Updated Annotations for Pseudomonas fluorescens FW300-N2E2

Updated annotations for Pseudomonas fluorescens FW300-N2E2

116 genes with updated (or confirmed) annotations:

Pf6N2E2_1146 : 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5)
Original description: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
SEED: Butyryl-CoA dehydrogenase (EC 1.3.99.2)
KEGG: no annotation
Rationale: Specifically important for: L-Isoleucine. 2-methylbutanoyl-CoA is an intermediate in isoleucine catabolism.

Pf6N2E2_1226 : DNA damage response nuclease
Original description: Hypothetical protein, restriction endonuclease-like 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.

Pf6N2E2_159 : DNA damage resistance protein
Original description: FIG00953874: hypothetical protein
SEED: FIG00953874: hypothetical protein
KEGG: no annotation
Rationale: PFam PF07867.7 (DUF1654). Conserved specific phenotype for cisplatin resistance, in an operon with an endonuclease, and close homologs are regulated by LexA

Pf6N2E2_1650 : Sucrose alpha-glucosidase (EC 3.2.1.48)
Original description: Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)
SEED: Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)
KEGG: beta-fructofuranosidase
Rationale: Specifically important for utilizing Sucrose. Automated validation from mutant phenotype: the predicted function (3.2.1.48-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_1668 : Xylonate dehydratase (EC 4.2.1.82)
Original description: Xylonate dehydratase (EC 4.2.1.82)
SEED: Xylonate dehydratase (EC 4.2.1.82)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_1959 : D-sorbitol dehydrogenase (EC 1.1.1.14)
Original description: Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
SEED: Multiple polyol-specific dehydrogenase (EC 1.1.1.-)
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Sorbitol. This is the first step in sorbitol degradation.

Pf6N2E2_1960 : ABC transporter for D-sorbitol, ATPase component
Original description: Various polyols ABC transporter, ATP-binding component
SEED: Various polyols ABC transporter, ATP-binding component
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Sorbitol

Pf6N2E2_1961 : ABC transporter for D-sorbitol, permease component 2
Original description: Various polyols ABC transporter, permease component 2
SEED: Various polyols ABC transporter, permease component 2
KEGG: sorbitol/mannitol transport system permease protein
Rationale: # Specifically important in carbon source D-Sorbitol. We do not have fitness data for the putative first subunit Pf6N2E2_1962.

Pf6N2E2_1962 : ABC transporter for D-sorbitol, permease component 1
Original description: Various polyols ABC transporter, permease component 1
SEED: Various polyols ABC transporter, permease component 1
KEGG: no annotation
Rationale: # Reannotated based on fitness data for other genes in the operon. We have no fitness data for this gene.

Pf6N2E2_1963 : ABC transporter for D-sorbitol, periplasmic substrate-binding component
Original description: Various polyols ABC transporter, periplasmic substrate-binding protein
SEED: Various polyols ABC transporter, periplasmic substrate-binding protein
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Sorbitol

Pf6N2E2_1965 : Fructokinase (EC 2.7.1.4)
Original description: Fructokinase (EC 2.7.1.4)
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Sorbitol. Automated validation from mutant phenotype: the predicted function (FRUCTOKINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_2047 : D-glucosaminate dehydratase (EC 4.3.1.9)
Original description: D-serine deaminase (EC 4.3.1.18)
SEED: D-serine deaminase (EC 4.3.1.18)
KEGG: no annotation
Rationale: Specifically important for: D-Glucosamine Hydrochloride. This enzyme had not previously been linked to a gene. This is the second step in catabolism of glucosamine, and the 'beta' form of the enzyme was expected to be PLP-dependent and about this size. Iwamoto et al (2003) purified a non-specific 'alpha' enzyme for this reaction (PMID: 12686150)

Pf6N2E2_2050 : ABC transporter for D-Glucosamine, putative ATPase component
Original description: ABC-type polar amino acid transport system, ATPase component
SEED: ABC-type polar amino acid transport system, ATPase component
KEGG: no annotation
Rationale: Lacks fitness data but is in a conserved operon with confirmed glucosamine utilization genes

Pf6N2E2_2051 : ABC transporter for D-Glucosamine Hydrochloride, permease component 1
Original description: Amino acid ABC transporter, permease protein
SEED: Amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride.

