Updated Annotations for Caulobacter crescentus NA1000

Updated annotations for Caulobacter crescentus NA1000

35 genes with updated (or confirmed) annotations:

CCNA_00003 : shikimate dehydrogenase (EC 1.1.1.25)
Original description: shikimate 5-dehydrogenase
SEED: Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
KEGG: shikimate dehydrogenase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00507.

CCNA_00096 : asparaginase (EC 3.5.1.1)
Original description: L-asparaginase
SEED: Isoaspartyl aminopeptidase (EC 3.4.19.5) @ Asp-X dipeptidase
KEGG: beta-aspartyl-peptidase (threonine type)
Rationale: Specifically important for utilization of asparagine as a nitrogen source

CCNA_00435 : L-proline transporter
Original description: amino acid transporter
SEED: amino acid transporter
KEGG: basic amino acid/polyamine antiporter, APA family
Rationale: Mildly important for growth with proline as the carbon or nitrogen source, and detrimental in most other conditions.

CCNA_00452 : N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Original description: N-acetylglucosamine-6-phosphate deacetylase
SEED: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
KEGG: N-acetylglucosamine-6-phosphate deacetylase
Rationale: Specifically important for utilizing N-Acetyl-D-Glucosamine. Automated validation from mutant phenotype: the predicted function (NAG6PDEACET-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CCNA_00453 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: glucosamine-6-phosphate deaminase
SEED: Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
KEGG: glucosamine--fructose-6-phosphate aminotransferase (isomerizing)
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.

CCNA_00528 : 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.

CCNA_00650 : nitrate transporter
Original description: MFS superfamily nitrate/nitrite transporter NarK
SEED: Nitrate/nitrite transporter
KEGG: MFS transporter, NNP family, nitrate/nitrite transporter
Rationale: Specific phenotype: utilization of nitrate; probably a nitrate transporter only (51% identical to B.subtilis nasA) but could be a nitrate/nitrite antiporter (29% id to Q9RA46)

CCNA_00651 : Nitrite reductase (NAD(P)H) (EC 1.7.1.4)
Original description: nitrite reductase (NAD(P)H) catalytic subunit
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.

CCNA_00653 : Nitrate reductase (EC 1.7.99.4)
Original description: assimilatory nitrate reductase catalytic subunit
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.

CCNA_00857 : D-xylose transporter
Original description: glucose/fructose transport protein
SEED: D-xylose proton-symporter XylE
KEGG: MFS transporter, SP family, sugar:H+ symporter
Rationale: Specifically important for D-xylose utilization. Also see PMC2168598 and PMC344409. May also be important for lactose utilization, which is not explained.

CCNA_00862 : Xylonate dehydratase (EC 4.2.1.82)
Original description: xylonate dehydratase xylD
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.

CCNA_00864 : D-xylose 1-dehydrogenase (EC 1.1.1.175)
Original description: xylose dehydrogenase xylB
SEED: D-xylose 1-dehydrogenase (EC 1.1.1.175)
KEGG: no annotation
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (1.1.1.175) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CCNA_00866 : 2-keto-3-deoxyxylonate dehydratase XylX (EC 4.2.1.141)
Original description: fumarylacetoacetate hydrolase family protein
SEED: predicted 2-keto-3-deoxyxylonate dehydratase
KEGG: no annotation
Rationale: Important for utilizing D-Xylose. It was previously reported to be involved in xylose catabolism and named xylX (see CC0823 and PMC1855722). It is distantly related to the characterized 2-keto-3-deoxyxylonate dehydratase from Haloferax volcanii (PMC2785657)

CCNA_01019 : Beta-glucosidase (EC 3.2.1.21)
Original description: beta-glucosidase
SEED: Beta-glucosidase (EC 3.2.1.21)
KEGG: beta-glucosidase
Rationale: Specifically important for utilizing D-Salicin. Automated validation from mutant phenotype: the predicted function (3.2.1.21) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

CCNA_01194 : TonB-dependent receptor for sucrose and raffinose (SucA)
Original description: TonB-dependent receptor
SEED: Predicted sucrose-specific TonB-dependent receptor
KEGG: no annotation
Rationale: Specific phenotype: utilization of D-Raffinose. Raffinose is probably cleaved in the cytoplasm by CCNA_02368, implying raffinose transport. This also transports sucrose (PMID:30054816)

CCNA_01356 : 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29)
Original description: 5-dehydro-2-deoxygluconokinase IolC
SEED: 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
KEGG: 5-dehydro-2-deoxygluconokinase
Rationale: Important for utilizing 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.

