Updated annotations for Pseudomonas stutzeri RCH2

74 genes with updated (or confirmed) annotations:

Psest_1077 : acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8)
Original description: 3-oxoacid CoA-transferase, B subunit
SEED: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5)
KEGG: 3-oxoacid CoA-transferase subunit B
Rationale: Specifically important for: L-tyrosine disodium salt; L-Leucine. This role makes sense because of its involvement in acetoacetate catabolism (from tyrosine or leucine). It had been annotated as succinyl-CoA:3-ketoacid-coenzyme A transferase (a broader range of substrates and with succinyl-CoA not acetyl-CoA as donor). Similar to E. coli atoA (52% identical), which has this activity.

Psest_1078 : acetyl-CoA:acetoacetate CoA transferase, A subunit (EC 2.8.3.8)
Original description: 3-oxoacid CoA-transferase, A subunit
SEED: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5)
KEGG: 3-oxoacid CoA-transferase subunit A
Rationale: Specifically important for: L-Leucine. Important on tyrosine as well. This role makes sense because of its involvement in acetoacetate catabolism (from tyrosine or leucine). It had been annotated as succinyl-CoA:3-ketoacid-coenzyme A transferase (a broader range of substrates and with succinyl-CoA not acetyl-CoA as donor). Similar to E. coli atoD (46% identical), which has the same activity.

Psest_1083 : 3-methylcrotonyl-CoA carboxylase, beta subunit (EC 6.4.1.4)
Original description: Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
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 (METHYLCROTONYL-COA-CARBOXYLASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_1084 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: Acyl-CoA dehydrogenases
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 (1.3.8.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Psest_1122 : putative adhesin (DUF1302)
Original description: Protein of unknown function (DUF1302).
SEED: FIG067310: hypothetical protein
KEGG: no annotation
Rationale: Similar to PA3923, which binds laminin (PMC6890786) and is involved in biofilm formation (PMC8547006), so this is probably an adhesin.

Psest_1123 : adhesin-associated sorting protein (DUF1329)
Original description: Protein of unknown function (DUF1329).
SEED: FIG002188: hypothetical protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Psest_1122). DUF1329 is distantly related to lolB, which inserts lipoproteins into the outer membrane. So we predict that DUF1329 is involved in sorting the adhesin to the outer membrane.

Psest_1156 : outer membrane component of uptake system, probably for ferrous iron
Original description: Uncharacterized protein conserved in bacteria
SEED: no annotation
KEGG: hypothetical protein
Rationale: PFam PF07433.7 (DUF1513). In a conserved cofit operon with two efeO-like genes (Psest_1159,Psest_1157) and a efeB-like gene (Psest_1158)

Psest_1178 : D-glycerate 2-kinase (EC 2.7.1.-)
Original description: Putative glycerate kinase
SEED: D-glycerate 2-kinase (EC 2.7.1.-)
KEGG: hydroxypyruvate reductase
Rationale: Specifically important for: Glycolic Acid. Either glycerate kinase or hydroxypyruvate reductase could be involved in glycolate utilization (via glyoxylate and tartronate-semialdehyde, which can be converted to glycerate, perhaps via hydroxypyruvate). However this protein is similar to TM1585 (also PDB:2b8nA or GCK_THEMA), which is a glycerate kinase. We were not able to find a rationale for KEGG's annotation as hydroxypyruvate reductase. (SEED_correct)

Psest_1181 : Glyoxylate carboligase (EC 4.1.1.47)
Original description: glyoxylate carboligase
SEED: Glyoxylate carboligase (EC 4.1.1.47)
KEGG: tartronate-semialdehyde synthase
Rationale: Specifically important for utilizing Glycolic Acid. Automated validation from mutant phenotype: the predicted function (GLYOCARBOLIG-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_1335 : Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Original description: Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
SEED: Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
KEGG: long-chain acyl-CoA synthetase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ACYLCOASYN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_0155 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide 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.

Psest_1636 : putative transporter, required for glycine utilization
Original description: Predicted membrane protein
SEED: no annotation
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

Psest_1923 : adhesin-associated BNR repeat protein
Original description: Uncharacterized protein related to plant photosystem II stability/assembly factor
SEED: FIG002465: BNR repeat protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Psest_1122). This is also predicted to be an outer membrane protein.

