Updated annotations for Pseudomonas fluorescens FW300-N2E3

115 genes with updated (or confirmed) annotations:

AO353_00805 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase
SEED: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) large subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_00810 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase
SEED: Nitrite reductase [NAD(P)H] small subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) small subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_00815 : Nitrate reductase (EC 1.7.99.4)
Original description: nitrate reductase
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: periplasmic nitrate reductase NapA
Rationale: Specifically important for utilizing Sodium nitrate and Sodium nitrite. Automated validation from mutant phenotype: the predicted function (1.7.99.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_03040 : ABC transporter for L-Arginine and L-Citrulline, ATPase component
Original description: amino acid transporter
SEED: Arginine/ornithine ABC transporter, ATP-binding protein AotP
KEGG: no annotation
Rationale: Specific phenotype on L-Arginine. Also important on citrulline.

AO353_03045 : ABC transporter for L-Arginine and L-Citrulline, permease component 1
Original description: amino acid ABC transporter permease
SEED: Arginine/ornithine ABC transporter, permease protein AotM
KEGG: arginine/ornithine transport system permease protein
Rationale: Specific phenotypes on L-Arginine; L-Arginine. also important for citrulline

AO353_03050 : ABC transporter for L-Arginine and L-Citrulline, permease component 2
Original description: ABC transporter
SEED: Arginine/ornithine ABC transporter, permease protein AotQ
KEGG: no annotation
Rationale: Specific phenotypes on L-Arginine; L-Arginine; L-Arginine. possibly citrulline as well

AO353_03055 : ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component
Original description: ABC transporter substrate-binding protein
SEED: Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
KEGG: arginine/ornithine transport system substrate-binding protein
Rationale: Specific phenotype on L-Arginine; L-Citrulline.

AO353_03060 : 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.

AO353_03400 : 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 AO353_25910 is also important for mannose utilization, which would complete the pathway.

AO353_03500 : Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2)
Original description: glycine dehydrogenase
SEED: Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
KEGG: glycine dehydrogenase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (1.4.4.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_03810 : Alpha-ketoglutarate permease, MFS superfamily
Original description: MFS transporter
SEED: Dicarboxylate MFS transporter
KEGG: MFS transporter, MHS family, alpha-ketoglutarate permease
Rationale: Specific phenotype on a-ketoglutarate. 86% identical to the a-ketoglutarate transporter in P. aeruginosa (PA5530, see PMCID: PMC4097582) and 56% similar to E. coli kgtP. (KEGG_correct)

AO353_04450 : 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.

AO353_04455 : 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-6-phosphate isomerase
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.

AO353_04460 : N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF)
Original description: PTS N-acetyl-D-glucosamine transporter
SEED: PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: phosphocarrier protein
Rationale: Specifically important for NAG utilization. (SEED_correct)

AO353_04465 : 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: Specifically important for NAG utilization. SEED incorrectly implies that this contains the IIA component as well. (KEGG_correct)

AO353_04830 : required for acetate efflux, together with NodT, MFP and FUSC proteins (AO353_04840, AO353_04825, and AO353_04835)
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.

AO353_05115 : 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.

AO353_05485 : Fructose-specific PTS system, I, HPr, and IIA components
Original description: PTS fructose transporter subunit IIA
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: phosphocarrier protein
Rationale: Specifically important for fructose utilization. The enzyme II B/C components of this PTS system are in AO353_05475 which is cofit and is correctly annotated. AO353_05485 is 73% identical to PA3562, which is also part of a fructose-specific system (PMC:PMC2542419)

AO353_05930 : L-tryptophan transporter
Original description: amino acid permease
SEED: Phenylalanine-specific permease
KEGG: no annotation
Rationale: Specifically important for utilization of tryptophan as a nitrogen source.

AO353_05935 : 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.

AO353_05950 : Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1)
Original description: anthranilate 1,2-dioxygenase large subunit
SEED: Benzoate 1,2-dioxygenase alpha subunit (EC 1.14.12.10)
KEGG: anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunit
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (1.14.12.1-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_05955 : Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1)
Original description: benzoate 1,2-dioxygenase small subunit
SEED: Benzoate 1,2-dioxygenase beta subunit (EC 1.14.12.10)
KEGG: anthranilate 1,2-dioxygenase (deaminating, decarboxylating) small subunit
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (1.14.12.1-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_05970 : Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
Original description: tryptophan 2,3-dioxygenase
SEED: Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
KEGG: tryptophan 2,3-dioxygenase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (RXN-8665) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_05975 : 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.

