GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudomonas simiae WCS417

Best path

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

Also see fitness data for the top candidates

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa PS417_08865
paaK phenylacetate-CoA ligase PS417_15170 PS417_22070
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PS417_23400
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PS417_10680 PS417_13845
paaZ1 oxepin-CoA hydrolase PS417_13845 PS417_10680
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PS417_06710 PS417_10515
paaF 2,3-dehydroadipyl-CoA hydratase PS417_13845 PS417_10680
paaH 3-hydroxyadipyl-CoA dehydrogenase PS417_07575 PS417_21215
paaJ2 3-oxoadipyl-CoA thiolase PS417_06710 PS417_10515
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PS417_11520 PS417_09065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PS417_13845 PS417_13835
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PS417_13845 PS417_10680
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PS417_26235
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit PS417_16595
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 PS417_13850 PS417_04135
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PS417_13845 PS417_07575
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
H281DRAFT_04042 phenylacetate:H+ symporter PS417_23700 PS417_22235
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaT phenylacetate transporter Paa
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 PS417_19210 PS417_07580
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit PS417_14930
pimF 6-carboxyhex-2-enoyl-CoA hydratase PS417_07575 PS417_21215

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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