GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudomonas fluorescens GW456-L13

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa PfGW456L13_2421 PfGW456L13_4275
paaK phenylacetate-CoA ligase PfGW456L13_2428 PfGW456L13_1910
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PfGW456L13_2427
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PfGW456L13_2426
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PfGW456L13_2425
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PfGW456L13_2423 PfGW456L13_2523
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PfGW456L13_2433 PfGW456L13_3388
paaZ1 oxepin-CoA hydrolase PfGW456L13_2419 PfGW456L13_2433
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PfGW456L13_2419
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PfGW456L13_2430 PfGW456L13_4590
paaF 2,3-dehydroadipyl-CoA hydratase PfGW456L13_2434 PfGW456L13_2984
paaH 3-hydroxyadipyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_2432
paaJ2 3-oxoadipyl-CoA thiolase PfGW456L13_4590 PfGW456L13_2430
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PfGW456L13_3458 PfGW456L13_2522
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PfGW456L13_2433 PfGW456L13_2984
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PfGW456L13_1104
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 PfGW456L13_4886 PfGW456L13_2629
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 PfGW456L13_2419
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PfGW456L13_2983 PfGW456L13_1630
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
H281DRAFT_04042 phenylacetate:H+ symporter PfGW456L13_4291 PfGW456L13_4400
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PfGW456L13_2984
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 PfGW456L13_2498 PfGW456L13_2157
pimC pimeloyl-CoA dehydrogenase, small subunit PfGW456L13_2494
pimD pimeloyl-CoA dehydrogenase, large subunit PfGW456L13_2495 PfGW456L13_2536
pimF 6-carboxyhex-2-enoyl-CoA hydratase PfGW456L13_412 PfGW456L13_4041

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