Psest_1924 : adhesin-associated MmpL efflux pump
Original description: Predicted exporters of the RND superfamily
SEED: FIG005548: transport protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (Psest_1122). The MmpL family is involved in efflux of lipids or siderophores (see IPR004869); we speculate that this exports a lipid or saccharide that is attached to the adhesin.

Psest_1928 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase [NAD(P)H], large subunit
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.

Psest_1944 : NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form
Original description: NAD-specific glutamate dehydrogenase
SEED: NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form
KEGG: no annotation
Rationale: Specifically important for utilizing L-Glutamic acid monopotassium salt monohydrate. Automated validation from mutant phenotype: the predicted function (GLUTAMATE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_2014 : Isocitrate lyase (EC 4.1.3.1)
Original description: Isocitrate lyase
SEED: Isocitrate lyase (EC 4.1.3.1)
KEGG: isocitrate lyase
Rationale: Specifically important for utilizing Sodium butyrate and Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_2055 : cytochrome c550
Original description: Cytochrome c, mono- and diheme variants
SEED: Cytochrome C550 (Soluble cytochrome C)
KEGG: no annotation
Rationale: Specific phenotype: utilization of Ethanol. This is the electron acceptor for quinoprotein ethanol dehydrogenase, see PMID:10075429

Psest_0205 : tricarboxylate porin
Original description: outer membrane porin, OprD family.
SEED: Tricarboxylate porin OpdH
KEGG: no annotation
Rationale: Specific phenotype: utilization of Tricitrate. Similar to P. aeruginosa OdpH

Psest_2123 : fusion of gluconokinase (EC 2.7.1.12) and the small permease component of the D-gluconate TRAP transporter
Original description: carbohydrate kinase, thermoresistant glucokinase family
SEED: Gluconokinase (EC 2.7.1.12)
KEGG: gluconokinase
Rationale: This protein has pleiotropic phenotypes which are not explained, but it is most important for fitness with D-gluconate as the carbon source, consistent with its putative roles as part of the tripartite gluconate transport system and as gluconate kinase. Also, the N-terminal part is 49% identical to PP3416 or gnuK from P. putida, which is the catabolic gluconate kinase (PMC1951859). The SEED and KEGG annotations ignore the dctQ-like C-terminal portion.

Psest_2124 : D-gluconate TRAP transporter, large permease component
Original description: TRAP transporter, DctM subunit
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: no annotation
Rationale: specific phenotype on D-gluconate and no other transporter is apparent in the fitness data.

Psest_2125 : D-gluconate TRAP transporter, periplasmic component
Original description: tripartite ATP-independent periplasmic transporter solute receptor, DctP family
SEED: TRAP-type transport system, periplasmic component, predicted N-acetylneuraminate-binding protein
KEGG: no annotation
Rationale: specific phenotype on D-gluconate and no other transporter is apparent in the fitness data

Psest_2235 : DNA damage response nuclease
Original description: VRR-NUC domain.
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.

Psest_2276 : Aldehyde dehydrogenase (EC 1.2.1.3)
Original description: NAD-dependent aldehyde dehydrogenases
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Specifically important for utilizing Ethanol. Automated validation from mutant phenotype: the predicted function (RXN66-3) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_2436 : Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Original description: methylmalonic acid 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.

Psest_2437 : Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
Original description: Enoyl-CoA hydratase/carnithine racemase
SEED: Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (METHYLACYLYLCOA-HYDROXY-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_2438 : 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.

Psest_2439 : 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: Enoyl-CoA hydratase/carnithine racemase
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.

Psest_2440 : isobutyryl-CoA dehydrogenase (EC 1.3.8.5)
Original description: Acyl-CoA dehydrogenases
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Important for valine utilization as N source, and isobutyryl-CoA is an intermediate in valine catabolism. SEED annotated it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction

Psest_2445 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: Acyl-CoA dehydrogenases
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Specifically important for: L-Isoleucine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction. 2-methylbutanoyl-CoA is an intermediate in isoleucine catabolism

Psest_3078 : L-proline:Na+ symporter
Original description: sodium/proline symporter
SEED: Proline/sodium symporter PutP (TC 2.A.21.2.1) @ Propionate/sodium symporter
KEGG: sodium/proline symporter
Rationale: Specifically important for proline utilization. 76% identical to PutP (Q9I5F5) from P. aeruginosa.

Psest_3079 : L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2)
Original description: delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)
SEED: 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.

