Updated Annotations for Burkholderia phytofirmans PsJN

Updated annotations for Burkholderia phytofirmans PsJN

86 genes with updated (or confirmed) annotations:

BPHYT_RS02015 : phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8)
Original description: MFS transporter
SEED: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
KEGG: indolepyruvate ferredoxin oxidoreductase
Rationale: Specifically important for: L-Phenylalanine. Annotated as indolepyruvate ferredoxin oxidoreductase, which has the same EC number; alternatively, could be a decarboxylase, but did not identify a separate aldehyde dehydrogenase

BPHYT_RS02045 : Fructokinase (EC 2.7.1.4)
Original description: sugar kinase
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Sorbitol. Automated validation from mutant phenotype: the predicted function (FRUCTOKINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS02050 : D-mannose isomerase (EC 5.3.1.7)
Original description: N-acylglucosamine 2-epimerase
SEED: D-mannose isomerase (EC 5.3.1.7)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose; D-Sorbitol; D-Fructose. Often annotated as N-acylglucosamine 2-epimerase, but phenotype on mannose is consistent with annotation as mannose isomerase. Its role on sorbitol (which is probably oxidized to sorbose or fructose by BPHYT_RS16120) or fructose is unclear - this might be a polar effect on fructokinase (BPHYT_RS02045), as there is a stronger phenotype for insertions with the antibiotic resistance marker in the non-coding orientation

BPHYT_RS02730 : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine-6-phosphate deacetylase
SEED: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
KEGG: N-acetylglucosamine-6-phosphate deacetylase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (NAG6PDEACET-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS02735 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: iron dicitrate transport regulator FecR
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (GLUCOSAMINE-6-P-DEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS02740 : N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF)
Original description: PTS glucose transporter subunit IIA
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) / PTS system, glucose-specific IIA component
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specifically important on NAG and cofit with the IIBC component nearby (BPHYT_RS02745). 58% identical to nagF or H16_A0311 of R. eutropha, which is important for NAG utilization (PMCid:PMC3127587). 58% similar to PA3760, which is required for NAG utilization in P. aeruginosa (PMCid:PMC2542419)

BPHYT_RS02745 : N-acetylglucosamine-specific PTS system, IIBC components (nagE)
Original description: PTS system N-acetylglucosamine-specific transporter subunit IIBC
SEED: PTS system, N-acetylglucosamine-specific IIA component / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component
KEGG: PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component
Rationale: Specifically important on NAG and cofit with the I-HPr-IIA component nearby (BPHYT_RS02740). CDD or PFam do not show any sign of this gene containing a IIA component, so the SEED annotation is misleading. 62% similar to H16_A0312 (nagE) and 58% similar to PA3761, which are both involved in NAG utilization (PMCid:PMC3127587, PMCid:PMC2542419). KEGG_correct.

BPHYT_RS03150 : Phosphoglycerate dehydrogenase (EC:1.1.1.95)
Original description: FAD-linked oxidase
SEED: FAD/FMN-containing dehydrogenases
KEGG: no annotation
Rationale: Auxotrophic, and rescued by L-serine or gly-glu. Glycine could yield serine via hydroxymethyltransferase, so this is consistent with a role in serine synthesis. BPHYT_RS31960 is also a possibility but gene context suggests that has a role in catabolism and has little phenotype; BPHYT_RS01425 is a possibility, but fitness data suggests it is cell wall related (auxotroph)

BPHYT_RS03220 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG:
Rationale: Specifically important for: Tween 20; Trisodium citrate dihydrate. Tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation. The phenotype on citrate is milder and is not explained, but it is conserved. (SEED_correct)

BPHYT_RS03625 : Histidinol-phosphatase (EC:3.1.3.15)
Original description: phosphoserine phosphatase
SEED: Phosphoserine phosphatase (EC 3.1.3.3)
KEGG: no annotation
Rationale: Auxotrophic, and rescued by histidne. It is usually annotated as phosphoserine phosphatase but that does not match its phenotypes and there is another putative serB. The only homolog of the traditional hisB phosphatase part is the essential protein BPHYT_RS03340, which seems more likely to be ghmB for cell wall synthesis. (auxotroph)

