Updated Annotations for Pseudomonas fluorescens GW456-L13

Updated annotations for Pseudomonas fluorescens GW456-L13

80 genes with updated (or confirmed) annotations:

PfGW456L13_1114 : L-threonine aldolase (EC 4.1.2.5)
Original description: Low-specificity L-threonine aldolase (EC 4.1.2.48)
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.

PfGW456L13_1170 : 5-aminopentanamidase (EC 3.5.1.30)
Original description: 5-aminopentanamidase (EC 3.5.1.30)
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.

PfGW456L13_1171 : Lysine 2-monooxygenase (EC 1.13.12.2)
Original description: Lysine 2-monooxygenase (EC 1.13.12.2)
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.

PfGW456L13_161 : putative transporter, required for glycine utilization
Original description: putative membrane protein
SEED: putative membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

PfGW456L13_1866 : Aminomethyltransferase (EC 2.1.2.10)
Original description: Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)
SEED: Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)
KEGG: aminomethyltransferase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (2.1.2.10) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_1868 : Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2)
Original description: Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
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.

PfGW456L13_1869 : glycine cleavage system H protein (EC 1.4.1.27)
Original description: Glycine cleavage system H protein
SEED: Glycine cleavage system H protein
KEGG: glycine cleavage system H protein
Rationale: Specific phenotype: utilization of L-Threonine (threonine is broken down via glycine)

PfGW456L13_1894 : ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
Original description: Glucose ABC transport system, periplasmic sugar-binding protein
SEED: Glucose ABC transport system, periplasmic sugar-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on D-Fructose; L-Aspartic Acid; D-Galactose; L-Lysine. The nitrogen source phenotypes for aspartate and lysine are with glucose as the carbon source. May also transport fructose.

PfGW456L13_1895 : ABC transporter for D-Galactose and D-Glucose, permease component 1
Original description: Glucose ABC transport system, inner membrane component 1
SEED: Glucose ABC transport system, inner membrane component 1
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Galactose; N L-Lysine. glucose is the C source for the N source experiments with a phenotype (i.e. lysine); may also transport fructose.

PfGW456L13_1896 : ABC transporter for D-Galactose and D-Glucose, permease component 2
Original description: Glucose ABC transport system, inner membrane component 2
SEED: Glucose ABC transport system, inner membrane component 2
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotypes on D-Galactose; N L-Lysine. glucose is the C source for the N source experiments with a phenotype (i.e. lysine); may also transport fructose.

PfGW456L13_1897 : ABC transporter for D-Galactose and D-Glucose, ATPase component
Original description: Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
SEED: Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specific phenotype on D-Galactose; L-Lysine; L-Aspartic Acid. The nitrogen source phenotypes for aspartate and lysine are with glucose as the carbon source. May also transport fructose.

PfGW456L13_1974 : Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
Original description: Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
SEED: Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71)
KEGG: succinylglutamic semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCGLUALDDEHYD-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_1977 : Succinylglutamate desuccinylase (EC 3.5.1.96)
Original description: Succinylglutamate desuccinylase (EC 3.5.1.96)
SEED: Succinylglutamate desuccinylase (EC 3.5.1.96)
KEGG: succinylglutamate desuccinylase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCGLUDESUCC-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_2016 : C4-dicarboxylate transporter
Original description: Aerobic C4-dicarboxylate transporter for fumarate, L-malate, D-malate, succunate, aspartate
SEED: no annotation
KEGG: aerobic C4-dicarboxylate transport protein
Rationale: Specific phenotype: utilization of L-Malic acid, succinate, Tween 20; the phenotype on Tween 20 is not explained

PfGW456L13_2118 : L-arabinolactonase (EC 3.1.1.15)
Original description: L-arabinolactonase (EC 3.1.1.15)
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONOLACTONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_2119 : L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48)
Original description: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
SEED: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
KEGG: no annotation
Rationale: Specifically important for: D-Galactose; L-Arabinose. Both of these sugars are catabolized via a 1-dehydrogenase followed by lactonase and dehydratase reactions. This is the only dehydrogenase is specifically important for either of these carbon sources in several Pseudomonas, except for an alpha-ketoglutarate semialdehyde dehydrogenase that is expected to be the last dedicated step in L-arabinose catabolism (i.e., Pf6N2E2_612). L-arabinose and D-galactose are chemically similar and some dehydrogenases are already known to act on both substrates.

