GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Phaeobacter inhibens BS107

Best path

paaT, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase PGA1_c26800 PGA1_c34070
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PGA1_c04080
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PGA1_c04070
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PGA1_c04060
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PGA1_c04040
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PGA1_c26820 PGA1_c16990
paaZ1 oxepin-CoA hydrolase PGA1_c26830 PGA1_262p00800
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PGA1_c26830 PGA1_262p00800
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PGA1_c04090 PGA1_c34350
paaF 2,3-dehydroadipyl-CoA hydratase PGA1_c36500 PGA1_262p01980
paaH 3-hydroxyadipyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
paaJ2 3-oxoadipyl-CoA thiolase PGA1_c04090 PGA1_c34350
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PGA1_c17930 PGA1_c03390
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PGA1_262p01980 PGA1_c26820
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
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 PGA1_c10430 PGA1_c25750
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 PGA1_c26830 PGA1_262p00800
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PGA1_c10280 PGA1_c17340
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PGA1_c36500
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit PGA1_c28890 PGA1_c27640
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 PGA1_c22730 PGA1_c04120
pimC pimeloyl-CoA dehydrogenase, small subunit PGA1_c04140
pimD pimeloyl-CoA dehydrogenase, large subunit PGA1_c04130 PGA1_c12060
pimF 6-carboxyhex-2-enoyl-CoA hydratase PGA1_c22740 PGA1_c04110
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 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 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