GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Cupriavidus basilensis 4G11

Best path

ppa, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa RR42_RS06400
paaK phenylacetate-CoA ligase RR42_RS23755 RR42_RS18265
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A RR42_RS23725
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B RR42_RS23730
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C RR42_RS23735
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E RR42_RS23745 RR42_RS31980
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase RR42_RS18255 RR42_RS19805
paaZ1 oxepin-CoA hydrolase RR42_RS05755 RR42_RS35145
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase RR42_RS23750 RR42_RS35145 with RR42_RS24800
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase RR42_RS35915 RR42_RS26090
paaF 2,3-dehydroadipyl-CoA hydratase RR42_RS18250 RR42_RS23710
paaH 3-hydroxyadipyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
paaJ2 3-oxoadipyl-CoA thiolase RR42_RS35915 RR42_RS26090
Alternative steps:
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase RR42_RS23690 RR42_RS25125
badI 2-ketocyclohexanecarboxyl-CoA hydrolase RR42_RS23695 RR42_RS18250
badK cyclohex-1-ene-1-carboxyl-CoA hydratase RR42_RS23710 RR42_RS18250
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 RR42_RS03755 RR42_RS05535
bamI class II benzoyl-CoA reductase, BamI subunit RR42_RS05540
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 RR42_RS35120 RR42_RS07500
boxB benzoyl-CoA epoxidase, subunit B RR42_RS35125 RR42_RS07505
boxC 2,3-epoxybenzoyl-CoA dihydrolase RR42_RS07510 RR42_RS35130
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase RR42_RS35145
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase RR42_RS00895 RR42_RS28565
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase RR42_RS28050 RR42_RS23710
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RR42_RS18250 RR42_RS23710
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
gcdH glutaryl-CoA dehydrogenase RR42_RS15400 RR42_RS28565
H281DRAFT_04042 phenylacetate:H+ symporter RR42_RS33495 RR42_RS28305
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase RR42_RS34260
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase RR42_RS11095
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit RR42_RS15975
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 RR42_RS25210 RR42_RS10260
pimC pimeloyl-CoA dehydrogenase, small subunit RR42_RS36390 RR42_RS36650
pimD pimeloyl-CoA dehydrogenase, large subunit RR42_RS05595 RR42_RS36645
pimF 6-carboxyhex-2-enoyl-CoA hydratase RR42_RS35270 RR42_RS11095

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.

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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 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