BPHYT_RS03870 : xanthine dehydrogenase, molybdopterin binding subunit (EC 1.17.1.4)
Original description: aldehyde oxidase
SEED: Xanthine dehydrogenase, molybdenum binding subunit (EC 1.17.1.4)
KEGG: xanthine dehydrogenase large subunit
Rationale: Specific phenotype: utilization of Deoxyribonucleic acid

BPHYT_RS04730 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: oxidoreductase
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

BPHYT_RS04765 : 2-deoxy-D-ribonate transporter
Original description: major facilitator transporter
SEED: D-galactonate transporter
KEGG: no annotation
Rationale: Important for the utilization of deoxyribonate. Similar to the putative deoxyribonate transporter in several other bacteria.

BPHYT_RS04775 : 2-deoxy-D-ribonate 3-dehydrogenase
Original description: 3-ketoacyl-ACP reductase
SEED: SHORT CHAIN DEHYDROGENASE
KEGG: no annotation
Rationale: Important for deoxyribonate utilization. Similar to the deoxyribonate dehydrogenase of P. simiae (PS417_07245)

BPHYT_RS07555 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: histidine ammonia-lyase
SEED: Histidine ammonia-lyase (EC 4.3.1.3)
KEGG: histidine ammonia-lyase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (HISTIDINE-AMMONIA-LYASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS07585 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate amidohydrolase
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: N-formylglutamate deformylase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (N-FORMYLGLUTAMATE-DEFORMYLASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS07675 : ABC transporter for L-Arginine, permease component 2
Original description: histidine/lysine/arginine/ornithine ABC transporter permease HisQ
SEED: Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Very important for utilization of L-arginine

BPHYT_RS07680 : ABC transporter for L-Arginine, permease component 1
Original description: histidine/lysine/arginine/ornithine ABC transporter permease HisM
SEED: Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Specific phenotypes on L-Arginine. no phenotype on histidine

BPHYT_RS07685 : ABC transporter for L-Arginine, putative ATPase component
Original description: histidine ABC transporter ATP-binding protein
SEED: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
KEGG: histidine transport system ATP-binding protein
Rationale: This is presumably the ATPase component but lacks fitness data.

BPHYT_RS07720 : Succinylglutamate desuccinylase (EC 3.5.1.96)
Original description: succinylglutamate desuccinylase
SEED: Succinylglutamate desuccinylase (EC 3.5.1.96)
KEGG: succinylglutamate desuccinylase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCGLUDESUCC-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS07735 : ABC transporter for L-Arginine, periplasmic substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
KEGG: lysine/arginine/ornithine transport system substrate-binding protein
Rationale: Specific phenotype on L-Arginine. Not near the permease components

BPHYT_RS08815 : L-asparaginase (EC 3.5.1.1)
Original description: L-asparaginase
SEED: L-asparaginase (EC 3.5.1.1)
KEGG: L-asparaginase
Rationale: Specifically important for utilizing L-Asparagine. Automated validation from mutant phenotype: the predicted function (ASPARAGHYD-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS11290 : 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43)
Original description: bifunctional glyoxylate/hydroxypyruvate reductase B
SEED: 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43)
KEGG: gluconate 2-dehydrogenase
Rationale: Specifically important for: D-Gluconic Acid sodium salt. Gluconate is probably primarily catabolized via gluconate kinase (BPHYT_RS16720) and the Entner-Doudoroff pathway (starting with phosphogluconate dehydratase, BPHYT_RS16735). However it appears that there is a side pathway involving gluconate 2-dehydrogenase (BPHYT_RS14520, which has no phenotype because this side path is not beneficial), 2-ketogluconate kinase (BPHYT_RS11300, no fitness data), and 2-ketogluconate-6-P reductase (this gene). A similar side path is known in P. putida (PMCID:PMC4646247) and this gene is similar to the P. putida 2-ketoglutarate-6-phosphate reductase (PP3376). (SEED_correct)

