GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudovibrio axinellae Ad2

Best path

paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Rules

Overview: Phenylacetate utilization in GapMind is based on MetaCyc pathway phenylacetate degradation I (aerobic via phenylacetyl-CoA dehydrogenase, link) and pathway II (anaerobic via benzoyl-CoA, link).

54 steps (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase PsAD2_RS12305
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PsAD2_RS12240
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PsAD2_RS12245
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PsAD2_RS12250
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PsAD2_RS12260 PsAD2_RS19860
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PsAD2_RS12315 PsAD2_RS22715
paaZ1 oxepin-CoA hydrolase PsAD2_RS22715 PsAD2_RS12315
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PsAD2_RS12320
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PsAD2_RS08175 PsAD2_RS01745
paaF 2,3-dehydroadipyl-CoA hydratase PsAD2_RS08800 PsAD2_RS22715
paaH 3-hydroxyadipyl-CoA dehydrogenase PsAD2_RS22445 PsAD2_RS11955
paaJ2 3-oxoadipyl-CoA thiolase PsAD2_RS08175 PsAD2_RS01745
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PsAD2_RS01745 PsAD2_RS08175
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PsAD2_RS18845 PsAD2_RS01750
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PsAD2_RS08800 PsAD2_RS22715
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PsAD2_RS08800 PsAD2_RS22715
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit PsAD2_RS23390
bamH class II benzoyl-CoA reductase, BamH subunit PsAD2_RS23385 PsAD2_RS17110
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit
boxA benzoyl-CoA epoxidase, subunit A
boxB benzoyl-CoA epoxidase, subunit B
boxC 2,3-epoxybenzoyl-CoA dihydrolase
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PsAD2_RS16670 PsAD2_RS22225
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PsAD2_RS08800 PsAD2_RS16425
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PsAD2_RS08800 PsAD2_RS22445
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PsAD2_RS22445 PsAD2_RS11955
gcdH glutaryl-CoA dehydrogenase PsAD2_RS08770 PsAD2_RS22225
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit
padD phenylacetyl-CoA dehydrogenase, PadD subunit
padE phenylglyoxylate dehydrogenase, gamma subunit
padF phenylglyoxylate dehydrogenase, delta subunit
padG phenylglyoxylate dehydrogenase, alpha subunit
padH phenylglyoxylate dehydrogenase, epsilon subunit
padI phenylglyoxylate dehydrogenase, beta subunit
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PsAD2_RS01745 PsAD2_RS08175
pimC pimeloyl-CoA dehydrogenase, small subunit PsAD2_RS23295 PsAD2_RS13050
pimD pimeloyl-CoA dehydrogenase, large subunit PsAD2_RS23300 PsAD2_RS13055
pimF 6-carboxyhex-2-enoyl-CoA hydratase PsAD2_RS22445 PsAD2_RS11955
ppa phenylacetate permease ppa

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory