Updated annotations for Pseudomonas simiae WCS417

118 genes with updated (or confirmed) annotations:

PS417_05090 : ferric citrate outer membrane transporter (fecA)
Original description: transporter
SEED: Iron(III) dicitrate transport protein FecA @ Iron siderophore receptor protein
KEGG: iron complex outermembrane recepter protein
Rationale: Specific phenotype on citrate; 63% identical to E. coli fecA; SEED_correct

PS417_05405 : L-alanine and D-alanine permease
Original description: D-alanine/D-serine/glycine permease
SEED: D-serine/D-alanine/glycine transporter
KEGG: amino acid transporter, AAT family
Rationale: Important for utilizing both isomers of alanine, and no other transporter is apparent. Both phenotypes are conserved.

PS417_05575 : Glycerol kinase (EC 2.7.1.30)
Original description: glycerol kinase
SEED: Glycerol kinase (EC 2.7.1.30)
KEGG: glycerol kinase
Rationale: Specifically important for utilizing Glycerol. Automated validation from mutant phenotype: the predicted function (GLYCEROL-KIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PS417_06615 : ABC transporter for branched-chain amino acids, substrate-binding component
Original description: leucine ABC transporter substrate-binding protein
SEED: High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system substrate-binding protein
Rationale: Important for L-leucine utilization and detrimental for L-valine utilization. Not important for isoleucine utilization, but lose homologs are (AO353_17125, Pf1N1B4_3218), so probably transporters isoleucine as well. Close homologs are mildly important for phenylalanine utilization (i.e., PP_1141), so may transport phenylalanine as well.

PS417_06700 : 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.

PS417_06705 : 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.

PS417_00715 : required for octanoate transport, together with NodT, MFP, and FUSC proteins (PS417_00725, PS417_00720, PS417_00710)
Original description: membrane protein
SEED: membrane protein, putative
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). A conserved cofit operon. This and orthologous operons are important for growth in 20 mM octanoate (as the carbon source), which is probably toxic. This operon could also be for uptake rather than efflux.

PS417_07240 : Transcriptional regulator of deoxyribose catabolism
Original description: GntR family transcriptional regulator
SEED: Predicted regulator PutR for proline utilization, GntR family
KEGG: no annotation
Rationale: # Specifically important in carbon source 2-Deoxy-D-Ribose. Conserved synteny (in an apparent operon) with the SDR and the beta-keto acid cleavage enzyme suggested that it might regulate the operon. Motif analysis found a conserved palindrome GTGATCAC upstream of the operon that matches the motif for AkgR from Rhodobacter sphaeroides (PMCID: GTGATCAC), which is 32% identical to PS417_07240.

PS417_07245 : 2-deoxy-D-ribonate 3-dehydrogenase
Original description: 3-ketoacyl-ACP reductase
SEED: SHORT CHAIN DEHYDROGENASE
KEGG: no annotation
Rationale: Specifically important in carbon source 2-Deoxy-D-Ribose; also important for deoxyribonate utilization, so this is the second dehydrogenase in the pathway

PS417_07250 : 2-deoxy-3-keto-D-ribonoate cleavage enzyme
Original description: hypothetical protein
SEED: hypothetical protein AF1210
KEGG: no annotation
Rationale: # Specifically important in carbon source 2-Deoxy-D-Ribose; carbon source 2-Deoxy-D-ribonic acid lithium salt; this is a beta keto acid cleavage enzyme, see PMID:24240508

PS417_07255 : Deoxyribonolactonase
Original description: calcium-binding protein
SEED: Senescence marker protein-30
KEGG: no annotation
Rationale: # Specifically important in carbon source 2-Deoxy-D-Ribose; a putative lactonase

PS417_07260 : 2-deoxy-D-ribonate transporter 2
Original description: MFS transporter
SEED: Major facilitator superfamily MFS_1
KEGG: no annotation
Rationale: Specifically important for utilization of deoxyribose and deoxyribonate. Because deoxyribose is probably oxidized in the periplasm, this is probably a deoxyribonate transporter. It belongs to the MFS superfamily, and is in conserved proximity to other deoxyribonate utilization genes. Another MFS transporter, PS417_07265, is also important for utilizing deoxyribose and deoxyribonate, which is not explained..