BPHYT_RS12305 : Malate synthase (EC 2.3.3.9)
Original description: malate synthase
SEED: Malate synthase (EC 2.3.3.9)
KEGG: malate synthase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (MALSYN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS13300 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: phenylhydantoinase
SEED: Dihydropyrimidinase (EC 3.5.2.2)
KEGG: dihydropyrimidinase
Rationale: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (3.5.2.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

BPHYT_RS13545 : 3-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35)
Original description: 3-hydroxyacyl-CoA dehydrogenase
SEED: Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
KEGG: 3-hydroxyacyl-CoA dehydrogenase
Rationale: # Specifically important in carbon source L-Phenylalanine. Phenylalanine is catabolized via phenylacetyl-CoA. This protein contains both a 3-hydroxyacyl-CoA dehydrogenase domain, which fits with the requirement for 3-hydroxyadipyl-CoA dehydrogenase in the phenylacetate pathway, and a enoyl-CoA hydratase domain, whose role is uncertain. (BPHYT_RS17335 is probably the trans-2,3-dehydroadipyl-CoA hydratase)

BPHYT_RS13910 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
Original description: 5-dehydro-2-deoxygluconokinase
SEED: 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
KEGG: 5-dehydro-2-deoxygluconokinase
Rationale: # Specifically important in carbon source m-Inositol. This protein is a fusion of 5-keto-deoxygluconate kinase and DUF2090. As DUF2090 has distant similarity to aldolases, it may provide the missing 5-dehydro-2-deoxyphosphogluconate aldolase activity.

BPHYT_RS13920 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: xylose isomerase
SEED: Inosose dehydratase (EC 4.2.1.44)
KEGG: inosose dehydratase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (MYO-INOSOSE-2-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS13925 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: 5-deoxyglucuronate isomerase
SEED: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
KEGG: 5-deoxy-glucuronate isomerase
Rationale: Specifically important for utilizing m-Inositol.

BPHYT_RS14905 : Aromatic-amino-acid transaminase (EC 2.6.1.57)
Original description: histidinol-phosphate aminotransferase
SEED: Biosynthetic Aromatic amino acid aminotransferase beta (EC 2.6.1.57)
KEGG: histidinol-phosphate aminotransferase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (2.6.1.57) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

BPHYT_RS16025 : Kynurenine formamidase, bacterial (EC 3.5.1.9)
Original description: kynurenine formamidase
SEED: Kynurenine formamidase, bacterial (EC 3.5.1.9)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (ARYLFORMAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS16030 : Kynureninase (EC 3.7.1.3)
Original description: kynureninase
SEED: Kynureninase (EC 3.7.1.3)
KEGG: kynureninase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (KYNURENINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS16050 : xylitol 2-dehydrogenase (EC 1.1.1.9)
Original description: iditol 2-dehydrogenase
SEED: Xylitol dehydrogenase (EC 1.1.1.9)
KEGG: L-iditol 2-dehydrogenase
Rationale: Specifically important for: Xylitol. (SEED_correct)

BPHYT_RS16095 : ABC transporter for D-Sorbitol, ATPase component
Original description: sugar ABC transporter ATP-binding protein
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: sorbitol/mannitol transport system ATP-binding protein
Rationale: Specific phenotype on D-Sorbitol.

BPHYT_RS16105 : ABC transporter for D-Sorbitol, permease component 1
Original description: mannitol ABC transporter permease
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol.

BPHYT_RS16110 : ABC transporter for D-Sorbitol, permease component 2
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 1
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol.

BPHYT_RS16115 : ABC transporter for D-Sorbitol, periplasmic substrate-binding component
Original description: sugar ABC transporter substrate-binding protein
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: sorbitol/mannitol transport system substrate-binding protein
Rationale: Specific phenotype on D-Sorbitol.

