4_pro_2, Bacterial aa3 type cytochrome c oxidase subunit IV
PF07879	PHB_acc_N, PHB/PHA accumulation regulator DNA-binding domain
PF07886	BA14K, BA14K-like protein
PF07940	Hepar_II_III, Heparinase II/III-like protein
PF08239	SH3_3, Bacterial SH3 domain
PF08269	Cache_2, Cache domain
PF08362	TetR_C_3, YcdC-like protein, C-terminal region
PF08379	Bact_transglu_N, Bacterial transglutaminase-like N-terminal region
PF08471	Ribonuc_red_2_N, Class II vitamin B12-dependent ribonucleotide reductase
PF08521	2CSK_N, Two-component sensor kinase N-terminal
PF08548	Peptidase_M10_C, Peptidase M10 serralysin C terminal
PF08755	YccV-like, Hemimethylated DNA-binding protein YccV like
PF08808	RES, RES domain
PF08871	ExoV, ExoV-like protein
PF08904	DUF1849, Domain of unknown function (DUF1849)
PF09296	NUDIX-like, NADH pyrophosphatase-like rudimentary NUDIX domain
PF09297	zf-NADH-PPase, NADH pyrophosphatase zinc ribbon domain
PF09326	DUF1982, Domain of unknown function (DUF1982)
PF00211	Guanylate_cyc, Adenylate and Guanylate cyclase catalytic domain
PF00743	FMO-like, Flavin-binding monooxygenase-like
PF01152	Bac_globin, Bacterial-like globin
PF01642	MM_CoA_mutase, Methylmalonyl-CoA mutase
PF01730	UreF, UreF
PF01774	UreD, UreD urease accessory protein
PF01794	Ferric_reduct, Ferric reductase like transmembrane component
PF01968	Hydantoinase_A, Hydantoinase/oxoprolinase
PF01970	DUF112, Integral membrane protein DUF112
PF02167	Cytochrom_C1, Cytochrome C1 family
PF02514	CobN-Mg_chel, CobN/Magnesium Chelatase
PF02534	TraG, TraG/TraD family
PF02551	Acyl_CoA_thio, Acyl-CoA thioesterase
PF02571	CbiJ, Precorrin-6x reductase CbiJ/CobK
PF02633	Creatininase, Creatinine amidohydrolase
PF02643	DUF192, Uncharacterized ACR, COG1430
PF02790	COX2_TM, Cytochrome C oxidase subunit II, transmembrane domain
PF03450	CO_deh_flav_C, CO dehydrogenase flavoprotein C-terminal domain
PF03459	TOBE, TOBE domain
PF03824	NicO, High-affinity nickel-transport protein
PF03861	ANTAR, ANTAR domain
PF03928	DUF336, Domain of unknown function (DUF336)
PF03932	CutC, CutC family
PF03972	MmgE_PrpD, MmgE/PrpD family
PF03975	CheD, CheD
PF04169	DUF404, Domain of unknown function (DUF404)
PF04174	DUF407, Domain of unknown function (DUF407)
PF04204	HTS, Homoserine O-succinyltransferase
PF04263	TPK_catalytic, Thiamin pyrophosphokinase, catalytic domain
PF04329	DUF470, Family of unknown function (DUF470)
PF04331	DUF472, Family of unknown function (DUF472)
PF04367	DUF502, Protein of unknown function (DUF502)
PF04401	DUF540, Protein of unknown function (DUF540)
PF04463	DUF523, Protein of unknown function (DUF523)
PF04748	Polysacc_deac_2, Divergent polysaccharide deacetylase
PF04828	DUF636, Protein of unknown function (DUF636)
PF04932	Wzy_C, O-Antigen Polymerase
PF05016	Plasmid_stabil, Plasmid stabilisation system protein
PF05025	RbsD_FucU, RbsD / FucU transport protein family
PF05088	Bac_GDH, Bacterial NAD-glutamate dehydrogenase
PF05194	UreE_C, UreE urease accessory protein, C-terminal domain
PF05378	Hydant_A_N, Hydantoinase/oxoprolinase N-terminal region
PF05673	DUF815, Protein of unknown function (DUF815)
PF05981	CreA, CreA protein
PF05992	SbmA_BacA, SbmA/BacA-like family
PF06104	DUF949, Bacterial protein of unknown function (DUF949)
PF06472	ABC_membrane_2, ABC transporter transmembrane region 2
PF06803	DUF1232, Protein of unknown function (DUF1232)
PF07366	SnoaL, SnoaL-like polyketide cyclase
PF07995	GSDH, Glucose / Sorbosone dehydrogenase
PF08291	Peptidase_M15_3, Peptidase M15
PF08327	AHSA1, Activator of Hsp90 ATPase homolog 1-like protein
PF08482	HrpB_C, ATP-dependent helicase C-terminal
PF00032	Cytochrom_B_C, Cytochrome b(C-terminal)/b6/petD
PF02133	Transp_cyt_pur, Permease for cytosine/purines, uracil, thiamine, allantoin
PF03562	MltA, MltA specific insert domain
PF04379	DUF525, Protein of unknown function (DUF525)
PF04960	Glutaminase, Glutaminase

