GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudomonas putida KT2440

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa PP_3272 PP_1743
paaK phenylacetate-CoA ligase PP_3279 PP_4550
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PP_3278
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PP_3277
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PP_3276
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PP_3274 PP_1163
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PP_3283 PP_3726
paaZ1 oxepin-CoA hydrolase PP_3270 PP_3283
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PP_3270
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PP_3280 PP_1377
paaF 2,3-dehydroadipyl-CoA hydratase PP_3284 PP_2217
paaH 3-hydroxyadipyl-CoA dehydrogenase PP_2136 PP_3282
paaJ2 3-oxoadipyl-CoA thiolase PP_1377 PP_3280
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PP_1946 PP_1852
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PP_3283 PP_2217
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PP_2217 PP_3284
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PP_0311
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 PP_2184 PP_4123
bamI class II benzoyl-CoA reductase, BamI subunit PP_2185
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 PP_3270 PP_0708
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PP_2216 PP_4064
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PP_2217 PP_3284
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
gcdH glutaryl-CoA dehydrogenase PP_0158 PP_4064
H281DRAFT_04042 phenylacetate:H+ symporter PP_0927 PP_4495
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PP_2217
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 PP_2051 PP_2137
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase PP_2136 PP_2047

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