AO353_05985 : 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Original description: 3-hydroxyisobutyrate dehydrogenase
SEED: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
KEGG: 3-hydroxyisobutyrate dehydrogenase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (3-HYDROXYISOBUTYRATE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_05990 : Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Original description: methylmalonate-semialdehyde dehydrogenase
SEED: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (RXN-11213) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_06780 : DNA repair helicase Lhr
Original description: ATP-dependent DNA helicase
SEED: Lhr-like helicases
KEGG: no annotation
Rationale: # Specifically important in stress Cisplatin. Similar to the full length of Lhr from Mycobacterium smegmatis, which is a helicase that is suspected to be involved in DNA repair (see PMC3656269) (SEED_correct)

AO353_07335 : 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

AO353_07340 : yeaH component of nitrogen-related signalling system (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

AO353_07345 : 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

AO353_07420 : 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 utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (LYSINE-2-MONOOXYGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_07425 : 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 utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_07485 : 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: Sodium butyrate; Tween 20. The phenotype on Tween 20 suggests that it has activity on longer substrates as well as on butyryl-CoA (SEED_correct)

AO353_07660 : sarcosine oxidase (5,10-methylenetetrahydrofolate-forming), beta subunit (EC 1.5.3.24)
Original description: sarcosine oxidase subunit beta
SEED: Sarcosine oxidase beta subunit (EC 1.5.3.1)
KEGG: sarcosine oxidase, subunit beta
Rationale: Specific phenotype: utilization of Carnitine. Cartnitine is broken down via glycine betaine (trimethyl glycine) and sacrosine (N-methylglycine)

AO353_07665 : Serine hydroxymethyltransferase (EC 2.1.2.1)
Original description: serine hydroxymethyltransferase
SEED: Serine hydroxymethyltransferase (EC 2.1.2.1)
KEGG: glycine hydroxymethyltransferase
Rationale: Specific phenotype: utilization of Carnitine. Carnitine is broken down via glycine.

AO353_07670 : L-threonine aldolase (EC 4.1.2.5)
Original description: threonine aldolase
SEED: Low-specificity L-threonine aldolase (EC 4.1.2.48)
KEGG: threonine aldolase
Rationale: Specifically important for utilizing L-Threonine. Automated validation from mutant phenotype: the predicted function (4.1.2.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_07705 : DgcB Dimethylglycine demethylase subunit B (EC 1.5.3.-)
Original description: (Fe-S)-binding protein
SEED: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
KEGG: no annotation
Rationale: Specifically important for: Carnitine Hydrochloride. Dimethylglycine is an intermediate in L-carnitine metabolism; this gene is similar to PA5399 or dgcB (PMCID: PMC2293255)

AO353_07710 : DgcA Dimethylglycine demethylase subunit A
Original description: N-methylproline demethylase
SEED: DgcA Dimethylglycine demethylase subunit A
KEGG:
Rationale: Specifically important for: Carnitine Hydrochloride. Carnitine is catabolized via glycine betaine (trimethylglycine) and then demethylated twice to sarcosine (N-methylglycine) (PMCID: PMC2293255) (SEED_correct)

AO353_07740 : ABC transporter for Carnitine, substrate-binding component
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 phenotypes on Carnitine Hydrochloride. Similar to CaiX (see PMID:19919675). This transporter may also have a second SBP, AO353_07780, similar to CbcX, which is reported to be an alternate SBP for choline or glycine utilization (ibid). However _07780 is also important for carnitine utilization - it might be an additional necessary subunit of this transporter.