References

Tian, Y. and A. W. Dickerman (2007). "GeneTrees: a phylogenomics resource for prokaryotes." Nucleic Acids Res. 35(Database issue): D328-31. Epub 2006 Dec 6.

Supplementary Information: Methods

DNA sequencing and assembly. Two DNA libraries with 2-4 kb or 4-8 kb insert sizes were generated for each Agrobacterium genome by mechanical shearing of DNA and cloning into pUC18. After Sanger-based shotgun sequencing of the libraries, the reads (~87,000 for K84 and ~82,000 for S4) were assembled and edited using Phred, Phrap, and Consed (1-3) . Gaps were closed by PCR targeted sequencing. All rRNA operons were amplified with specific flanking primers, sequenced and assembled individually. All nucleotides with Phred scores <40 were re-sequenced using an independent PCR fragment as template. The error rate is estimated to be <1:10,000. The genome sequences are available through GenBank (4) and the interactive Agrobacterium genomes database (5) maintained by the Setubal group at the Virginia Bioinformatics Institute (6) .

Comparative genomics analyses. Ortholog families for Fig. 3 were obtained with orthoMCL (7) . Ortholog alignments were obtained with custom Perl scripts. Circular representations of these alignments were obtained with the tool genomeViz (8) . Analysis of potential intragenome transfers (Tables S3-S21) involved the Multi-Genome Homology Comparison (9) and Phylogenetic Profiler (10) Web-based tools. Completed bacterial genomes listed in NCBI as having more than one chromosome were initially examined and only those cases where the additional chromosome(s) carried a substantial number of essential genes were maintained. Within this subset, three cases in which two or more closely related genera appear to share a common origin of additional chromosomes were analyzed in greater detail. If intragenome transfer is a robust explanation for the origin of additional chromosomes, then the “transferred” genes should occur in clusters within which the synteny from the initial ancestral chromosome I was maintained. The additional chromosomes of two related genera A and B were searched for such shared gene clusters that are present on chromosome I of a unichromosomal relative C but are no longer found on chromosome I in genera A and B. An initial homology lower limit of 60% identity was used and once clusters were identified the lower limit was adjusted to 40% identity to determine the fullest extent of each shared gene cluster. Preliminary versions of Tables S3-S21 were checked against the ortholog alignments, and minor corrections and additions were done to obtain the final set of tables.

Analysis of the repABC systems of Agrobacterium. The RepA, RepB, and RepC protein sequences from Agrobacterium tumefaciens were used as a query against the NCBI database as of May, 2007 using the NCBI BlastP program (11) . The top 100 matches were used for analysis. The sequences of each protein were aligned using the Muscle program (12) ; phylogenetic and molecular evolutionary analyses were conducted using MEGA, version 4 (13) .