PfGW456L13_2411 : Acetyl-CoA C-acetyltransferase (EC 2.3.1.9)
Original description: 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (ACETYL-COA-ACETYLTRANSFER-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_2685 : Glycine hydroxymethyltransferase (EC 2.1.2.1)
Original description: Serine hydroxymethyltransferase (EC 2.1.2.1)
SEED: Serine hydroxymethyltransferase (EC 2.1.2.1)
KEGG: glycine hydroxymethyltransferase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (2.1.2.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_2738 : electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1)
Original description: benzoate dioxygenase, ferredoxin reductase component; Anthranilate dioxygenase reductase
SEED: benzoate dioxygenase, ferredoxin reductase component; Anthranilate dioxygenase reductase
KEGG: anthranilate dioxygenase reductase
Rationale: # Specifically important in carbon source L-Tryptophan. Tryptophan is catabolized via kynurenine and anthranilate, so this system acts on anthranilate, not benzoate. The subunits of the other component are PfGW456L13_2739 and PfGW456L13_2740.

PfGW456L13_2739 : Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1)
Original description: Benzoate 1,2-dioxygenase beta subunit (EC 1.14.12.10)
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.

PfGW456L13_2740 : Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1)
Original description: Benzoate 1,2-dioxygenase alpha subunit (EC 1.14.12.10)
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.

PfGW456L13_2842 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: Oxidoreductase probably involved in sulfite reduction
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

PfGW456L13_2867 : D-glucosaminate dehydratase (EC 4.3.1.9)
Original description: D-serine deaminase (EC 4.3.1.18)
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)

PfGW456L13_2935 : 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Original description: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
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 (RXN-10815) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_2982 : 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
Original description: 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
SEED: 3-ketoacyl-CoA thiolase (EC 2.3.1.16)
KEGG: acetyl-CoA C-acetyltransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (METHYLACETOACETYLCOATHIOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_2983 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG:
Rationale: Specifically important for utilizing L-Isoleucine, which is oxidized via 2-methylbutanoyl-CoA

PfGW456L13_2985 : isobutyryl-CoA dehydrogenase (EC 1.3.8.5)
Original description: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG:
Rationale: Specifically important for: L-Valine. Isobutyryl-CoA is an intermediate in valine degradation. SEED annotates it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction

PfGW456L13_2986 : 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
SEED: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (3.1.2.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_303 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
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.

PfGW456L13_3036 : Fructokinase (EC 2.7.1.4)
Original description: Fructokinase (EC 2.7.1.4)
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.

PfGW456L13_3038 : mannitol 2-dehydrogenase (EC 1.1.1.67)
Original description: Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
SEED: Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
KEGG: no annotation
Rationale: Specific phenotype: utilization of D-Mannose; mannose is apparently converted to fructose via mannitol; very simlar to O08355

PfGW456L13_316 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate deformylase (EC 3.5.1.68)
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: formiminoglutamase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (3.5.1.68) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_317 : Imidazolonepropionase (EC 3.5.2.7)
Original description: Imidazolonepropionase (EC 3.5.2.7)
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.

PfGW456L13_320 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: Histidine ammonia-lyase (EC 4.3.1.3)
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.

PfGW456L13_326 : Urocanate hydratase (EC 4.2.1.49)
Original description: Urocanate hydratase (EC 4.2.1.49)
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.

PfGW456L13_330 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
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.

PfGW456L13_3314 : D-galactono-lactonase (EC 3.1.1.-)
Original description: 3-carboxymuconate cyclase
SEED: 3-carboxymuconate cyclase
KEGG: no annotation
Rationale: Specifically important for: D-Galactose. A 1,5-lactone is probably the product of D-galactose dehydrogenase (PfGW456L13_2119), althought it might rearrange to a 1,4-lactone. Related to E. coli ybhE or pgl, which is 6-phospho-D-glucono-1,5-lactonase.

PfGW456L13_3317 : 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43)
Original description: SUGAR TRANSPORTER
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.)