Psest_3297 : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: histidinol-phosphate aminotransferase
SEED: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
KEGG: histidinol-phosphate aminotransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01141.

Psest_3299 : 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.

Psest_3354 : 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.

Psest_3355 : fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
Original description: phosphoenolpyruvate-protein phosphotransferase
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) / Fructose-specific phosphocarrier protein HPr (EC 2.7.1.69) / PTS system, fructose-specific IIA component (EC 2.7.1.69)
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specifically important for utilizing D-Fructose.

Psest_3366 : Biosynthetic arginine decarboxylase (EC 4.1.1.19)
Original description: arginine decarboxylase, biosynthetic
SEED: Biosynthetic arginine decarboxylase (EC 4.1.1.19)
KEGG: arginine decarboxylase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGDECARBOX-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_3511 : 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-tyrosine disodium salt. Automated validation from mutant phenotype: the predicted function (MALEYLACETOACETATE-ISOMERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_3512 : fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2)
Original description: 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway)
SEED: Fumarylacetoacetate hydrolase family protein
KEGG: no annotation
Rationale: Specifically important for: L-tyrosine disodium salt; casamino acids. The annotation of psa:PST_0871 has been updated to fumarylacetoacetate (FAA) hydrolase [EC:3.7.1.2], which is a step in tyrosine catabolism (KEGG_correct)

Psest_3513 : 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.

Psest_3514 : 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-tyrosine disodium salt. Automated validation from mutant phenotype: the predicted function (4-HYDROXYPHENYLPYRUVATE-DIOXYGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_0346 : small component of pyruvate/D-alanine transporter (TIGR03647)
Original description: putative solute:sodium symporter small subunit
SEED: FIG152265: Sodium:solute symporter associated protein
KEGG: no annotation
Rationale: Important for utilization of D-alanine and pyruvate, along with Psest_0347. Belongs to TIGR03647, which was predicted to be the small subunit of a transporter.

Psest_3516 : Leucine dehydrogenase (EC 1.4.1.9)
Original description: Glutamate dehydrogenase/leucine dehydrogenase
SEED: Leucine dehydrogenase (EC 1.4.1.9)
KEGG: leucine dehydrogenase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (1.4.1.9) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Psest_3517 : branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate
Original description: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
SEED: Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits
KEGG: indolepyruvate ferredoxin oxidoreductase
Rationale: Specifically important for: L-Leucine; L-Isoleucine. This oxidizes and decarboxylates the alpha-keto acid that is produced by a branched chain amino acid dehydrogenase (4-methyl-2-oxopentanoate or (S)-3-methyl-2-oxopentanoate). This is also improtant for utilization of valine as a nitrogen source implying a third substrate (3-methyl-2-oxobutanoate).

Psest_0347 : large component of pyruvate/D-alanine transporter (actP-like)
Original description: probable sodium:solute symporter, VC_2705 subfamily
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: Important for utilization of D-alanine and pyruvate, along with Psest_0346.

Psest_0354 : Malate synthase G (EC 2.3.3.9)
Original description: malate synthase G
SEED: Malate synthase G (EC 2.3.3.9)
KEGG: malate synthase
Rationale: Specifically important for utilizing Sodium butyrate and Tween 20. Automated validation from mutant phenotype: the predicted function (MALSYN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_3793 : D-alanine dehydrogenase (EC 1.4.99.-)
Original description: Glycine/D-amino acid oxidases (deaminating)
SEED: D-amino acid dehydrogenase small subunit (EC 1.4.99.1)
KEGG: D-amino-acid dehydrogenase
Rationale: Specifically important for utilizing D-Alanine. Automated validation from mutant phenotype: the predicted function (DALADEHYDROG-RXN) was linked to the condition via a SEED subsystem. A more specific reaction was selected manually.

Psest_3839 : D-lactate/glycolate dehydrogenase, iron-sulfur subunit GlcF (EC 1.1.99.6; EC 1.1.99.14)
Original description: Fe-S oxidoreductase
SEED: Glycolate dehydrogenase (EC 1.1.99.14), iron-sulfur subunit GlcF
KEGG: glycolate oxidase iron-sulfur subunit
Rationale: Specifically important for: Glycolic Acid; Sodium D-Lactate. This is the first step in both D-lactate and glycolate oxidation.