PS417_07265 : 2-deoxy-D-ribonate transporter 1
Original description: membrane protein
SEED: Nitrate/nitrite transporter
KEGG: no annotation
Rationale: Specifically important for utilization of deoxyribose and deoxyribonate. Because deoxyribose is probably oxidized in the periplasm, this is probably a deoxyribonate transporter. It belongs to the MFS superfamily, and is in conserved proximity to other deoxyribonate utilization genes. Another putative transporter (PS417_07260) is also important for utilizing deoxyribose and deoxyribonate, which is not explained.

PS417_08035 : adenine transporter (MFS superfamily)
Original description: transporter
SEED: Putative transport protein
KEGG: no annotation
Rationale: specific phenotype on adenine and no other transporter was identified by the fitness data. Also mildly important on adenosine, which could reflect extracellular conversion to adenine

PS417_08810 : glyoxylate carboligase (EC 4.1.1.47)
Original description: glyoxylate carboligase
SEED: Glyoxylate carboligase (EC 4.1.1.47)
KEGG: tartronate-semialdehyde synthase
Rationale: Specific phenotype: utilization of 2'-Deoxyinosine, Deoxyribonucleic acid, Inosine. (purines are catabolized via urate, allantoin, glyoxylate)

PS417_08860 : small component of pyruvate transporter (yjcH-like)
Original description: membrane protein
SEED: Putative membrane protein, clustering with ActP
KEGG: no annotation
Rationale: Specifically important for pyruvate utilization. 59% identical to E. coli yjcH.

PS417_08865 : large component of pyruvate transporter (actP-like)
Original description: acetate permease
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: Specifically important for pyruvate utilization.

PS417_10880 : cytochrome c component of deoxyribose dehydrogenase
Original description: alcohol dehydrogenase
SEED: Putative diheme cytochrome c-553
KEGG: no annotation
Rationale: Specifically important in carbon source 2-Deoxy-D-Ribose. This gene is in a conserved cluster with the iorAB-like subunits of deoxyribose dehydrogenase and has a similar (if weaker) fitness pattern. It is probably the electron acceptor in vivo.

PS417_10885 : Deoxyribose 1-dehydrogenase, beta subunit
Original description: isoquinoline 1-oxidoreductase
SEED: Isoquinoline 1-oxidoreductase beta subunit (EC 1.3.99.16)
KEGG: isoquinoline 1-oxidoreductase, beta subunit
Rationale: # Specifically important in carbon source 2-Deoxy-D-Ribose; not required for deoxyribonoate utilization; related to iorB

PS417_10890 : Deoxyribose 1-dehydrogenase, alpha subunit
Original description: (2Fe-2S)-binding protein
SEED: Isoquinoline 1-oxidoreductase alpha subunit (EC 1.3.99.16)
KEGG: isoquinoline 1-oxidoreductase, alpha subunit
Rationale: # Specifically important in carbon source 2-Deoxy-D-Ribose; not required for deoxyribonoate utilization; related to iorA

PS417_10925 : malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18)
Original description: methylmalonate-semialdehyde dehydrogenase
SEED: Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for: m-Inositol. 3-oxopropionate or malonate semialdehyde is an intermediate in myo-inositol catabolism

PS417_10945 : Xylose isomerase (EC 5.3.1.5)
Original description: xylose isomerase
SEED: Xylose isomerase (EC 5.3.1.5)
KEGG: xylose isomerase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PS417_11000 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: dihydroxy-acid dehydratase
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for: L-Arabinose. L-arabonate is an intermediate in the oxidation of L-arabinose (SEED_correct)

PS417_11005 : L-arabinose transporter
Original description: MFS transporter
SEED: Nitrate/nitrite transporter
KEGG: no annotation
Rationale: Specific phenotype: utilization of L-Arabinose. A strong and conserved phenotype.

