Updated Annotations for Pedobacter sp. GW460-11-11-14-LB5

Updated annotations for Pedobacter sp. GW460-11-11-14-LB5

57 genes with updated (or confirmed) annotations:

CA265_RS00660 : uvrA paralog in Bacteroidetes
Original description: excinuclease ABC subunit A
SEED: Excinuclease ABC subunit A paralog in greater Bacteroides group
KEGG: excinuclease ABC subunit A
Rationale: # Very important for resisting cisplatin. Both the "standard" uvrA and this gene were important for cisplatin resistance. (SEED_correct)

CA265_RS03615 : 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.

CA265_RS05010 : anthranilate phosphoribosyltransferase (EC 2.4.2.18)
Original description: anthranilate phosphoribosyltransferase
SEED: Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
KEGG: anthranilate phosphoribosyltransferase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01245.

CA265_RS05025 : tryptophan synthase, alpha subunit (EC 4.2.1.20)
Original description: tryptophan synthase subunit alpha
SEED: Tryptophan synthase alpha chain (EC 4.2.1.20)
KEGG: tryptophan synthase alpha chain
Rationale: # This gene and its ortholog in Echinicola vietnamensis are essential, which is consistent with a role in amino acid biosynthesis. 76% identical to AAFF35_06155, which complements a trpA- strain of E. coli (data of PMID:39375541)

CA265_RS06120 : UDP-glucose--hexose-1-phosphate uridylyltransferase (EC 2.7.7.12)
Original description: galactose-1-phosphate uridylyltransferase
SEED: Galactose-1-phosphate uridylyltransferase (EC 2.7.7.10)
KEGG: UDPglucose--hexose-1-phosphate uridylyltransferase
Rationale: Specifically important for utilizing D-Galactose; this is part of the Leloir pathway

CA265_RS06125 : galactokinase, -1-phosphate forming (EC 2.7.1.6)
Original description: galactokinase
SEED: Galactokinase (EC 2.7.1.6)
KEGG: galactokinase
Rationale: Specifically important for utilizing D-Galactose. Automated validation from mutant phenotype: the predicted function (2.7.1.6) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CA265_RS06130 : D-galactose transporter
Original description: sodium transporter
SEED: putative sodium/hexose cotransport protein
KEGG: solute:Na+ symporter, SSS family
Rationale: Specifically important for D-galactose utilization

CA265_RS06165 : nitrite transporter, HPP family
Original description: HPP family protein
SEED: CBS-domain-containing membrane protein
KEGG: no annotation
Rationale: # Specifically detrimental during growth at high nitrite concentrations. Related to Synpcc7942_1745, which is a nitrite transporter (PMID:24904028)

CA265_RS08615 : L-arabinose isomerase (EC 5.3.1.4)
Original description: L-arabinose isomerase
SEED: L-arabinose isomerase (EC 5.3.1.4)
KEGG: L-arabinose isomerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (ARABISOM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS08620 : L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
Original description: L-ribulose-5-phosphate 4-epimerase
SEED: L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4)
KEGG: L-ribulose-5-phosphate 4-epimerase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (RIBULPEPIM-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS08625 : Ribulokinase (EC 2.7.1.16)
Original description: ribulokinase
SEED: Ribulokinase (EC 2.7.1.16)
KEGG: L-ribulokinase
Rationale: Specifically important for utilizing L-Arabinose. Automated validation from mutant phenotype: the predicted function (RXN0-5116) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS09085 : DNA repair nuclease, ligase-associated (TIGR04123)
Original description: phosphoesterase
SEED: FIG006285: ICC-like protein phosphoesterase
KEGG: no annotation
Rationale: # Specifically important in stress Cisplatin. This family was previously annotated as a DNA ligase-associated metallophosphoesterase (TIGR04123). A member of this family (PdeM) has been studied biochemically and found to have nuclease activity, but it was not known if DNA was the physiological substrate (see PMC4320098).

