GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

H281DRAFT_04042, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
H281DRAFT_04042 phenylacetate:H+ symporter H281DRAFT_04042 H281DRAFT_01668
paaK phenylacetate-CoA ligase H281DRAFT_05720 H281DRAFT_04125
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A H281DRAFT_05858
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B H281DRAFT_05857
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C H281DRAFT_05856
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E H281DRAFT_05854
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase H281DRAFT_05722 H281DRAFT_03491
paaZ1 oxepin-CoA hydrolase H281DRAFT_04594 H281DRAFT_00370
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase H281DRAFT_05724 H281DRAFT_00370 with H281DRAFT_02531
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase H281DRAFT_05723 H281DRAFT_01504
paaF 2,3-dehydroadipyl-CoA hydratase H281DRAFT_05725 H281DRAFT_02514
paaH 3-hydroxyadipyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
paaJ2 3-oxoadipyl-CoA thiolase H281DRAFT_05723 H281DRAFT_01504
Alternative steps:
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase H281DRAFT_00643 H281DRAFT_03703
badI 2-ketocyclohexanecarboxyl-CoA hydrolase H281DRAFT_02741 H281DRAFT_05725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase H281DRAFT_05725 H281DRAFT_02514
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit H281DRAFT_02472
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 H281DRAFT_04572 H281DRAFT_03941
bamI class II benzoyl-CoA reductase, BamI subunit H281DRAFT_03942 H281DRAFT_04573
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 H281DRAFT_00375
boxB benzoyl-CoA epoxidase, subunit B H281DRAFT_00374
boxC 2,3-epoxybenzoyl-CoA dihydrolase H281DRAFT_00373
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase H281DRAFT_00370
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase H281DRAFT_01204 H281DRAFT_06133
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase H281DRAFT_05725 H281DRAFT_01137
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
gcdH glutaryl-CoA dehydrogenase H281DRAFT_04737 H281DRAFT_01204
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 H281DRAFT_00917 H281DRAFT_04626
pimC pimeloyl-CoA dehydrogenase, small subunit H281DRAFT_00359 H281DRAFT_04587
pimD pimeloyl-CoA dehydrogenase, large subunit H281DRAFT_04586 H281DRAFT_00360
pimF 6-carboxyhex-2-enoyl-CoA hydratase H281DRAFT_00916 H281DRAFT_00361
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