Updated annotations for Pseudomonas fluorescens FW300-N2C3

122 genes with updated (or confirmed) annotations:

AO356_00010 : ABC transporter for D-Sorbitol, ATPase component
Original description: ABC transporter ATP-binding protein
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: no annotation
Rationale: Specific phenotype on D-Sorbitol.

AO356_00015 : ABC transporter for D-Sorbitol, permease component 1
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Sorbitol; D-Sorbitol. (no phenotype on mannitol)

AO356_00020 : ABC transporter for D-Sorbitol, permease component 2
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 1
KEGG: no annotation
Rationale: Specific phenotypes on D-Sorbitol; D-Sorbitol. (no phenotype on mannitol)

AO356_00025 : 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: no annotation
Rationale: Specific phenotype on D-Sorbitol.

AO356_00035 : 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.

AO356_00450 : D-glucosaminate dehydratase (EC 4.3.1.9)
Original description: amino acid deaminase
SEED: D-serine deaminase (EC 4.3.1.18)
KEGG: no annotation
Rationale: Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150)

AO356_00465 : ABC transporter for D-Glucosamine, putative ATPase component
Original description: ATP-binding protein
SEED: ABC-type polar amino acid transport system, ATPase component
KEGG: no annotation
Rationale: This is presumably the ATPase component of the operon, but lacks fitness data.

AO356_00470 : ABC transporter for D-Glucosamine, permease component 1
Original description: ABC transporter permease
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride. Detrimental on D-serine as N source

AO356_00475 : ABC transporter for D-Glucosamine, permease component 2
Original description: amino acid ABC transporter permease
SEED: amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride. Detrimental on D-serine as N source

AO356_00480 : ABC transporter for D-Glucosamine, periplasmic substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
KEGG: no annotation
Rationale: Specific phenotype on D-Glucosamine Hydrochloride.

AO356_00560 : 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

AO356_00940 : uridine/adenosine nucleosidase (EC 3.2.2.3; EC 3.2.2.7)
Original description: nucleoside hydrolase
SEED: Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1)
KEGG: no annotation
Rationale: Specifically important for: Uridine. Also important on adenosine. Annotated by SEED as acting on uridine and inosine, and the fitness data suggests that it might also act on inosine (subtle phenotype)

AO356_00950 : Ribokinase (EC 2.7.1.15)
Original description: ribokinase
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_00980 : DNA damage resistance protein
Original description: hypothetical protein
SEED: FIG00953874: hypothetical protein
KEGG: no annotation
Rationale: PFam PF07867.7 (DUF1654). Conserved (somewhat specific) phenotype for cisplatin resistance, in operon with endonuclease, and close homologs are regulated by LexA

AO356_01105 : putative hydrolase, required for lysine catabolism
Original description: hypothetical protein
SEED: FIG00960493: hypothetical protein
KEGG: no annotation
Rationale: PFam PF07063.9 (DUF1338). This gene is specifically important for utilizing lysine, and this phenotype is conserved. It might be the decarboxylating 2-oxoadipate hydrolase of the D-lysine oxidase pathway, which has not been linked to a gene, or the crotonyl-CoA hydratase in the glutaryl-CoA degradation pathway.

AO356_01580 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (RXN0-2301) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_01585 : 3-methylcrotonyl-CoA carboxylase, beta subunit (EC 6.4.1.4)
Original description: methylcrotonoyl-CoA carboxylase
SEED: Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
KEGG: 3-methylcrotonyl-CoA carboxylase beta subunit
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (6.4.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_01590 : Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
Original description: gamma-carboxygeranoyl-CoA hydratase
SEED: Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
KEGG: methylglutaconyl-CoA hydratase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (METHYLGLUTACONYL-COA-HYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_01595 : 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit (EC 6.4.1.4)
Original description: 3-methylcrotonyl-CoA carboxylase
SEED: Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
KEGG: 3-methylcrotonyl-CoA carboxylase alpha subunit
Rationale: Specifically important for utilizing L-Leucine.

