GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Azohydromonas australica DSM 1124

Best path

ppa, 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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa H537_RS0109875 H537_RS0110095
paaK phenylacetate-CoA ligase H537_RS0102655 H537_RS0105900
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A H537_RS0105965
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B H537_RS0105960
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C H537_RS0105955
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E H537_RS0105950 H537_RS0117830
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase H537_RS0102665 H537_RS0134075
paaZ1 oxepin-CoA hydrolase H537_RS0117800 H537_RS0114955
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase H537_RS0105910 H537_RS0117800
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase H537_RS0133460 H537_RS0103580
paaF 2,3-dehydroadipyl-CoA hydratase H537_RS0100790 H537_RS0111045
paaH 3-hydroxyadipyl-CoA dehydrogenase H537_RS0132195 H537_RS0116855
paaJ2 3-oxoadipyl-CoA thiolase H537_RS0102630 H537_RS0133460
Alternative steps:
atoB acetyl-CoA C-acetyltransferase H537_RS0122115 H537_RS0129600
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase H537_RS0110980 H537_RS0101065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase H537_RS0115550 H537_RS0100790
badK cyclohex-1-ene-1-carboxyl-CoA hydratase H537_RS0111045 H537_RS0100790
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 H537_RS0135705
bamH class II benzoyl-CoA reductase, BamH subunit H537_RS0135700 H537_RS0108175
bamI class II benzoyl-CoA reductase, BamI subunit H537_RS41585
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 H537_RS0136330
boxB benzoyl-CoA epoxidase, subunit B H537_RS0136335 H537_RS0129360
boxC 2,3-epoxybenzoyl-CoA dihydrolase H537_RS0136340
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase H537_RS0117800
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase H537_RS0124695 H537_RS0111035
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase H537_RS0100790 H537_RS0127180
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H537_RS0100790 H537_RS0111045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H537_RS0132195 H537_RS0116855
gcdH glutaryl-CoA dehydrogenase H537_RS0120055 H537_RS0115055
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase H537_RS0115550
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit H537_RS40960 H537_RS44475
padD phenylacetyl-CoA dehydrogenase, PadD subunit H537_RS0103355
padE phenylglyoxylate dehydrogenase, gamma subunit H537_RS0100025
padF phenylglyoxylate dehydrogenase, delta subunit
padG phenylglyoxylate dehydrogenase, alpha subunit
padH phenylglyoxylate dehydrogenase, epsilon subunit H537_RS0103715 H537_RS0129470
padI phenylglyoxylate dehydrogenase, beta subunit
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase H537_RS0115020 H537_RS0132200
pimC pimeloyl-CoA dehydrogenase, small subunit H537_RS0115050 H537_RS0138715
pimD pimeloyl-CoA dehydrogenase, large subunit H537_RS0115045 H537_RS0138710
pimF 6-carboxyhex-2-enoyl-CoA hydratase H537_RS0115025 H537_RS0138660

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 Apr 09 2024. 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