Updated Annotations for Sphingomonas koreensis DSMZ 15582

Updated annotations for Sphingomonas koreensis DSMZ 15582

37 genes with updated (or confirmed) annotations:

Ga0059261_0351 : N-acetylglutamylphosphate reductase (EC 1.2.1.38)
Original description: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)
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. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01850.

Ga0059261_1047 : 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 (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.

Ga0059261_1051 : 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.

Ga0059261_1166 : Beta-glucosidase (EC 3.2.1.21)
Original description: Beta-glucosidase-related glycosidases
SEED: Periplasmic beta-glucosidase (EC 3.2.1.21)
KEGG: no annotation
Rationale: Specifically important for utilizing D-Cellobiose. 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.

Ga0059261_1280 : 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 most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00070.

Ga0059261_1497 : required for sulfate utilization, putative electron source for sulfite reductase CysI
Original description: Protein of unknown function (DUF2849)
SEED: Conserved hypothetical protein probably involved in sulfate reduction
KEGG: no annotation
Rationale: PFam PF11011.4 (DUF2849). conserved cofit with sulfite reductase and has a complementary pattern of gene presence as cysJ

Ga0059261_1499 : required for sulfate utilization, putative electron transport protein for sulfite reductase
Original description: Uncharacterized protein conserved in bacteria
SEED: Oxidoreductase probably involved in sulfite reduction
KEGG: no annotation
Rationale: PFam PF06073.8 (DUF934). conserved cofitness with sulfite reductase; auxotrophic

Ga0059261_1577 : L-glutamine and L-histidine transporter
Original description: amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
SEED: amino acid transporter
KEGG: basic amino acid/polyamine antiporter, APA family
Rationale: Specific phenotype on glutamine; also important for histidine utilization; detrimental to fitness on some other amino acids (proline, alanine) which may indicate that it likes these amino acids

Ga0059261_1581 : Maltose or maltodextrin glucosidase (EC 3.2.1.20)
Original description: Glycosidases
SEED: Maltodextrin glucosidase (EC 3.2.1.20)
KEGG: no annotation
Rationale: Specifically important for: D-Maltose monohydrate; a-Cyclodextrin. The first step in catabolism of maltose or longer maltodextrin polymers. The phenotype on maltose implies that maltose is also a substrate, which was ambiguous with the original SEED annotation (SEED_correct)

Ga0059261_1644 : Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6)
Original description: Predicted phosphosugar isomerases
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.

Ga0059261_1645 : 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.

Ga0059261_1647 : N-acetylglucosamine phosphotransferase system, IIB/IIC components (EC 2.7.1.193)
Original description: PTS system, N-acetylglucosamine-specific IIBC component
SEED: PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
KEGG: PTS system, N-acetylglucosamine-specific IIB component ; PTS system, N-acetylglucosamine-specific IIC component
Rationale: Specific phenotype: utilization of N-Acetyl-D-Glucosamine

Ga0059261_1776 : Fructokinase (EC 2.7.1.4)
Original description: Transcriptional regulator/sugar kinase
SEED: Fructokinase (EC 2.7.1.4)
KEGG: fructokinase
Rationale: Specifically important for utilizing D-Fructose. Automated validation from mutant phenotype: the predicted function (2.7.1.4) was linked to the condition via a SEED subsystem. This annotation was also checked manually.

Ga0059261_1777 : D-fructose transporter, sugar porter family
Original description: MFS transporter, sugar porter (SP) family
SEED: no annotation
KEGG: no annotation
Rationale: Specific phenotype on fructose and raffinose; during growth on raffinose, it is probably cleaved to sucrose in the periplasm (by Ga0059261_1166), so this probably is important on raffinose because of the fructose uptake

Ga0059261_1778 : beta-fructosidase for D-raffinose catabolism (EC 3.2.1.26)
Original description: Beta-fructosidases (levanase/invertase)
SEED: Sucrose-6-phosphate hydrolase (EC 3.2.1.B3)
KEGG: no annotation
Rationale: Specifically important for: D-Raffinose pentahydrate. Uncertain if it acts on raffinose or sucrose (raffinose could be cleaved to galactose + sucrose first). Alternatively, SEED suggests that it hydrolyzes sucrose-6-phosphate, but the basis for this is unclear.