BPHYT_RS16120 : sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14)
Original description: sorbitol dehydrogenase
SEED: Sorbitol dehydrogenase (EC 1.1.1.14)
KEGG: D-sorbitol dehydrogenase (acceptor)
Rationale: Specifically important for: D-Sorbitol. The KEGG EC number implies that sorbose would be the product, but it is not clear how sorbose would be consumed. The only other genes with specific phenotypes on sorbitol are an ABC transporter, the fructokinase BPHYT_RS02045, and an apparent polar effect on mannose isomerase BPHYT_RS02050. Also this protein is 60% similar to DHSO_RHOSH (polS), which is annotated in UniProt as forming sorbose but is believed to form D-fructose, see PMID: 15805591 (SEED_correct)

BPHYT_RS16285 : Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Original description: branched-chain amino acid aminotransferase
SEED: Branched-chain amino acid aminotransferase (EC 2.6.1.42)
KEGG: branched-chain amino acid aminotransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (BRANCHED-CHAINAMINOTRANSFERILEU-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS16405 : galactonate dehydratase [EC: 4.2.1.6]
Original description: galactonate dehydratase
SEED: Gluconate dehydratase (EC 4.2.1.39)
KEGG: galactonate dehydratase
Rationale: Specifically important for: D-Galactose. galactonate is an intermediate in galactose oxidation (KEGG_correct)

BPHYT_RS16720 : Gluconokinase (EC 2.7.1.12)
Original description: gluconate kinase
SEED: Gluconokinase (EC 2.7.1.12)
KEGG: gluconokinase
Rationale: Specifically important for utilizing D-Gluconic Acid sodium salt. Automated validation from mutant phenotype: the predicted function (GLUCONOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS16725 : gluconate:H+ symporter (gntT)
Original description: permease
SEED: Gluconate transporter family protein
KEGG: gluconate:H+ symporter, GntP family
Rationale: Specific phenotype on gluconate and 72% identical to the gluconate permease (gntT, ACIAD0544) of A. baylayi ADP1 (PMCid:PMC4254613). KEGG_correct

BPHYT_RS16915 : L-arabinono-1,4-lactonase; galactonolactonase
Original description: gluconolaconase
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: L-arabinonolactonase
Rationale: specifically important for utilization of L-arabinose and D-galactose; it is not certain whether the galactose dehydrogenase (BPHYT_RS16920) forms the 1,5-lactone or the 1,4-lactone.

BPHYT_RS16920 : L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48)
Original description: 3-oxoacyl-ACP reductase
SEED: Putative oxidoreductase in arabinose utilization cluster
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Arabinose; carbon source D-Galactose. Some other dehydrogenases are known to act on both of these substrates.

BPHYT_RS16925 : D-galactose ABC transporter, permease component
Original description: arabinose ABC transporter permease
SEED: L-arabinose transport system permease protein (TC 3.A.1.2.2)
KEGG: L-arabinose transport system permease protein
Rationale: Specifically important for D-galactose utilization

BPHYT_RS16930 : D-galactose ABC transporter, ATPase component
Original description: arabinose ABC transporter ATP-binding protein
SEED: L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
KEGG: L-arabinose transport system ATP-binding protein
Rationale: Specifically important for D-galactose utilization

BPHYT_RS16935 : D-galactose ABC transporter, substrate-binding component
Original description: arabinose ABC transporter substrate-binding protein
SEED: L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
KEGG: L-arabinose transport system substrate-binding protein
Rationale: Specifically important for D-galactose utilization

BPHYT_RS16950 : 2-dehydro-3-deoxygalactonokinase DgoK (EC 2.7.1.58)
Original description: 2-dehydro-3-deoxygalactonokinase
SEED: 2-dehydro-3-deoxygalactonokinase (EC 2.7.1.58)
KEGG: 2-dehydro-3-deoxygalactonokinase
Rationale: specifically important for D-galactose utilization

BPHYT_RS17335 : 2,3-dehydroadipyl-CoA hydratase / enoyl-CoA hydratase (EC 4.2.1.17)
Original description: enoyl-CoA hydratase
SEED: Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for utilization of phenylacetate and phenylalanine. 51% identical to the characterized enzyme (paaF = Q845K2) from Pseudomonas sp. Y2, which is part of the aerobic phenylacetyl-CoA pathway. Also, 83% identical to enoyl-CoA hydratase Crt2 = H16_A3307 from Ralstonia eutropha (PMID:30243533).