AO356_01905 : L-aspartate transporter
Original description: amino acid:proton symporter
SEED: Proton/glutamate symport protein @ Sodium/glutamate symport protein
KEGG: no annotation
Rationale: Specifically important for aspartate utilization

AO356_02560 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: FAD-binding molybdopterin dehydrogenase
SEED: Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A (1.17.1.4)
KEGG: xanthine dehydrogenase small subunit
Rationale: Specifically important for utilizing Inosine. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_02565 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: xanthine dehydrogenase
SEED: Xanthine dehydrogenase, molybdenum binding subunit (EC 1.17.1.4)
KEGG: xanthine dehydrogenase large subunit
Rationale: Specifically important for utilizing Inosine. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_03600 : putative efflux pump, required for thallium (I) resistance
Original description: hypothetical protein
SEED: Protein of unknown function UPF0060
KEGG: hypothetical protein
Rationale: PFam PF02694.11 (UPF0060). conserved specific phenotype of UPF0060

AO356_03975 : Phenylalanine 4-monooxygenase (EC 1.14.16.1)
Original description: phenylalanine 4-monooxygenase
SEED: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
KEGG: phenylalanine-4-hydroxylase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.14.16.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_03985 : L-phenylalanine transaminase (EC 2.6.1.57)
Original description: aromatic amino acid aminotransferase
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aromatic-amino-acid transaminase
Rationale: Specifically important for utilizing L-Phenylalanine.

AO356_05200 : D-mannose isomerase (EC 5.3.1.7)
Original description: sugar isomerase
SEED: N-acylglucosamine 2-epimerase (EC 5.1.3.8)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose. Often annotated as N-acylglucosamine 2-epimerase, but this is also distantly related to the D-mannose isomerase Sama_0560. The putative fructokinase AO356_00035 is also important for consuming mannose, which would complete the pathway.

AO356_05495 : ABC transporter for L-Lysine, 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-Lysine. Note that this organism has a second ABC transporter that is also important for lysine utilization, which is not explained.

AO356_05500 : ABC transporter for L-Lysine, permease component 1
Original description: amino acid ABC transporter permease
SEED: Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is important for lysine utilization, which is not explained.

AO356_05505 : ABC transporter for L-Lysine, permease component 2
Original description: amino acid ABC transporter permease
SEED: Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_05515 : ABC transporter for L-Lysine, ATPase component
Original description: amino acid transporter
SEED: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
KEGG: histidine transport system ATP-binding protein
Rationale: Specific phenotype on L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_06970 : 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.

AO356_07325 : fructose phosphotransferase system, IIB/IIC components (EC 2.7.1.202)
Original description: PTS fructose transporter subunit IIBC
SEED: PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
KEGG: PTS system, fructose-specific IIB component ; PTS system, fructose-specific IIC component
Rationale: Specific phenotype: utilization of D-Fructose

AO356_07330 : 1-phosphofructokinase (EC 2.7.1.56)
Original description: 1-phosphofructokinase
SEED: 1-phosphofructokinase (EC 2.7.1.56)
KEGG: 1-phosphofructokinase
Rationale: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (1PFRUCTPHOSN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_07335 : fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
Original description: PTS fructose transporter subunit IIA
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specifically important for utilizing D-Fructose.

AO356_07550 : L-lactate and D-lactate permease (lctP family)
Original description: L-lactate permease
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: This gene is often annotated as a L-lactate transporter but has a specific phenotype on D-lactate as well. Although it is difficult to rule out polar effects on the lactate dehydrogenase genes downstream, this gene's phenotype on D-lactate is conserved and is observed on both strands, and no other D-lactate transporter was identified by the mutant fitness data. (There is a zinc ABC transporter with a specific defect on D-lactate, but it is very similar to znuABC of P. aeruginosa, i.e. AO356_11480 is 65% identical to PA5498, so it is unlikely to be a lactate transporter.) Furthermore, the annotation as lactate permease seems to be derived from E. coli glcA or yghK, which transports both isomers of lactate (PMID:11283302). (KEGG_correct)

AO356_08325 : predicted copper homeostasis protein
Original description: hypothetical protein
SEED: Putative multicopper oxidases
KEGG: no annotation
Rationale: PFam PF11162.4 (DUF2946). conserved cofit with TonB-dependent copper receptor (AO356_08330), and cofit with copper chaperone CopZ (AO356_08320)

AO356_08365 : Urease maturation and nickel insertion protein UreD
Original description: urease accessory protein UreD
SEED: Urease accessory protein UreD
KEGG: urease accessory protein
Rationale: Important for utilization of urea as N source. For the specific role of UreD, see PMID:23539618

AO356_08390 : Urease (EC 3.5.1.5)
Original description: urease subunit alpha
SEED: Urease alpha subunit (EC 3.5.1.5)
KEGG: urease subunit alpha
Rationale: Specifically important for utilizing Urea. Automated validation from mutant phenotype: the predicted function (3.5.1.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_09525 : 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.