PfGW456L13_3320 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: L-arabonate dehydratase (EC 4.2.1.25)
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_3503 : Beta-ureidopropionase (EC 3.5.1.6)
Original description: Beta-ureidopropionase (EC 3.5.1.6)
SEED: Beta-ureidopropionase (EC 3.5.1.6)
KEGG: N-carbamoyl-L-amino-acid hydrolase
Rationale: Specifically important for utilizing Cytosine; 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.

PfGW456L13_3505 : uridine/cytosine permease
Original description: Possible pyrimidine permease in reductive pathway
SEED: Possible pyrimidine permease in reductive pathway
KEGG: nucleobase:cation symporter-1, NCS1 family
Rationale: Specific phenotype: utilization of Cytosine, Uridine; 39% identical to nucleobase transporter A8J166

PfGW456L13_3506 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: Dihydropyrimidinase (EC 3.5.2.2)
SEED: Dihydropyrimidinase (EC 3.5.2.2)
KEGG: dihydropyrimidinase
Rationale: Specifically important for utilizing Cytosine. 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.

PfGW456L13_3508 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
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.

PfGW456L13_3540 : branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit (EC 1.2.4.4)
Original description: Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
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.

PfGW456L13_3541 : branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit (EC 1.2.4.4)
Original description: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
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.

PfGW456L13_3542 : Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168)
Original description: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
SEED: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
KEGG: 2-oxoisovalerate dehydrogenase E2 component (dihydrolipoyl transacylase)
Rationale: Specifically important for utilizing L-Isoleucine; L-Valine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_3543 : Dihydrolipoyl dehydrogenase (EC 1.8.1.4)
Original description: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
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-Valine. 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.

PfGW456L13_359 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
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.

PfGW456L13_3648 : D-serine ammonia-lyase (EC 4.3.1.18)
Original description: D-serine dehydratase (EC 4.3.1.18)
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.

PfGW456L13_3649 : D-serine permease
Original description: D-serine permease DsdX
SEED: D-serine permease DsdX
KEGG: gluconate:H+ symporter, GntP family
Rationale: Specific phenotype: utilization of D-Serine

PfGW456L13_3822 : Catechol 1,2-dioxygenase (EC 1.13.11.1)
Original description: Catechol 1,2-dioxygenase (EC 1.13.11.1)
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.

PfGW456L13_3823 : Muconolactone isomerase (EC 5.3.3.4)
Original description: Muconolactone isomerase (EC 5.3.3.4)
SEED: Muconolactone isomerase (EC 5.3.3.4)
KEGG: muconolactone D-isomerase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (MUCONOLACTONE-DELTA-ISOMERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_4101 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
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.

PfGW456L13_4103 : Nitrate reductase (EC 1.7.99.4)
Original description: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: periplasmic nitrate reductase NapA
Rationale: Specifically important for utilizing Sodium nitrate. 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.

PfGW456L13_4288 : Kynureninase (EC 3.7.1.3)
Original description: Kynureninase (EC 3.7.1.3)
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.

PfGW456L13_4291 : L-tryptophan transporter
Original description: Aromatic amino acid transport protein AroP
SEED: Aromatic amino acid transport protein AroP
KEGG: amino acid transporter, AAT family
Rationale: Specifically important for utilization of tryptophan as a carbon source.

PfGW456L13_4292 : Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
Original description: Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
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.

PfGW456L13_4293 : Kynurenine formamidase, bacterial (EC 3.5.1.9)
Original description: Kynurenine formamidase, bacterial (EC 3.5.1.9)
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.

PfGW456L13_4394 : Phenylalanine 4-monooxygenase (EC 1.14.16.1)
Original description: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
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.

PfGW456L13_4396 : tyrosine aminotransferase (EC 2.6.1.57)
Original description: Aspartate aminotransferase (EC 2.6.1.1)
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aromatic-amino-acid transaminase
Rationale: Specifically important for: L-Phenylalanine. Phenylalanine is hydroxylated to tyrosine (by PfGW456L13_4394) before deamination. KEGG has same EC# but less specific

PfGW456L13_4527 : tricarboxylate transporter component TctB
Original description: Tricarboxylate transport protein TctB
SEED: Tricarboxylate transport protein TctB
KEGG: putative tricarboxylic transport membrane protein
Rationale: Specific phenotype: utilization of Tricitrate

PfGW456L13_4591 : 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6)
Original description: 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6); Glutaconate CoA-transferase subunit B (EC 2.8.3.12)
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.

