GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Rhodococcus qingshengii djl-6-2

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa C1M55_RS22765
paaK phenylacetate-CoA ligase C1M55_RS27950 C1M55_RS08200
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A C1M55_RS27975
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B C1M55_RS27970
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C C1M55_RS27965
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E C1M55_RS27955 C1M55_RS08985
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase C1M55_RS27980 C1M55_RS08860
paaZ1 oxepin-CoA hydrolase C1M55_RS28000 C1M55_RS26225
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase C1M55_RS28000
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase C1M55_RS26675 C1M55_RS04430
paaF 2,3-dehydroadipyl-CoA hydratase C1M55_RS19610 C1M55_RS12340
paaH 3-hydroxyadipyl-CoA dehydrogenase C1M55_RS07980 C1M55_RS25285
paaJ2 3-oxoadipyl-CoA thiolase C1M55_RS26675 C1M55_RS04430
Alternative steps:
atoB acetyl-CoA C-acetyltransferase C1M55_RS28700 C1M55_RS07210
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase C1M55_RS27655 C1M55_RS30565
badI 2-ketocyclohexanecarboxyl-CoA hydrolase C1M55_RS08580 C1M55_RS19610
badK cyclohex-1-ene-1-carboxyl-CoA hydratase C1M55_RS19610 C1M55_RS20280
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit C1M55_RS06770
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 C1M55_RS13750
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 C1M55_RS28000
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase C1M55_RS25280 C1M55_RS19625
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase C1M55_RS19610 C1M55_RS01960
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C1M55_RS19610 C1M55_RS12340
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C1M55_RS07980 C1M55_RS25285
gcdH glutaryl-CoA dehydrogenase C1M55_RS24690 C1M55_RS09530
H281DRAFT_04042 phenylacetate:H+ symporter C1M55_RS07700 C1M55_RS22525
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase C1M55_RS27575
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit
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 C1M55_RS27635 C1M55_RS21060
pimC pimeloyl-CoA dehydrogenase, small subunit C1M55_RS20160 C1M55_RS25340
pimD pimeloyl-CoA dehydrogenase, large subunit C1M55_RS20165 C1M55_RS25345
pimF 6-carboxyhex-2-enoyl-CoA hydratase C1M55_RS14320

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