AO356_09590 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate deformylase
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: formiminoglutamase
Rationale: Specifically important for: L-Histidine. KEGG suggests formimidoyl-L-glutamate as the substrate, while SEED suggests N-formylglutamate. This gene is cofit with iminohydrolase (which produces N-formylglutamate) which suggests that the SEED annotation is correct. (SEED_correct)

AO356_09595 : Imidazolonepropionase (EC 3.5.2.7)
Original description: imidazolonepropionase
SEED: Imidazolonepropionase (EC 3.5.2.7)
KEGG: imidazolonepropionase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (IMIDAZOLONEPROPIONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_09605 : 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.

AO356_09610 : ABC transporter for L-Histidine, ATPase component
Original description: hypothetical protein
SEED: Histidine ABC transporter, ATP-binding protein (TC 3.A.1)
KEGG: glycine betaine/proline transport system ATP-binding protein
Rationale: Specific phenotype on L-Histidine. This gene cluster also includes a permease of the nucleobase-cation-symport family (AO356_09625) that is important for histidine utilization but whose role is unclear. (SEED_correct)

AO356_09615 : ABC transporter for L-Histidine, permease component
Original description: ABC transporter permease
SEED: Histidine ABC transporter, permease protein (TC 3.A.1)
KEGG: glycine betaine/proline transport system permease protein
Rationale: Specific phenotypes on L-Histidine.

AO356_09620 : ABC transporter for L-Histidine, periplasmic substrate-binding component
Original description: histidine ABC transporter substrate-binding protein
SEED: Histidine ABC transporter, histidine-binding protein (TC 3.A.1)
KEGG: glycine betaine/proline transport system substrate-binding protein
Rationale: Specific phenotype on L-Histidine. This gene cluster also includes a permease of the nucleobase-cation-symport family (AO356_09625) that is important for histidine utilization but whose role is unclear

AO356_09630 : Urocanate hydratase (EC 4.2.1.49)
Original description: urocanate hydratase
SEED: Urocanate hydratase (EC 4.2.1.49)
KEGG: urocanate hydratase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (UROCANATE-HYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_09635 : histidine utilization regulatory protein hutD
Original description: hypothetical protein
SEED: Conserved hypothetical protein (perhaps related to histidine degradation)
KEGG: hypothetical protein
Rationale: Specifically important for: L-Histidine. Believed to prevent overexpression of the hut operon (not an enzyme) (PMC:1950622)

AO356_09645 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: N-formimino-L-glutamate deiminase
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_09800 : 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.

AO356_09895 : ABC transporter for L-Lysine, ATPase component
Original description: amino acid transporter
SEED: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
KEGG: no annotation
Rationale: Has weaker phenotypes on lysine than the other components, but is in an apparent operon and has the correct domain. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_09900 : ABC transporter for L-Lysine, periplasmic substrate-binding component
Original description: amino acid ABC transporter
SEED: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
KEGG: no annotation
Rationale: Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_09905 : ABC transporter for L-Lysine, permease component 1
Original description: ABC transporter permease
SEED: Arginine ABC transporter, permease protein ArtQ
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on L-Lysine; L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_09910 : ABC transporter for L-Lysine, permease component 2
Original description: ABC transporter permease
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotype on L-Lysine. Note that this organism has a second ABC transporter operon that is also important for lysine utilization, which is not explained.

AO356_10030 : Agmatine deiminase (EC 3.5.3.12)
Original description: agmatine deiminase
SEED: Agmatine deiminase (EC 3.5.3.12)
KEGG: agmatine deiminase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (AGMATINE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_10845 : succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13)
Original description: CoA-transferase
SEED: L-carnitine dehydratase/bile acid-inducible protein F
KEGG: no annotation
Rationale: Specifically important for: L-Lysine. Glutaryl-CoA is an intermediate in lysine catabolism and this reaction would be a way to form it from glutarate before oxidation by AO356_10850. Other reactions in this pathway were also found but the only candidate for glutarate semialdehyde dehydrogenase, AO356_26740, had little phenotype.) Note that this EC number is primarily associated with forming (S)-3-hydroxy-methylglutaryl-CoA.

AO356_11100 : L-asparaginase (EC 3.5.1.1)
Original description: 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.