Pf6N2E2_2052 : ABC transporter for D-Glucosamine Hydrochloride, permease component 2
Original description: amino acid ABC transporter, permease protein
SEED: amino acid ABC transporter, permease protein
KEGG: polar amino acid transport system permease protein
Rationale: Specific phenotypes on D-Glucosamine Hydrochloride; D-Glucosamine Hydrochloride. ko:K02029 : polar amino acid transport system permease protein

Pf6N2E2_2053 : ABC transporter for D-Glucosamine, periplasmic substrate-binding component
Original description: Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
SEED: Glutamine ABC transporter, periplasmic glutamine-binding protein (TC 3.A.1.3.2)
KEGG: no annotation
Rationale: Specific phenotype on D-Glucosamine Hydrochloride.

Pf6N2E2_2074 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: Oxidoreductase probably involved in sulfite reduction
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

Pf6N2E2_2102 : Glutaminase (EC 3.5.1.2)
Original description: Glutaminase (EC 3.5.1.2)
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.

Pf6N2E2_2111 : Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit A
Original description: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5)
SEED: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A (EC 2.8.3.5)
KEGG: 3-oxoacid CoA-transferase subunit A
Rationale: Very important on cartinine and also important on L-phenylalanine and L-leucine. Acts on dehydrocarnitine during carnitine catabolism to give dehydrocarnitine-CoA. Probably also acts on acetoacetate, which is an intermediate in the degradation of phenylalanine (via tyrosine and homogentistate) and leucine (from HMG-CoA lyase). Both substrates are 3-oxoacids, but not sure if succinyl-CoA is the source of the CoA as annotated. Note that acetoacetyl-CoA is probably cleaved to acetyl-CoA by _2113 (downstream). Similar to DhcA = PA1999.

Pf6N2E2_2112 : Dehydrocarnitine CoA-transferase and acetoacetate CoA-transferase, subunit B
Original description: Succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B (EC 2.8.3.5)
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: Carnitine Hydrochloride; L-Phenylalanine. Also important on L-leucine. Converts dehydrocarnitine to dehydrocarnitine-CoA during carnitine catabolism. Probably also acts on acetoacetate, which is an intermediate in the degradation of phenylalanine (via tyrosine and homogentistate) and leucine (from HMG-CoA lyase). Both substrates are 3-oxoacids, but not sure if succinyl-CoA is the source of the CoA as annotated. Similar to DhcB = PA2000.

Pf6N2E2_2191 : Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Original description: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
SEED: Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
KEGG: no annotation
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.

Pf6N2E2_2192 : 3-methylcrotonyl-CoA carboxylase, beta subunit (EC 6.4.1.4)
Original description: Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
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 (6.4.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_2193 : Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
Original description: Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
SEED: Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
KEGG: methylglutaconyl-CoA hydratase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (METHYLGLUTACONYL-COA-HYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_2194 : 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit (EC 6.4.1.4)
Original description: Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
SEED: Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)
KEGG: 3-methylcrotonyl-CoA carboxylase alpha subunit
Rationale: Specifically important for utilizing L-Leucine.

Pf6N2E2_2376 : nitrate transporter
Original description: Nitrate/nitrite transporter
SEED: Nitrate/nitrite transporter
KEGG: MFS transporter, NNP family, nitrate/nitrite transporter
Rationale: Specific phenotype: utilization of nitrate. Similar B.subtilis nasA, which is a nitrate transporter (not a nitrate/nitrite antiporter)

Pf6N2E2_2378 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
SEED: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
KEGG: nitrite reductase (NAD(P)H) large subunit
Rationale: Specifically important for utilizing Sodium nitrate. Automated validation from mutant phenotype: the predicted function (1.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_2380 : Nitrate reductase (EC 1.7.99.4)
Original description: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
SEED: Assimilatory nitrate reductase large subunit (EC:1.7.99.4)
KEGG: nitrate reductase catalytic subunit
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.

Pf6N2E2_2427 : DNA damage response gene with a putative DNA binding domain and often regulated by LexA (PA0922-like)
Original description: Transcriptional regulators
SEED: Transcriptional regulators
KEGG: no annotation
Rationale: Conserved and specific phenotype: important for resisting cisplatin.