CA265_RS09125 : Methylglutaconyl-CoA hydratase (EC 4.2.1.18)
Original description: methylglutaconyl-CoA hydratase
SEED: Enoyl-CoA hydratase (EC 4.2.1.17)
KEGG: methylglutaconyl-CoA hydratase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (4.2.1.18) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CA265_RS09995 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase (NAD(P)H)
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.

CA265_RS10015 : Nitrate reductase (EC 1.7.99.4)
Original description: NAD(P)H-nitrite 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.

CA265_RS11300 : N-acetylglucosamine kinase (EC 2.7.1.59)
Original description: sugar kinase
SEED: Glucokinase (EC 2.7.1.2)
KEGG: glucokinase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (2.7.1.59) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CA265_RS11605 : Proline dehydrogenase (EC 1.5.5.2)
Original description: proline dehydrogenase
SEED: Carbapenem antibiotics biosynthesis protein carD
KEGG: proline dehydrogenase
Rationale: Specifically important for utilizing L-Proline. Automated validation from mutant phenotype: the predicted function (1.5.5.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CA265_RS11630 : prephenate and/or arogenate dehydratase (EC 4.2.1.51)
Original description: prephenate dehydratase
SEED: Prephenate dehydratase (EC 4.2.1.51)
KEGG: prephenate dehydratase
Rationale: Important for fitness in defined media unless phenylalanine is provided. 34% identical to prephenate/arogenate dehydratase from Oryza sativa (Q6Z3Y3). It is uncertain whether dehydration occurs first or transamination (to arogenate) occurs first.

CA265_RS11635 : chorismate mutase (EC 5.4.99.5); 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54)
Original description: 3-deoxy-7-phosphoheptulonate synthase
SEED: 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate synthase I beta (EC 2.5.1.54) / Chorismate mutase I (EC 5.4.99.5)
KEGG: chorismate mutase
Rationale: Important for fitness in most defined media. The N-terminal DHAP region is only 36% identical to the Pyrococcus enzyme (Q8U0A9) but the active site and substrate-binding residues are conserved. The C-terminal chorismate mutase region is diverged but hits PF01817 and no other chorismate mutase was found in the genome except for a paralog that has little phenotype (CA264_13110)

CA265_RS12710 : pif1-like DNA repair helicase
Original description: ATP-dependent endonuclease
SEED: RecD-like DNA helicase Atu2026
KEGG: exodeoxyribonuclease V
Rationale: # Specifically important in stress Cisplatin; stress Nalidixic acid sodium salt; stress Lomefloxacin hydrochloride. Contains a pif1-like helicase domain and probably part of the RecD superfamily (see CDD). (SEED_correct)

CA265_RS13115 : Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Original description: hydroxymethylglutaryl-CoA lyase
SEED: Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
KEGG: hydroxymethylglutaryl-CoA lyase
Rationale: Specifically important for utilizing L-Leucine. Automated validation from mutant phenotype: the predicted function (HYDROXYMETHYLGLUTARYL-COA-LYASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS14455 : L-lysine 6-transaminase (EC 2.6.1.36)
Original description: L-lysine 6-transaminase
SEED: Probable L-lysine-epsilon aminotransferase (EC 2.6.1.36) (L-lysine aminotransferase) (Lysine 6-aminotransferase)
KEGG: L-lysine 6-transaminase
Rationale: Specifically important for utilizing L-Lysine. Automated validation from mutant phenotype: the predicted function (L-LYSINE-AMINOTRANSFERASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS15340 : periplasmic glucoside 3-dehydrogenase (lacC subunit) (EC 1.1.99.13)
Original description: twin-arginine translocation pathway signal protein
SEED: no annotation
KEGG: no annotation
Rationale: Specifically important in carbon source D-Salicin; carbon source D-Trehalose dihydrate; carbon source D-Cellobiose; carbon source Beta-Lactose (all are glucosides). Related to lacC of Caulobacter crescentus which is a component of lactose 3-dehydrogenase.

