GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Sinorhizobium meliloti 1021

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase SMc00261
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A SM_b21640
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B SM_b21639
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C SM_b21638
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E SM_b21636 SMc00981
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase SM_b21633 SMc01669
paaZ1 oxepin-CoA hydrolase SM_b21635 SM_b21633
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase SM_b21635
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase SM_b20589 SMc03879
paaF 2,3-dehydroadipyl-CoA hydratase SMc01153 SMc01669
paaH 3-hydroxyadipyl-CoA dehydrogenase SMc02227 SMc00727
paaJ2 3-oxoadipyl-CoA thiolase SM_b20589 SMc03879
Alternative steps:
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SMc03878 SMc00268
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SMc01669 SMc01153
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SMc01153 SM_b21633
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 SMa1525 SMc02525
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 SM_b21635
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase SMa1400 SM_b21121
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SMc01153 SMc01669
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
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 SM_b20589 SMc03879
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase SM_b21632 SMc02227
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 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