AO356_12580 : gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.99); 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
Original description: aldehyde dehydrogenase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: no annotation
Rationale: Specifically important for utilization of putrescine (as part of the gamma-glutamyl-putrescine pathway) and L-arginine. Similar to kauB = PP_5278 = Q88CA3, a 4-guanidinobutyraldehyde dehydrogenase from P. putida that is involved in arginine degradation.

AO356_13135 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: gamma-glutamylputrescine synthetase
SEED: no annotation
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride. This is the first step in putrescine catabolism

AO356_13140 : Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
Original description: gamma-glutamyl-gamma-aminobutyrate hydrolase
SEED: Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
KEGG: putative glutamine amidotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. this is part of the gamma-glutamyl-putrescine pathway for putrescine catabolism (SEED_correct)

AO356_13150 : 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: Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC3147493)

AO356_13160 : putrescine ABC transporter, substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Putrescine ABC transporter putrescine-binding protein PotF (TC 3.A.1.11.2)
KEGG: putrescine transport system substrate-binding protein
Rationale: Specific phenotype: utilization of Putrescine Dihydrochloride. 68% identical to a spermidine SBP (P. aeruginosa spuE), so it may well transport spermidine as well

AO356_13805 : ABC transporter for Carnitine, ATPase component
Original description: choline ABC transporter ATP-binding protein
SEED: L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system ATP-binding protein
Rationale: Specific phenotype on Carnitine Hydrochloride. Likely to be a choline or glycine betaine transporter as well (with AO356_13855 as the SBP)

AO356_13810 : ABC transporter for Carnitine, permease component
Original description: choline ABC transporter permease subunit
SEED: L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system permease protein
Rationale: Specific phenotypes on Carnitine Hydrochloride; Carnitine Hydrochloride.

AO356_13815 : ABC transporter for Carnitine, periplasmic substrate-binding component 1
Original description: glycine/betaine ABC transporter substrate-binding protein
SEED: L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system substrate-binding protein
Rationale: Specific phenotype on Carnitine Hydrochloride. This protein is similar to CaiX of P. syringae or P. aeruginosa (Psyr_2916 and PA5388) which has been shown to be a L-carnitine SBP (see PMID:19919675). Another gene in the cluster, AO356_13855, is also a SBP and is specifically important for L-carnitine utilization. AO356_13855 is similar to CbcX of P. aeruginosa or P. syringae (PA5378 or Psyr_4709) which is specific for choline or glycine betaine (ibid). Nevertheless, insertions in _13855 have a specific defect for carnitine utilization. It is possible that these insertions are polar on the beta-cleavage enzyme (_13850) which is required for carnitine catabolism. However insertions in _13855 in either orientation have a strong phenotype.

AO356_13840 : L-carnitine 3-dehydrogenase, thioesterase-like subunit CdhB (EC 1.1.1.108)
Original description: 4-hydroxybenzoyl-CoA thioesterase
SEED: no annotation
KEGG: acyl-CoA thioester hydrolase
Rationale: Specifically important for: Carnitine Hydrochloride. This is CdhB (PA5385), a subunit of L-carnitine 3-dehydrogenase. See PMC2857723.

AO356_13845 : Carnitine 3-dehydrogenase (EC 1.1.1.108)
Original description: 3-hydroxybutyryl-CoA dehydrogenase
SEED: Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
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.

AO356_14110 : Putative D-serine transporter
Original description: chloramphenical resistance permease RarD
SEED: Protein rarD
KEGG: chloramphenicol-sensitive protein RarD
Rationale: Specific phenotype: utilization of D-Serine. This is a conserved phenotype, although AO356_05055 (DsdX) is also involved in D-serine uptake. 31% identical to PA14_1916, which is thought to be a citrate transporter based on genetic evidence (PMC9765132). Belongs to the rarD family (often annotated as chloramphenicol resistance, but the molecular function of E. coli rarD is not known)

AO356_14165 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG: no annotation
Rationale: Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct)

AO356_14190 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG: no annotation
Rationale: Specifically important for: Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct)

AO356_14225 : 5-aminopentanamidase (EC 3.5.1.30)
Original description: carbon-nitrogen hydrolase
SEED: 5-aminopentanamidase (EC 3.5.1.30)
KEGG: no annotation
Rationale: Specifically important for: L-Lysine. this is an early step in the oxidation of lysine (SEED_correct)

