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Table 4 Proposed annotation refinements

From: Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

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%