GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Ruegeria conchae TW15

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase G7G_RS0102260 G7G_RS0100765
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A G7G_RS0102220
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B G7G_RS0102225
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C G7G_RS0102230
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E G7G_RS0102240
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase G7G_RS0102270 G7G_RS0106810
paaZ1 oxepin-CoA hydrolase G7G_RS0102290 G7G_RS0102270
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase G7G_RS0102290
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase G7G_RS0102215 G7G_RS0116445
paaF 2,3-dehydroadipyl-CoA hydratase G7G_RS0116465 G7G_RS0122460
paaH 3-hydroxyadipyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
paaJ2 3-oxoadipyl-CoA thiolase G7G_RS0102215 G7G_RS0116445
Alternative steps:
atoB acetyl-CoA C-acetyltransferase G7G_RS0122070 G7G_RS0116445
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase G7G_RS0114145 G7G_RS0122065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase G7G_RS0116465
badK cyclohex-1-ene-1-carboxyl-CoA hydratase G7G_RS0116465 G7G_RS0122460
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 G7G_RS0117610 G7G_RS0102730
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 G7G_RS0102290
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase G7G_RS0117695 G7G_RS0106645
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase G7G_RS0116465 G7G_RS0111395
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G7G_RS0116465 G7G_RS0104515
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
gcdH glutaryl-CoA dehydrogenase G7G_RS0107335 G7G_RS0117695
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 G7G_RS0109635 G7G_RS0105860
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 G7G_RS0102215 G7G_RS0122070
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit G7G_RS0110000
pimF 6-carboxyhex-2-enoyl-CoA hydratase G7G_RS0102205
ppa phenylacetate permease ppa G7G_RS0105940

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