Ga0059261_1893 : Xylonolactonase (EC 3.1.1.68)
Original description: Gluconolactonase
SEED: Xylonolactonase (EC 3.1.1.68)
KEGG: no annotation
Rationale: Specifically important for: D-Xylose. xylonolactone is an intermediate in the oxidation of xylose (SEED_correct)

Ga0059261_1894 : D-xylose 1-dehydrogenase (EC 1.1.1.175)
Original description: Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
SEED: D-xylose 1-dehydrogenase (EC 1.1.1.175)
KEGG: no annotation
Rationale: Specifically important for: D-Xylose. the first step in xylose oxidation (SEED_correct)

Ga0059261_1895 : 2-keto-3-deoxyxylonate dehydratase (EC 4.2.1.141)
Original description: Fumarylacetoacetate (FAA) hydrolase family protein
SEED: Fumarylacetoacetate hydrolase family protein
KEGG: no annotation
Rationale: # Specifically important in carbon source D-Xylose. 31% identical to HVO_B0027, which is 2-keto-3-deoxyxylonate dehydratase (see PMC2785657). Ga0059261_1895 is also 61% identical to xylX from Caulobacter crescentus, which is also required for xylose utilization (PMC1855722) and is believed to have this activity as well.

Ga0059261_1896 : Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
Original description: NAD-dependent aldehyde dehydrogenases
SEED: Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26)
KEGG: NADP-dependent aldehyde dehydrogenase
Rationale: Specifically important for: D-Xylose. The KEGG annotation is vague; xylose is oxidized to alpha-ketoglutarate semialdehyde (SEED_correct)

Ga0059261_1941 : DNA damage response helicase, ligase-associated
Original description: DEXH box helicase, DNA ligase-associated
SEED: ATP-dependent helicase, DEAD/DEAH box family, associated with Flp pilus assembly
KEGG: ATP-dependent helicase Lhr and Lhr-like helicase
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Related to Lhr, which is either a DNA:DNA or DNA:RNA helicase, but lacks the long C-terminal extension that might have a regulatory role (see putative winged helix domain in E. coli lhr). This is also related to the archael protein saci_1500, which has also been linked to DNA damage response, as a mutant is sensitive to UV (PMID: 26148716)

Ga0059261_1942 : putative efflux pump, required for thallium (I) resistance
Original description: Uncharacterized conserved protein
SEED: Protein of unknown function UPF0060
KEGG: hypothetical protein
Rationale: PFam PF02694.11 (UPF0060). conserved specific phenotype of UPF0060

Ga0059261_2035 : Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
Original description: histidinol-phosphatase, inositol monophosphatase family
SEED: Histidinol-phosphatase [alternative form] (EC 3.1.3.15)
KEGG: no annotation
Rationale: Annotated as this by multiple resources. (auxotroph) (SEED_correct)

Ga0059261_2051 : diaminopimelate decarboxylase (EC 4.1.1.20)
Original description: diaminopimelate decarboxylase
SEED: Diaminopimelate decarboxylase (EC 4.1.1.20)
KEGG: diaminopimelate decarboxylase
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR01048.

Ga0059261_2194 : shikimate dehydrogenase (EC 1.1.1.25)
Original description: shikimate dehydrogenase (EC 1.1.1.25)
SEED: Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
KEGG: shikimate dehydrogenase
Rationale: # Cofit with other chorismate synthesis genes. Also known as BDW16_RS10815, which complements an aroE- strain of E. coli (data of PMID:39375541)

Ga0059261_2298 : prephenate and/or arogenate dehydrogenase (EC 1.3.1.13)
Original description: Prephenate dehydrogenase
SEED: Prephenate and/or arogenate dehydrogenase (unknown specificity) (EC 1.3.1.12)(EC 1.3.1.43)
KEGG: prephenate dehydrogenase
Rationale: Important for fitness in defined media. 31% identical to arogenate dehydrogenase from Arabidopsis (Q9LMR3). The substrate could be prephenate (dehydrogenation first) or arogenate (transamination followed by dehydrogenation).