Pf6N2E2_2630 : Phenylalanine 4-monooxygenase (EC 1.14.16.1)
Original description: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
SEED: Phenylalanine-4-hydroxylase (EC 1.14.16.1)
KEGG: phenylalanine-4-hydroxylase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.14.16.1) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_2632 : tyrosine aminotransferase (EC 2.6.1.57)
Original description: Aspartate aminotransferase (EC 2.6.1.1)
SEED: Aspartate aminotransferase (EC 2.6.1.1)
KEGG: aromatic-amino-acid transaminase
Rationale: Specifically important for: L-Phenylalanine. Phenylalanine is first hydroxylated to tyrosine (Pf6N2E2_2630) and then transaminated. KEGG has same EC# but less specific. (KEGG_correct)

Pf6N2E2_2878 : required for 4-hydroxybenzoate and octanoate transport, together with MFP and FUSC proteins (Pf6N2E2_2877, Pf6N2E2_2879)
Original description: FIG00953813: hypothetical protein
SEED: FIG00953813: hypothetical protein
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). A conserved cofit operon. Important for utilization of octanoate and 4-hydroxybenzoate, which are probably toxic at the high concentrations used (5-20 mM), but it could also be for uptake rather than efflux.

Pf6N2E2_2914 : 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2)
Original description: P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
SEED: P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
KEGG: p-hydroxybenzoate 3-monooxygenase
Rationale: Specifically important for utilizing 4-Hydroxybenzoic Acid. Automated validation from mutant phenotype: the predicted function (1.14.13.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_2921 : ABC transporter for L-leucine/L-phenylalanine/D-alanine, substrate-binding component LivK
Original description: High-affinity leucine-specific transport system, periplasmic binding protein LivK (TC 3.A.1.4.1)
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 utilization of leucine, phenylanine, or D-alanine. Slightly important for utilization of isoleucine as a carbon source and detrimental when isoleucine is the nitrogen source.

Pf6N2E2_2923 : ABC transporter for L-leucine/L-phenylalanine/D-alanine, permease component 1 LivH
Original description: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
SEED: High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system permease protein
Rationale: Important for utilization of leucine, phenylanine, or D-alanine. Slightly important for utilization of isoleucine as a carbon source and detrimental when isoleucine is the nitrogen source.

Pf6N2E2_2924 : ABC transporter for L-leucine/L-isoleucine/L-phenylalanine/D-alanine, permease component 2 LivM
Original description: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system permease protein
Rationale: Important for utilization of leucine, phenylanine, or D-alanine. Slightly important for utilization of isoleucine as a carbon source and detrimental when isoleucine is the nitrogen source.

Pf6N2E2_2925 : ABC transporter for L-leucine/L-isoleucine/L-phenylalanine/D-alanine, ATPase component 1 LivG
Original description: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Important for utilization of leucine, phenylanine, or D-alanine. Slightly important for utilization of isoleucine as a carbon source and detrimental when isoleucine is the nitrogen source.

Pf6N2E2_2926 : ABC transporter for L-leucine/L-isoleucine/L-phenylalanine/D-alanine, ATPase component 2 LivF
Original description: Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Important for utilization of leucine, phenylanine, or D-alanine. Slightly important for utilization of isoleucine as a carbon source and detrimental when isoleucine is the nitrogen source.

Pf6N2E2_2958 : ABC transporter for L-Lysine, periplasmic substrate-binding component
Original description: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
SEED: Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
KEGG: lysine/arginine/ornithine transport system substrate-binding protein
Rationale: Specific phenotype on L-Lysine; Gly-Glu. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear.

Pf6N2E2_2959 : ABC transporter for L-Lysine, permease component 1
Original description: Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
SEED: Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Specific phenotypes on L-Lysine. Also important on gly-glu. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear.

Pf6N2E2_2960 : ABC transporter for L-Lysine, permease component 2
Original description: Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
SEED: Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)
KEGG: histidine transport system permease protein
Rationale: Specific phenotype on Gly-Glu; L-Lysine. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear.

Pf6N2E2_2962 : ABC transporter for L-Lysine, ATPase component
Original description: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
SEED: Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
KEGG: histidine transport system ATP-binding protein
Rationale: Very important for L-lysine and gly-glu utilization. There is another dedicated transporter for the dipeptide gly-glu so the basis of that phenotype is unclear.

Pf6N2E2_3251 : histidinol-phosphate aminotransferase (EC 2.6.1.9)
Original description: Histidinol-phosphate aminotransferase (EC 2.6.1.9)
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.