PS417_11015 : Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: ketoglutarate semialdehyde dehydrogenase
SEED: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: NADP-dependent aldehyde dehydrogenase
Rationale: Specifically important for: L-Arabinose. alpha-ketoglutarate semialdehyde is an intermediate in the oxidation of L-arabinose (SEED_correct)

PS417_11020 : L-arabinolactonase (EC 3.1.1.15)
Original description: gluconolaconase
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Specifically important for: L-Arabinose. a step in L-arabinose oxidation (SEED_correct)

PS417_11520 : Sorbitol dehydrogenase (EC 1.1.1.14)
Original description: sorbitol dehydrogenase
SEED: Sorbitol dehydrogenase (EC 1.1.1.14)
KEGG: no annotation
Rationale: Specifically important for: D-Sorbitol. The first step in sorbitol degradation (SEED_correct)

PS417_11850 : 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.

PS417_11855 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: xylose isomerase
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.

PS417_11860 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: 5-deoxyglucuronate isomerase
SEED: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
KEGG: 5-deoxy-glucuronate isomerase
Rationale: Specifically important for utilizing m-Inositol.

PS417_11870 : 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 hydrolase
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.

PS417_11875 : 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.

PS417_11885 : Inositol transport system sugar-binding protein
Original description: rhizopine-binding protein
SEED: Inositol transport system sugar-binding protein
KEGG: simple sugar transport system substrate-binding protein
Rationale: specific phenotype on inositol. SEED_correct

PS417_11890 : Inositol transport system ATP-binding protein
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 inositol. SEED_correct

PS417_11895 : Inositol transport system permease protein
Original description: ABC transporter
SEED: Inositol transport system permease protein
KEGG: simple sugar transport system permease protein
Rationale: specific phenotype on inositol. SEED_correct

PS417_12055 : xylitol ABC transporter, substrate-binding component
Original description: sugar ABC transporter substrate-binding protein
SEED: Inositol transport system sugar-binding protein
KEGG: ribose transport system substrate-binding protein
Rationale: Specifically important for utilizing xylitol.

PS417_12060 : xylitol ABC transporter, permease component
Original description: sugar ABC transporter permease
SEED: Inositol transport system permease protein
KEGG: ribose transport system permease protein
Rationale: Specifically important for utilizing xylitol.

PS417_12065 : xylitol ABC transporter, ATPase component
Original description: D-ribose transporter ATP-binding protein
SEED: Inositol transport system ATP-binding protein
KEGG: ribose transport system ATP-binding protein
Rationale: Specifically important for utilizing xylitol.

PS417_12125 : 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)

PS417_12555 : 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: phosphogluconate 2-dehydrogenase
Rationale: Variably important for glucose utilization, especially with nitrogen sources other than ammonia. 72% identical to the characterized KguD from P.putida (PP3376, see PMC4646247)

PS417_12700 : ABC transporter for D-Mannitol and D-Sorbitol, ATPase component
Original description: ABC transporter ATP-binding protein
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: sorbitol/mannitol transport system ATP-binding protein
Rationale: Specific phenotype on D-Sorbitol; D-Mannitol. Also important for D-mannose utilization, but is closely related to a P. aeruginosa system that is apparently not a mannose transporter (the substrate-binding component PA2338 does not bind mannose, see PMC6829864).

PS417_12705 : ABC transporter for D-Mannitol and D-Sorbitol, permease component 1
Original description: mannitol ABC transporter permease
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Specific phenotypes on D-Mannitol; D-Sorbitol. Also important for D-mannose utilization, but closely related to a P. aeruginosa system that is apparently not a mannose transporter (the substrate-binding component PA2338 does not bind mannose, see PMC6829864).

PS417_12710 : ABC transporter for D-Mannitol and D-Sorbitol, permease component 2
Original description: sugar ABC transporter permease
SEED: Various polyols ABC transporter, permease component 1
KEGG: sorbitol/mannitol transport system permease protein
Rationale: Very important for utilization of D-sorbitol, D-mannitol. Also important for D-mannose utilization, but closely related to a P. aeruginosa system that is apparently not a mannose transporter (the substrate-binding component PA2338 does not bind mannose, see PMC6829864).

