GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudomonas benzenivorans DSM 8628

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa BLS63_RS05935
paaK phenylacetate-CoA ligase BLS63_RS09790 BLS63_RS09785
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 BLS63_RS03815
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BLS63_RS19940 BLS63_RS21395
paaZ1 oxepin-CoA hydrolase BLS63_RS19940 BLS63_RS21705
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BLS63_RS16765 BLS63_RS22810
paaF 2,3-dehydroadipyl-CoA hydratase BLS63_RS18235 BLS63_RS21705
paaH 3-hydroxyadipyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
paaJ2 3-oxoadipyl-CoA thiolase BLS63_RS16765 BLS63_RS22810
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BLS63_RS22810 BLS63_RS21120
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLS63_RS06695 BLS63_RS22805
badI 2-ketocyclohexanecarboxyl-CoA hydrolase
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLS63_RS21705 BLS63_RS21395
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BLS63_RS25245
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit BLS63_RS10705
bamH class II benzoyl-CoA reductase, BamH subunit BLS63_RS10700 BLS63_RS01490
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 BLS63_RS26370 BLS63_RS24295
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLS63_RS21705 BLS63_RS06660
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLS63_RS21705 BLS63_RS07890
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
gcdH glutaryl-CoA dehydrogenase BLS63_RS14585 BLS63_RS24330
H281DRAFT_04042 phenylacetate:H+ symporter
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
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 BLS63_RS24670 BLS63_RS12420
pimC pimeloyl-CoA dehydrogenase, small subunit BLS63_RS21710 BLS63_RS07275
pimD pimeloyl-CoA dehydrogenase, large subunit BLS63_RS17700
pimF 6-carboxyhex-2-enoyl-CoA hydratase BLS63_RS10750 BLS63_RS07890

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.

Links

Downloads

Related tools

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