GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Stutzerimonas stutzeri A1501

Best path

ppa, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa PST_RS07285 PST_RS19425
paaK phenylacetate-CoA ligase PST_RS14845 PST_RS00545
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 PST_RS03120 PST_RS09740
paaZ1 oxepin-CoA hydrolase PST_RS08835 PST_RS03120
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PST_RS08835
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PST_RS06390 PST_RS16155
paaF 2,3-dehydroadipyl-CoA hydratase PST_RS09740 PST_RS06175
paaH 3-hydroxyadipyl-CoA dehydrogenase PST_RS08735 PST_RS00510
paaJ2 3-oxoadipyl-CoA thiolase PST_RS06390 PST_RS16155
Alternative steps:
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PST_RS10135 PST_RS03535
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PST_RS09740
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS03120
bamB class II benzoyl-CoA reductase, BamB subunit
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
bamI class II benzoyl-CoA reductase, BamI subunit
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 PST_RS16120 PST_RS09700
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS06175
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
H281DRAFT_04042 phenylacetate:H+ symporter PST_RS13100
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase PST_RS04505
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 PST_RS18400
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 PST_RS12565 PST_RS06390
pimC pimeloyl-CoA dehydrogenase, small subunit PST_RS00520
pimD pimeloyl-CoA dehydrogenase, large subunit PST_RS00515 PST_RS08590
pimF 6-carboxyhex-2-enoyl-CoA hydratase PST_RS00510 PST_RS08735

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