BPHYT_RS17340 : 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PaaZ (EC:1.2.1.91)
Original description: aldehyde dehydrogenase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ
KEGG: no annotation
Rationale: Specifically important for utilization of phenylalanine and phenylacetate. This dehydrogenase (also known as PaaZ) is part of the aerobic phenylacetyl-CoA degradation pathway. 86% identical to BCAL0408 from B. cenocepacia, which is also involved in phenylacetate degradation and was proposed to be PaaZ (PMC2580687).

BPHYT_RS17345 : bifunctional thiolase PaaJ: 3-oxo-5,6-didehydrosuberyl-CoA thiolase (EC 2.3.1.223); 3-oxoadipyl-CoA thiolase (EC 2.3.1.174)
Original description: acetyl-CoA acetyltransferase
SEED: Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
KEGG: acetyl-CoA acyltransferase
Rationale: Specifically important for utilization of phenylacetate and phenylalanine. This is probably the bifunctional thiolase in the aerobic phenylacetyl-CoA degradation pathway (also known as PaaJ).

BPHYT_RS17540 : L-aspartate/L-glutamate/L-glutamine:H+ symporter
Original description: amino acid:proton symporter
SEED: Amino acid transporter
KEGG: no annotation
Rationale: Specifically important for utilization of glutamine, glutamate, or asparagine.

BPHYT_RS17670 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: phosphoribosyl-ATP pyrophosphatase
SEED: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
KEGG: phosphoribosyl-ATP pyrophosphohydrolase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR03188.

BPHYT_RS17685 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

BPHYT_RS17700 : imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)
Original description: imidazoleglycerol-phosphate dehydratase
SEED: Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)
KEGG: imidazoleglycerol-phosphate dehydratase
Rationale: # Important for fitness in minimal media, unless histidine is provided as a carbon or nitrogen source.

BPHYT_RS17715 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase
SEED: ATP phosphoribosyltransferase (EC 2.4.2.17)
KEGG: ATP phosphoribosyltransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00070.

BPHYT_RS19330 : glycine cleavage system P protein (EC 1.4.4.2)
Original description: glycine dehydrogenase (decarboxylating)
SEED: Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
KEGG: no annotation
Rationale: Specific phenotype: utilization of Gly-Glu

BPHYT_RS19340 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: serine dehydratase
SEED: L-serine dehydratase, beta subunit (EC 4.3.1.17) / L-serine dehydratase, alpha subunit (EC 4.3.1.17)
KEGG: L-serine dehydratase
Rationale: Specifically important for utilizing L-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

BPHYT_RS19730 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: dihydroxy-acid dehydratase
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct)

BPHYT_RS22245 : transporter for D-alanine, D-lactate, and pyruvate (MctP)
Original description: sodium:solute symporter
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: solute:Na+ symporter, SSS family
Rationale: Specific phenotype: utilization of 2-Deoxyadenosine 5-monophosphate, D-Alanine, Deoxyribonucleic acid, pyruvate. The DNA and dAMP phenotypes are not explained

BPHYT_RS22380 : Carnitine 3-dehydrogenase (EC 1.1.1.108)
Original description: 3-hydroxybutyryl-CoA dehydrogenase
SEED: 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157)
KEGG: 3-hydroxybutyryl-CoA dehydrogenase
Rationale: Specifically important for utilizing Carnitine Hydrochloride. Automated validation from mutant phenotype: the predicted function (CARNITINE-3-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS22715 : L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
Original description: cytochrome C biogenesis protein CcdA
SEED: L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43)
KEGG: dihydrodipicolinate synthase
Rationale: important for L-arabinose utilization and 70% similar to araD from A. brasilense (KDADA_AZOBR, PMID:16950779). SEED_correct

