Updated Annotations for Pseudomonas putida KT2440

Updated annotations for Pseudomonas putida KT2440

41 genes with updated (or confirmed) annotations:

PP_0154 : Succinyl-CoA:acetate CoA-transferase (EC 2.8.3.18)
Original description: propionyl-CoA:succinate CoA transferase
SEED: Acetyl-CoA hydrolase (EC 3.1.2.1)
KEGG: acetyl-CoA hydrolase
Rationale: # Specifically important in carbon source Sodium acetate; carbon source Potassium acetate. 48% identical to B3EY95 from Acetobacter, which uses succinyl-CoA to form acetyl-CoA and aids growth on acetate, see PMID:18502856

PP_0292 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide 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.

PP_0294 : Choline / carnitine / glycine betaine ABC transporter, ATPase component
Original description: choline / betaine / carnitine ABC transporter - ATP binding subunit
SEED: L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system ATP-binding protein
Rationale: Specific phenotype: utilization of Carnitine, Choline. Probably part of a glycine-betaine transporter as well (see PA5376 and TC 3.A.1.12.12)

PP_0302 : L-carnitine 3-dehydrogenase (EC 1.1.1.108)
Original description: L-carnitine dehydrogenase
SEED: no annotation
KEGG: 3-hydroxybutyryl-CoA dehydrogenase
Rationale: Specific phenotype: utilization of Carnitine

PP_0765 : putative adhesin (DUF1302)
Original description: conserved exported protein of unknown function
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.

PP_0766 : adhesin-associated sorting protein (DUF1329)
Original description: conserved exported protein of unknown function
SEED: FIG002188: hypothetical protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (PP_0765). 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.

PP_0965 : 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.

PP_0967 : 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.

PP_1167 : D-glucuronate / D-galacturonate TRAP transporter, large permease component
Original description: putative TRAP dicarboxylate transporter, DctM subunit
SEED: TRAP-type C4-dicarboxylate transport system, large permease component
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucuronate and D-galacturonate

PP_1168 : D-glucuronate / D-galacturonate TRAP transporter, small permease component
Original description: putative TRAP dicarboxylate transporter, DctQ subunit
SEED: TRAP-type C4-dicarboxylate transport system, small permease component
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucuronate and D-galacturonate

PP_1169 : D-glucuronate / D-galacturonate TRAP transporter, solute receptor component
Original description: TRAP dicarboxylate transporter, DctP subunit
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucuronate and D-galacturonate

PP_1170 : D-glucaro-1,5-lactonase UxuL
Original description: Gluconolactonase
SEED: Gluconolactonase (EC 3.1.1.17)
KEGG: no annotation
Rationale: Specifically important for utilization of D-glucuronate. Glucuronate appears to be oxidized by an oxidative pathway via uronate dehydrogenase (PP_1171). PP_1170 is 72% identical to PSPTO_1052 or UxuL, which a glucaro-1,5-lactonase and a galactaro-1,5-lactonase (see PMC6304669).

PP_1171 : Uronate dehydrogenase (EC 1.1.1.203)
Original description: uronate dehydrogenase
SEED: Uronate dehydrogenase (EC 1.1.1.203)
KEGG: no annotation
Rationale: Specifically important for utilizing D-Glucuronic Acid. Automated validation from mutant phenotype: the predicted function (1.1.1.203) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PP_2018 : adhesin-associated BNR repeat protein
Original description: BNR domain protein
SEED: FIG002465: BNR repeat protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (PP_0765). This is also predicted to be an outer membrane protein.

PP_2019 : adhesin-associated MmpL efflux pump
Original description: putative multidrug efflux transporter, RND family
SEED: FIG005548: transport protein
KEGG: no annotation
Rationale: Conserved cofit with a putative adhesin (PP_0765). 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.

PP_2349 : nitrite transporter, HPP family
Original description: CBS domain protein
SEED: CBS domain protein
KEGG: CBS domain-containing membrane protein
Rationale: # Specifically important in nitrogen source Sodium nitrite. Related to Synpcc7942_1745, which can be a nitrite uptake transporter (PMID:24904028). Besides the HPP domain, it encodes two cytoplasmic CBS domains, which might play a regulatory role.

