Table 4 Proposed annotation refinements
Gene Locus | Current Annotation (Burkholderia.com) | Proposed Reannotation | Protein name | Protein ID | Evidence |
|---|---|---|---|---|---|
BCAL0691, BCAL2945 | Putative cytidylyltransferase, D-beta-D-heptose 7-phosphate kinase | Bifunctional protein RfaE domain II and I, respectively, sugar kinase/adenylyltransferase | RfaE | - | Modelling evidence, RfaE is necessary for biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis; BLAST search of RfaE from P. aeruginosa gave E values of 9E-35 and 1E-75, respectively |
BCAL0780 | Putative multiphosphoryl transfer protein | Glucose-specific enzyme IIA component of PTS | Crr | TC-4.A.1.1.1 | BIOLOG assays indicated growth on glucose; BLAST search of Crr from E.coli gave an E value of 1E-28 and Identities of 40% |
BCAL0781 | Phosphotransferase system, IIbc component | Glucose/N-acetyl glucosamine-specific IIC component | PtsG/NagE | - | Evidence from BIOLOG assays; BLAST search of PtsG, NagE from E.coli gave E values of 3E-107, 7E-151 and Identities of 43%, 56%, respectively |
BCAL0802 | Gene locus is not assigned in Burkholderia Genome Database and KEGG | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | IspE | EC-2.7.1.148 | Modelling evidence, IspE is necessary for biosynthesis of polyprenyl-PP, a precursor for ubiquinone biosynthesis; BLAST E value of 4E-172; assigned gene locus of BCAL0802 (from 872938 to 873820) in GeneDB database |
BCAL1281 | Hypothetical protein | Ornithine N-acyltransferase | OlsB | EC-2.3.1.- | Physiological evidence from Weissenmayer et al. (2002); OlsB is required for the first step of ornithine-derived lipid biosynthesis; BLAST E value of 1E-29 |
BCAL1431, BCAL1432, BCAL1433 | Putative sugar transport system | Galactose transport | MglB, MglA, MglC | TC-3.A.1.2.3 | BIOLOG assays indicated growth on galactose; and BLAST E values (< 2E-23) |
BCAL1933, BCAL1934 | Putative formyltransferase, NAD-dependent epimerase/dehydratase family protein | UDP-Ara4N formyltransferase, UDP-4'-keto-5'-carboxypentose decarboxylase | ArnA1, ArnA2 | - | Evidence from Ortega et al. (2006). Unlike other bacteria in which arnA is a single gene encoding a bifunctional enzyme, two distinct genes were found in J2315 (arnA1 and arnA2) and both are required for Ara4N biosynthesis |
BCAL2388 | Hypothetical protein | Glucose-1-phosphate adenylyltransferase | - | EC-2.7.7.27 | Modelling evidence, a missing protein is required for glycogen biosynthesis; and BLAST search against UNIPROT database gave an E value of 9E-58 |
BCAL3280 | Putative carbon-nitrogen hydrolase protein | Succinamic acid amidohydrolase | - | EC-3.5.1.3 | BIOLOG assays indicated growth on succinamic acid; modelling showed a missing protein in this pathway; BLAST search against UNIPROT database gave an E value of 3E-46 |
BCAL3365 | Putative gluconate permease | D-gluconate: H+ symporter | GntP | TC-2.A.8.1.3 | BIOLOG assays indicated growth on D-Gluconic acid; modelling revealed a lack of transporter; BLAST E values of 4E-68 |
BCAM0469 | Putative aldehyde dehydrogenase | Aldehyde dehydrogenase A, NAD-linked | AldA | EC-1.2.1.21 | Modelling evidence: a gene is missing to synthesize glycolaldehyde which is required for biosynthesis of vitamin B6; BLAST E value of 2E-74 |
BCAM1404 | Probable exported glycosyl hydrolase | Sucrose-6-phosphate hydrolase | ScrB | EC-3.2.1.26 | BIOLOG assays indicated growth on sucrose; modelling showed missing protein along the pathway; gene locus identified from annotation as 93% similarity from Staphylococcus aureus and E value of 1E-33 |
BCAM2340, BCAM2338, BCAM2336 | Putative (R)-3-hydroxydecanoyl-ACP: CoA transacylase, putative glycosyltransferase, putative sugar transferase | Rhamnosyltransferase chain A, Rhamnosyltransferase chain B, Rhamnosyltransferase 2 | RhlA, RhlB, RhlC | - | Strong physiological evidence from Dubeau et. al. (2009): Burkholderia cepacia complex (Bcc) can synthesize rhamnolipids; high homologous similarity of RhlA, RhlB, RhlC found in B. cenocepacia J2315 when compared with P. aeruginosa PAO1 and B. thailandensis |
BCAM2496, BCAM2497, BCAM2498 | Binding-protein-dependent transport system protein, ABC transporter ATP-binding protein, extracellular solute-binding protein | Thiamin transport via ATP-binding protein | ThiP, ThiQ, ThiB | TC-3.A.1.19.1 | Genetic evidence: J2315 is unable to biosynthesize thiamin, which is an important cofactor to grow, by itself and could only obtain it from culture medium; BLAST search of ThiP, ThiQ, ThiB from E.coli got good result |
BCAM2723 | Putative outer membrane porin protein | Pyroglutatmate porin OpdO | OpdO | TC-1.B.25.1.7 | Evidence from BIOLOG assays; BLAST search of OpdO from P. aeruginosa PAO1 versus the B. cenocepacia J2315 genome gave an E value of 4E-32 |
BCAM2795 | Hypothetical protein | 1,4-lactonase | - | EC-3.1.1.25 | BIOLOG assays indicated growth on galactose; modelling suggested a protein is missing in this pathway; BLAST search of 1,4-lactonase from Xanthomonas campestris gave an E value of 4E-55 and identities of 42% |