CCNA_01360 : Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
Original description: malonate-semialdehyde dehydrogenase IolA
SEED: Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)
KEGG: methylmalonate-semialdehyde dehydrogenase
Rationale: Specifically important for utilizing m-Inositol. Automated validation from mutant phenotype: the predicted function (RXN-2902) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CCNA_01698 : 3-keto-glycoside 1,2-lyase
Original description: endo-1,3-1,4-beta glucanase-related protein
SEED: putative multi-domain protein
KEGG: no annotation
Rationale: Specifically important in carbon source D-Raffinose pentahydrate. Raffinose utilization which appears to proceed via the 3-ketoglycoside pathway. This protein is in a conserved cluster with the 3-ketoglycoside pathway starting with lacABC. Distantly related to BT2157, which is a 3-ketoglycoside lyase. This protein has a signal peptide so is probably periplasmic. Note that another protein from this family (CCNA_01705) is also involved. Because raffinose is a trisaccharide, it is not clear which cleavage is performed by CCNA_01698.

CCNA_01700 : 2-hydroxy-3-keto-glucal / 2-hydroxy-3-keto-galactal transporter
Original description: nucleoside permease
SEED: FIG00481863: hypothetical protein
KEGG: no annotation
Rationale: Important for utilization of raffinose, lactose, and salicin. In a conserved cluster with the 3-ketoglycoside pathway starting with lacABC. The 3-ketoglycosides are probably cleaved in the periplasm by various lyases (CCNA_01698, CCNA_01705, CCNA_01701) and the 2-hydroxy-3-keto-glucal or -galactal is probably hydrated in the cytoplasm (CCNA_01703), so this transporter probably acts on 2-hydroxy-3-keto-glucal or -galactal.

CCNA_01701 : 3-keto-glycoside 1,2-lyase
Original description: xylose isomerase family protein
SEED: Sugar phosphate isomerases/epimerases
KEGG: no annotation
Rationale: Important for the utilization of lactose, salicin, and raffinose. In a conserved cluster with the 3-ketoglycoside pathway starting with lacABC. Distantly related to BT2156, which is a 3-keto-beta-glycoside 1,2-lyase. Lactose and salicin are beta-glycosides but raffinose has two alpha linkages for its hexoses, which suggests that CCNA_01700 acts on alpha-glycosides as well. Note that another lyase (CCNA_01705) is also involved in lactose and raffinose utilization; the two enzymes may be partially redundant. CCNA_01701 has a signal peptide and is expected to be periplasmic

CCNA_01702 : 3-ketohexose reductase (NADH)
Original description: NAD-dependent oxidoreductase
SEED: Nucleoside-diphosphate-sugar epimerases
KEGG: no annotation
Rationale: Important for the utilization of lactose, salicin, and raffinose. In a conserved cluster with the 3-ketoglycoside pathway starting with lacABC. 28% identical to 3-ketoglucose reductase lgdC (BCB28826.1, see PMC7676230), which uses NADH as the electron donor. Probably cytoplasmic.

CCNA_01703 : 3-ketohexose dehydratase
Original description: IolE-related protein
SEED: Inosose isomerase (EC 5.3.99.-)
KEGG: no annotation
Rationale: Important for the utilization of lactose, salicin, and raffinose. In a conserved cluster with the 3-ketoglycoside pathway starting with lacABC. 74% identical to 3-ketoglucose dehydratase AtHyd (PMC10628242). This is probably cytoplasmic.

CCNA_01704 : lacB: cytochrome c2 component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Original description: cytochrome c
SEED: Cytochrome c2
KEGG: cytochrome c
Rationale: Specifically important in carbon source Beta-Lactose, and also important for carbon sources salicin and raffinose. Previously proposed to be a component of lactose 3-dehydrogenase (PMCID:PMC2863468)

CCNA_01705 : 3-keto-glycoside 1,2-lyase
Original description: hypothetical protein
SEED: FIG00482450: hypothetical protein
KEGG: no annotation
Rationale: Specifically important for the utilization of lactose, as part of the 3-ketoglycoside pathway. (3'-ketolactose is formed by LacABC, which are encoded on either side.) Also involved in raffinose utilization. Distantly related to the 3-keto-glycoside 1,2-lyase BT2157, which is more active on alpha substrates, but the role in lactose utilization implies that CCNA_01705 is active on beta-galactosides.

