GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Marinobacter adhaerens HP15

Best path

paaT, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Also see fitness data for the top candidates

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase HP15_2696 HP15_3926
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A HP15_2697
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B HP15_2698
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C HP15_2699
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E HP15_2701
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HP15_2692 HP15_4094
paaZ1 oxepin-CoA hydrolase HP15_2702 HP15_4094
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase HP15_2702
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase HP15_2695 HP15_5
paaF 2,3-dehydroadipyl-CoA hydratase HP15_12 HP15_908
paaH 3-hydroxyadipyl-CoA dehydrogenase HP15_1512 HP15_2693
paaJ2 3-oxoadipyl-CoA thiolase HP15_2695 HP15_5
Alternative steps:
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HP15_4143 HP15_2784
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HP15_4142
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HP15_12 HP15_2692
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 HP15_4173 HP15_1573
bamI class II benzoyl-CoA reductase, BamI subunit HP15_4174
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 HP15_2702
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase HP15_907 HP15_2
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HP15_908 HP15_4142
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
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 HP15_3943 HP15_1513
pimC pimeloyl-CoA dehydrogenase, small subunit HP15_3928
pimD pimeloyl-CoA dehydrogenase, large subunit HP15_3929 HP15_53
pimF 6-carboxyhex-2-enoyl-CoA hydratase HP15_3941 HP15_1512
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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