Updated annotations for Pseudomonas fluorescens FW300-N1B4

60 genes with updated (or confirmed) annotations:

Pf1N1B4_1013 : L-serine ammonia-lyase (EC 4.3.1.17)
Original description: L-serine dehydratase (EC 4.3.1.17)
SEED: L-serine dehydratase (EC 4.3.1.17)
KEGG: L-serine dehydratase
Rationale: Specifically important for utilizing L-Serine. Automated validation from mutant phenotype: the predicted function (4.3.1.17) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf1N1B4_1067 : 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.

Pf1N1B4_1109 : 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
SEED: 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Specifically important for: D-Galacturonic Acid monohydrate. ketoglutarate semialdehyde is an intermedate in the oxidation of galacturonate (SEED_correct)

Pf1N1B4_1110 : 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
Original description: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
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.

Pf1N1B4_1146 : fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components
Original description: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
SEED: Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
KEGG: phosphocarrier protein
Rationale: Specifically important for utilizing D-Fructose.

Pf1N1B4_1229 : Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Original description: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
SEED: Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (RXN-11213) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_1296 : Biosynthetic arginine decarboxylase (EC 4.1.1.19)
Original description: Biosynthetic arginine decarboxylase (EC 4.1.1.19)
SEED: Biosynthetic arginine decarboxylase (EC 4.1.1.19)
KEGG: arginine decarboxylase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (ARGDECARBOX-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_1554 : predicted FeS cluster maintenance protein
Original description: FIG028220: hypothetical protein co-occurring with HEAT repeat protein
SEED: FIG028220: hypothetical protein co-occurring with HEAT repeat protein
KEGG: no annotation
Rationale: PFam PF06155.8 (DUF971). Conserved cofitness with mrp/apbC (Pf1N1B4_731)

Pf1N1B4_1566 : 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 many defined media and cofit with phosphoribosyl-AMP cyclohydrolase (Pf1N1B4_1565). Hits TIGR03188.

Pf1N1B4_1578 : 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.

Pf1N1B4_1579 : 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.

Pf1N1B4_1582 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: Histidine ammonia-lyase (EC 4.3.1.3)
SEED: Histidine ammonia-lyase (EC 4.3.1.3)
KEGG: histidine ammonia-lyase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (HISTIDINE-AMMONIA-LYASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_1587 : 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.

Pf1N1B4_1591 : Formiminoglutamic iminohydrolase (EC 3.5.3.13)
Original description: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
SEED: Formiminoglutamic iminohydrolase (EC 3.5.3.13)
KEGG: formimidoylglutamate deiminase
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMATE-DEIMINASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_1624 : 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.

Pf1N1B4_2023 : 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.

Pf1N1B4_2254 : Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
Original description: Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11)
SEED: no annotation
KEGG: glutamine synthetase
Rationale: Specifically important for: Putrescine Dihydrochloride. This is the first step in putrescine catabolism. Some close homologs are annotated as this by SEED, so not sure why it was missed. Also, another gene is annotated as this activity (Pf1N1B4_4354) but has no phenotype.

Pf1N1B4_2262 : Lysine ABC transporter, permease component
Original description: Putrescine transport system permease protein PotH (TC 3.A.1.11.2)
SEED: Putrescine transport system permease protein PotH (TC 3.A.1.11.2)
KEGG: putrescine transport system permease protein
Rationale: Specific phenotype: utilization of L-Lysine, Cytidine. The lysine phenotype is stronger and is conserved.

Pf1N1B4_2429 : Carnitine 3-dehydrogenase (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 utilizing Carnitine Hydrochloride. Automated validation from mutant phenotype: the predicted function (CARNITINE-3-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_2454 : Serine hydroxymethyltransferase (EC 2.1.2.1)
Original description: Serine hydroxymethyltransferase (EC 2.1.2.1)
SEED: Serine hydroxymethyltransferase (EC 2.1.2.1)
KEGG: glycine hydroxymethyltransferase
Rationale: Specific phenotype: utilization of Carnitine (carnitine is broken down via glycine betaine and glycine)

Pf1N1B4_2504 : 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.

Pf1N1B4_2505 : 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.