AO356_14230 : lysine 2-monooxygenase (EC 1.13.12.2)
Original description: amine oxidase
SEED: Lysine 2-monooxygenase (EC 1.13.12.2)
KEGG: tryptophan 2-monooxygenase
Rationale: Specifically important for: L-Lysine. this is the first step in the oxidation of lysine (SEED_correct)

AO356_14305 : ycgB component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: SpoVR family protein
SEED: FIG004684: SpoVR-like protein
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

AO356_14310 : yeaH component of nitrogen-related signalling system yeaH (of yeaGH-ycgB)
Original description: hypothetical protein
SEED: FIG002076: hypothetical protein
KEGG: hypothetical protein
Rationale: PFam PF04285.8 (DUF444). conserved cofitness; yeaG is a protein kinase

AO356_14315 : yeaG component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: serine/threonine protein kinase
SEED: Serine protein kinase (prkA protein), P-loop containing
KEGG: serine protein kinase
Rationale: conserved cofitness; yeaG is a protein kinase

AO356_16835 : Maleylacetoacetate isomerase (EC 5.2.1.2)
Original description: maleylacetoacetate isomerase
SEED: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
KEGG: maleylacetoacetate isomerase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (5.2.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_17240 : required for acetate efflux, together with NodT, MFP and FUSC proteins (AO356_17230, AO356_17245, and AO356_17235)
Original description: Na+-dependent transporter
SEED: Na+-dependent transporters of the SNF family
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). A conserved cofit operon. This operon and orthologous operons are important on acetate as a carbon source and cholin acetate as a stress, which suggests that acetate is a substrate.

AO356_17535 : N-acetylglucosamine-specific PTS system, IIBC components (nagE)
Original description: PTS N-acetyl-D-glucosamine transporter
SEED: PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
KEGG: PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component
Rationale: Specific phenotype on NAG as a carbon source. Not sure why SEED think s this includes the IIA component. (KEGG_correct)

AO356_17540 : N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF)
Original description: PTS N-acetyl-D-glucosamine transporter
SEED: no annotation
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specific phenotype on NAG as a carbon source. Not sure why SEED think s this includes the IIA component. (KEGG_correct)

AO356_17550 : 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.

AO356_17670 : L-alanine and D-alanine permease
Original description: D-alanine/D-serine/glycine permease
SEED: D-serine/D-alanine/glycine transporter
KEGG: amino acid transporter, AAT family
Rationale: Specific phenotype on D-alanine and L-alanine

AO356_17790 : alpha-ketoglutarate permease (MHS family)
Original description: MFS transporter
SEED: Dicarboxylate MFS transporter
KEGG: MFS transporter, MHS family, alpha-ketoglutarate permease
Rationale: Specific phenotype on a-ketoglutarate. Not important for the utilization of other dicarboxylates (succinate or malate). 83% identical to PA5530, which is reported to transport a-ketoglutarate and also glutarate (PMC4097582). KEGG_correct

AO356_18450 : outer membrane component of uptake system, probably for ferrous iron
Original description: hypothetical protein
SEED: no annotation
KEGG: hypothetical protein
Rationale: PFam PF07433.7 (DUF1513). In a conserved cofit operon with an efeO-like gene (AO356_18455) and an efeB-like gene (AO356_18460). Another efeO-like gene (AO356_05015) is cofit but not nearby.

AO356_18530 : L-tyrosine transporter
Original description: aromatic amino acid transporter
SEED: Aromatic amino acid transport protein AroP
KEGG: amino acid transporter, AAT family
Rationale: Specific phenotype with tyrosine as the nitrogen source. Not important if phenylalanine is the nitrogen source.

AO356_18695 : Acetyl-coenzyme A synthetase (EC 6.2.1.1)
Original description: acetyl-CoA synthetase
SEED: Acetyl-coenzyme A synthetase (EC 6.2.1.1)
KEGG: acetyl-CoA synthetase
Rationale: Specifically important for utilizing Ethanol. Automated validation from mutant phenotype: the predicted function (ACETATE--COA-LIGASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_18700 : L-Arginine ABC transporter, periplasmic substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
KEGG: no annotation
Rationale: Specific phenotype on L-Arginine. (SEED_correct)

AO356_18705 : L-Arginine ABC transporter, permease component 2
Original description: ABC transporter
SEED: Arginine/ornithine ABC transporter, permease protein AotQ
KEGG: arginine/ornithine transport system permease protein
Rationale: Specific phenotype on L-Arginine. (SEED_correct)