Phylogenetic comparisons among the Rhizobiaceae. A database of all multiply-alignable homology groups was developed using the methods previously described (14) for six representatives of the Rhizobiaceae plus nine outgroups in the Rhizobiales (taxa listed in Table S1 (5) ). All homology groups which had a single gene in each of the 15 taxa were selected (486 total) and this compilation was filtered to remove any which did not have all members on the largest replicon within the Rhizobiaceae genomes, yielding a total of 423 homology groups (Table S2 (5) ). The sequences were aligned using Muscle (12) within each group and filtered to remove poorly aligned regions using Gblocks (15) . Trees were inferred by MrBayes (16) individually from each alignment and from a concatenation of all 423 consisting of 133,351 aligned amino acid positions, using the 'WAG' amino-acid substitution model and gamma-distributed rate variation. After burn-in, the concatenated set converged to a single topology with 100% support at all nodes. The plurality-rule consensus of single-protein genes matched the topology of the concatenated data, though with variable support numbers.

Niche Map Construction. A niche map was constructed as previously described (17) . In brief, a total of 625 prokaryotic genome sequences obtained from the National Center for Biotechnological Information Microbial Genomes database (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi, accessed: 01.15.2008). The predicted proteome of each organism was then compared against a local database of Pfam protein domains (18) using RPSBLAST (11) . For each bacterium, a protein domain profile was constructed by calculating the total number of instances a particular Pfam ID was found in the prokaryote’s genome. These profiles were then clustered using Spearman’s rank correlation, and a combination of force-directed placement and multi-dimensional scaling was used to assign an (x, y) coordinate to each prokaryote in the plane. This ordination was then visualized as a topographical map in three dimensions using the computer program VxInsight. The map consists of a number of mountains, and the height of each mountain corresponds to the number of prokaryotes found in that particular area. Mountain numbers were then assigned by ranking each mountain based on their total number of composite prokaryotes in ascending order.

Rhizobiaceae Pfam Analysis. To determine the set of Pfams unique to the Rhizobiaceae in mountain NM13 on the niche map, the set of Pfams found in all seven members of this family were initially calculated. Only those Pfams that were found in less than two-thirds of all other prokaryotes on the niche map were retained. Finally, this list was parsed against a generated list of Pfams that were found in all 46 of the other a-proteobacteria in NM13.

Comparative single protein analysis (used to create figure S1). Genomes were clustered by gene content by constructing a matrix of pairwise distances between bacterial proteomes. Pairwise distances were estimated using the following procedure. Using NCBI BlastP, each protein in genome A was compared to the proteome of genome B. The similarity of the top hit in genome B was noted for each protein in genome A. All such A to B comparisons were summarized by calculating the percentage of the proteins in A which had a match in B of at least certain similarity. That is, a table was created showing what fraction of proteome A had matches of at least 100% identity in B, what fraction had matches of at least 99% identity, what fraction had 98%, and so on. If A and B were the same proteome, this table would contain values of 1.0 for all percents identity from 100% to 1%. The sum of the differences between the actual fractions observed and those which would arise from having identical proteomes is our pairwise distance measure. The proteomic comparison was repeated for all possible pairwise comparisons. A dendrogram illustrating how the genomes cluster (and their relative distances) with this scheme can be easily derived from the matrix of pairwise distances using the neighbor-joining method implemented in PHYLIP. This proteomic comparison method also appears robust with respect to highly divergent and even largely disjoint protein sets: the archeon Pyrococcus furiosus branches deeply from the gamma proteobacteria, while the small genome of Buchnera aphidicola, for example, clusters with Wigglesworthia (data not shown). In spirit, this clustering method is similar to the more rigorous average amino acid identity (AAI) measure proposed by Konstantinidis and Tiedje (19) ; like theirs, our method shows that entire proteome comparisons largely recapitulate standard 16S rRNA phylogeny yet provide insights into the correlation of genome and ecological role as well as highlighting possible horizontal gene transfer.

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