Psest_3840 : D-lactate/glycolate dehydrogenase, FAD binding subunit GlcE (EC 1.1.99.6; EC 1.1.99.14)
Original description: FAD/FMN-containing dehydrogenases
SEED: Glycolate dehydrogenase (EC 1.1.99.14), FAD-binding subunit GlcE
KEGG: glycolate oxidase FAD binding subunit
Rationale: Specifically important for: Sodium D-Lactate; Glycolic Acid.

Psest_3841 : D-lactate/glycolate dehydrogenase, FAD-linked subunit GlcD (EC 1.1.99.6; EC 1.1.99.14)
Original description: glycolate oxidase, subunit GlcD
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: glycolate oxidase
Rationale: Specifically important for: Sodium D-Lactate; Glycolic Acid. This is the first step in both D-lactate and glycolate oxidation.

Psest_3864 : Histidinol-phosphatase (EC:3.1.3.15)
Original description: HAD-superfamily subfamily IB hydrolase, TIGR01490
SEED: Phosphoserine phosphatase (EC 3.1.3.3)
KEGG: no annotation
Rationale: Annotated as HAD-superfamily IB hydrolase or sometimes as phosphoserine phosphatase (serB). However Psest_0489 seems to be serB and has auxotrophic phenotypes, so this is more likely the missing phosphatase for histidine synthesis. Fitness data for close homologs in other pseudomonads is consistent with this interpretation. (auxotroph)

Psest_3944 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: phosphoribosyl-ATP pyrophosphohydrolase
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.

Psest_4075 : symporter for L-glutamate, L-glutamine, and L-proline
Original description: Na+/H+-dicarboxylate symporters
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for utilization of L-glutamate, L-glutamine, or L-proline as carbon soruces. Glutamine is probably cleaved by a cytoplasmic glutaminaes (Psest_4081), so glutamine is probably a substrate. Mildly detrimental during tyrosine utilization, so tyrosine might also be a substrate.

Psest_4081 : 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.

Psest_4131 : alpha-ketoglutarate sensor protein (mifS)
Original description: Signal transduction histidine kinase regulating C4-dicarboxylate transport system
SEED: C4-dicarboxylate transport sensor protein
KEGG: two-component system, NtrC family, C4-dicarboxylate transport sensor histidine kinase DctB
Rationale: Specific phenotype on a-ketoglutarate and 56% identical to PA5512 (mifS), which regulates a-ketoglutarate transport in P. aeruginosa (PMC4482717). The transporter in this organism is Psest_0084:0085.

Psest_4132 : alpha-ketoglutarate DNA-binding response regulator (mifR)
Original description: Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains
SEED: Nitrogen regulation protein NtrX
KEGG: two-component system, NtrC family, C4-dicarboxylate transport response regulator DctD
Rationale: Specific phenotype on a-ketoglutarate and 75% identical to PA5511 (mifR), which regulates a-ketoglutarate transport in P. aeruginosa (PMC4482717). The transporter in this organism is Psest_0084:0085.

Psest_0419 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: Acyl-CoA dehydrogenases
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG: no annotation
Rationale: Specifically important for: L-tyrosine disodium salt; Sodium butyrate; Tween 20. tween 20 hydrolyzes to a mix of C12, C14, and C16 fatty acids; this is probably part of beta oxidation (SEED_correct)

Psest_4269 : C4-dicarboxylate transporter, DctQ subunit
Original description: TRAP-type C4-dicarboxylate transport system, small permease component
SEED: TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter
KEGG: C4-dicarboxylate transporter, DctQ subunit
Rationale: Important for succinate and fumarate utilization (KEGG_correct). The other components (Psest_4268 and Psest_4270) were already annotated correctly

Psest_4288 : Glutamate--putrescine ligase (EC 6.3.1.11)
Original description: Glutamine synthetase
SEED: Glutamine synthetase (EC 6.3.1.2)
KEGG: glutamine synthetase
Rationale: Specifically important for utilizing L-Arginine and Putrescine Dihydrochloride. Automated validation from mutant phenotype: the predicted function (RXN0-3901) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_0450 : Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Original description: branched-chain amino acid aminotransferase, group I
SEED: Branched-chain amino acid aminotransferase (EC 2.6.1.42)
KEGG: branched-chain amino acid aminotransferase
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (BRANCHED-CHAINAMINOTRANSFERILEU-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Psest_0482 : yqiA-like hydrolase, affects the cell envelope
Original description: Predicted esterase
SEED: Putative esterase, FIGfam005057
KEGG: no annotation
Rationale: PFam PF05728.8 (UPF0227). Conserved phenotypes: important for resisting carbenicillin and doxycycline

Psest_0557 : Urease (EC 3.5.1.5)
Original description: urease, alpha subunit
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.