CA265_RS15345 : periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13)
Original description: GMC family oxidoreductase
SEED: Glucose-methanol-choline (GMC) oxidoreductase:NAD binding site
KEGG: no annotation
Rationale: Specifically important in carbon source D-Trehalose dihydrate; carbon source D-Salicin; carbon source Beta-Lactose; carbon source D-Cellobiose (all are glucosides). Related to lacA of Caulobacter crescentus which is a component of lactose 3-dehydrogenase.

CA265_RS15350 : 3-ketohexose reductase (NADH)
Original description: oxidoreductase
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: no annotation
Rationale: Important for utilization of various glucosides (trehalose, salicin, lactose, and cellobiose). In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. 28% identical to 3-ketoglucose reductase lgdC (BCB28826.1, see PMC7676230), which uses NADH as the electron donor.

CA265_RS15355 : 3-ketohexose dehydratase
Original description: AP endonuclease
SEED: Inosose isomerase (EC 5.3.99.-)
KEGG: no annotation
Rationale: Specifically important in carbon source D-Salicin; carbon source D-Trehalose dihydrate; carbon source D-Cellobiose; carbon source Beta-Lactose. In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. Similar to the Agrobacterium enzyme (AtHyd, PMC10628242). The role in beta-lactose utilization suggests that it is a 3-ketogalactose dehydratase as well as a 3-ketoglucose dehydratase..

CA265_RS15360 : predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Original description: cytochrome C552
SEED: Cytochrome c551/c552
KEGG: no annotation
Rationale: Although we do not have fitness data for this gene, a similar protein (Echvi_1841) is also part of a cluster with glucoside 3-dehydrogenase (lacAC) and has similar phenotypes. This is probably the cytochrome c subunit, replacing lacB.

CA265_RS15375 : 2-hydroxy-3-keto-glucal / 2-hydroxy-3-keto-galactal transporter
Original description: MFS transporter
SEED: FIG00481863: hypothetical protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Salicin; carbon source D-Trehalose dihydrate; carbon source Beta-Lactose; carbon source D-Cellobiose (all glucosides or galactosides). In a conserved cluster with the 3-ketoglycoside pathway starting with lacAC. The 3-ketoglycoside is probably cleaved in the periplasm (CA265_RS22975 or CA265_RS15370 for alpha-glycosides, CA265_RS15380 for beta-glycosides), to give 2-hydroxy-3-keto-glucal or -galactal. Hydration to 3-ketoglucose or 3-ketogalactose probably occurs in the cytoplasm (CA265_RS15355), so this is probably a 2-hydroxy-3-keto-glucal / 2-hydro-3-keto-galatcal transporter.

CA265_RS15380 : 3-keto-beta-glycoside 1,2-lyase
Original description: hydroxypyruvate isomerase
SEED: Hydroxypyruvate isomerase (EC 5.3.1.22)
KEGG: hydroxypyruvate isomerase
Rationale: # Specifically important in carbon source Lactitol. May also be involved in lactulose utilization. 33% identical to 3-keto-beta-glycoside 1,2-lyase BT2156. May be partly redundant with downstream homologs (CA265_RS15385, CA265_RS15390). Has a potential signal peptide so is probably periplasmic.

CA265_RS15435 : glycine transporter
Original description: hypothetical protein
SEED: putative membrane protein
KEGG: no annotation
Rationale: Specific phenotype: utilization of Glycine. Belongs to the UPF0126 family of transporters (see PMID:29769716)

CA265_RS15670 : 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
Original description: 4-hydroxy-tetrahydrodipicolinate reductase
SEED: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
KEGG: dihydrodipicolinate reductase
Rationale: A conserved essential gene. This activity is necessary to explain lysine biosynthesis. 34% identical to dapB from Thermotoga maritima (Q9X1K8).

CA265_RS15810 : acetohydroxybutanoate synthase regulatory subunit (EC 2.2.1.6)
Original description: acetolactate synthase small subunit
SEED: Acetolactate synthase small subunit (EC 2.2.1.6)
KEGG: acetolactate synthase I/III small subunit
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00119.