Pf6N2E2_3253 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase (EC 2.4.2.17)
SEED: ATP phosphoribosyltransferase (EC 2.4.2.17)
KEGG: ATP phosphoribosyltransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00070.

Pf6N2E2_3553 : Urease (EC 3.5.1.5)
Original description: Urease gamma subunit (EC 3.5.1.5)
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.

Pf6N2E2_3556 : Urease (EC 3.5.1.5)
Original description: Urease alpha subunit (EC 3.5.1.5)
SEED: Urease alpha subunit (EC 3.5.1.5)
KEGG: no annotation
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.

Pf6N2E2_3577 : ABC transporter for L-leucine/L-isoleucine/D-alanine, ATPase component 1 LivG
Original description: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
SEED: Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
KEGG: branched-chain amino acid transport system ATP-binding protein
Rationale: Specific phenotype: utilization of D-Alanine, L-Leucine, and weaker phenotypes on L-Isoleucine

Pf6N2E2_3621 : putative transporter, required for glycine utilization
Original description: putative membrane protein
SEED: putative membrane protein
KEGG: no annotation
Rationale: PFam PF03458.9 (UPF0126). conserved specific phenotype of UPF0126

Pf6N2E2_3637 : yqiA-like hydrolase, affects the cell envelope
Original description: Putative esterase, FIGfam005057
SEED: Putative esterase, FIGfam005057
KEGG: no annotation
Rationale: PFam PF05728.8 (UPF0227). conserved phenotypes: important for resisting doxycycline and for octanoate utilization (also a putative stress)

Pf6N2E2_3783 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
SEED: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
KEGG: phosphoribosyl-ATP pyrophosphohydrolase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR03188.

Pf6N2E2_3797 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate deformylase (EC 3.5.1.68)
SEED: N-formylglutamate deformylase (EC 3.5.1.68)
KEGG: formiminoglutamase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (3.5.1.68) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_3798 : Imidazolonepropionase (EC 3.5.2.7)
Original description: Imidazolonepropionase (EC 3.5.2.7)
SEED: Imidazolonepropionase (EC 3.5.2.7)
KEGG: imidazolonepropionase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (IMIDAZOLONEPROPIONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_3799 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: Histidine ammonia-lyase (EC 4.3.1.3)
SEED: Histidine ammonia-lyase (EC 4.3.1.3)
KEGG: histidine ammonia-lyase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (4.3.1.3) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_3805 : Urocanate hydratase (EC 4.2.1.49)
Original description: Urocanate hydratase (EC 4.2.1.49)
SEED: Urocanate hydratase (EC 4.2.1.49)
KEGG: urocanate hydratase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (UROCANATE-HYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_3808 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: no annotation
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.

Pf6N2E2_3839 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

Pf6N2E2_4013 : 5-aminovalerate transaminase (EC 2.6.1.48)
Original description: 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
SEED: 5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (2.6.1.48) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_4087 : L-asparaginase (EC 3.5.1.1)
Original description: L-asparaginase (EC 3.5.1.1)
SEED: L-asparaginase (EC 3.5.1.1)
KEGG: L-asparaginase
Rationale: Specifically important for utilizing L-Asparagine. Automated validation from mutant phenotype: the predicted function (ASPARAGHYD-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_4383 : gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.99); 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54)
Original description: Aldehyde dehydrogenase (EC 1.2.1.3)
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: no annotation
Rationale: Important on putrescine; this is the dehydrogenase reaction in the gamma-glutamyl-putrescine pathway. Similar to the 4-guanidinobutyraldehyde dehydrogenase kauB from P. putida, which is involved in arginine catabolism, and 99% id. to AO356_12580, which has a phenotype on arginine. So Pf6N2E2_4383 probably has both activities.

