GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Burkholderia phytofirmans PsJN

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa BPHYT_RS25605 BPHYT_RS11800
paaK phenylacetate-CoA ligase BPHYT_RS17360 BPHYT_RS21775
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A BPHYT_RS18250
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B BPHYT_RS18255
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C BPHYT_RS18260
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E BPHYT_RS18270
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BPHYT_RS17350 BPHYT_RS28620
paaZ1 oxepin-CoA hydrolase BPHYT_RS06755 BPHYT_RS13360
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase BPHYT_RS17340 BPHYT_RS13360
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BPHYT_RS17345 BPHYT_RS29385
paaF 2,3-dehydroadipyl-CoA hydratase BPHYT_RS17335 BPHYT_RS25360
paaH 3-hydroxyadipyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
paaJ2 3-oxoadipyl-CoA thiolase BPHYT_RS17345 BPHYT_RS29385
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BPHYT_RS30440 BPHYT_RS04770
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BPHYT_RS28620 BPHYT_RS17335
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BPHYT_RS17335 BPHYT_RS17350
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BPHYT_RS25200
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 BPHYT_RS06650 BPHYT_RS14990
bamI class II benzoyl-CoA reductase, BamI subunit BPHYT_RS14995 BPHYT_RS06655
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 BPHYT_RS13335
boxB benzoyl-CoA epoxidase, subunit B BPHYT_RS13340
boxC 2,3-epoxybenzoyl-CoA dihydrolase BPHYT_RS13345
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase BPHYT_RS13360
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BPHYT_RS20780 BPHYT_RS28040
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BPHYT_RS17335 BPHYT_RS10815
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
H281DRAFT_04042 phenylacetate:H+ symporter BPHYT_RS15500 BPHYT_RS21680
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 BPHYT_RS24535
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 BPHYT_RS09565 BPHYT_RS03230
pimC pimeloyl-CoA dehydrogenase, small subunit BPHYT_RS13555 BPHYT_RS25385
pimD pimeloyl-CoA dehydrogenase, large subunit BPHYT_RS06715 BPHYT_RS13550
pimF 6-carboxyhex-2-enoyl-CoA hydratase BPHYT_RS09560 BPHYT_RS13545

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, 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