PS417_12715 : ABC transporter for D-Mannitol and D-Sorbitol, periplasmic substrate-binding protein
Original description: sugar ABC transporter substrate-binding protein
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: sorbitol/mannitol transport system substrate-binding protein
Rationale: Specific phenotype on D-Sorbitol; D-Mannitol. Also important for D-mannose utilization, Also important for D-mannose utilization, but closely related to a P. aeruginosa system that is apparently not a mannose transporter (the substrate-binding component PA2338 does not bind mannose, see PMC6829864).

PS417_13835 : 3-hydroxyisobutyryl-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. KEGG no longer makes any prediction (see pfo:Pfl01_2864). 3-hydroxy-isobutanoyl-CoA is an intermediate in valine degradation. (SEED_correct)

PS417_13840 : isobutyryl-CoA dehydrogenase (EC 1.3.8.5)
Original description: acyl-CoA dehydrogenase
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG:
Rationale: Specifically important for: L-Valine. SEED annotates it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in valine catabolism

PS417_13850 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: acyl-CoA dehydrogenase
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Specifically important for: L-Isoleucine. SEED has it as butyryl-CoA dehydrogenase, which is also expected to perform this reaction in isoleucine catabolism

PS417_14725 : 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.

PS417_14730 : 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.

PS417_14735 : Nitrate reductase (EC 1.7.99.4)
Original description: reductase
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: no annotation
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.

PS417_01575 : 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.

PS417_17015 : 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.

PS417_01705 : 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.

PS417_01720 : 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.

PS417_17330 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: dihydropyrimidine dehydrogenase
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: no annotation
Rationale: Specifically important for utilizing Cytidine. 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.

PS417_17360 : D-galacturonate dehydrogenase (EC 1.1.1.203)
Original description: NAD-dependent dehydratase
SEED: UDP-glucose 4-epimerase (EC 5.1.3.2)
KEGG: no annotation
Rationale: Specifically important for: D-Galacturonic Acid monohydrate. KEGG now annotates it as uronate dehydrogenase which is correct (although less specific) (KEGG_correct)

PS417_17365 : galactaro-1,5-lactonase
Original description: gluconolactonase
SEED: Gluconolactonase (EC 3.1.1.17)
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Galacturonic Acid monohydrate. This is the second step after D-galacturonate dehydrogenase (PS417_17360) and forms meso-galactarate, which is the substrate of PS417_04210. The substrate is probably the 1,5-lactone, not the 1,4-lactone, given the characterization of the D-galacturonate dehydrogenase from Agrobacterium tumefaciens (PMID:24450804), which is 51% identical to PS417_17360.

PS417_17420 : ethanol oxidation regulatory protein ercA
Original description: alcohol dehydrogenase
SEED: Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
KEGG: no annotation
Rationale: Strongest phenotype is on ethanol. Similar to ercA (PA1991) which apparently has a regulatory role (PMCID: PMC3754586) rather than being directly involved in catabolism. Consistent with a regulatory role, this gene has pleiotropic phenotypes. The main ethanol dehydrogenase is probably PS417_17460.

PS417_17460 : Quinoprotein ethanol dehydrogenase QedA (EC 1.1.2.8)
Original description: quinonprotein alcohol dehydrogenase
SEED: Quino(hemo)protein alcohol dehydrogenase, PQQ-dependent (EC 1.1.99.8)
KEGG: alcohol dehydrogenase (cytochrome c)
Rationale: Important for ethanol utilization. Milder phenotypes on L-Arginine and L-Citrulline are not explained. 90% identical to A8R3S4 , which acts on longer primary alcohols as well

PS417_17550 : branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit (EC 1.2.4.4)
Original description: 2-oxoisovalerate dehydrogenase
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, beta subunit
Rationale: Specifically important for utilizing L-Isoleucine; L-Leucine.

PS417_17560 : Dihydrolipoyl dehydrogenase (EC 1.8.1.4)
Original description: dihydrolipoamide dehydrogenase
SEED: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
KEGG: dihydrolipoamide dehydrogenase
Rationale: Specifically important for utilizing L-Leucine; L-Isoleucine. 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.