Pf6N2E2_4509 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: glutamine synthetase family protein
SEED: no annotation
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride. This synthetase reaction is the first step in putrescine catabolism

Pf6N2E2_4510 : Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
Original description: Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
SEED: Gamma-glutamyl-GABA hydrolase (EC 3.5.1.94)
KEGG: putative glutamine amidotransferase
Rationale: Specifically important for: Putrescine Dihydrochloride. part of putrescine catabolism via gamma-glutamyl-putrescine (SEED_correct)

Pf6N2E2_4512 : Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Original description: Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
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)

Pf6N2E2_456 : 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Original description: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
SEED: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
KEGG: 4-hydroxyphenylpyruvate dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (RXN-10815) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_4681 : ABC transporter for Carnitine, ATPase component
Original description: L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)
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 on Carnitine Hydrochloride. This ABC transporter might also take up choline or glycine-betaine, in conjunction with another SBP, Pf6N2E2_4683

Pf6N2E2_4682 : ABC transporter for Carnitine, permease component
Original description: L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
SEED: L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system permease protein
Rationale: Specific phenotypes on Carnitine Hydrochloride. This ABC transporter might also take up choline or glycine-betaine, in conjunction with another SBP, Pf6N2E2_4683

Pf6N2E2_4689 : L-carnitine 3-dehydrogenase, B subunit (EC 1.1.1.108)
Original description: FIG143042: Thioesterase-like protein
SEED: no annotation
KEGG: acyl-CoA thioester hydrolase
Rationale: Specifically important for: Carnitine Hydrochloride. Similar to CdhB = PA5385

Pf6N2E2_4690 : L-carnitine 3-dehydrogenase, A subunit (EC 1.1.1.108)
Original description: Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
SEED: Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
KEGG: 3-hydroxybutyryl-CoA dehydrogenase
Rationale: Specifically important for: Carnitine Hydrochloride. Similar to CdhA = PA5386

Pf6N2E2_4692 : dehydrocarnitine cleavage enzyme (EC 2.3.1.-)
Original description: FIG004891: hypothetical protein in carnitine cluster
SEED: FIG004891: hypothetical protein in carnitine cluster
KEGG: no annotation
Rationale: Specifically important for: Carnitine Hydrochloride. Similar to CdhC = PA5387

Pf6N2E2_4693 : ABC transporter for Carnitine Hydrochloride, periplasmic substrate-binding component
Original description: L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1)
SEED: L-proline glycine betaine binding ABC transporter protein ProX (TC 3.A.1.12.1)
KEGG: glycine betaine/proline transport system substrate-binding protein
Rationale: Specific phenotype on Carnitine Hydrochloride. Similar to CaiX. There might also be another SBP, Pf6N2E2_4683 (similar to CbcX) that is expected to be specific for choline and glycine-betaine. However _4683 is important for carnitine utilization as well and it does not appear to be a polar effect, so it could be another subunit.

Pf6N2E2_4704 : Dimethylglycine dehydrogenase (ferredoxin), FeS subunit DgcB (EC 1.5.7.-)
Original description: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
SEED: Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
KEGG: no annotation
Rationale: Specific phenotype: utilization of Carnitine. DgcB is quite similar to csal_0991, which is the putative FeS component of a N,N-dimethylglycine/sarcosine dehydrogenase that forms formaldehyde and glycine (PMC2293255). However the Pseudomonas enzyme probably acts primarily on dimethylglycine in vivo, as another sarcosine-specific system is important for carnitine utilization (Pf6N2E2_4720).

Pf6N2E2_4777 : 5-aminopentanamidase (EC 3.5.1.30)
Original description: 5-aminopentanamidase (EC 3.5.1.30)
SEED: 5-aminopentanamidase (EC 3.5.1.30)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (5-AMINOPENTANAMIDASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_4778 : Lysine 2-monooxygenase (EC 1.13.12.2)
Original description: Lysine 2-monooxygenase (EC 1.13.12.2)
SEED: Lysine 2-monooxygenase (EC 1.13.12.2)
KEGG: tryptophan 2-monooxygenase
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (LYSINE-2-MONOOXYGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_478 : Dihydrolipoyl dehydrogenase (EC 1.8.1.4)
Original description: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
SEED: Dihydrolipoamide dehydrogenase of branched-chain alpha-keto acid dehydrogenase (EC 1.8.1.4)
KEGG: dihydrolipoamide dehydrogenase
Rationale: Specifically important for utilizing L-Leucine. 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.