CA265_RS15855 : 2-isopropylmalate synthase (EC 2.3.3.13)
Original description: 2-isopropylmalate synthase
SEED: 2-isopropylmalate synthase (EC 2.3.3.13)
KEGG: 2-isopropylmalate synthase
Rationale: Important for fitness in defined media unless leucine is provided. 54% identical to 2-isopropylmalate synthase from Leptospira interrogans (Q8F445).

CA265_RS15860 : threonine deaminase (EC 4.3.1.19)
Original description: threonine dehydratase
SEED: Threonine dehydratase biosynthetic (EC 4.3.1.19)
KEGG: threonine dehydratase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR02079.

CA265_RS16075 : Cytidine deaminase (EC 3.5.4.5)
Original description: cytidine deaminase
SEED: Cytidine deaminase (EC 3.5.4.5)
KEGG: cytidine deaminase
Rationale: Specifically important for utilizing Cytidine. Automated validation from mutant phenotype: the predicted function (CYTIDEAM2-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS18485 : arginosuccinate lyase (EC 4.3.2.1)
Original description: argininosuccinate lyase
SEED: Argininosuccinate lyase (EC 4.3.2.1)
KEGG: argininosuccinate lyase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00838.

CA265_RS18500 : N-succinylcitrulline desuccinylase (EC 3.5.1.-)
Original description: acetylornithine deacetylase
SEED: Acetylornithine deacetylase (EC 3.5.1.16)
KEGG: acetylornithine deacetylase
Rationale: Important for fitness in most defined media, except when arginine is provided. Distantly related to succinyl-diaminopimelate desuccinylases, so this probably provides the missing N-succinylcitrulline desuccinylase activity. See PMC7311316.

CA265_RS18505 : pyrroline-5-carboxylate reductase (EC 1.5.1.2)
Original description: pyrroline-5-carboxylate reductase
SEED: Pyrroline-5-carboxylate reductase (EC 1.5.1.2)
KEGG: pyrroline-5-carboxylate reductase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00112.

CA265_RS18540 : N-succinylglutamylphosphate reductase (EC 1.2.1.38)
Original description: N-acetyl-gamma-glutamyl-phosphate reductase
SEED: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
KEGG: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
Rationale: Important for fitness in most defined media, except when arginine or citrulline is provided. Hits TIGR01850, which is described as N-acetyl-gamma-glutamyl-phosphate reductase, but Bacteroidetes use succinylated intermediates for arginine synthesis (see PMC7311316).

CA265_RS19745 : shikimate dehydrogenase (EC 1.1.1.25)
Original description: shikimate dehydrogenase
SEED: Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
KEGG: shikimate dehydrogenase
Rationale: A conserved essential gene. This activity is necessary to explain chorismate biosynthesis. 33% identical to shikimate dehydrogenase from Geobacillus kaustophilus (Q5KWX7).

CA265_RS19855 : D-galacturonate transporter ExuT
Original description: MFS transporter
SEED: Hexuronate transporter
KEGG: MFS transporter, ACS family, hexuronate transporter
Rationale: Specifically important for D-galacturonate utilization.

CA265_RS19860 : 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14)
Original description: bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase
SEED: 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
KEGG: 2-dehydro-3-deoxyphosphogluconate aldolase / 4-hydroxy-2-oxoglutarate aldolase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (KDPGALDOL-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS19865 : 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
Original description: carbohydrate kinase
SEED: 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
KEGG: 2-dehydro-3-deoxygluconokinase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (DEOXYGLUCONOKIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS19870 : Glucuronate isomerase (EC 5.3.1.12)
Original description: glucuronate isomerase
SEED: Uronate isomerase (EC 5.3.1.12)
KEGG: glucuronate isomerase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (5.3.1.12) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CA265_RS19875 : Altronate dehydratase (EC 4.2.1.7)
Original description: altronate hydrolase
SEED: Altronate dehydratase (EC 4.2.1.7)
KEGG: altronate hydrolase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (ALTRODEHYDRAT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS19880 : Altronate oxidoreductase (EC 1.1.1.58)
Original description: altronate oxidoreductase
SEED: Altronate oxidoreductase (EC 1.1.1.58)
KEGG: tagaturonate reductase
Rationale: Specifically important for utilizing D-Galacturonic Acid monohydrate. Automated validation from mutant phenotype: the predicted function (ALTRO-OXIDOREDUCT-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS20855 : glutamate 5-kinase (EC 2.7.2.11)
Original description: glutamate 5-kinase
SEED: Glutamate 5-kinase (EC 2.7.2.11)
KEGG: glutamate 5-kinase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01027.

