GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Belnapia rosea CPCC 100156

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase BLR02_RS03515
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BLR02_RS21360 BLR02_RS13145
paaZ1 oxepin-CoA hydrolase BLR02_RS13145 BLR02_RS02380
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BLR02_RS13910 BLR02_RS00935
paaF 2,3-dehydroadipyl-CoA hydratase BLR02_RS23955 BLR02_RS09775
paaH 3-hydroxyadipyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
paaJ2 3-oxoadipyl-CoA thiolase BLR02_RS13910 BLR02_RS00935
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BLR02_RS13910 BLR02_RS06650
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLR02_RS23080 BLR02_RS06485
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BLR02_RS23085 BLR02_RS23955
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLR02_RS23955 BLR02_RS02380
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 BLR02_RS18705 BLR02_RS23805
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 BLR02_RS23270 BLR02_RS03525
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLR02_RS23955 BLR02_RS04715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR02_RS23955 BLR02_RS03400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
gcdH glutaryl-CoA dehydrogenase BLR02_RS06730 BLR02_RS03525
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BLR02_RS23085
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit BLR02_RS18115 BLR02_RS01185
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 BLR02_RS00935 BLR02_RS13910
pimC pimeloyl-CoA dehydrogenase, small subunit BLR02_RS03410 BLR02_RS20985
pimD pimeloyl-CoA dehydrogenase, large subunit BLR02_RS03405 BLR02_RS20980
pimF 6-carboxyhex-2-enoyl-CoA hydratase BLR02_RS03400
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 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