GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Sphingopyxis indica DS15

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase CHB69_RS06840 CHB69_RS07220
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 CHB69_RS05385 CHB69_RS02790
paaZ1 oxepin-CoA hydrolase CHB69_RS12770 CHB69_RS02790
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase CHB69_RS08555 CHB69_RS16130
paaF 2,3-dehydroadipyl-CoA hydratase CHB69_RS13675 CHB69_RS12770
paaH 3-hydroxyadipyl-CoA dehydrogenase CHB69_RS16340 CHB69_RS02805
paaJ2 3-oxoadipyl-CoA thiolase CHB69_RS08555 CHB69_RS16130
Alternative steps:
atoB acetyl-CoA C-acetyltransferase CHB69_RS16345 CHB69_RS02585
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CHB69_RS06000 CHB69_RS15165
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CHB69_RS13675 CHB69_RS12925
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CHB69_RS13675 CHB69_RS12770
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 CHB69_RS04110
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 CHB69_RS13685 CHB69_RS03045
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CHB69_RS13675 CHB69_RS18650
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CHB69_RS13675 CHB69_RS12770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CHB69_RS16340 CHB69_RS02805
gcdH glutaryl-CoA dehydrogenase CHB69_RS11225 CHB69_RS03045
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
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 CHB69_RS16130 CHB69_RS08555
pimC pimeloyl-CoA dehydrogenase, small subunit CHB69_RS03675 CHB69_RS13605
pimD pimeloyl-CoA dehydrogenase, large subunit CHB69_RS03670 CHB69_RS00075
pimF 6-carboxyhex-2-enoyl-CoA hydratase CHB69_RS13660
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 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