AO356_18710 : L-Arginine ABC transporter, permease component 1
Original description: amino acid ABC transporter permease
SEED: Arginine/ornithine ABC transporter, permease protein AotM
KEGG: no annotation
Rationale: Specific phenotypes on L-Arginine; L-Arginine. (SEED_correct)

AO356_18715 : L-Arginine ABC transporter, ATPase component
Original description: amino acid transporter
SEED: Arginine/ornithine ABC transporter, ATP-binding protein AotP
KEGG: no annotation
Rationale: Important for utiliizing L-arginine. Detrimental on L-lysine which might indicate that it leaks lysine. (SEED_correct)

AO356_18980 : sodium:C4-dicarboxylate symporter (dctA)
Original description: C4-dicarboxylate transporter
SEED: no annotation
KEGG: aerobic C4-dicarboxylate transport protein
Rationale: Important for utilization of malate, succinate, or fumarate (all C4 dicarboxylates) as carbon sources. 81% identical to PA1183 from P. aeruginosa (PMC3165536), which is also involved in growth with these substrates. KEGG_correct

AO356_19460 : allantoinase (EC 3.5.2.5)
Original description: allantoinase
SEED: Uricase (urate oxidase) (EC 1.7.3.3)
KEGG: no annotation
Rationale: Specifically important for: Inosine. This protein is similar to hpxB from Klebsiella, which is allantoinase, an step in the degradation of purines such as adenine or hypoxanthine (inosine is the nucleoside of hypoxanthine). See PMID:19060149

AO356_19465 : 5-hydroxyisourate hydrolase [EC: 3.5.2.17]
Original description: 5-hydroxyisourate hydrolase
SEED: no annotation
KEGG: 5-hydroxyisourate hydrolase
Rationale: Specifically important for: Inosine. 5-hydroxyisourate is an intermediate in purine degradation (KEGG_correct)

AO356_20235 : L-arabinolactonase (EC 3.1.1.15) / D-galactonolactonase (EC 3.1.1.25)
Original description: gluconolaconase
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Specifically important for: L-Arabinose; D-Galactose. The SEED prediction explains the phenotype on L-arabinose but not on D-galactose. L-arabinose and D-galactose are chemically similar and some dehydrogenases act on both substrates, so it is not surprising that a lactonase would hydrolase both of their products. The dehydrogenase is probably AO356_20240. (SEED_correct)

AO356_20240 : L-arabinose 1-dehydrogenase (EC 1.1.1.46)
Original description: short-chain dehydrogenase
SEED: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
KEGG: no annotation
Rationale: This is specifically important for L-arabinose utilization. Some closely related proteins in other Pseudomonas are important for D-galactose utilization as well, so this is probably also a D-galactose 1-dehydrogenase. However mutants in this gene had little phenotype in D-galactose (two replicates). No other dehydrogenase was identified as specifically important on D-galactose.

AO356_20280 : 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: Specific phenotype: utilization of D-Galactose

AO356_21495 : gamma-glutamylputrescine oxidase (EC 1.4.3.-)
Original description: gamma-glutamylputrescine oxidoreductase
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: gamma-glutamylputrescine oxidase
Rationale: Specifically important for: Putrescine Dihydrochloride. part of the pathway for oxidizing putrescine via gamma-glutamyl-putrescine (KEGG_correct)

AO356_21640 : acetyl-CoA C-acetyltransferase [EC: 2.3.1.9]
Original description: acetyl-CoA acetyltransferase
SEED: no annotation
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for: L-Lysine; Carnitine Hydrochloride. acetyl-CoA acetyltransferase is required for the breakdown of acetoacetyl-CoA, which is an intermediate in lysine degradation (via glutaryl-CoA) and in carnitine degradation (from the beta cleavage enzyme, see PMID: 24240508) (KEGG_correct)

AO356_21690 : Glutaminase (EC 3.5.1.2)
Original description: glutaminase A
SEED: Glutaminase (EC 3.5.1.2)
KEGG: glutaminase
Rationale: Specifically important for utilizing L-Glutamine. Automated validation from mutant phenotype: the predicted function (GLUTAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_22845 : 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Original description: 4-hydroxyphenylpyruvate dioxygenase
SEED: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
KEGG: 4-hydroxyphenylpyruvate dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.27) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_22970 : 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, BRANCHED-CHAINAMINOTRANSFERLEU-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_22975 : Dihydrolipoyl dehydrogenase (EC 1.8.1.4)
Original description: dihydrolipoamide dehydrogenase
SEED: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
KEGG: dihydrolipoamide dehydrogenase
Rationale: Specifically important for utilizing L-Isoleucine; L-Leucine. Automated validation from mutant phenotype: the predicted function (1.8.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_22985 : branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit (EC 1.2.4.4)
Original description: 2-oxoisovalerate dehydrogenase
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, beta subunit
Rationale: Specifically important for utilizing L-Isoleucine.