AO353_07750 : carnitine 3-dehydrogenase [EC:1.1.1.108]
Original description: 3-hydroxybutyryl-CoA dehydrogenase
SEED: no annotation
KEGG: 3-hydroxybutyryl-CoA dehydrogenase
Rationale: Specifically important for: Carnitine Hydrochloride. Not sure why SEED missed this: some very similar proteins are annotated correctly. pba:PSEBR_a5237 has been updated in KEGG and is now annotated as the carnitine dehydrogenase. (KEGG_correct)

AO353_07755 : betainyl-CoA thiolase (EC 3.1.2.-)
Original description: 4-hydroxybenzoyl-CoA thioesterase
SEED: no annotation
KEGG: acyl-CoA thioester hydrolase
Rationale: Specifically important for: Carnitine Hydrochloride. This is part of the degradation of carnitine (K. Bastard et al, Nature Chem Biol. 2014). Since KEGG had this EC number you could argue that it is correct, but it made a very vague prediction.

AO353_07780 : Carnitine ABC transporter, substrate-binding component CaiX
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: utilization of Carnitine. Similar to PA5388. See PMID:19919675

AO353_07785 : 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. no phenotype in choline stress; annotated as glycine betaine or proline transport. Another issue is that carnitine might be oxidized to choline which is then excreted (MetaCyc Pathway: L-carnitine degradation II) but this would not support growth with carnitine as either C or N source (no C or N extracted). Note that both carnitine and choline are catabolized via glycine betaine and this is clustered with glycine betaine degradation genes. This ABC transporter might also transport choline or glycine betaine with a different SBP (AO353_07780).

AO353_07790 : 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 phenotypes on Carnitine Hydrochloride. Note that both carnitine and choline are catabolized via glycine betaine and this is clustered with glycine betaine degradation genes. This ABC transporter might also transport choline or glycine betaine with a different SBP (AO353_07780).

AO353_08585 : 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, PMC:3147493)

AO353_08595 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: gamma-glutamylputrescine synthetase
SEED: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
KEGG: glutamine synthetase
Rationale: Specifically important for: Potassium acetate; L-Arginine; Putrescine Dihydrochloride; L-Citrulline. This is the first step in putrescine degradation and is important for the usage of putrescine as either C or N source. The phenotypes on citrulline and arginine might indicate a side pathway where they are converted to putrescine via ornithine decarboxylase (SEED_correct)

AO353_09960 : 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.

AO353_11505 : succinate-semialdehyde dehydrogenase (EC 1.2.1.16)
Original description: succinate-semialdehyde dehydrogenase
SEED: no annotation
KEGG: glutarate semialdehyde dehydrogenase
Rationale: Specifically important for: L-Citrulline; L-Arginine; Putrescine Dihydrochloride. succinate semialdehyde is an intermediate in putrescine catabolism. KEGG has updated its annotation (K00135, see pman:OU5_3276) to include both succinate semialdehyde and glutarate semialdehyde as substrates. The other phenotypes are milder and might indicate a side pathway of conversion of citrulline and arginine to putrescine via ornithine decarboxylase. (KEGG_correct)

AO353_11510 : 5-aminovalerate transaminase (EC 2.6.1.48)
Original description: 4-aminobutyrate aminotransferase
SEED: 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
KEGG: 5-aminovalerate aminotransferase
Rationale: Specifically important for utilizing L-Lysine. This confirms that it is involved in L-lysine catabolism via 5-aminovalerate. A milder phenotype on putrescine suggests that it is also likely to be a 4-aminobutyrate transaminase.

AO353_11740 : DNA damage response protein (yhgF like)
Original description: transcription accessory protein
SEED: Transcription accessory protein (S1 RNA-binding domain)
KEGG: uncharacterized protein
Rationale: Conserved and mostly specific phenotype: important for resisting cisplatin. Also important for resisting ionizing radiation in E. coli

AO353_12085 : 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.

AO353_12235 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: N-formimino-L-glutamate deiminase
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: formimidoylglutamate deiminase
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.

AO353_12250 : 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.

AO353_12275 : histidine permease
Original description: proline-specific permease
SEED: Histidine transport protein (permease)
KEGG: amino acid transporter, AAT family
Rationale: Specific phenotype on histidine. 86% identical to PFLU0368, which is required for histidine utilization (PMCID: PMC1950622). SEED_correct

AO353_12280 : 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.

AO353_12285 : 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)

AO353_12360 : 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.

