GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Nocardioides dokdonensis FR1436

Best path

paaT, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase I601_RS05795 I601_RS04470
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A I601_RS08030
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B I601_RS08035
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C I601_RS08040
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E I601_RS08050 I601_RS14170
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase I601_RS10740 I601_RS11365
paaZ1 oxepin-CoA hydrolase I601_RS08400 I601_RS17105
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase I601_RS17535 I601_RS03035
paaF 2,3-dehydroadipyl-CoA hydratase I601_RS19165 I601_RS17105
paaH 3-hydroxyadipyl-CoA dehydrogenase I601_RS04220 I601_RS05790
paaJ2 3-oxoadipyl-CoA thiolase I601_RS17535 I601_RS03035
Alternative steps:
atoB acetyl-CoA C-acetyltransferase I601_RS03035 I601_RS19250
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase I601_RS11285 I601_RS16775
badI 2-ketocyclohexanecarboxyl-CoA hydrolase I601_RS07275 I601_RS19165
badK cyclohex-1-ene-1-carboxyl-CoA hydratase I601_RS19165 I601_RS11365
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit I601_RS04875
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 I601_RS03870
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 I601_RS04215 I601_RS08940
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase I601_RS19165 I601_RS16330
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I601_RS19165 I601_RS05525
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I601_RS04220 I601_RS05790
gcdH glutaryl-CoA dehydrogenase I601_RS02110 I601_RS10230
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 I601_RS19750
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 I601_RS03035 I601_RS17150
pimC pimeloyl-CoA dehydrogenase, small subunit I601_RS02070 I601_RS02110
pimD pimeloyl-CoA dehydrogenase, large subunit I601_RS02065 I601_RS03050
pimF 6-carboxyhex-2-enoyl-CoA hydratase I601_RS17540
ppa phenylacetate permease ppa I601_RS07700 I601_RS07725

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.

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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:

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