Pf1N1B4_3431 : ABC transporter for L-Arginine and L-Citrulline, 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; L-Citrulline.

Pf1N1B4_3432 : ABC transporter for L-Arginine and L-Citrulline, permease component 1
Original description: Arginine/ornithine ABC transporter, permease protein AotQ
SEED: Arginine/ornithine ABC transporter, permease protein AotQ
KEGG: arginine/ornithine transport system permease protein
Rationale: Specific phenotypes on L-Arginine; L-Citrulline.

Pf1N1B4_3433 : ABC transporter for L-Arginine and L-Citrulline, permease component 2
Original description: Arginine/ornithine ABC transporter, permease protein AotM
SEED: Arginine/ornithine ABC transporter, permease protein AotM
KEGG: arginine/ornithine transport system permease protein
Rationale: Specific phenotypes on L-Arginine; L-Citrulline.

Pf1N1B4_3435 : ABC transporter for L-Arginine and L-Citrulline, 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 utilization of L-Arginine or L-Citrulline. Detrimental to fitness in some other minimal media experiments.

Pf1N1B4_3440 : Succinylornithine transaminase (EC 2.6.1.81)
Original description: Succinylornithine transaminase (EC 2.6.1.81)
SEED: Succinylornithine transaminase (EC 2.6.1.81)
KEGG: acetylornithine/N-succinyldiaminopimelate aminotransferase
Rationale: Specifically important for utilizing L-Arginine. Automated validation from mutant phenotype: the predicted function (SUCCORNTRANSAM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_3672 : 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: Specifically important for pyruvate utilization. 62% identical to E. coli yjcH.

Pf1N1B4_3673 : 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: Specifically important for pyruvate utilization.

Pf1N1B4_3835 : 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.

Pf1N1B4_3984 : 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.

Pf1N1B4_4042 : Isocitrate lyase (EC 4.1.3.1)
Original description: Isocitrate lyase (EC 4.1.3.1)
SEED: Isocitrate lyase (EC 4.1.3.1)
KEGG: isocitrate lyase
Rationale: Specifically important for utilizing Tween 20. Automated validation from mutant phenotype: the predicted function (ISOCIT-CLEAV-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_409 : 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

Pf1N1B4_410 : 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

Pf1N1B4_411 : 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

Pf1N1B4_412 : 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: 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, apart from a 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.

Pf1N1B4_413 : 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.

Pf1N1B4_4279 : 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase IolD (EC 3.7.1.22)
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.

Pf1N1B4_4511 : D-galacturonate dehydrogenase (EC 1.1.1.203)
Original description: UDP-glucose 4-epimerase (EC 5.1.3.2)
SEED: UDP-glucose 4-epimerase (EC 5.1.3.2)
KEGG: no annotation
Rationale: Important on D-galacturonate; KEGG now has pfo:Pfl01_3452 as uronate dehydrogenase which is correct but less specific (KEGG_correct)

Pf1N1B4_4623 : 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.)

Pf1N1B4_4787 : 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: Important for isoleucine utilization. 2-methylbutaonyl-CoA is an intermediate in the standard pathway and no other gene for the methylbutanoyl-CoA dehydrogenase was apparent in the fitness data.

Pf1N1B4_4790 : 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
Original description: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
SEED: 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for utilizing L-Valine. Automated validation from mutant phenotype: the predicted function (3.1.2.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Pf1N1B4_4934 : 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.

Pf1N1B4_5112 : sucrose ABC transporter, substrate-binding component
Original description: Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
SEED: Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
KEGG: multiple sugar transport system substrate-binding protein
Rationale: Specific phenotype on sucrose

Pf1N1B4_5113 : sucrose ABC transporter, permease component 1
Original description: Maltose/maltodextrin ABC transporter, permease protein MalF
SEED: Maltose/maltodextrin ABC transporter, permease protein MalF
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotype on sucrose

Pf1N1B4_5114 : sucrose ABC transporter, permease component 2
Original description: Maltose/maltodextrin ABC transporter, permease protein MalG
SEED: Maltose/maltodextrin ABC transporter, permease protein MalG
KEGG: multiple sugar transport system permease protein
Rationale: Specific phenotype on sucrose

Pf1N1B4_5115 : sucrose ABC transporter, ATPase component
Original description: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
SEED: Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
KEGG: maltose/maltodextrin transport system ATP-binding protein
Rationale: Specific phenotype on sucrose

Pf1N1B4_5116 : 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.