AO353_12420 : predicted FeS cluster maintenance protein
Original description: 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
SEED: FIG028220: hypothetical protein co-occurring with HEAT repeat protein
KEGG: no annotation
Rationale: PFam PF06155.8 (DUF971). conserved cofitness with yggX (AO353_12045), nfuA (AO353_21625)

AO353_12810 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: transcriptional regulator
SEED: Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
KEGG: proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.2.1.88, 1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_13110 : putative transporter, required for glycine utilization
Original description: hypothetical protein
SEED: putative membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

AO353_13495 : 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.

AO353_13515 : Urease (EC 3.5.1.5)
Original description: urease subunit gamma
SEED: Urease gamma subunit (EC 3.5.1.5)
KEGG: urease subunit gamma
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.

AO353_13585 : predicted copper homeostasis protein
Original description: hypothetical protein
SEED: FIG00955840: hypothetical protein
KEGG: no annotation
Rationale: PFam PF11162.4 (DUF2946). conserved cofit with TonB-dependent copper receptor (AO353_13570) and perhaps with copper chaperone CopZ (AO353_13580)

AO353_15500 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: serine dehydratase
SEED: L-serine dehydratase (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.

AO353_15550 : Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Original description: homogentisate 1,2-dioxygenase
SEED: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
KEGG: homogentisate 1,2-dioxygenase
Rationale: Specifically important for utilizing L-tyrosine disodium salt. Automated validation from mutant phenotype: the predicted function (HOMOGENTISATE-12-DIOXYGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_15560 : 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.

AO353_15980 : trehalose PTS system, EII-BC components TreB
Original description: trehalose permease IIC protein
SEED: PTS system, trehalose-specific IIB component (EC 2.7.1.69) / PTS system, trehalose-specific IIC component (EC 2.7.1.69)
KEGG: PTS system, trehalose-specific IIB component ; PTS system, trehalose-specific IIC component
Rationale: Specifically important for trehalose utilization.

AO353_15985 : Alpha,alpha-phosphotrehalase (EC 3.2.1.93)
Original description: trehalose-6-phosphate hydrolase
SEED: Trehalose-6-phosphate hydrolase (EC 3.2.1.93)
KEGG: trehalose-6-phosphate hydrolase
Rationale: Specifically important for utilizing D-Trehalose dihydrate. Automated validation from mutant phenotype: the predicted function (3.2.1.93) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_15995 : trehalose-specific PTS system, I, HPr, and IIA components
Original description: PTS mannose transporter subunit IIC
SEED: PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / 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: Specific phenotype on trehalose. The IIB/IIC components are provided by AO353_15980. 45% similar to a NAG PTS system (PA3760, PMC:PMC2542419)

AO353_16120 : D-alanine and L-alanine transporter
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 as the carbon source. Also important for utilizing L-alanine as a carbon source. Both of these phenotypes are conserved. For D-alanine as a nitrogen source, there is a mild phenotype, and it may be partly redundant with another amino acid transporter (AO353_04615:04600). Sometimes annotated as a glycine transporter, but neither it nor its orthologs are important on glycine.

AO353_16275 : ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component
Original description: amino acid ABC transporter ATP-binding protein
SEED: Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system ATP-binding protein
Rationale: # Reannotated based on fitness data for other genes in the operon. We have no fitness data for this gene.

AO353_16280 : ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1
Original description: amino acid ABC transporter permease
SEED: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: # Specifically important in carbon source L-Aspartic Acid; pH ; carbon source L-Asparagine; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine

AO353_16285 : ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2
Original description: amino acid ABC transporter permease
SEED: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: # Specifically important in carbon source L-Aspartic Acid; pH ; carbon source L-Asparagine; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine

AO353_16290 : ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component
Original description: ABC transporter
SEED: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system substrate-binding protein
Rationale: # Specifically important in carbon source L-Aspartic Acid; carbon source L-Asparagine; pH ; carbon source L-Glutamic acid monopotassium salt monohydrate; carbon source L-Glutamine

