TABLE 4.

Similarity analysis of gene paralogues and orthologues

Duplicated gene(s)	No. of copies in R. sphaeroides	Function	% Identitya	Close match		Treec
				Organism	% Identityb	Type	Bootstrap value
CI-CI
pucB1/pucB2	2	Light entrapment	100	Rhodovulum sulfidophilum	80	B	94
pucA1/pucA2	2	Light entrapment	58	R. sulfidophilum	54	A	55
dxsI/dxsII	2	Isoprenoid synthesis	66	Rhodobacter capsulatus	75	A	100
flgG	2	Flagellum biosynthesis	42	Caulobacter crescentus	47	A	82
flgI	2	Flagellum biosynthesis	42	C. crescentus	50	A	43
flhA	2	Flagellum biosynthesis	32	C. crescentus	32	A	100
fliI	2	Flagellum biosynthesis	36	C. crescentus	44	A	76
fliP	2	Flagellum biosynthesis	39	Sinorhizobium meliloti	40	A	57
fliQ	2	Flagellum biosynthesis	47	S. meliloti	40	B	62
fliR	2	Flagellum biosynthesis	33	S. meliloti	27	A	42
fliN	2	Flagellum biosynthesis	35	C. crescentus	37	A	79
fliF	2	Flagellum biosynthesis	30	C. crescentus	30	B	73
flhB	2	Flagellum biosynthesis	33	C. crescentus	32	B	98
flgH	2	Flagellum biosynthesis	30	C. crescentus	42	A	100
flgF	2	Flagellum biosynthesis	33	C. crescentus	42	B	57
flgE	2	Flagellum biosynthesis	25	S. meliloti	29	A	90
flgC	2	Flagellum biosynthesis	28	Bradyrhizobium japonicum	39	A	100
flgB	2	Flagellum biosynthesis	31	Pseudomonas aeruginosa	46	B	57
nuoA	2	Electron transport protein	36	R. capsulatus	85	A	85
nuoB	2	Electron transport protein	53	R. capsulatus	88	A	80
nuoD	2	Electron transport protein	42	R. capsulatus	83	A	98
nuoF	2	Electron transport protein	38	R. capsulatus	88	A	99
nuoH	2	Electron transport protein	42	R. capsulatus	82	A	100
nuoI	2	Electron transport protein	43	R. capsulatus	88	A	96
nuoL	2	Electron transport protein	30	R. capsulatus	33	A	98
fnrL	2	Anaerobic regulator	33	R. capsulatus	77	A	41
rpoN	2	Sigma factor	41	R. capsulatus	50	A	100
hemN/Z	4	Coproporphyrinogen III oxidase	24	S. meliloti	43	B	54
cheA	4	Chemotaxis histidine kinase	35	C. crescentus	47	A	99
cheB	2	MCPd-glutamate methylesterase	41	C. crescentus	45	A	70
cheR	3	MCP-glutamate methyltransferase	33	C. crescentus	48	A	100
cheW	4	Chemotaxis protein	33	C. crescentus	48	A	100
CI-CII
rdxA/rdxB	2	Electron transport protein	67	R. capsulatus	67	A	97
qoxA	2	Electron transport protein	45	S. meliloti	48	A	62
qor	2	Electron transport protein	31	R. capsulatus	54	A	100
cbbGI/cbbGII	2	Carbon assimilation	84	Paraccocus denitrificans	84	B	77
hemA/hemT	2	ALAe synthase (tetrapyrrole biosynthesis)	54	R. capsulatus	76	A	100
cbbTI/cbbTII	2	Carbon assimilation	58	R. capsulatus	66	A	100
cbbAI/cbbAII	2	Carbon assimilation	78	R. capsulatus	89	A	78
cbbFI/cbbFII	2	Carbon assimilation	67	R. capsulatus	69	A	99
cbbPI/cbbPII	2	Carbon assimilation	86	R. capsulatus	86	B	71
cbbMI/cbbMII	2	Carbon assimilation	31	R. capsulatus	94	A	100
groEL	3	HSP60	40	R. capsulatus	70	A	100
groES	2	HSP10	35	R. capsulatus	84	A	99

^aAmino acid identity for duplicate pair.

^bAmino acid identity with orthologue.

^cPhylogenetic relationship.

^dMCP, membrane-spanning chemoreceptor proteins.

^eALA, 5-aminolevulinic acid.