GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Thauera aminoaromatica S2

Best path

ppa, paaK, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa C665_RS12865 C665_RS13515
paaK phenylacetate-CoA ligase C665_RS03175 C665_RS06105
padB phenylacetyl-CoA dehydrogenase, PadB subunit C665_RS06145 C665_RS04875
padC phenylacetyl-CoA dehydrogenase, PadC subunit C665_RS06140 C665_RS04870
padD phenylacetyl-CoA dehydrogenase, PadD subunit C665_RS06135
padG phenylglyoxylate dehydrogenase, alpha subunit C665_RS06120
padI phenylglyoxylate dehydrogenase, beta subunit C665_RS06110
padE phenylglyoxylate dehydrogenase, gamma subunit C665_RS06130
padF phenylglyoxylate dehydrogenase, delta subunit C665_RS06125
padH phenylglyoxylate dehydrogenase, epsilon subunit C665_RS06115 C665_RS03645
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit C665_RS06195
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit C665_RS06190
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit C665_RS06185
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit C665_RS06200 C665_RS06195
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase C665_RS06180 C665_RS11710
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase C665_RS06170 C665_RS04310
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase C665_RS06175
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase C665_RS04230 C665_RS03170
gcdH glutaryl-CoA dehydrogenase C665_RS15135 C665_RS12450
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C665_RS16150 C665_RS16085
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C665_RS04225 C665_RS00910
atoB acetyl-CoA C-acetyltransferase C665_RS12455 C665_RS01835
Alternative steps:
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase C665_RS01145 C665_RS01140
badI 2-ketocyclohexanecarboxyl-CoA hydrolase C665_RS11710 C665_RS10355
badK cyclohex-1-ene-1-carboxyl-CoA hydratase C665_RS16150 C665_RS16085
bamB class II benzoyl-CoA reductase, BamB subunit C665_RS03640
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit
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 C665_RS07555 C665_RS05430
bamI class II benzoyl-CoA reductase, BamI subunit C665_RS07550 C665_RS17595
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 C665_RS12450 C665_RS13930
H281DRAFT_04042 phenylacetate:H+ symporter
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A C665_RS03160
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B C665_RS03155
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C C665_RS03150
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E C665_RS03140
paaF 2,3-dehydroadipyl-CoA hydratase C665_RS16150 C665_RS16085
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C665_RS03190 C665_RS11710
paaH 3-hydroxyadipyl-CoA dehydrogenase C665_RS04225 C665_RS03185
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase C665_RS03170 C665_RS04230
paaJ2 3-oxoadipyl-CoA thiolase C665_RS03170 C665_RS04230
paaT phenylacetate transporter Paa
paaZ1 oxepin-CoA hydrolase C665_RS03190 C665_RS16150
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase C665_RS03195
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase C665_RS04215

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 24 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:

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