Psest_0560 : Urease (EC 3.5.1.5)
Original description: urease, gamma subunit
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.

Psest_0566 : urea ABC transporter, permease component
Original description: urea ABC transporter, permease protein UrtB
SEED: Urea ABC transporter, permease protein UrtB
KEGG: branched-chain amino acid transport system permease protein
Rationale: Specific phenotype: utilization of Parabanic Acid. Parabanic acid is probably hydrolyzed to urea before uptake

Psest_0774 : cytosine permease
Original description: Purine-cytosine permease and related proteins
SEED: Cytosine permease
KEGG: cytosine permease
Rationale: Specific phenotype: utilization of Cytosine

Psest_0779 : tyrosine aminotransferase (EC 2.6.1.57)
Original description: Aspartate/tyrosine/aromatic aminotransferase
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aromatic-amino-acid transaminase
Rationale: Specifically important for: L-tyrosine disodium salt. This is cofit with 4-hydroxyphenylpyruvate dioxygenase (Psest_0779) which would be the second step in tyrosine catabolism (KEGG_correct)

Psest_0084 : alpha-ketoglutarate TRAP transporter, 4TM/12TM components
Original description: TRAP transporter, 4TM/12TM fusion protein
SEED: TRAP transporter, 4TM/12TM fusion protein, unknown substrate 1
KEGG: no annotation
Rationale: specific phenotype on a-ketoglutarate and no other transporter for this substrate is apparent in the fitness data. (Mutants in another TRAP system, Psest_4268:Psest_4270, have a much milder defect in a-ketoglutarate utilization).

Psest_0863 : maltose ABC transporter, substrate-binding component MalE
Original description: Maltose-binding periplasmic proteins/domains
SEED: Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
KEGG: maltose/maltodextrin transport system substrate-binding protein
Rationale: Specifically important for utilizing D-Maltose monohydrate.

Psest_0085 : alpha-ketoglutarate TRAP transporter, solute receptor component
Original description: TRAP transporter solute receptor, TAXI family
SEED: TRAP transporter solute receptor, unknown substrate 1
KEGG: no annotation
Rationale: specific phenotype on a-ketoglutarate and no other transporter for this substrate is apparent in the fitness data. (Mutants in another TRAP system, Psest_4268:Psest_4270, have a much milder defect in a-ketoglutarate utilization).

Psest_0864 : maltose ABC transporter, permease component 1 (MalF)
Original description: ABC-type sugar transport systems, permease components
SEED: Maltose/maltodextrin ABC transporter, permease protein MalF
KEGG: maltose/maltodextrin transport system permease protein
Rationale: Specifically important for utilizing D-Maltose monohydrate

Psest_0865 : maltose ABC transporter, permease component 2 (MalG)
Original description: ABC-type maltose transport systems, permease component
SEED: Maltose/maltodextrin ABC transporter, permease protein MalG
KEGG: maltose/maltodextrin transport system permease protein
Rationale: Specifically important for utilizing D-Maltose monohydrate.

Psest_0870 : Alpha-glucosidase (EC 3.2.1.20)
Original description: Glycosidases
SEED: Maltodextrin glucosidase (EC 3.2.1.20)
KEGG: alpha-glucosidase
Rationale: Specifically important for utilizing D-Maltose monohydrate. Automated validation from mutant phenotype: the predicted function (3.2.1.20) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Psest_0871 : maltose ABC transporter, ATPase component MalK
Original description: ABC-type sugar transport systems, ATPase components
SEED: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
KEGG: maltose/maltodextrin transport system ATP-binding protein
Rationale: Specifically important for utilizing D-Maltose monohydrate.

Psest_0955 : D,L-lactate:H+ symporter
Original description: L-lactate transport
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: Important for utilization of L,-lactate, D-lactate, D,L-lactate. Also important in many nitrogen source experiments with D,L-lactate as the carbn source.

Or download reannotations for Pseudomonas stutzeri RCH2 or for all organisms as tab-delimited tables