GapMind for catabolism of small carbon sources


phenylacetate catabolism in Magnetospirillum magneticum AMB-1

Best path

ppa, paaK, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB


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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa AMB_RS21920 AMB_RS13720
paaK phenylacetate-CoA ligase AMB_RS13855 AMB_RS06320
padB phenylacetyl-CoA dehydrogenase, PadB subunit AMB_RS06300 AMB_RS10170
padC phenylacetyl-CoA dehydrogenase, PadC subunit AMB_RS10175 AMB_RS06305
padD phenylacetyl-CoA dehydrogenase, PadD subunit AMB_RS06310 AMB_RS10180
padG phenylglyoxylate dehydrogenase, alpha subunit AMB_RS08485
padI phenylglyoxylate dehydrogenase, beta subunit AMB_RS08495
padE phenylglyoxylate dehydrogenase, gamma subunit AMB_RS08475
padF phenylglyoxylate dehydrogenase, delta subunit AMB_RS08480
padH phenylglyoxylate dehydrogenase, epsilon subunit AMB_RS08490 AMB_RS14720
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit AMB_RS10810
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit AMB_RS10815
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit AMB_RS10820
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit AMB_RS10805 AMB_RS10810
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AMB_RS10825 AMB_RS03265
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase AMB_RS10835
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AMB_RS10830
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AMB_RS13850 AMB_RS04295
gcdH glutaryl-CoA dehydrogenase AMB_RS16315 AMB_RS03480
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
Alternative steps:
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AMB_RS13035 AMB_RS13020
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AMB_RS03265 AMB_RS13070
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AMB_RS03265 AMB_RS13070
bamB class II benzoyl-CoA reductase, BamB subunit AMB_RS14710
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 AMB_RS13985 AMB_RS17165
bamI class II benzoyl-CoA reductase, BamI subunit AMB_RS00865 AMB_RS13980
boxA benzoyl-CoA epoxidase, subunit A AMB_RS00895
boxB benzoyl-CoA epoxidase, subunit B AMB_RS00890
boxC 2,3-epoxybenzoyl-CoA dihydrolase AMB_RS00885
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase AMB_RS00880
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AMB_RS18215 AMB_RS18150
H281DRAFT_04042 phenylacetate:H+ symporter
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
paaF 2,3-dehydroadipyl-CoA hydratase AMB_RS03265 AMB_RS13070
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AMB_RS00905 AMB_RS20905
paaH 3-hydroxyadipyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AMB_RS13850 AMB_RS13060
paaJ2 3-oxoadipyl-CoA thiolase AMB_RS13850 AMB_RS13060
paaT phenylacetate transporter Paa
paaZ1 oxepin-CoA hydrolase AMB_RS00880 AMB_RS00905
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AMB_RS00880
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AMB_RS03480
pimF 6-carboxyhex-2-enoyl-CoA hydratase AMB_RS15050

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 17 2021. The underlying query database was built on Sep 17 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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