CCNA_01706 : lacA: subunit of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Original description: BetA-family choline dehydrogenase
SEED: Glucose-methanol-choline (GMC) oxidoreductase:NAD binding site
KEGG: no annotation
Rationale: Specifically important in carbon source D-Raffinose pentahydrate; carbon source Beta-Lactose; carbon source. Previously shown to be required for and induced by growth on lactose and to be a component of lactose 3-dehydrogenase (PMCID:PMC2863468)

CCNA_01707 : lacC: subunit of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13)
Original description: gluconate 2-dehydrogenase subunit 3-family protein
SEED: FIG00480828: hypothetical protein
KEGG: no annotation
Rationale: Important for the utilization of lactose, salicin, and raffinose. Previously proposed to be a component of lactose 3-dehydrogenase (PMCID:PMC2863468)

CCNA_01969 : aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23)
Original description: aspartyl-tRNA synthetase
SEED: Aspartyl-tRNA synthetase (EC 6.1.1.12) @ Aspartyl-tRNA(Asn) synthetase (EC 6.1.1.23)
KEGG: aspartyl-tRNA synthetase
Rationale: A conserved essential gene. This activity is necessary to explain asparagine biosynthesis. 43% identical to the enzyme from Bacillus subtilis (O32038)

CCNA_01982 : glutamyl-tRNA(Glx) synthetase (EC 6.1.1.24)
Original description: glutamyl-tRNA synthetase
SEED: Glutamyl-tRNA synthetase (EC 6.1.1.17) @ Glutamyl-tRNA(Gln) synthetase (EC 6.1.1.24)
KEGG: glutamyl-tRNA synthetase
Rationale: A conserved essential gene. This activity is necessary to explain glutamine synthesis. Similar to both glutamyl-tRNA(Glu) and glutamyl-tRNA(Glx) synthetases (i.e. from E. coli or the organellar enzyme from Arabidopsis, which is probably transamidating, see PMID:3340166)

CCNA_02122 : DNA repair nuclease, ligase-associated (TIGR04123)
Original description: DNA ligase-associated metallophosphoesterase
SEED: FIG006285: ICC-like protein phosphoesterase
KEGG: no annotation
Rationale: # Very important for resisting 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).

CCNA_03103 : shikimate kinase (EC 2.7.1.71)
Original description: shikimate kinase
SEED: Shikimate kinase I (EC 2.7.1.71)
KEGG: shikimate kinase
Rationale: Important for fitness in most defined media, and highly cofit with shikimate 5-dehydrogenase (CCNA_00003). 39% identical to shikimate kinase from Acinetobacter baumannii (A0A0M3KL09)

CCNA_03284 : Adenosine deaminase (EC 3.5.4.4)
Original description: adenosine deaminase
SEED: Adenosine deaminase (EC 3.5.4.4)
KEGG: adenosine deaminase
Rationale: Specifically important for utilizing Adenosine. Automated validation from mutant phenotype: the predicted function (ADENODEAMIN-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

CCNA_03626 : ATP phosphoribosyltransferase (EC 2.4.2.17)
Original description: ATP phosphoribosyltransferase
SEED: ATP phosphoribosyltransferase (EC 2.4.2.17)
KEGG: ATP phosphoribosyltransferase
Rationale: Important for fitness in many defined media, and cofit with histidinol dehydrogenase (CCNA_02431). Hits TIGR00070.

CCNA_03750 : threonine deaminase (EC 4.3.1.19)
Original description: threonine dehydratase
SEED: Threonine dehydratase (EC 4.3.1.19)
KEGG: threonine dehydratase
Rationale: Important for fitness in most defined media. Hits TIGR01127.

CCNA_03852 : 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16)
Original description: phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase
SEED: Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
KEGG: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00007.

CCNA_03854 : phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
Original description: phosphoribosyl-ATP pyrophosphatase
SEED: Phosphoribosyl-ATP pyrophosphatase (EC 3.6.1.31)
KEGG: phosphoribosyl-ATP pyrophosphohydrolase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR03188.

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