Updated annotations for Escherichia coli BW25113

16 genes with updated (or confirmed) annotations:

b0757 galK : galactokinase GalK (EC 2.7.1.6)
Original description: galactokinase (NCBI)
SEED: Galactokinase (EC 2.7.1.6)
KEGG: galactokinase
Rationale: Specific phenotype: utilization of D-Galactose

b1188 ycgB : ycgB component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: hypothetical protein (NCBI)
SEED: no annotation
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

b1189 dadA : D-amino acid dehydrogenase (quinone) DadA (EC 1.4.5.1)
Original description: D-amino acid dehydrogenase small subunit (NCBI)
SEED: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
KEGG: D-amino-acid dehydrogenase
Rationale: Specific phenotype: utilization of D-Alanine

b1415 aldA : Lactaldehyde / glycolaldehyde dehydrogenase aldA (EC 1.2.1.22; EC 1.2.1.21)
Original description: aldehyde dehydrogenase A, NAD-linked (NCBI)
SEED: Aldehyde dehydrogenase A (EC 1.2.1.22) / Glycolaldehyde dehydrogenase (EC 1.2.1.21)
KEGG: lactaldehyde dehydrogenase / glycolaldehyde dehydrogenase
Rationale: Specific phenotype: utilization of L-Fucose. Also detoxifies glycolaldehyde (PMC4585216)

b1783 yeaG : yeaG component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: conserved protein with nucleoside triphosphate hydrolase domain (NCBI)
SEED: no annotation
KEGG: serine protein kinase
Rationale: conserved cofitness; yeaG is a protein kinase

b1784 yeaH : yeaH component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: hypothetical protein (NCBI)
SEED: UPF0229 protein YeaH
KEGG: hypothetical protein
Rationale: PFam PF04285.8 (DUF444). conserved cofitness; yeaG is a protein kinase

b2184 yejH : DNA damage response helicase (yejH or radD)
Original description: predicted ATP-dependet helicase (NCBI)
SEED: ATP-dependent RNA helicase YejH
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiation and UV radiation (PMID:25425430)

b2504 yfgG : Negative regulator of nickel and cobalt uptake (YfgG)
Original description: hypothetical protein (NCBI)
SEED: Putative inner membrane protein
KEGG: no annotation
Rationale: YfgG is important for resisting cobalt and nickel stress, as is its ortholog in Klebsiella (BWI76_RS21010). Furthermore, overexpression of yfgG confers increased resistance to cobalt (PMID:30659179). YfgG has strong negative cofitness with the Mg/Ni/Co transporter corA, as does its ortholog in Klebsiella. YfgG is a small putative membrane protein and might bind corA to inhibit it or reduce its abundance (by analogy to the magnesium transporter MtgE and the small membrane protein MtgS that binds and stabilizes MtgS.)

b2943 galP : galactose:H+ symporter (galP)
Original description: D-galactose transporter (NCBI)
SEED: Arabinose-proton symporter
KEGG: MFS transporter, SP family, galactose:H+ symporter
Rationale: A characterized E. coli protein, see EcoCyc. Not sure why SEED has it as transporting arabinose. KEGG_correct.

b2979 glcD : glycolate dehydrogenase, putative FAD-linked subunit
Original description: glycolate oxidase subunit, FAD-linked (NCBI)
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: glycolate oxidase
Rationale: Specific phenotype: utilization of Glycolic Acid

b3528 dctA : C4 dicarboxylate/orotate:H+ symporter (DctA)
Original description: C4-dicarboxylate transport protein (NCBI)
SEED: Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate
KEGG: aerobic C4-dicarboxylate transport protein
Rationale: Specific phenotype: utilization of L-Malic acid, succinate; also transports other C4 dicarboxylates, aspartate, and orotate (see ecocyc)

b3543 dppB : dipeptide ABC transporter, membrane subunit (DppB)
Original description: dipeptide transporter (NCBI)
SEED: Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
KEGG: dipeptide transport system permease protein
Rationale: Specific phenotype: utilization of Gly-DL-Asp, Gly-Glu

b3599 mtlA : Mannitol phosphotransferase system, IIA/IIB/IIC components (EC 2.7.1.197)
Original description: fused mannitol-specific PTS enzymes: IIA components/IIB components/IIC components (NCBI)
SEED: PTS system, mannitol-specific IIC component (EC 2.7.1.69) / PTS system, mannitol-specific IIB component (EC 2.7.1.69) / PTS system, mannitol-specific IIA component
KEGG: PTS system, mannitol-specific IIA component ; PTS system, mannitol-specific IIB component ; PTS system, mannitol-specific IIC component
Rationale: Specific phenotype: utilization of D-Mannitol

b3603 lldP : (R)-lactate / (S)-lactate / glycolate:H+ symporter LldP
Original description: L-lactate permease (NCBI)
SEED: L-lactate permease
KEGG: L-lactate permease
Rationale: This protein is annotated by EcoCyc as transporting both stereoisomers of lactate and glycolate, which is consistent with our genetic data and a more detailed study (PMID:11785976). The previous study found that yghK (glcA) also transported glycolate and was important for glycolyate utilization. We instead observed a very subtle defect of the glcA mutant during growth on glycolate (fitness = -0.5).

b3748 rbsD : D-ribose pyranase [EC:5.4.99.62]
Original description: D-ribose high-affinity transport system; membrane-associated protein (VIMSS)
SEED: Ribose ABC transport system, high affinity permease RbsD (TC 3.A.1.2.1)
KEGG: D-ribose pyranase
Rationale: This is a ribose pyranase, not a transporter, see PMID:15060078 or UniProt:RBSD_ECOLI (KEGG_correct)

b4068 yjcH : required for glycolate transport, with actP
Original description: conserved inner membrane protein involved in acetate transport (NCBI)
SEED: Putative membrane protein, clustering with ActP
KEGG: no annotation
Rationale: PFam PF04341.8 (DUF485). This gene is specifically important for glycolate utilization and is conserved cofit with actP.

Or download reannotations for Escherichia coli BW25113 or for all organisms as tab-delimited tables