GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Chryseobacterium arthrosphaerae CC-VM-7

Best path

H281DRAFT_04042, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
H281DRAFT_04042 phenylacetate:H+ symporter BBI00_RS13465
paaK phenylacetate-CoA ligase BBI00_RS22560 BBI00_RS21905
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A BBI00_RS22550
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B BBI00_RS22545
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C BBI00_RS22540
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E BBI00_RS22555 BBI00_RS04645
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BBI00_RS22515 BBI00_RS21810
paaZ1 oxepin-CoA hydrolase BBI00_RS22475
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase BBI00_RS22475
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BBI00_RS22490 BBI00_RS04610
paaF 2,3-dehydroadipyl-CoA hydratase BBI00_RS21810 BBI00_RS22515
paaH 3-hydroxyadipyl-CoA dehydrogenase BBI00_RS04620 BBI00_RS08465
paaJ2 3-oxoadipyl-CoA thiolase BBI00_RS22490 BBI00_RS06705
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BBI00_RS06705 BBI00_RS04415
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BBI00_RS16110 BBI00_RS07550
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BBI00_RS06575 BBI00_RS21810
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BBI00_RS21810
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BBI00_RS21550
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 BBI00_RS19395
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 BBI00_RS22475
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BBI00_RS01605 BBI00_RS05370
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BBI00_RS21810 BBI00_RS22515
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BBI00_RS21810 BBI00_RS22510
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BBI00_RS04620 BBI00_RS08465
gcdH glutaryl-CoA dehydrogenase BBI00_RS04080 BBI00_RS21510
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 BBI00_RS17060
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 BBI00_RS04610 BBI00_RS22490
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
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