GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudomonas fluorescens FW300-N2E2

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa Pf6N2E2_5849
paaK phenylacetate-CoA ligase Pf6N2E2_2873 Pf6N2E2_2872
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Pf6N2E2_5315
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Pf6N2E2_1934 Pf6N2E2_1840
paaZ1 oxepin-CoA hydrolase Pf6N2E2_1834 Pf6N2E2_1147
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Pf6N2E2_2835 Pf6N2E2_2113
paaF 2,3-dehydroadipyl-CoA hydratase Pf6N2E2_1834 Pf6N2E2_1147
paaH 3-hydroxyadipyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
paaJ2 3-oxoadipyl-CoA thiolase Pf6N2E2_2835 Pf6N2E2_2113
Alternative steps:
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Pf6N2E2_1839 Pf6N2E2_1323
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Pf6N2E2_1934 Pf6N2E2_1147
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1834
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Pf6N2E2_4704
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 Pf6N2E2_1468 Pf6N2E2_273
bamI class II benzoyl-CoA reductase, BamI subunit Pf6N2E2_1467
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf6N2E2_1146 Pf6N2E2_5333
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1922
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
H281DRAFT_04042 phenylacetate:H+ symporter Pf6N2E2_5633 Pf6N2E2_5459
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf6N2E2_1522
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 Pf6N2E2_2539 Pf6N2E2_2289
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Pf6N2E2_1922 Pf6N2E2_2290

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