GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Kocuria turfanensis HO-9042

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa AYX06_RS16640
paaK phenylacetate-CoA ligase AYX06_RS08125 AYX06_RS17015
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A AYX06_RS08135
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B AYX06_RS08140
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C AYX06_RS08145
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E AYX06_RS08155
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AYX06_RS08340 AYX06_RS10100
paaZ1 oxepin-CoA hydrolase AYX06_RS08110 AYX06_RS08340
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AYX06_RS08110
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AYX06_RS08085 AYX06_RS05785
paaF 2,3-dehydroadipyl-CoA hydratase AYX06_RS08340 AYX06_RS10100
paaH 3-hydroxyadipyl-CoA dehydrogenase AYX06_RS10095 AYX06_RS13475
paaJ2 3-oxoadipyl-CoA thiolase AYX06_RS08085 AYX06_RS05785
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AYX06_RS08025 AYX06_RS08085
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AYX06_RS10315 AYX06_RS08805
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AYX06_RS06280 AYX06_RS10100
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AYX06_RS08340 AYX06_RS10100
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
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 AYX06_RS08110
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AYX06_RS12200 AYX06_RS12220
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AYX06_RS08340 AYX06_RS10100
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AYX06_RS08340 AYX06_RS10100
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AYX06_RS10095 AYX06_RS13475
gcdH glutaryl-CoA dehydrogenase AYX06_RS10120 AYX06_RS13480
H281DRAFT_04042 phenylacetate:H+ symporter AYX06_RS08205 AYX06_RS16200
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AYX06_RS10100
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit AYX06_RS12275
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 AYX06_RS08085 AYX06_RS10305
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase AYX06_RS13475

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