PfGW456L13_4592 : 3-oxoadipate CoA-transferase subunit A (EC 2.8.3.6)
Original description: 3-oxoadipate CoA-transferase subunit A (EC 2.8.3.6); Glutaconate CoA-transferase subunit A (EC 2.8.3.12)
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.

PfGW456L13_4770 : ABC transporter for L-Asparagine and possibly other L-amino acids, periplasmic substrate-binding component
Original description: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
SEED: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system substrate-binding protein
Rationale: Specific phenotype on L-Asparagine; Sodium octanoate. Detrimental on glutamine and might leak it. The mild phenotype on octanoate is not explained.

PfGW456L13_4771 : ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1
Original description: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: Specific phenotypes on L-Asparagine; L-Asparagine. also has weak phenotypes on other a.a., but not on aspartate; weak phenotype on glutamate; also is detrimental during growth on glutamine (along with a downstream HK-RR), which could imply that it leaks glutamate; ko:K10003 : glutamate/aspartate transport system permease protein

PfGW456L13_4772 : ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2
Original description: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: Specific phenotypes on L-Asparagine; L-Asparagine. also has weak phenotypes on other a.a., but not on aspartate; weak phenotype on glutamate; also is detrimental during growth on glutamine (along with a downstream HK-RR), which could imply that it leaks glutamate; K10002 : glutamate/aspartate transport system permease protein

PfGW456L13_4773 : ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component
Original description: Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system ATP-binding protein
Rationale: This is presumably the ATPase component but lacks fitness data.

PfGW456L13_4830 : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
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.

PfGW456L13_4831 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
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.

PfGW456L13_495 : Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20)
Original description: Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
SEED: Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)
KEGG: glutarate semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (GLUTARATE-SEMIALDEHYDE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PfGW456L13_4954 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: L-serine dehydratase (EC 4.3.1.17)
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.

PfGW456L13_4962 : Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Original description: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
SEED: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
KEGG: homogentisate 1,2-dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PfGW456L13_5001 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase (EC 2.4.2.17)
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.

PfGW456L13_506 : required for octanoate transport, together with NodT, MFP, and FUSC proteins (PfGW456L13_504, PfGW456L13_505, PfGW456L13_507)
Original description: membrane protein, putative
SEED: membrane protein, putative
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). A conserved cofit operon. This and orthologous operons are important for utilization of octanoate, which is probably toxic at 20 mM, but it could also be for uptake rather than efflux.

PfGW456L13_5118 : D-lactate dehydrogenase (quinone), FeS subunit (EC 1.1.5.12)
Original description: Predicted D-lactate dehydrogenase, Fe-S protein, FAD/FMN-containing
SEED: Predicted D-lactate dehydrogenase, Fe-S protein, FAD/FMN-containing
KEGG: no annotation
Rationale: Specific phenotype: utilization of D-Lactate, Glycerol. The phenotype on glycerol is not explained (is there is a side pathway via glycerate?)

PfGW456L13_5145 : 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
Original description: 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31)
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.

PfGW456L13_5146 : Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Original description: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
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.

PfGW456L13_740 : L-asparaginase (EC 3.5.1.1)
Original description: L-asparaginase (EC 3.5.1.1)
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.

PfGW456L13_805 : gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.99); 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
Original description: Aldehyde dehydrogenase (EC 1.2.1.3)
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: 4-guanidinobutyraldehyde dehydrogenase / NAD-dependent aldehyde dehydrogenase
Rationale: Specifically important for utilization of putrescine as part of the gamma-glutamyl-putrescine pathway. 87% identical to 4-guanidinobutyraldehyde dehydrogenase (kauB = PP_5278 = Q88CA3) from P. putida, which is involved in arginine degradation, and 93% identical to AO356_12580, which is mildly important on arginine. So PfGW456L13_805 probably acts on both substrates.

PfGW456L13_925 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
SEED: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride. The first step in putrescine catabolism. (SEED_correct)

Or download reannotations for Pseudomonas fluorescens GW456-L13 or for all organisms as tab-delimited tables