BPHYT_RS23155 : Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Original description: aminotransferase
SEED: Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
KEGG: putrescine aminotransferase
Rationale: Important for utilization of putrescine as C or N source. This is the only transamination reaction in putrescine catabolism via gamma-glutamylputrescine (formed by BPHYT_RS23160), gamma-glutamylpurescine oxidase (possibly redundant, BPHYT_RS23125 or BPHYT_RS22700, neither has a phenotype), gamma-glutamylbutyraldehyde dehydrogenase (BPHYT_RS23175), and gamma-glutamyl-gamma-aminobutyrate hydrolase (probably BPHYT_RS23165, but no fitness data). Another gene (BPHYT_RS22435) likely has this activity as well, and is important (but with a weaker phenotype) on putresine as a carbon source. However that gene is not important with putrescine as a nitrogen source, which suggests that this gene is providing the activity.

BPHYT_RS23160 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: glutamine synthetase
SEED: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride. The first step in putrescine catabolism via gamma-glutamyl-putrescine (SEED_correct)

BPHYT_RS24000 : L-histidine ABC transporter, substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: ABC-type amino acid transport/signal transduction systems, periplasmic component/domain
KEGG: octopine/nopaline transport system substrate-binding protein
Rationale: Specifically important for histidine utilization.

BPHYT_RS24005 : L-histidine ABC transporter, permease component 1
Original description: ABC transporter permease
SEED: ABC-type arginine transport system, permease component
KEGG: octopine/nopaline transport system permease protein
Rationale: Specifically important for histidine utilization.

BPHYT_RS24010 : L-histidine ABC transporter, permease component 2
Original description: ABC transporter permease
SEED: ABC-type arginine/histidine transport system, permease component
KEGG: octopine/nopaline transport system permease protein
Rationale: Specifically important for histidine utilization.

BPHYT_RS24015 : L-histidine ABC transporter, ATPase component
Original description: ATP-binding protein
SEED: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
KEGG: octopine/nopaline transport system ATP-binding protein
Rationale: No fitness data for the gene, but the other components of the putative transporter are upstream (BPHYT_RS24000:BPHYT_RS24010) and are specifically important for histidine utilization.

BPHYT_RS24155 : 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Original description: 5-dehydro-4-deoxyglucarate dehydratase
SEED: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
KEGG: 5-dehydro-4-deoxyglucarate dehydratase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

BPHYT_RS25805 : deoxyribose kinase (EC 2.7.1.15)
Original description: ribokinase
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important in carbon source 2-Deoxy-D-Ribose

BPHYT_RS25810 : acetaldehyde dehydrogenase (EC 1.2.1.3)
Original description: aldehyde dehydrogenase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Specifically important in carbon source 2-Deoxy-D-Ribose. Acetaldehyde is expected to be produced by the deoxyribose 5-phosphate aldolase.

BPHYT_RS26965 : L-lactate dehydrogenase, LldG subunit
Original description: hypothetical protein
SEED: Predicted L-lactate dehydrogenase, hypothetical protein subunit SO1518
KEGG: hypothetical protein
Rationale: Specifically important for utilization of L-lactate and D,L-lactate as well as L-rhamnose and L-fucose, which are catabolized via L-lactate. This gene has additional phenotypes which were not found for the other subunits and are not explained.

BPHYT_RS26970 : L-lactate dehydrogenase, LldF subunit
Original description: 4Fe-4S ferredoxin
SEED: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
KEGG: no annotation
Rationale: Specifically important for utilization of L-lactate and D,L-lactate as well as L-rhamnose and L-fucose, which are catabolized via L-lactate

BPHYT_RS26975 : L-lactate dehydrogenase, LldE subunit
Original description: Fe-S oxidoreductase
SEED: Predicted L-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE
KEGG: no annotation
Rationale: Specifically important for utilization of L-lactate and D,L-lactate as well as L-rhamnose and L-fucose, which are catabolized via L-lactate.

BPHYT_RS28235 : L-rhamnose-1-dehydrogenase ( EC 1.1.1.173)
Original description: short-chain dehydrogenase
SEED: L-rhamnose-1-dehydrogenase ( EC 1.1.1.173)
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Rhamnose monohydrate. This is the first step in its catabolism.