AO356_22990 : branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit (EC 1.2.4.4)
Original description: 2-oxoisovalerate dehydrogenase
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, alpha subunit
Rationale: Specifically important for utilizing L-Isoleucine.

AO356_23085 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydropyrimidine dehydrogenase
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: no annotation
Rationale: Specifically important for utilizing Cytosine. Automated validation from mutant phenotype: the predicted function (1.3.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_23095 : 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.

AO356_23105 : Beta-ureidopropionase (EC 3.5.1.6)
Original description: allantoate amidohydrolase
SEED: Beta-ureidopropionase (EC 3.5.1.6)
KEGG: no annotation
Rationale: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (3.5.1.6) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_23160 : 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.

AO356_23165 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: myo-inosose-2 dehydratase
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.

AO356_23170 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: 5-deoxy-glucuronate isomerase
SEED: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
KEGG: 5-deoxy-glucuronate isomerase
Rationale: Specifically important for utilizing m-Inositol.

AO356_23175 : malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18)
Original description: methylmalonate-semialdehyde dehydrogenase
SEED: Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for: m-Inositol. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism

AO356_23185 : 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD (EC 3.7.1.22)
Original description: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
SEED: Epi-inositol hydrolase (EC 3.7.1.-)
KEGG: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase
Rationale: Specifically important for utilizing m-Inositol.

AO356_23190 : Inositol 2-dehydrogenase (EC 1.1.1.18)
Original description: inositol 2-dehydrogenase
SEED: Myo-inositol 2-dehydrogenase (EC 1.1.1.18)
KEGG: myo-inositol 2-dehydrogenase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (1.1.1.18) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO356_24205 : Alpha,alpha-trehalase (EC 3.2.1.28)
Original description: trehalase
SEED: Trehalase (EC 3.2.1.28); Periplasmic trehalase precursor (EC 3.2.1.28)
KEGG: alpha,alpha-trehalase
Rationale: Specifically important for utilizing D-Trehalose dihydrate. Automated validation from mutant phenotype: the predicted function (TREHALA-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_24585 : 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)

AO356_24595 : 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43)
Original description: FAH family protein
SEED: SUGAR TRANSPORTER
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.)

AO356_26355 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: acyl-CoA dehydrogenase
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Important for isoleucine utilization. 2-methylbutaonyl-CoA is an intermediate in the standard pathway and no other gene for the methylbutanoyl-CoA dehydrogenase was apparent in the fitness data.

AO356_26995 : DNA damage response nuclease
Original description: nuclease
SEED: Hypothetical protein, restriction endonuclease-like VRR-NUC domain
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Contains a VRR-NUC domain that is predicted to have nuclease activity.

AO356_27695 : Xylulose kinase (EC 2.7.1.17)
Original description: xylulose kinase
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLULOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO356_28020 : ethanol oxidation regulatory protein ercA
Original description: alcohol dehydrogenase
SEED: Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
KEGG: no annotation
Rationale: Specifically important for: Ethanol. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. AO356_28055 is probably the main ethanol dehydrogenase. (not an enzyme)

AO356_28500 : 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.

AO356_28540 : D-mannose transporter
Original description: hexuronate transporter
SEED: Hexuronate transporter
KEGG: no annotation
Rationale: Specific phenotype on D-mannose as the carbon source. No other transporter was apparent in the fitness data.

AO356_28590 : sucrose alpha-glucosidase (EC 3.2.1.48)
Original description: glycosyl hydrolase family 32
SEED: Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)
KEGG: beta-fructofuranosidase
Rationale: Specifically important for sucrose utilization; sucrose is probably taken up by thuEFGK-like AO356_28570:AO356_28585

AO356_28760 : Xylonate dehydratase (EC 4.2.1.82)
Original description: dihydroxy-acid dehydratase
SEED: Xylonate dehydratase (EC 4.2.1.82)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Pseudomonas fluorescens FW300-N2C3 or for all organisms as tab-delimited tables