TABLE 1.

Proposed reannotations of gene functions resulting from the curation and reconciliation process

B. cenocepacia		B. multivorans		Proposed annotation	Gene name	Protein ID	Evidence
Locus tag	Current annotation	Locus tag	Current annotation
BCAS0031	Hypothetical protein	Bmul_6140	Hypothetical protein	l-2,4-Diaminobutyric acid transaminase	doeD	EC 2.6.1.-	E values of 1E−154 and 1E−155, respectively, to Helo_3661 in H. elongata (40)
BCAM1003	Putative epimerase	Bmul_4613	NAD-dependent epimerase/dehydratase	GDP-d-mannose reductase	bceM	EC 1.1.1.187	E values of 1E−141 and 1E−129, respectively, to Bcep1808_4471 in B. vietnamiensis (41)
BCAS0105	Hypothetical protein	—	—	dTDP-4-dehydrorhamnose reductase	rfbD	EC 1.1.1.133	E value of 1E−139 to Bmul_6045, which is annotated as a dTDP-4-dehydrorhamnose reductase
BCAM2148	Hypothetical protein	Bmul_3704	Hypothetical protein	Malate dehydrogenase	mdh	EC 1.1.1.37	E values of 7E−30 and 3E−27 to BCAM1263 and Bmul_4451, respectively, which are annotated as malate/l-lactate dehydrogenases
BCAS0285	Hypothetical protein	—	—	Argininosuccinate lyase	argH	EC 4.3.2.1	CDD E value of 3E−27 to argininosuccinate lyase; E value of 9E-17 to Bcep1808_5167, which is annotated as an argininosuccinate lyase in B. vietnamiensis
—a	—	Bmul_6038	Hypothetical protein	4-Carboxy-4-hydroxy-2-oxoadipate (CHA) aldolase	galC	EC 4.1.3.17	CDD E value of 1E−95 to CHA aldolase; E value of 2E−80 and 95% coverage to PP_2514 in Pseudomonas putida (81); no ortholog in B. cenocepacia
BCAM0581	Enoyl-CoA hydratase	Bmul_5121	Enoyl-CoA hydratase	3-Hydroxydodecanoyl-ACP hydratase/cis-2-dodecenoyl-ACP thioesterase			In vitro characterization of BCAM0581 showed bifunctional product (40); Bmul_5121 has E value of 1E−162 to BCAM0581
—	—	Bmul_3969	Autoinducer synthesis protein	N-Acylhomoserine lactone synthase	cepI	EC 2.3.1.184	E value of 8E−81 to BCAM1870, which is annotated as cepI
BCAL2418	Hypothetical protein	Bmul_0955	6-Phosphogluconolactonase	Gluconolactonase	ppgL	EC 3.1.1.17	E values of 2E−84 and 2E−83 to PA4204 in P. aeruginosa, which codes for a characterized periplasmic gluconolactonase (43)
BCAL1668	Putative amino acid transport system	Bmul_1621	Extracellular solute-binding protein	Cysteine ABC transporter	cjaA	CjaA	E values of 1E−25 and 1E−25 to Cj0982 in Campylobacter jejuni, which was shown to be a high-affinity cysteine transporter (44)
BCAS0145, BCAL1224, BCAS0735, BCAM1221, BCAM0361	Metallo peptidase, allantoate amidohydrolase	Bmul_5349, Bmul_4490, Bmul_2063, Bmul_5235	Allantoate amidohydrolase	β-Ureidopropionase		EC 3.5.1.6	All genes have E values of <1E−100 to PP_0614 in P. putida, which was shown to be a β-ureidopropionase (82)
BCAL1428	Putative amine catabolism-related protein	Bmul_1894	Xylose isomerase domain-containing protein	myo-Inosose-2 dehydratase	iolE	EC 4.2.1.44	E values of 2E−56 and 4E−58 to SMc00433 in Sinorhizobium meliloti (46)
BCAL1429	Putative TPP-binding acetolactate synthase	Bmul_1893	Thiamine pyrophosphate protein	3d-(3,5/4)-Trihydroxycyclohexane-1,2-dione hydrolase	iolD		E values of 1E−168 and 1E−166 to SMc01166 in S. meliloti (46)
BCAL1427	myo-Inositol catabolism protein	Bmul_1895	myo-Inositol catabolism IolB domain-containing protein	5-Deoxy-d-glucuronate isomerase	iolB	EC 5.3.1.-	E values of 3E−71 and 2E−71 to SMc00432 in S. meliloti (46)
BCAL1430	Putative carbohydrate kinase	Bmul_1892	Ribokinase-like domain-containing protein	5-Dehydro-2-deoxygluconokinase	iolC	EC 2.7.1.92	E values of 1E−147 and 1E−143 to SMc01165 in S. meliloti (46)
BCAL2435	Na+/solute symporter family protein	Bmul_0940	Na+/solute symporter	Monocarboxylate permease	mctP	MctP	E values of 1E−161 and 1E−155 to mctP in Rhizobium leguminosarum, which was shown to code for a pyruvate transporter (47)

^aDashes indicate the absence of a corresponding reannotation in one of the genomes.