Pf6N2E2_479 : Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168)
Original description: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
SEED: Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)
KEGG: 2-oxoisovalerate dehydrogenase E2 component (dihydrolipoyl transacylase)
Rationale: Specifically important for utilizing L-Leucine; L-Isoleucine. Automated validation from mutant phenotype: the predicted function (2.3.1.168) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_4799 : ycgB component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: FIG004684: SpoVR-like protein
SEED: FIG004684: SpoVR-like protein
KEGG: no annotation
Rationale: conserved cofitness; yeaG is a protein kinase

Pf6N2E2_480 : 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4)
Original description: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, beta subunit
Rationale: Specifically important for utilizing L-Isoleucine. Automated validation from mutant phenotype: the predicted function (1.2.4.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_4800 : yeaH component of nitrogen-related signalling system yeaH (of yeaGH-ycgB)
Original description: FIG002076: hypothetical protein
SEED: FIG002076: hypothetical protein
KEGG: hypothetical protein
Rationale: PFam PF04285.8 (DUF444). conserved cofitness; yeaG is a protein kinase

Pf6N2E2_4801 : yeaG component of nitrogen-related signalling system (of yeaGH-ycgB)
Original description: Serine protein kinase (prkA protein), P-loop containing
SEED: Serine protein kinase (prkA protein), P-loop containing
KEGG: serine protein kinase
Rationale: conserved cofitness; yeaG is a protein kinase

Pf6N2E2_481 : branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit (EC 1.2.4.4)
Original description: Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
SEED: Branched-chain alpha-keto acid dehydrogenase, E1 component, alpha subunit (EC 1.2.4.4)
KEGG: 2-oxoisovalerate dehydrogenase E1 component, alpha subunit
Rationale: Specifically important for utilizing L-Isoleucine.

Pf6N2E2_496 : Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2)
Original description: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
SEED: Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2)
KEGG: no annotation
Rationale: Specifically important for utilizing Cytosine. 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.

Pf6N2E2_498 : Dihydropyrimidinase (EC 3.5.2.2)
Original description: Dihydropyrimidinase (EC 3.5.2.2)
SEED: Dihydropyrimidinase (EC 3.5.2.2)
KEGG: dihydropyrimidinase
Rationale: Specifically important for utilizing Cytosine. Automated validation from mutant phenotype: the predicted function (3.5.2.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_512 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
Original description: 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
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.

Pf6N2E2_513 : Myo-inosose-2 dehydratase (EC 4.2.1.44)
Original description: Inosose dehydratase (EC 4.2.1.44)
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.

Pf6N2E2_514 : 5-deoxy-D-glucuronate isomerase (EC 5.3.1.30)
Original description: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
SEED: 5-deoxy-glucuronate isomerase (EC 5.3.1.-)
KEGG: 5-deoxy-glucuronate isomerase
Rationale: Specifically important for utilizing m-Inositol.

Pf6N2E2_515 : malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18)
Original description: Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
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

Pf6N2E2_517 : Epi-inositol hydrolase (EC 3.7.1.-)
Original description: Epi-inositol hydrolase (EC 3.7.1.-)
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. Automated validation from mutant phenotype: the predicted function (RXN-14149) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_5290 : Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Original description: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
SEED: Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
KEGG: homogentisate 1,2-dioxygenase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (1.13.11.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_5292 : Maleylacetoacetate isomerase (EC 5.2.1.2)
Original description: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
SEED: Maleylacetoacetate isomerase (EC 5.2.1.2) @ Glutathione S-transferase, zeta (EC 2.5.1.18)
KEGG: maleylacetoacetate isomerase
Rationale: Specifically important for utilizing L-Phenylalanine. Automated validation from mutant phenotype: the predicted function (5.2.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_5305 : Fe(3+) dicitrate transport protein FecA
Original description: Iron(III) dicitrate transport protein FecA @ Iron siderophore receptor protein
SEED: Iron(III) dicitrate transport protein FecA @ Iron siderophore receptor protein
KEGG: iron complex outermembrane recepter protein
Rationale: Specific phenotype: utilization of Tricitrate

Pf6N2E2_5373 : required for cephalothin efflux, together with NodT, MFP and FUSC proteins (Pf6N2E2_5371, Pf6N2E2_5374, Pf6N2E2_5372)
Original description: Na+-dependent transporters of the SNF family
SEED: Na+-dependent transporters of the SNF family
KEGG: no annotation
Rationale: PFam PF07869.8 (DUF1656). A conserved cofit operon. Specifically important for resisting cephalothin.

Pf6N2E2_5402 : ABC transporter for D-Alanine, periplasmic substrate-binding component
Original description: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
SEED: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system substrate-binding protein
Rationale: Very important for D-alanine utilization. This transporter may also uptake L-histidine.

