The genome of Rhizobium leguminosarum has recognizable core and accessory components

Young, J Peter W; Crossman, Lisa C; Johnston, Andrew WB; Thomson, Nicholas R; Ghazoui, Zara F; Hull, Katherine H; Wexler, Margaret; Curson, Andrew RJ; Todd, Jonathan D; Poole, Philip S; Mauchline, Tim H; East, Alison K; Quail, Michael A; Churcher, Carol; Arrowsmith, Claire; Cherevach, Inna; Chillingworth, Tracey; Clarke, Kay; Cronin, Ann; Davis, Paul; Fraser, Audrey; Hance, Zahra; Hauser, Heidi; Jagels, Kay; Moule, Sharon; Mungall, Karen; Norbertczak, Halina; Rabbinowitsch, Ester; Sanders, Mandy; Simmonds, Mark; Whitehead, Sally; Parkhill, Julian

doi:10.1186/gb-2006-7-4-r34

Table 4 The σ factors of Rlv3841

From: The genome of Rhizobium leguminosarum has recognizable core and accessory components

Gene and name (if known)^a	GC3s, quartop^b	Closest homologs^c
		Species	Gene	BLAST e value
RL0422 (RpoN, used for N assimilation)	0.791 Y	S. meliloti	SMc01139	0.0
		A. tumefaciens	AGR_C_581	0.0
		M. loti	mll3196	2E-161
		Brucella suis	BR0158	3E-156
RL0788	0.732 N	Pseudomonas fluorescens	Pflu02001224	9E-56
		Erwinia carotovora	ECA2017	E-43
		Burkholderia ambifaria	BambDRAFT_3017	9E-30
		S. meliloti	SMa01432	2E-27
		A.tumefaciens	AGR_C_2739	2E-16
		M.loti	mlr77732	E-16
RL1138	0.714 N	Ralstonia eutropha	Reut_B3794	E-47
		Bradyrhizobium japonicum	bll6484	2E-44
		Silicibacter pomeroyi	SPO31254	E-29
		M. loti	mlr7773	7E-29
		A. tumefaciens	AGR_C_2739	2E-28
		S. meliloti	SMc01419	9E-23
RL3020	0.749 Y	A. tumefaciens	AGR_C_4121	6E-56
		B. suis	BRA0021	2E-32
		Burkholderia fungorum	Bcep02004893	7E-32
		Caulobacter crescentus	CC3253	2E-30
		M. loti	mll3493	4E-25
		S. meliloti	SMb20531	2E-18
RL3235	0.777 N	S. meliloti	SMc01419	E-48
		A. tumefaciens	AGR_C_3679p	9E-44
		Sphingopyxis alaskensis	SalaDRAFT_1954	5E-23
		B. japonicum	bll2628	6E-23
		M. loti	mlr04075	E-18
RL3402 (RpoD, 'housekeeping' σ)	0.823 Y	A. tumefaciens	AGR_C_3929p	0.0
		S. meliloti	SMc01563	0.0
		B. suis	BR1479	0.0
		M. loti	mll2466	0.0
RL3509	0.758 N	S. meliloti	SMc02713	2E-38
		S. alaskensis	SalaDRAFT_1954	4E-18
		Burkholderia cepacia	Bcepa03005434	5E-18
		Novosphingobium aromaticivorans	DSM 12444	2E-17
		A. tumefaciens	AGR_C_3679	E-14
		M. loti	mlr7773	5E-12
RL3703 (RpoZ)	0.790 Y	S. meliloti	SMc01506	5E-84
		B. suis	BR1658	3E-80
		Bartonella henselae	BH13830	5E-73
		A. tumefaciens	AGR_L_1386p	5E-68
		M. loti	mll3697	7E-68
RL3766 (RpoH, heat shock σ)	0.794 Y	A. tumefaciens	AGR_C_4439p	2E-155
		S. meliloti	SMc00646	3E-148
		M. loti	mlr3741	5E-138
		B. suis	BR1650	E-133
RL4524	0.780 N	M. loti	mlr8088	5E-38
		Rhodospirillum rubrum	Rrub02003750	3E-37
		Rhodobacter sphaeroides	'rpoE'	3E-34
		Magnetospirillum magnetotacticum	Magn03011107	E-33
		S. meliloti	None listed in top 50 matches
		A. tumefaciens	None listed in top 50 matches
RL4614 (RpoH2, heat shock σ)	0.771 N	S. meliloti	SMc03873	5E-118
		M. loti	mlr3862	2E-98
		B. suis	BR1763	5E-97
		B. henselae	BH15210	3E-95
		A. tumefaciens	AGR_C_4439p^d	7E-58
pRL10385	0.720 N	M. loti	mll1224	2E-52
		Microbulbifer degradans	Mdeg02003584	E-28
		R. sphaeroides	Rsph03003515	E-27
		Solibacter usitatus	AcidDRAFT_4778	6E-22
		S. meliloti	None listed in top 50 matches
		A. tumefaciens	None listed in top 50 matches
pRL11007 (EcfR)	0.778 N	M. loti	mlr0407	4E-57
		R. sphaeroides	Rsph03002607	E-45
		M. magnetotacticum	Magn03006880	8E-39
		Bordetella parapertussis	BPP1584	4E-37
		A. tumefaciens	AGR_L_1386p	3E-24
		S. meliloti	SMa0143	2E-22
pRL110418	0.794 N	B. japonicum	blr7812	2E-83
		Streptomyces avermitilis	SAV7424	7E-74
		Nocardia farcina	nfa4970	3E-73
		Frankia sp.	Francci3DRAFT_3517	7E-66
		M. loti	mll6869	8E-33
		S. meliloti	None listed in top 50 matches
		A. tumefaciens	None listed in top 50 matches
pRL120319 (RpoI, iron uptake sigma)	0.640 N	Azotobacter vinelandii	AvinDRAFT_4065	4E-20
		Pseudomonas aeruginosa	'pvdS'^e	3E-18
		S. meliloti	SMc04203	8E-09
		A. tumefaciens	AGR_pAT_442	2E-08
pRL120580	0.587 N	Rhodopseudomonas palustris	RPA0550	4E-40
		R. rubrum	Rrub02003750	8E-38
		M. magnetotacticum	Magn03011107	5E-37
		Pseudomonas syringae	PSPTO1043	3E-28
		M. loti	mlr8088	4E-26
		A. tumefaciens	AGR_C_3605	6E-14
		S. meliloti	None listed in top 50 matches

^aRhizobium leguminosarum biovar viciae 3841 (Rlv3841) locus tags are shown and, if the gene has been named in R. leguminosarum, this name is shown. ^bGC3s (G+C content of silent third positions of codons), member of quartop (yes [Y]/no [N]). ^cEach of the Rlv3841 sigma factors was used in BLASTP searches (maximum of 50 matches). The sequences and the locus tag numbers, together with the 'e' values, are shown for the top four matches. In those genera (Brucella, Pseudomonas, Streptomyces, Burkholderia) with more than one sequenced species, only one example is shown for each genus. In those cases in which one or more of the species used in the quartop analysis is not in the top four matches, these are also included. ^dA. tumefaciens has only one rpoH gene (AGR_C_4439p) whereas R. leguminosarum, M. loti, and S. meliloti have two. AGR_C_4439p is more closely related to Rlv3841 RpoH1 (RL3766) than to Rlv3841 RpoH2 (RL4614). ^eAlso known as PfrI in P. putida, and PbrA in P. fluorescens.

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