AO353_17195 : 3-oxoadipate CoA-transferase subunit A (EC 2.8.3.6)
Original description: 3-oxoadipate--succinyl-CoA transferase
SEED: 3-oxoadipate CoA-transferase subunit A (EC 2.8.3.6); Glutaconate CoA-transferase subunit A (EC 2.8.3.12)
KEGG: glutaconate CoA-transferase, subunit A
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (2.8.3.6) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_17200 : 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6)
Original description: 3-oxoadipate--succinyl-CoA transferase
SEED: 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6); Glutaconate CoA-transferase subunit B (EC 2.8.3.12)
KEGG: glutaconate CoA-transferase, subunit B
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (2.8.3.6) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_17230 : Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Original description: 3-oxoadipate enol-lactonase
SEED: Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
KEGG: 3-oxoadipate enol-lactonase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (3-OXOADIPATE-ENOL-LACTONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_18575 : tyrosine aminotransferase (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: L-Phenylalanine. Phenylalanine is catabolized via tyrosine and transamination to 4-hydroxyphenylpyruvate, so tyrosine is the relevant substrate. (KEGG_correct)

AO353_18585 : 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; L-tyrosine disodium salt. 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.

AO353_19235 : DNA damage response gene with a putative DNA binding domain (PA0922-like)
Original description: transcriptional regulator
SEED: Transcriptional regulators
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Also some homologs are regulated by LexA.

AO353_20350 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: isovaleryl-CoA dehydrogenase
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: isovaleryl-CoA dehydrogenase
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.

AO353_20835 : 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.

AO353_20845 : 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: purine nucleosidase
Rationale: Important on adenosine and uridine; annotated by SEED as for uridine and inosine; fitness defect on uridine is subtle but is confirmed by observations for close homologs (SEED_correct)

AO353_21335 : 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.

AO353_21340 : 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.

AO353_21345 : 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.

AO353_21360 : 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.

AO353_21365 : 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.

AO353_21385 : m-Inositol ABC transporter, ATPase component (itaA)
Original description: D-ribose transporter ATP-binding protein
SEED: Inositol transport system ATP-binding protein
KEGG: simple sugar transport system ATP-binding protein
Rationale: Specific phenotype on m-Inositol and 63% identical to SMb20173 or itaA, which also has this function (see PMC2597717). The periplasmic substrate-binding component (AO353_21380) is not included in this table because it was annotated correclty in both resources. SEED_correct

AO353_21390 : m-Inositol ABC transporter, permease component (iatP)
Original description: ABC transporter
SEED: Inositol transport system permease protein
KEGG: simple sugar transport system permease protein
Rationale: Specific phenotype on m-Inositol and 71% identical to SMb20174 or itaP, which also has this function (see PMC2597717). The periplasmic substrate-binding component (AO353_21380) is not included in this table because it was annotated correclty in both resources. SEED_correct

AO353_21710 : 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: # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride

AO353_21715 : ABC transporter for D-glucosamine, permease component 1
Original description: amino acid ABC transporter permease
SEED: amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride

AO353_21720 : ABC transporter for D-glucosamine, permease component 2
Original description: ABC transporter permease
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: # Specifically important in nitrogen source D-Glucosamine Hydrochloride; carbon source D-Glucosamine Hydrochloride

AO353_21725 : ABC transporter for D-glucosamine, ATPase component
Original description: ATP-binding protein
SEED: ABC-type polar amino acid transport system, ATPase component
KEGG: polar amino acid transport system ATP-binding protein
Rationale: # Reannotated based on fitness data for other genes in the operon. We have no fitness data for this gene.

AO353_21740 : 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)

AO353_23525 : Catechol 1,2-dioxygenase (EC 1.13.11.1)
Original description: catechol 1,2-dioxygenase
SEED: Catechol 1,2-dioxygenase (EC 1.13.11.1)
KEGG: catechol 1,2-dioxygenase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (CATECHOL-12-DIOXYGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

AO353_24750 : 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.

AO353_25210 : D-serine ammonia-lyase (EC 4.3.1.18)
Original description: D-serine dehydratase
SEED: D-serine dehydratase (EC 4.3.1.18)
KEGG: D-serine dehydratase
Rationale: Specifically important for utilizing D-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.18) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_25255 : large subunit of pyruvate transporter (CstA)
Original description: carbon starvation protein A
SEED: Carbon starvation protein A
KEGG: no annotation
Rationale: Specifically important for pyruvate utilization. Related to E. coli cstA, which is involved in pyruvate transport along with ybdD (PMID:29358499). Also similar to pyruvate transporter btsT (formerly yjiY). It is not certain if AO353_25255 functions with a ybdD-like component: the downstream gene, AO353_25260, is ybdD-like and has subtle defects during growth on pyruvate.