PP_2448 : Gamma-glutamylputrescine oxidase (EC 1.4.3.-)
Original description: gamma-glutamylputrescine oxidase
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: gamma-glutamylputrescine oxidase
Rationale: Specific phenotype: utilization of Putrescine Dihydrochloride

PP_2791 : 4-hydroxypentanoyl-CoA kinase, subunit LvaA
Original description: Aminoglycoside phosphotransferase
SEED: aminoglycoside phosphotransferase
KEGG: no annotation
Rationale: Specific phenotype: utilization of 4-Hydroxyvalerate, Levulinic Acid. See PMID:28947739

PP_2909 : glutarate hydroxylase
Original description: carbon starvation induced protein
SEED: Carbon starvation induced protein CsiD
KEGG: no annotation
Rationale: Specifically important in carbon source 2-Piperidinone; carbon source 5-Aminovaleric acid. This is part of the pathway from L-lysine and 5-aminovalerate to succinate. For detailed rationale and biochemical evidence, see https://doi.org/10.1101/450254

PP_3356 : p-coumarate CoA-ligase (EC 6.2.1.12)
Original description: feruloyl-CoA-synthetase
SEED: no annotation
KEGG: feruloyl-CoA synthase
Rationale: Specifically important in carbon source p-Coumaric acid. This is the first step in its catabolism.

PP_3357 : p-hydroxybenzaldehyde dehydrogenase vdh (EC 1.2.1.64)
Original description: vanillin dehydrogenase
SEED: Vanillin dehydrogenase (Hydroxybenzaldehyde dehydrogenase) (EC 1.2.1.28)
KEGG: no annotation
Rationale: Specifically important in carbon source p-Coumaric acid. This gene is known as vdh and has vanillin dehydrogenase activity, but it is not required for growth on vanillin (PMID:25026441). Instead, its primary substrate in vivo seems to be p-hydroxybenzaldehyde (which is the product of hydroxycinnamoyl-CoA hydratase-lyase)

PP_3358 : hydroxycinnamoyl-CoA hydratase-lyase (EC 4.1.2.61)
Original description: hydroxycinnamoyl-CoA hydratase-lyase
SEED: 4-hydroxycinnamoyl CoA hydratase/lyase (Enoyl-CoA hydratase/lyase) (EC 4.2.1.17)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important in carbon source p-Coumaric acid. This is the second step in p-coumaric acid catabolism. (Hydroxycinnamoyl-CoA is a synonym for p-coumaryl-CoA.)

PP_3492 : isobutyryl-CoA dehydrogenase (EC 1.3.8.5)
Original description: short-chain acyl-CoA dehydrogenase
SEED: no annotation
KEGG:
Rationale: Specific phenotype: utilization of L-Valine (mild phenotype, but confirmed by conservation)

PP_3590 : aromatic-amino-acid transaminase (EC 2.6.1.57)
Original description: D-lysine aminotransferase
SEED: Biosynthetic Aromatic amino acid aminotransferase alpha (EC 2.6.1.57)
KEGG: aromatic-amino-acid transaminase
Rationale: Required for utilization of phenylalanine or tyrosine as the sole nitrogen source (PMID:38323821). Has phenotypes on a variety of carbon sources, which probably indicates a (partly genetically-redundant) biosynthetic role as well. May also act on isoleucine or on 2-aminoadipate, as part of pipecolate degradation (PMC9004399). Was previously proposed to be D-lysine aminotransferase, but is not important for utilizing D-lysine (PMID:38323821). 71% identical to E. coli tyrB.

PP_3593 : L-lysine and D-lysine ABC transporter, substrate-binding component
Original description: Amino acid ABC transporter, periplasmic binding protein
SEED: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
KEGG: polar amino acid transport system substrate-binding protein
Rationale: Specifically important for utilization of L-lysine and D-lysine.

PP_3594 : L-lysine and D-lysine ABC transporter, permease component 1
Original description: Amino acid ABC transporter, membrane protein
SEED: Arginine transport system permease protein ArtQ
KEGG: polar amino acid transport system permease protein
Rationale: Specifically important for utilization of L-lysine and D-lysine.

PP_3595 : L-lysine and D-lysine ABC transporter, permease component 2
Original description: Amino acid ABC transporter, membrane protein
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specifically important for utilization of L-lysine and D-lysine.

PP_3597 : L-lysine and D-lysine ABC transporter, ATPase component
Original description: Amino-acid ABC transporter, ATP-binding protein
SEED: Lipoprotein releasing system ATP-binding protein LolD
KEGG: no annotation
Rationale: Specifically important for utilization of L-lysine and D-lysine.

