GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Rhodanobacter denitrificans 2APBS1

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
H281DRAFT_04042 phenylacetate:H+ symporter R2APBS1_RS05445 R2APBS1_RS12170
paaK phenylacetate-CoA ligase
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 R2APBS1_RS12580 R2APBS1_RS06035
paaZ1 oxepin-CoA hydrolase R2APBS1_RS06035 R2APBS1_RS12580
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase R2APBS1_RS03900 R2APBS1_RS08710
paaF 2,3-dehydroadipyl-CoA hydratase R2APBS1_RS12580 R2APBS1_RS06035
paaH 3-hydroxyadipyl-CoA dehydrogenase R2APBS1_RS08705 R2APBS1_RS10950
paaJ2 3-oxoadipyl-CoA thiolase R2APBS1_RS03900 R2APBS1_RS08710
Alternative steps:
atoB acetyl-CoA C-acetyltransferase R2APBS1_RS12475 R2APBS1_RS08710
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase R2APBS1_RS11655 R2APBS1_RS18280
badI 2-ketocyclohexanecarboxyl-CoA hydrolase R2APBS1_RS12580
badK cyclohex-1-ene-1-carboxyl-CoA hydratase R2APBS1_RS12580 R2APBS1_RS06035
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 R2APBS1_RS07190
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 R2APBS1_RS06205 R2APBS1_RS12465
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase R2APBS1_RS12580
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase R2APBS1_RS12580 R2APBS1_RS10950
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase R2APBS1_RS08705 R2APBS1_RS10950
gcdH glutaryl-CoA dehydrogenase R2APBS1_RS06240 R2APBS1_RS06205
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase R2APBS1_RS06990
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 R2APBS1_RS08710 R2APBS1_RS03900
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase R2APBS1_RS10950
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.

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