GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Escherichia coli BW25113

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa b4067
paaK phenylacetate-CoA ligase b1398 b1805
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A b1388
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B b1389
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C b1390
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E b1392
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase b1394 b1393
paaZ1 oxepin-CoA hydrolase b1387 b1394
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase b1387
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase b1397 b2224
paaF 2,3-dehydroadipyl-CoA hydratase b1393 b1394
paaH 3-hydroxyadipyl-CoA dehydrogenase b3846 b2341
paaJ2 3-oxoadipyl-CoA thiolase b1397 b2224
Alternative steps:
atoB acetyl-CoA C-acetyltransferase b2224 b2844
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase b1093 b2426
badI 2-ketocyclohexanecarboxyl-CoA hydrolase b2262
badK cyclohex-1-ene-1-carboxyl-CoA hydratase b1393 b1394
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
bamH class II benzoyl-CoA reductase, BamH subunit b2284
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit b4334
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit b4334
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 b1387
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase b1695
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase b1393 b2341
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
gcdH glutaryl-CoA dehydrogenase
H281DRAFT_04042 phenylacetate:H+ symporter b0112 b0576
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase b2262
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit b4072 b0895
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 b1397 b2224
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase b3846 b2341

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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