PS417_17580 : citrulline utilization hydrolase
Original description: amidinotransferase
SEED: no annotation
KEGG: no annotation
Rationale: Important on citrulline. This enzyme is distantly related to characterized arginine deiminases (see PF02274) and has conserved catalytic residues. It might be a citrullinase.

PS417_17720 : xylitol 2-dehydrogenase (EC 1.1.1.9)
Original description: iditol 2-dehydrogenase
SEED: Xylitol dehydrogenase (EC 1.1.1.9)
KEGG: L-iditol 2-dehydrogenase
Rationale: Specifically important for: Xylitol. This is the first step in xylitol degradation (SEED_correct)

PS417_18395 : D-ribose ABC transporter, permease component RbsC
Original description: ABC transporter permease
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: ribose transport system permease protein
Rationale: Specifically important for utilizing D-Ribose.

PS417_18400 : D-ribose ABC transporter, ATPase component RbsA
Original description: sugar ABC transporter ATPase
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: ribose transport system ATP-binding protein
Rationale: Specifically important for utilizing D-Ribose.

PS417_18405 : D-ribose ABC transporter, substrate-binding component RbsB
Original description: LacI family transcriptional regulator
SEED: Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
KEGG: ribose transport system substrate-binding protein
Rationale: No fitness data for this gene, but data for PS417_18400:18395 confirm this is the ABC transporter for ribose.

PS417_01850 : 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.

PS417_19130 : L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3)
Original description: lactate dehydrogenase
SEED: L-lactate dehydrogenase (EC 1.1.2.3)
KEGG: L-lactate dehydrogenase (cytochrome)
Rationale: Specifically important for utilizing Sodium L-Lactate. Automated validation from mutant phenotype: the predicted function (1.1.2.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PS417_19435 : urate hydroxylase (1.7.3.3)
Original description: membrane protein
SEED: FIG137887: membrane protein related to purine degradation
KEGG: no annotation
Rationale: Specific phenotype: utilization of Deoxyribonucleic acid, Inosine. (purines are catabolized via urate, allantoin, glyoxylate). 40% identical to A9CI11

PS417_20885 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: FAD-binding molybdopterin dehydrogenase
SEED: Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A (1.17.1.4)
KEGG: xanthine dehydrogenase small subunit
Rationale: Specifically important for utilizing Inosine. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PS417_20890 : Xanthine dehydrogenase (EC 1.17.1.4)
Original description: xanthine dehydrogenase
SEED: Xanthine dehydrogenase, molybdenum binding subunit (EC 1.17.1.4)
KEGG: xanthine dehydrogenase large subunit
Rationale: Specifically important for utilizing Inosine. Automated validation from mutant phenotype: the predicted function (1.17.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PS417_20960 : Nitrate-binding regulatory protein (nasS)
Original description: nitrate transporter
SEED: Nitrate ABC transporter, nitrate-binding protein
KEGG: sulfonate/nitrate/taurine transport system substrate-binding protein
Rationale: This protein is specifically important for the utilization of nitrate as a nitrogen source, but this may be a polar effect. It is74% identical to the nasS/PA1786 protein from P. aeruginosa (PMID:22493305) and to nasS from Azotobacter vinelandii (PMID:8748040), which binds nitrate and suppresses the activity of the transcriptional activator nasT. It is also more distantly related to the periplasmic substrate-binding components of nitrate ABC transporters (i.e., 37% identity to the N terminal part of ntrC/sll1452 and 36% identity to ntrA/sll1450), hence the misannotation as a transporter.

