Updated Annotations for Paraburkholderia bryophila 376MFSha3.1

Updated annotations for Paraburkholderia bryophila 376MFSha3.1

18 genes with updated (or confirmed) annotations:

H281DRAFT_00361 : (3S)-hydroxyadipyl-CoA dehydrogenase (EC 1.1.1.35) / enoyl-CoA hydratase domain
Original description: short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase
SEED: Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
KEGG: 3-hydroxyacyl-CoA dehydrogenase
Rationale: H281DRAFT_00361 is specifically important for phenylacetate utilization via the oxygenase pathway. This pathway require a (3S)-hydroxyadipyl-CoA dehydrogenase (forming 3-oxoadipyl-CoA), which is probably provided by the aldehyde dehydrogenase domain of H281DRAFT_00361. H281DRAFT_00361 is 49% identical to PimB from Rhodopseudomonas palustris; the pim operon is involved in dicarboxylic fatty acid degradation (PMID:15758219), which is consistent with activity on (3S)-hydroxyadipyl-CoA. H281DRAFT_00361 also has an enoyl-CoA hydratase domain, whose role (if any) in phenylacetate utilization is not clear.

H281DRAFT_00640 : putative regulator of deoxyribonate oxidation
Original description: AraC-type DNA-binding protein
SEED: Ornithine utilization regulator
KEGG: no annotation
Rationale: Conserved next to and has similar phenotypes as the deoxyribonate oxidation cluster. It is probably a transcriptional activator.

H281DRAFT_00641 : 2-deoxy-3-keto-D-ribonate cleavage enzyme
Original description: Uncharacterized conserved protein, DUF849 family
SEED: FIG00460329: hypothetical protein
KEGG: no annotation
Rationale: Important for utilization of deoxyribose and deoxyribonate. This is expected to be the next step after the oxidation of deoxyribonate. It would release glyceryl-CoA and acetoacetate.

H281DRAFT_00642 : 2-deoxy-D-ribonate transporter
Original description: Sugar phosphate permease
SEED: D-galactonate transporter
KEGG: no annotation
Rationale: Important for utilization of deoxyribonate and, to some extent, deoxyribose. This may be a deoxyribose transporter as well, or, deoxyribose might be oxidized in the periplasm.

H281DRAFT_00644 : 2-deoxy-D-ribonate 3-dehydrogenase
Original description: NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
SEED: D-beta-hydroxybutyrate dehydrogenase (EC 1.1.1.30)
KEGG: no annotation
Rationale: Important for utilization of deoxyribonate and deoxyribose. Similar to the deoxyribonate dehydrogenase of P. simiae (PS417_07245).

H281DRAFT_01112 : deoxynucleoside transporter, permease component 2
Original description: monosaccharide ABC transporter membrane protein, CUT2 family
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: simple sugar transport system permease protein
Rationale: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.

H281DRAFT_01113 : deoxynucleoside transporter, ATPase component
Original description: monosaccharide ABC transporter ATP-binding protein, CUT2 family
SEED: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
KEGG: simple sugar transport system ATP-binding protein
Rationale: No fitness data for this gene; it was reannotated based on the mutant phenotypes of its neighbors.

H281DRAFT_01114 : deoxynucleoside transporter, substrate-binding component
Original description: monosaccharide ABC transporter substrate-binding protein, CUT2 family
SEED: ABC transporter, periplasmic sugar-binding protein precursor
KEGG: simple sugar transport system substrate-binding protein
Rationale: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.

H281DRAFT_01115 : deoxynucleoside transporter, permease component 1
Original description: monosaccharide ABC transporter membrane protein, CUT2 family
SEED: Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)
KEGG: simple sugar transport system permease protein
Rationale: Important for utilization of dAMP and deoxyinosine. Because the fitness profiles for these compounds are very similar, dAMP is likely hydrolyzed before uptake, but this could also be a transporter for deoxynucleotides.

H281DRAFT_01116 : deoxyribose kinase (EC 2.7.1.15)
Original description: ribokinase
SEED: Ribokinase (EC 2.7.1.15)
KEGG: ribokinase
Rationale: Important for utilization of deoxyribose and deoxynucleosides. Deoxynucleosides might be hydrolyzed to deoxyribose.