BPHYT_RS32825 : Xylose isomerase (EC 5.3.1.5)
Original description: xylose isomerase
SEED: Xylose isomerase (EC 5.3.1.5)
KEGG: xylose isomerase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

BPHYT_RS34210 : 2,4-diketo-3-deoxy-L-rhamnonate hydrolase (EC 3.7.1.-)
Original description: ureidoglycolate lyase
SEED: 2,4-diketo-3-deoxy-L-fuconate hydrolase
KEGG: no annotation
Rationale: Specifically important for: L-Fucose; L-Rhamnose monohydrate. The substrate is also known as 2,4-diketo-3-deoxy-L-fuconate, and is an intermediate in both L-rhamnose and L-fucose degradation (SEED_correct)

BPHYT_RS34215 : 2-keto-3-deoxy-L-fuconate 4-dehydrogenase FucDH
Original description: oxidoreductase
SEED: 2-keto-3-deoxy-L-fuconate dehydrogenase
KEGG: no annotation
Rationale: Specifically important for L-fucose utilization; this is part of the oxidative pathway.

BPHYT_RS34220 : L-fucono-1,5-lactonase
Original description: amidohydrolase
SEED: L-fuconolactone hydrolase
KEGG: no annotation
Rationale: Specifically important for utilizing L-fucose.

BPHYT_RS34225 : L-fucose dehydrogenase (EC 1.1.1.122)
Original description: aldo/keto reductase
SEED: L-fuco-beta-pyranose dehydrogenase (EC 1.1.1.122)
KEGG: no annotation
Rationale: Specifically important for: L-Rhamnose monohydrate; L-Fucose. This is the only good candidate for the L-fucose dehydrogenase, but there is another putative rhamnose dehydrogenase (BPHYT_RS28235) that also seems to be required for rhamnose utilization. So the phenotype of this gene (BPHYT_RS34225) on rhamnose could be due to polar effects.

BPHYT_RS34230 : L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90)
Original description: hydrolase
SEED: L-fuconate dehydratase (EC 4.2.1.68), type 2
KEGG: altronate hydrolase
Rationale: Specifically important for: L-Rhamnose monohydrate; L-Fucose. annotated by SEED for fuconate activity only

BPHYT_RS34235 : putative accessory domain for L-fuconate/L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90)
Original description: hydrolase
SEED: Altronate dehydratase (EC 4.2.1.7)
KEGG: altronate hydrolase
Rationale: Important for L-fucose and perhaps L-rhamnose catabolism, but seems to have milder phenotypes than the adjacent dehydratase _RS34230. CDD suggests (see cd11613) that it might be a dimerization domain for the dehydratase, but that wouldn't make sense for a separate ORF. Some homologs of this gene are fused to the dehydratase (which has a GD_AH_C domain).

BPHYT_RS34240 : ABC transporter for L-rhamnose/L-fucose/xylitol, permease component
Original description: ATPase
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: simple sugar transport system permease protein
Rationale: Specifically important for utilizing L-rhamnose, L-fucose, and xylitol.

BPHYT_RS34245 : ABC transporter for L-rhamnose/L-fucose/xylitol, ATPase component
Original description: multidrug ABC transporter ATP-binding protein
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: simple sugar transport system ATP-binding protein
Rationale: Specifically important for utilizing L-rhamnose, L-fucose, and xylitol.

BPHYT_RS34250 : ABC transporter for L-rhamnose/L-fucose/xylitol, substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Ribose ABC transporter, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
KEGG: simple sugar transport system substrate-binding protein
Rationale: Specifically important for utilizing L-rhamnose, L-fucose, and xylitol.

BPHYT_RS35445 : 2-aminobenzoate-CoA ligase [EC: 6.2.1.32]
Original description: 2-aminobenzoate-CoA ligase
SEED: Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases
KEGG: 2-aminobenzoate-CoA ligase
Rationale: Specifically important for: L-Tryptophan. B. phytofirmans catabolizes tryptophan via 2-aminobenzoyl-CoA (KEGG_correct)

Or download reannotations for Burkholderia phytofirmans PsJN or for all organisms as tab-delimited tables