Ga0059261_2711 : homoserine dehydrogenase (EC 1.1.1.3)
Original description: homoserine dehydrogenase (EC 1.1.1.3)
SEED: Homoserine dehydrogenase (EC 1.1.1.3)
KEGG: homoserine dehydrogenase
Rationale: Divergent from characterized homoserine dehydrogenases but has the expected phenotype: important for fitness in the absence of amino acids and is most cofit with homoserine O-acetyltransferase Ga0059261_2301

Ga0059261_2928 : oxygen-dependent methionine synthase, putative oxygenase component MesX
Original description: Domain of unknown function (DUF1852)
SEED: FIG00919961: hypothetical protein
KEGG: no annotation
Rationale: # Required for methionine synthesis in the absence of cobalamin, along with MesD (Ga0059261_2929). This system requires oxygen, but not 5-methyltetrahydrofolate. See https://doi.org/10.1101/2020.04.21.054031

Ga0059261_2929 : oxygen-dependent methionine synthase, methyltransferase component MesD
Original description: methionine synthase (B12-independent) (EC 2.1.1.14)
SEED: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14)
KEGG: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Rationale: # Required for methionine synthesis in the absence of cobalamin. Contains the C-terminal domain of MetE (catalytic and homocysteine-binding) but not the N-terminal (folate-binding) domain. Requires MesX (Ga0059261_2928, DUF1852) and oxygen, but not 5-methyltetrahydrofolate. See https://doi.org/10.1101/2020.04.21.054031

Ga0059261_3194 : O-acetylhomoserine sulfhydrylase (EC:2.5.1.49)
Original description: Cystathionine beta-lyases/cystathionine gamma-synthases
SEED: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
KEGG: O-succinylhomoserine sulfhydrylase
Rationale: Annotated as this by multiple resources. KEGG suggests that it is O-succinylhomoserine sulfhydrylase but there is an O-acetyltransferase (Ga0059261_2301) with auxotrophic phenotypes (auxotroph) (SEED_correct)

Ga0059261_3253 : homoserine kinase (EC 2.7.1.39)
Original description: homoserine kinase (EC 2.7.1.39)
SEED: Homoserine kinase (EC 2.7.1.39)
KEGG: homoserine kinase type II
Rationale: Important for fitness in most defined media. Semi-automated annotation based on the auxotrophic phenotype and a hit to HMM TIGR00938.

Ga0059261_3512 : glutamate 5-kinase (EC 2.7.2.11)
Original description: glutamate 5-kinase
SEED: Glutamate 5-kinase (EC 2.7.2.11) / RNA-binding C-terminal domain PUA
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.

Ga0059261_3694 : threonine deaminase (EC 4.3.1.19)
Original description: threonine ammonia-lyase, medium form
SEED: Threonine dehydratase (EC 4.3.1.19)
KEGG: threonine dehydratase
Rationale: Important for fitness in most defined media. Hits TIGR01127.

Ga0059261_3899 : Alanine dehydrogenase (EC 1.4.1.1)
Original description: alanine dehydrogenase
SEED: Alanine dehydrogenase (EC 1.4.1.1)
KEGG: alanine dehydrogenase
Rationale: Specifically important for utilizing L-Alanine. Automated validation from mutant phenotype: the predicted function (ALANINE-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.

Ga0059261_3961 : 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.

Ga0059261_3962 : N-formylglutamate deformylase (EC 3.5.1.68)
Original description: N-formylglutamate amidohydrolase
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.

Ga0059261_3963 : 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.

Ga0059261_3964 : 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.

Or download reannotations for Sphingomonas koreensis DSMZ 15582 or for all organisms as tab-delimited tables