Pf6N2E2_5403 : ABC transporter for D-Alanine, permease component 2
Original description: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system permease protein
Rationale: Very important for D-alanine utilization. This transporter may also uptake L-histidine.

Pf6N2E2_5404 : ABC transporter for D-Alanine, permease component 1
Original description: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
KEGG: general L-amino acid transport system permease protein
Rationale: Specific phenotypes on D-Alanine. Also important for histidine utilization, so this may also take up L-histidine

Pf6N2E2_5405 : ABC transporter for D-Alanine, ATPase component
Original description: ABC-type polar amino acid transport system, ATPase component
SEED: ABC-type polar amino acid transport system, ATPase component
KEGG: general L-amino acid transport system ATP-binding protein
Rationale: Very important for D-alanine utilization. This transporter may also uptake L-histidine.

Pf6N2E2_5486 : Alpha-ketoglutarate permease
Original description: Dicarboxylate MFS transporter
SEED: Dicarboxylate MFS transporter
KEGG: MFS transporter, MHS family, alpha-ketoglutarate permease
Rationale: Specific phenotype: utilization of a-Ketoglutaric acid

Pf6N2E2_5556 : Aminomethyltransferase (EC 2.1.2.10)
Original description: Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)
SEED: Aminomethyltransferase (glycine cleavage system T protein) (EC 2.1.2.10)
KEGG: aminomethyltransferase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (2.1.2.10) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_5557 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: L-serine dehydratase (EC 4.3.1.17)
SEED: L-serine dehydratase (EC 4.3.1.17)
KEGG: L-serine dehydratase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (4.3.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_5558 : Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2)
Original description: Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
SEED: Glycine dehydrogenase [decarboxylating] (glycine cleavage system P protein) (EC 1.4.4.2)
KEGG: glycine dehydrogenase
Rationale: Specifically important for utilizing Glycine. Automated validation from mutant phenotype: the predicted function (1.4.4.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_5616 : outer membrane component of uptake system, probably for ferrous iron
Original description: putative exported protein
SEED: no annotation
KEGG: hypothetical protein
Rationale: PFam PF07433.7 (DUF1513). In a conserved cofit operon with an efeO-like gene (Pf6N2E2_5617) and an efeB-like gene (Pf6N2E2_5618). Another efeO-like gene (Pf6N2E2_2853) is cofit but not nearby.

Pf6N2E2_5660 : L-Arginine ABC transporter, periplasmic substrate-binding component
Original description: Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
SEED: Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
KEGG: no annotation
Rationale: Specific phenotype on L-Arginine. (SEED_correct)

Pf6N2E2_5661 : L-Arginine ABC transporter, permease protein AotQ
Original description: Arginine/ornithine ABC transporter, permease protein AotQ
SEED: Arginine/ornithine ABC transporter, permease protein AotQ
KEGG: no annotation
Rationale: Specific phenotypes on L-Arginine; L-Arginine. no data for ornithine (SEED_correct)

Pf6N2E2_5662 : L-Arginine ABC transporter, permease protein AotM
Original description: Arginine/ornithine ABC transporter, permease protein AotM
SEED: Arginine/ornithine ABC transporter, permease protein AotM
KEGG: no annotation
Rationale: Specific phenotypes on L-Arginine; L-Arginine. (SEED_correct)

Pf6N2E2_5663 : L-Arginine ABC transporter, ATPase component
Original description: Arginine/ornithine ABC transporter, ATP-binding protein AotP
SEED: Arginine/ornithine ABC transporter, ATP-binding protein AotP
KEGG: no annotation
Rationale: Very important for utilizing L-arginine. (SEED_correct)

Pf6N2E2_5848 : small component of pyruvate transporter (yjcH-like)
Original description: Putative membrane protein, clustering with ActP
SEED: Putative membrane protein, clustering with ActP
KEGG: no annotation
Rationale: Important for pyruvate utilization. 58% identical to E. coli yjcH.

Pf6N2E2_5849 : large component of pyruvate transporter (actP-like)
Original description: Acetate permease ActP (cation/acetate symporter)
SEED: Acetate permease ActP (cation/acetate symporter)
KEGG: cation/acetate symporter
Rationale: Important for pyruvate utilization.