PS417_21500 : C4 dicarboxylate transporter DctA
Original description: C4-dicarboxylate transporter
SEED: no annotation
KEGG: aerobic C4-dicarboxylate transport protein
Rationale: Specific phenotype: utilization of succinate. Subtly important for octanoate utilization, which is not explained. Close homologs are important for the utilization of malate or fumarate as well

PS417_21710 : Succinylornithine transaminase (EC 2.6.1.81)
Original description: acetylornithine aminotransferase
SEED: Succinylornithine transaminase (EC 2.6.1.81)
KEGG: acetylornithine/N-succinyldiaminopimelate aminotransferase
Rationale: Specifically important for: L-Arginine. succinylornithine transaminase is involved in L-arginine degradation via N-succinylarginine. Also this gene is cofit with other putative steps in that pathway (N-succinylarginine dihydrolase, succinylglutamate-semialdehyde dehydrogenase, succinylglutamate desuccinylase). In contrast, neither of the functions proposed by KEGG have an obvious relationship to arginine catabolism. (SEED_correct)

PS417_21735 : ABC transporter for L-Arginine, permease component 2
Original description: amino acid ABC transporter permease
SEED: Arginine/ornithine ABC transporter, permease protein AotM
KEGG: arginine/ornithine transport system permease protein
Rationale: Specific phenotype on L-Arginine. This gene is listed because other components of the arginine transporter are misannotated. (SEED_correct) (KEGG_correct)

PS417_21740 : ABC transporter for L-Arginine, permease component 1
Original description: ABC transporter
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotypes on L-Arginine; L-Arginine. KEGG annotation has been updated since the last public release (KEGG_correct)

PS417_21745 : ABC transporter for L-Arginine, 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. The ATPase component of this system is not clear. PS417_21725 is nearby and similar to aotP, but has no phenotype on arginine. It might be redundant with another ATPase? (SEED_correct) (KEGG_correct)

PS417_22065 : Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Original description: long-chain fatty acid--CoA ligase
SEED: Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
KEGG: long-chain acyl-CoA synthetase
Rationale: Specifically important for utilizing Sodium octanoate. 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.

PS417_22130 : glucose/xylose ABC transporter, ATPase component
Original description: sugar ABC transporter ATPase
SEED: Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-)
KEGG: multiple sugar transport system ATP-binding protein
Rationale: Specifically important for utilization of D-glucose 6-phosphate and D-xylose. Glucokinase (PS417_22685) is important for glucose-6-phosphate utilization, which implies that it is hydrolyzed to glucose before uptake.

PS417_22135 : glucose/xylose ABC transporter, permease component 1
Original description: sugar ABC transporter permease
SEED: Glucose ABC transport system, inner membrane component 2
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilization of D-glucose 6-phosphate and D-xylose. Glucokinase (PS417_22685) is important for glucose-6-phosphate utilization, which implies that it is hydrolyzed to glucose before uptake.

PS417_22140 : glucose/xylose ABC transporter, permease component 2
Original description: sugar ABC transporter permease
SEED: Glucose ABC transport system, inner membrane component 1
KEGG: multiple sugar transport system permease protein
Rationale: Specifically important for utilization of D-glucose 6-phosphate and D-xylose. Glucokinase (PS417_22685) is important for glucose-6-phosphate utilization, which implies that it is hydrolyzed to glucose before uptake.

PS417_22145 : glucose/xylose ABC transporter, periplasmic substrate-binding component
Original description: sugar ABC transporter substrate-binding protein
SEED: Glucose ABC transport system, periplasmic sugar-binding protein
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specifically important for utilization of D-glucose 6-phosphate and D-xylose. Glucokinase (PS417_22685) is important for glucose-6-phosphate utilization, which implies that it is hydrolyzed to glucose before uptake. PS417_22145 is 88% identical to GtsA from P. putida, which is well known as a glucose transporter, but is also involved in xylose uptake in strain S12 (PMC3340264).

PS417_22150 : 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. D-mannose isomerase is the first step in mannose catabolism. This gene is similar to the putative mannose isomerase Sama_0560 (PMID:20836887, PMCID: PMC4436071).

PS417_22360 : 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.

PS417_22370 : Aminomethyltransferase (EC 2.1.2.10)
Original description: glycine cleavage system protein T
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.

PS417_22685 : Glucokinase (EC 2.7.1.2)
Original description: glucokinase
SEED: Glucokinase (EC 2.7.1.2)
KEGG: glucokinase
Rationale: Specifically important for utilizing D-Trehalose dihydrate. Automated validation from mutant phenotype: the predicted function (GLUCOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PS417_22985 : 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.