AO353_25635 : citrulline utilization hydrolase
Original description: amidinotransferase
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for: L-Citrulline. This enzyme is distantly related to characterized arginine deiminases (see PF02274) and has conserved catalytic residues. It might be a citrullinase.

AO353_25665 : 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: crotonase
SEED: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
KEGG: enoyl-CoA hydratase
Rationale: # Specifically important for: L-Valine. Hydroxyisobutyryl-CoA is an intermediate in valine degradation. But is this the hydrolase (forming 3-hydroxyisobutyrate) as suggested by SEED, or is it the hydratase (or hydro-lyase in reverse) converting methylacrylyl-CoA to (S)-3-hydroxy-isobutanoyl-CoA, as suggested by KEGG? Characterized homologs are hydrolases (Q81DR3; Q5XIE6)

AO353_25670 : isobutyryl-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: Specifically important for: L-Valine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in valine catabolism

AO353_25680 : 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5)
Original description: acyl-CoA dehydrogenase
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG:
Rationale: Specifically important for: Sodium butyrate. SEED has it as butyryl-CoA dehydrogenase. Also important on isoleucine and valine, which implies that it acts on the other substrates as well

AO353_25685 : acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16)
Original description: acetyl-CoA acetyltransferase
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for: Sodium butyrate; L-Isoleucine. Degradation of acetoacetyl-CoA (EC 2.3.1.9) is consistent with a role in butyrate degradation. The role in Ile degradation suggests that 2-methylacetoacetyl-CoA is also a substrate (conversion to propionyl-CoA + acetyl-CoA). Hence the broader EC # 2.3.1.16.

AO353_25910 : Fructokinase (EC 2.7.1.4)
Original description: fructokinase
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Mannose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

AO353_26560 : Beta-ureidopropionase (EC 3.5.1.6)
Original description: allantoate amidohydrolase
SEED: Beta-ureidopropionase (EC 3.5.1.6)
KEGG: N-carbamoyl-L-amino-acid hydrolase
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.

AO353_26570 : 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.

AO353_26580 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydropyrimidine dehydrogenase
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: dihydropyrimidine dehydrogenase (NADP+)
Rationale: Specifically important for utilizing Uridine. 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.

AO353_26635 : 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; L-Leucine.

AO353_26685 : cobalt efflux pump
Original description: cation transporter
SEED: Cobalt-zinc-cadmium resistance protein CzcD
KEGG: no annotation
Rationale: Strong phenotypes on citrate (as a carbon source) but also on cobalt stress. The citrate phenotype may be due to iron deprivation (via chelation by the citrate) leading to heavy metal stress. The cobalt phenotype is more conserved. It is possible that nickel is also a substrate of this efflux pump, as a slight defect in nickel stress was observed, and this protein is 49% identical to the cobalt and nickel exporter dmeF (Atu0891) of Agrobacterium tumefaciens (PMID:27235438). AO353_26685 is annotated as performing zinc or cadium efflux as well (czcD), but unfortunately, we do not have data for those heavy metal stresses. However a role in zinc stress seems doubtful, as a close homolog in strain GW456-L13 is not important for resisting zinc.

AO353_26790 : 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.

AO353_26885 : phosphogluconate 2-dehydrogenase KguD (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: Specific phenotype: utilization of D-Gluconic Acid and of glucose with alternate N sources. See PMC1951859

AO353_26925 : 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.

AO353_29305 : 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. part of the gamma-glutamyl-putrescine pathway for degrading putrescine (SEED_correct)

AO353_29320 : putrescine ABC transporter, permease component
Original description: spermidine/putrescine ABC transporter permease
SEED: Putrescine transport system permease protein PotI (TC 3.A.1.11.2)
KEGG: putrescine transport system permease protein
Rationale: Specific phenotype: utilization of Putrescine Dihydrochloride

Or download reannotations for Pseudomonas fluorescens FW300-N2E3 or for all organisms as tab-delimited tables