CA265_RS21455 : Formiminoglutamase (EC 3.5.3.8)
Original description: arginase
SEED: Formiminoglutamase (EC 3.5.3.8)
KEGG: no annotation
Rationale: Specifically important for utilizing L-Histidine. Automated validation from mutant phenotype: the predicted function (FORMIMINOGLUTAMASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS21925 : Glucosamine-6-phosphate deaminase (EC 3.5.99.6)
Original description: glucosamine-6-phosphate deaminase
SEED: Glucosamine-6-phosphate deaminase (EC 3.5.99.6)
KEGG: glucosamine-6-phosphate deaminase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (GLUCOSAMINE-6-P-DEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CA265_RS22270 : Histidine ammonia-lyase (EC 4.3.1.3)
Original description: histidine ammonia-lyase
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.

CA265_RS22635 : phosphoserine phosphatase (EC 3.1.3.3)
Original description: phosphoserine phosphatase
SEED: D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
KEGG: D-3-phosphoglycerate dehydrogenase
Rationale: Important for fitness in most defined media and strongly cofit with 3-phosphoglycerate dehydrogenase (CA265_RS09010). CA265_RS22635 is distantly related (28% identity) to the chloroplast phosphoserine phosphatase of Arabidopsis (O82796). CA265_RS22635 also has a 3-phosphoglycerate dehydrogenase domain, but given the auxotrophic phenotypes of the other 3-phosphoglycerate dehydrogenase, it may not be catalytically active.

CA265_RS22975 : 3-keto-alpha-glucoside 1,2-lyase
Original description: hypothetical protein
SEED: putative multi-domain protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Trehalose dihydrate. Also important for utilization of maltitol, so it's probably active on other substrates as well. Distantly related to 3-keto-alpha-glycoside lyase BT2157 (see PMID:38898276, PMID:37932298). This protein has a signal peptide so is probably periplasmic.

CA265_RS23470 : homoserine kinase (EC 2.7.1.39)
Original description: homoserine kinase
SEED: Homoserine kinase (EC 2.7.1.39)
KEGG: homoserine kinase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00191.

CA265_RS23475 : aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3)
Original description: bifunctional aspartate kinase/homoserine dehydrogenase I
SEED: Aspartokinase (EC 2.7.2.4) / Homoserine dehydrogenase (EC 1.1.1.3)
KEGG: bifunctional aspartokinase / homoserine dehydrogenase 1
Rationale: Important for fitness in most defined media. The entire protein is 40% identical to a bifunctional aspartokinase/homoserine dehydrogenase from Arabidopsis chloroplast (O81852).

CA265_RS24655 : maltose phosphorylase (EC 2.4.1.8)
Original description: family 65 glycosyl hydrolase
SEED: Maltose phosphorylase (EC 2.4.1.8) / Trehalose phosphorylase (EC 2.4.1.64)
KEGG: no annotation
Rationale: Specifically important for utilizing D-maltose.

CA265_RS24665 : maltose transporter MalT
Original description: MFS transporter
SEED: Predicted maltose transporter MalT
KEGG: no annotation
Rationale: Specifically important for maltose utilization.

CA265_RS25090 : L-asparaginase (EC 3.5.1.1)
Original description: L-asparaginase 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.

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