PS417_23035 : D-trehalose PTS system, I, HPr, and IIA components
Original description: PTS mannose transporter subunit IIC
SEED: PTS system, glucose-specific IIA component (EC 2.7.1.69) / 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 for trehalose and no other trehalose transporter is apparent in the fitness data. The IIB and IIC components are provided by PS417_23050

PS417_23040 : D-trehalose outer membrane porin
Original description: maltoporin
SEED: Maltoporin (maltose/maltodextrin high-affinity receptor, phage lambda receptor protein)
KEGG: maltoporin
Rationale: Specific phenotype for trehalose (and conserved)

PS417_23045 : 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.

PS417_23050 : 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.

PS417_23650 : 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.

PS417_23660 : 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.

PS417_23665 : Muconolactone isomerase (EC 5.3.3.4)
Original description: muconolactone delta-isomerase
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.

PS417_23670 : Muconate cycloisomerase (EC 5.5.1.1)
Original description: muconate cycloisomerase
SEED: Muconate cycloisomerase (EC 5.5.1.1)
KEGG: muconate cycloisomerase
Rationale: Specifically important for utilizing L-Tryptophan. Automated validation from mutant phenotype: the predicted function (MUCONATE-CYCLOISOMERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

PS417_23685 : anthranilate 1,2-dioxygenase (deaminating, decarboxylating) large subunit [EC: 1.14.12.1]
Original description: anthranilate 1,2-dioxygenase
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: L-Tryptophan. anthranilate is an intermediate in the breakdown of tryptophan (via kynurenine) (KEGG_correct)

PS417_23690 : Anthranilate 1,2-dioxygenase (deaminating, decarboxylating) (EC 1.14.12.1)
Original description: benzene 1,2-dioxygenase
SEED: Anthranilate dioxygenase small subunit
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.

PS417_23695 : electron transfer component of the anthranilate 1,2-dioxygenase system (EC 1.14.12.1)
Original description: 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 PS417_23685 and PS417_23690.

PS417_23705 : 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.

PS417_23710 : 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.

PS417_24105 : D-lactate transporter (lctP family)
Original description: L-lactate permease
SEED: L-lactate permease
KEGG: lactate transporter, LctP family
Rationale: specific phenotype for D-lactate and no other transporter for D-lactate was apparent in the fitness data. Also important for utilization of D,L-lactate. Not clear if it transports L-lactate as well or not, but since it is in an apparent operon with a D-lactate dehydrogenase (PS417_24110), its main role is probably for transport of D-lactate.

PS417_02455 : putative transporter, required for glycine utilization
Original description: membrane protein
SEED: putative membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). Substrate is a conserved specific phenotype of UPF0126

PS417_25960 : Acyl-CoA dehydrogenase (EC 1.3.8.7)
Original description: acyl-CoA dehydrogenase
SEED: Acyl-CoA dehydrogenase (EC 1.3.8.7)
KEGG: no annotation
Rationale: Specifically important for: Sodium octanoate. presumably part of beta oxidation, but not sure why 2 different ones are required (could relate to different chain lengths) (SEED_correct)

PS417_25975 : 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 octanoate. presumably part of beta oxidation, but not sure why 2 different ones are required (could relate to different chain lengths) (SEED_correct)

PS417_27115 : putrescine ABC transporter, ATPase component
Original description: transporter
SEED: Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)
KEGG: putrescine transport system ATP-binding protein
Rationale: Specific phenotype: utilization of Putrescine Dihydrochloride

PS417_27130 : Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Original description: aminotransferase
SEED: Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
KEGG: putrescine aminotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. KEGG annotates this as putrescine aminotransferase, probably based on similarity to spuC (PA0299) of P. aeruginosa, but it is believed that only the g-glutamyl- pathway operates in P. aeruginosa (X. Yao et al 2011, PMC3147493)

PS417_27140 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: gamma-glutamylputrescine synthetase
SEED: glutamine synthetase family protein
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride; L-Arginine. The first step in the gamma-glutamyl-putrescine pathway