H281DRAFT_01117 : acetaldehyde dehydrogenase (EC 1.2.1.3)
Original description: aldehyde dehydrogenase (NAD+)
SEED: Aldehyde dehydrogenase (EC 1.2.1.3)
KEGG: aldehyde dehydrogenase (NAD+)
Rationale: Important for utilization of deoxyribose and deoxynucleosides. The acetaldehyde would be formed by deoxyribose 5-phosphate aldolase (H281DRAFT_01118)

H281DRAFT_03961 : xanthine dehydrogenase, small subunit (EC 1.17.1.4)
Original description: xanthine dehydrogenase small subunit
SEED: Xanthine dehydrogenase, iron-sulfur cluster and FAD-binding subunit A (1.17.1.4)
KEGG: xanthine dehydrogenase small subunit
Rationale: Specific phenotype: utilization of 2-Deoxyadenosine 5-monophosphate

H281DRAFT_04042 : phenylacetate transporter
Original description: aromatic amino acid:proton symporter, AAT family
SEED: Aromatic amino acid transport protein AroP
KEGG: amino acid transporter, AAT family
Rationale: Specifically important for phenylacetate utilization.

H281DRAFT_04594 : putative oxepin-CoA hydrolase (EC 3.3.2.12)
Original description: short chain enoyl-CoA hydratase /Enoyl-CoA hydratase
SEED: Enoyl-CoA hydratase/isomerase family protein, may be related to NAD-dependent histone deacetylation
KEGG: enoyl-CoA hydratase
Rationale: H281DRAFT_04594 is specifically important for phenylacetate utilization via the oxygenase pathway. This pathway requires an oxepin-CoA hydrolase, which is often provided by a (R)-specific enoyl-CoA hydratase (R-ECH) domain which is fused to 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase ("PaaZ"). But P. bryophila has a PacL-like semialdehyde dehydrogenase (H281DRAFT_05724), which lacks the R-ECH domain. H281DRAFT_04594 has an (S)-specific ECH domain and is probably the missing oxepin-CoA hydrolase. (There are no chiral centers in the oxepin-CoA reaction.) H281DRAFT_04594 is also related to paaF (2,3-dehydroadipyl-CoA hydratase), but that activity is probably provided by H281DRAFT_05725.

H281DRAFT_05722 : 1,2-epoxyphenylacetyl-CoA isomerase (EC 5.3.3.18)
Original description: short chain enoyl-CoA hydratase /Enoyl-CoA hydratase
SEED: Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for phenylacetate utilization. This is part of the aerobic phenylacetyl-CoA pathway.

H281DRAFT_05723 : bifunctional thiolase PaaJ: 3-oxo-5,6-didehydrosuberyl-CoA thiolase (EC 2.3.1.223); 3-oxoadipyl-CoA thiolase (EC 2.3.1.174)
Original description: acetyl-CoA acyltransferase
SEED: Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
KEGG: no annotation
Rationale: Specifically important for utilization of phenylacetate. This is probably the bifunctional thiolase in the aerobic phenylacetyl-CoA degradation pathway (also known as PaaJ).

H281DRAFT_05724 : 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PaaZ (EC:1.2.1.91)
Original description: phenylacetic acid degradation protein paaN
SEED: Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ
KEGG: no annotation
Rationale: Specifically important for utilization of phenylacetate. This dehydrogenase (also known as PaaZ) is part of the aerobic phenylacetyl-CoA degradation pathway. 86% identical to BCAL0408 from B. cenocepacia, which is also involved in phenylacetate degradation and was proposed to be PaaZ (PMC2580687).

H281DRAFT_05725 : 2,3-dehydroadipyl-CoA hydratase / enoyl-CoA hydratase (EC 4.2.1.17)
Original description: short chain enoyl-CoA hydratase
SEED: Phenylacetate degradation enoyl-CoA hydratase PaaA (EC 4.2.1.17)
KEGG: enoyl-CoA hydratase
Rationale: Specifically important for phenylacetate utilization. 51% identical to the characterized enzyme (paaF = Q845K2) from Pseudomonas sp. Y2, which is part of the aerobic phenylacetyl-CoA pathway. Also, 84% identical to enoyl-CoA hydratase Crt2 = H16_A3307 from Ralstonia eutropha (PMID:30243533).

Or download reannotations for Paraburkholderia bryophila 376MFSha3.1 or for all organisms as tab-delimited tables