PP_3598 : gamma-glutamyl-gamma-aminobutyrate hydrolase (EC: 3.5.1.94)
Original description: Peptidase C26
SEED: Para-aminobenzoate synthase, amidotransferase component (EC 2.6.1.85)
KEGG: putative glutamine amidotransferase
Rationale: # Specifically important in nitrogen source Putrescine Dihydrochloride; nitrogen source Propandiamine. 38% identical to E. coli PuuD. This reaction is the next step of putrescine degradation after gamma-glutamyl-putrescine ligase (PP_5184) and oxidase (PP_2448). The phenotype on propandiamine suggests that it is also active on 3-glutamyl-3-aminopropionate. See PMC9004399

PP_3599 : 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Original description: 5-dehydro-4-deoxyglucarate dehydratase
SEED: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
KEGG: 5-dehydro-4-deoxyglucarate dehydratase
Rationale: Specifically important for utilizing D-Glucuronic Acid. Automated validation from mutant phenotype: the predicted function (4.2.1.41) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PP_3621 : vanillin dehydrogenase, iorA-like component
Original description: isoquinoline 1-oxidoreductase subunit alpha
SEED: Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16)
KEGG: isoquinoline 1-oxidoreductase, alpha subunit
Rationale: Specifically important in carbon source Vanillin. This gene cluster is probably the major vanillin dehydrogenase in P. putida. This system is expected to use a molybdopterin cofactor, which explains why molybdate uptake is required for growth on vanillin (PMID:24136472).

PP_3622 : vanillin dehydrogenase, iorB-like component
Original description: putative Isoquinoline 1-oxidoreductase, beta subunit
SEED: Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
KEGG: isoquinoline 1-oxidoreductase, beta subunit
Rationale: Specifically important in carbon source Vanillin. This gene cluster is probably the major vanillin dehydrogenase in P. putida. This system is expected to use a molybdopterin cofactor, which explains why molybdate uptake is required for growth on vanillin (PMID:24136472).

PP_3623 : vanillin dehydrogenase, cytochrome c component
Original description: Alcohol dehydrogenase cytochrome c subunit
SEED: Putative diheme cytochrome c-553
KEGG: no annotation
Rationale: Specifically important in carbon source Vanillin. This gene cluster is probably the major vanillin dehydrogenase in P. putida. This system is expected to use a molybdopterin cofactor, which explains why molybdate uptake is required for growth on vanillin (PMID:24136472).

PP_3713 : 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: Specific phenotype: utilization of benzoic acid

PP_3721 : arginine:pyruvate transaminase AruH (EC 2.6.1.84)
Original description: Arginine--pyruvate transaminase AruH
SEED: Valine--pyruvate aminotransferase (EC 2.6.1.66)
KEGG: arginine:pyruvate transaminase
Rationale: Specific phenotype: utilization of L-Arginine. Similar to P.aeruginosa aruH (Q9HUI9)

PP_3948 : nicotinate dehydrogenase subunit B (EC 1.17.2.1)
Original description: nicotinate dehydrogenase subunit B
SEED: Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
KEGG: no annotation
Rationale: Specific phenotype: utilization of Nicotinic Acid. Also known as nicotinate hydroxylase

PP_4038 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: NADP-dependent dihydropyrimidine dehydrogenase subunit PreA
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: no annotation
Rationale: Specific phenotype: utilization of 3-aminobutyric acid, Uracil. The phenotype on 3-aminobutyrate is not explained

PP_4108 : 2-aminoadipate transaminase (EC 2.6.1.39)
Original description: putative 4-aminobutyrate aminotransferase
SEED: Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
KEGG: no annotation
Rationale: Specifically important in carbon source D-Lysine. D-lysine. This is part of the pathway from D-lysine to 2-oxoglutarate. For detailed rationale and biochemical evidence, see https://doi.org/10.1101/450254

PP_4493 : D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39)
Original description: putative oxidoreductase
SEED: Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD
KEGG: no annotation
Rationale: Specifically important in carbon source D-Lysine; carbon source L-Lysine; carbon source DL-2-Aminoadipic acid. This is part of the pathway from D-lysine to 2-oxoglutarate. For detailed rationale, see PMC6509195.

PP_5015 : 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.

PP_5260 : 2-oxoadipate decarboxylase/hydroxylase (2-hydroxyglutarate synthase)
Original description: metalloprotein, putative enzyme
SEED: FIG00960493: hypothetical protein
KEGG: no annotation
Rationale: Specifically important in carbon source L-Lysine; carbon source D-Lysine. This is part of the pathway from D-lysine to 2-oxoglutarate. For biochemical evidence that this enzyme forms 2-hydroxyglutarate, see https://doi.org/10.1101/450254

Or download reannotations for Pseudomonas putida KT2440 or for all organisms as tab-delimited tables