Pf1N1B4_5129 : D-galacturonate transporter ExuT
Original description: Hexuronate transporter
SEED: Hexuronate transporter
KEGG: MFS transporter, ACS family, hexuronate transporter
Rationale: Specifically important for D-galacturonate utilization.

Pf1N1B4_597 : D-mannose isomerase (EC 5.3.1.7)
Original description: N-acylglucosamine 2-epimerase (EC 5.1.3.8)
SEED: N-acylglucosamine 2-epimerase (EC 5.1.3.8)
KEGG: no annotation
Rationale: Specifically important for: D-Mannose. Often annotated as N-acylglucosamine 2-epimerase, but this is also distantly related to the D-mannose isomerase Sama_0560. This organism has a fructokinase (Pf1N1B4_4844, no data) which probably utilizes the resulting fructose.

Pf1N1B4_6029 : uridine nucleosidase (EC 3.2.2.3)
Original description: Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1)
SEED: Inosine-uridine preferring nucleoside hydrolase (EC 3.2.2.1)
KEGG: no annotation
Rationale: Important on uridine; annotated by SEED as for uridine and inosine; close homologs are important for utilizing uridine (SEED_correct)

Pf1N1B4_6031 : Ribokinase (EC 2.7.1.15)
Original description: Ribokinase (EC 2.7.1.15)
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Specifically important for utilizing D-Ribose. Automated validation from mutant phenotype: the predicted function (RIBOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Pf1N1B4_6033 : D-ribose ABC transporter, permease component RbsC
Original description: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: ribose transport system permease protein
Rationale: No fitness data for this gene, but the other putative components are upstream (Pf1N1B4_6035:Pf1N1B4_6034) and are specifically important for ribose utilization.

Pf1N1B4_6034 : D-ribose ABC transporter, ATPase component RbsA
Original description: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
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 ribose utilization. Also involved in utilization of ribonucleotides, which might be hydrolyzed before uptake.

Pf1N1B4_6035 : D-ribose ABC transporter, substrate-binding component RbsB
Original description: Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
SEED: Ribose ABC transport system, periplasmic ribose-binding protein RbsB (TC 3.A.1.2.1)
KEGG: ribose transport system substrate-binding protein
Rationale: Specifically important for ribose utilization. Also involved in utilization of ribonucleotides, which might be hydrolyzed before uptake.

Pf1N1B4_718 : 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 two efeO-like genes (Pf1N1B4_715,Pf1N1B4_717) and an efeB-like gene (Pf1N1B4_716)

Pf1N1B4_771 : ABC transporter for L-asparagine and L-glutamate, periplasmic substrate-binding component
Original description: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
SEED: Glutamate Aspartate periplasmic binding protein precursor GltI (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system substrate-binding protein
Rationale: # Specifically important in carbon source L-Asparagine. Also important for glutamate utilization.

Pf1N1B4_772 : ABC transporter for L-asparagine and L-glutamate, permease component 1
Original description: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: # Specifically important in carbon source L-Asparagine. Also important for glutamate utilization. We do not have fitness data for aspartate utilization - it may well transport aspartate as well. Also note that the aspariganase (Pf1N1B4_2023) is predicted to be cytoplasmic and is important for asparagine utilization, so we do not think that asparagine is converted to aspartate before uptake.

Pf1N1B4_773 : ABC transporter for L-asparagine and L-glutamate, permease subunit 2
Original description: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system permease protein
Rationale: # Important for glutamate and asparagine utilization and cofit with other components

Pf1N1B4_774 : ABC transporter for L-asparagine and L-glutamate, ATPase component
Original description: Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
SEED: Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)
KEGG: glutamate/aspartate transport system ATP-binding protein
Rationale: # Reannotated based on fitness data for other genes in the operon. We have no fitness data for this gene.

Or download reannotations for Pseudomonas fluorescens FW300-N1B4 or for all organisms as tab-delimited tables