Pf6N2E2_5966 : L-arabinolactonase (EC 3.1.1.15)
Original description: L-arabinolactonase (EC 3.1.1.15)
SEED: L-arabinolactonase (EC 3.1.1.15)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONOLACTONASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_5967 : L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48)
Original description: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
SEED: 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
KEGG: no annotation
Rationale: Important for utilization of L-arabinose and D-galactose in several Pseudomonas. Both of these sugars are catabolized via a 1-dehydrogenase followed by lactonase and dehydratase reactions. This is the only dehydrogenase is specifically important for either of these carbon sources in several Pseudomonas, except for an alpha-ketoglutarate semialdehyde dehydrogenase that is expected to be the last dedicated step in L-arabinose catabolism (i.e., Pf6N2E2_612). L-arabinose and D-galactose are chemically similar and some dehydrogenases are already known to act on both substrates. This gene might also be involved in D-gluconate utilization.

Pf6N2E2_5968 : ABC transporter for D-galactose/L-arabinose, substrate-binding component
Original description: L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
SEED: L-arabinose-binding periplasmic protein precursor AraF (TC 3.A.1.2.2)
KEGG: L-arabinose transport system substrate-binding protein
Rationale: Specifically important for utilizing D-galactose and L-arabinose

Pf6N2E2_5969 : ABC transporter for D-galactose/L-arabinose, ATPase component
Original description: L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
SEED: L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
KEGG: L-arabinose transport system ATP-binding protein
Rationale: Specifically important for utilizing D-galactose and L-arabinose

Pf6N2E2_5970 : ABC transporter for D-galactose/L-arabinose, permease component
Original description: L-arabinose transport system permease protein (TC 3.A.1.2.2)
SEED: L-arabinose transport system permease protein (TC 3.A.1.2.2)
KEGG: L-arabinose transport system permease protein
Rationale: Specifically important for utilizing D-galactose and L-arabinose

Pf6N2E2_6061 : Methylisocitrate lyase (EC 4.1.3.30)
Original description: Methylisocitrate lyase (EC 4.1.3.30)
SEED: Methylisocitrate lyase (EC 4.1.3.30)
KEGG: no annotation
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (4.1.3.30) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_6062 : 2-methylcitrate synthase (EC 2.3.3.5)
Original description: 2-methylcitrate synthase (EC 2.3.3.5)
SEED: 2-methylcitrate synthase (EC 2.3.3.5)
KEGG: 2-methylcitrate synthase
Rationale: Specifically important for utilizing Sodium propionate. Automated validation from mutant phenotype: the predicted function (2.3.3.5) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf6N2E2_609 : L-arabonate dehydratase (EC 4.2.1.25)
Original description: L-arabonate dehydratase (EC 4.2.1.25)
SEED: L-arabonate dehydratase (EC 4.2.1.25)
KEGG: dihydroxy-acid dehydratase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (L-ARABINONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_611 : 2-dehydro-3-deoxy-L-arabinonate dehydratase (EC 4.2.1.43)
Original description: SUGAR TRANSPORTER
SEED: SUGAR TRANSPORTER
KEGG: no annotation
Rationale: # Specifically important in carbon source L-Arabinose. Similar to PA2216 from Pseudomonas aeruginosa (see PMC:PMC4038344) and to gguC or araD1 (Atu2345) from Agrobacterium tumefaciens (see PMC: PMC3232879), which also have this activity. In Agrobacterium, this reaction is proposed to be a step in L-arabinose oxidation. (Note that 2-keto-3-deoxy-L-lyxonate and 2-keto-3-deoxy-L-arabinonate are the same compound.)

Pf6N2E2_612 : Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
SEED: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: NADP-dependent aldehyde dehydrogenase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (25-DIOXOVALERATE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf6N2E2_80 : gamma-glutamylputrescine oxidase (EC 1.4.3.-)
Original description: Nucleoside-diphosphate-sugar epimerases
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: gamma-glutamylputrescine oxidase
Rationale: Specifically important for: Putrescine Dihydrochloride. This is part of the gamma-glutamyl-putrescine pathway. (KEGG_correct)

Pf6N2E2_805 : Xylulose kinase (EC 2.7.1.17)
Original description: Xylulose kinase (EC 2.7.1.17)
SEED: Xylulose kinase (EC 2.7.1.17)
KEGG: xylulokinase
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLULOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Or download reannotations for Pseudomonas fluorescens FW300-N2E2 or for all organisms as tab-delimited tables