GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Desulfacinum infernum DSM 9756

Best path

paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase BUB04_RS14470 BUB04_RS07860
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
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BUB04_RS09760 BUB04_RS07705
paaZ1 oxepin-CoA hydrolase BUB04_RS09760 BUB04_RS15240
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
paaF 2,3-dehydroadipyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
paaH 3-hydroxyadipyl-CoA dehydrogenase BUB04_RS17405 BUB04_RS00230
paaJ2 3-oxoadipyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BUB04_RS03720 BUB04_RS00235
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BUB04_RS01135 BUB04_RS18395
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BUB04_RS01125 BUB04_RS03725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
bamB class II benzoyl-CoA reductase, BamB subunit BUB04_RS05725 BUB04_RS08160
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BUB04_RS11540
bamE class II benzoyl-CoA reductase, BamE subunit BUB04_RS05165 BUB04_RS20045
bamF class II benzoyl-CoA reductase, BamF subunit BUB04_RS05160 BUB04_RS15995
bamG class II benzoyl-CoA reductase, BamG subunit BUB04_RS10395 BUB04_RS09275
bamH class II benzoyl-CoA reductase, BamH subunit BUB04_RS10400 BUB04_RS09280
bamI class II benzoyl-CoA reductase, BamI subunit BUB04_RS10465 BUB04_RS05180
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit BUB04_RS07265
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit BUB04_RS07265
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 BUB04_RS12135 BUB04_RS03730
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BUB04_RS03725 BUB04_RS07705
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BUB04_RS17405 BUB04_RS00230
gcdH glutaryl-CoA dehydrogenase BUB04_RS03730 BUB04_RS05240
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BUB04_RS01125
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit BUB04_RS08705 BUB04_RS11390
padD phenylacetyl-CoA dehydrogenase, PadD subunit
padE phenylglyoxylate dehydrogenase, gamma subunit BUB04_RS06875 BUB04_RS02380
padF phenylglyoxylate dehydrogenase, delta subunit BUB04_RS06880
padG phenylglyoxylate dehydrogenase, alpha subunit BUB04_RS06885 BUB04_RS02390
padH phenylglyoxylate dehydrogenase, epsilon subunit
padI phenylglyoxylate dehydrogenase, beta subunit BUB04_RS06890 BUB04_RS02395
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BUB04_RS03720 BUB04_RS00235
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase BUB04_RS16430
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 Apr 09 2024. 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:

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