PS417_02710 : Urease maturation and nickel insertion protein UreE
Original description: urease accessory protein UreE
SEED: Urease accessory protein UreE
KEGG: urease accessory protein
Rationale: Specific phenotype: utilization of Inosine, Urea. (Inosine is broken down to ureidoglycolate, which is cleaved to glyoxylate and urea by PS417_19430.) For the specific role of UreE, see PMID:23539618

PS417_27745 : gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.99); 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
Original description: aldehyde dehydrogenase
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: 4-guanidinobutyraldehyde dehydrogenase / NAD-dependent aldehyde dehydrogenase
Rationale: Specifically important for putrescine utilization as part of the gamma-glutamylputrescine pathway. Similar to the 4-guanidinobutyraldehyde dehydrogenase from P. putida (kauB), which is involved in arginine catabolism, and 92% identical to AO356_12580, which is also involved in arginine catabolism. Mutants in PS417_27745 seem to have a very subtle defect in arginine catabolism; it probably has both activities.

PS417_02785 : 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.

PS417_28100 : glucose-6-phosphate 1-epimerase [EC: 5.1.3.15]
Original description: aldose epimerase
SEED: Aldose 1-epimerase
KEGG: glucose-6-phosphate 1-epimerase
Rationale: Specifically important for: D-Trehalose dihydrate; N-Acetyl-D-Glucosamine. NAG is phosphorylated by a PTS system, deacetylated (PS417_22985), and converted to fructose-6-phosphate by an aminotranferase (PS417_22990). One might expect the fructose-6-P to be converted to fructose-1,6-bisphosphate, but no gene for that is apparent in this organism or many other Pseudomonas (nor did the fitness data highlight any kinase). Instead, the fructose-6-phosphate is apparently converted to glucose-6-phosphate by the glucose-6-phosphate isomerase (PS417_23920) and oxidized by G6P dehydrogenase (PS417_22110). (Both of these genes are essential so we cannot confirm this.) G6P dehydrogenase is reportedly specific for the beta form, while G6P isomerase produces the alpha form of G6P, so it makes sense for a glucose-6-P epimerase to be involved (even though the reaction can occur spontaneously). This gene is also mildly important for trehalose utilization, which involves the hydrolysis of trehalose 6-phosphate to glucose-6-phosphate. Because trehalose has an alpha 1->1 linkage, the product is probably alpha-G6P. Thus, this gene's phenotypes are consistent with KEGG's annotation as glucose-6-phosphate 1-epimerase. (KEGG_correct)

PS417_03965 : fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
Original description: PTS fructose transporter subunit IIA
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: PTS system, fructose-specific IIA component ; phosphotransferase system, enzyme I, PtsI ; phosphocarrier protein FPr
Rationale: Specifically important for utilizing fructose and mannose. The phenotype on mannose is not explained.

PS417_04060 : dipeptide ABC transporter, permease component
Original description: peptide ABC transporter permease
SEED: Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)
KEGG: dipeptide transport system permease protein
Rationale: Specific phenotype: utilization of Gly-Glu. Nearly identical to AO353_05395, which is also important for utilization of Gly-DL-Asp

PS417_04195 : 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-Galacturonic Acid monohydrate. 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.

PS417_04200 : 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: aldehyde dehydrogenase
SEED: 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Specifically important for: D-Galacturonic Acid monohydrate. alpha-ketoglutarate semialdehyde is an intermediate in the oxidation of galacturonate (SEED_correct)

PS417_04205 : D-galacturonate transporter (MFS superfamily)
Original description: glucarate transporter
SEED: D-galactarate permease
KEGG: MFS transporter, ACS family, glucarate transporter
Rationale: Specific phenotype on galacturonate. This phenotype is conserved. There is also another putative hexuronate transporter that has a weaker phenotype on galacturonate (PS417_14775).

PS417_04210 : Galactarate dehydratase (EC 4.2.1.42)
Original description: galactarate dehydrogenase
SEED: D-galactarate dehydratase (EC 4.2.1.42)
KEGG: galactarate dehydratase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (4.2.1.42) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

PS417_04415 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase catalytic subunit
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.

Or download reannotations for Pseudomonas simiae WCS417 or for all organisms as tab-delimited tables