GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Xanthobacter autotrophicus Py2

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa XAUT_RS12220 XAUT_RS04965
paaK phenylacetate-CoA ligase XAUT_RS04510 XAUT_RS09365
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A XAUT_RS04485
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B XAUT_RS04490
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C XAUT_RS04495
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E XAUT_RS04505
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase XAUT_RS04520 XAUT_RS07010
paaZ1 oxepin-CoA hydrolase XAUT_RS04540 XAUT_RS07010
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase XAUT_RS04540 XAUT_RS04525
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase XAUT_RS05630 XAUT_RS04530
paaF 2,3-dehydroadipyl-CoA hydratase XAUT_RS04570 XAUT_RS16635
paaH 3-hydroxyadipyl-CoA dehydrogenase XAUT_RS04535 XAUT_RS04610
paaJ2 3-oxoadipyl-CoA thiolase XAUT_RS05630 XAUT_RS04530
Alternative steps:
atoB acetyl-CoA C-acetyltransferase XAUT_RS23630 XAUT_RS15615
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase XAUT_RS04590 XAUT_RS06800
badI 2-ketocyclohexanecarboxyl-CoA hydrolase XAUT_RS04595 XAUT_RS04520
badK cyclohex-1-ene-1-carboxyl-CoA hydratase XAUT_RS16635 XAUT_RS04570
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit XAUT_RS04625
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 XAUT_RS17550 XAUT_RS23440
bamI class II benzoyl-CoA reductase, BamI subunit XAUT_RS17545
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 XAUT_RS04540
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase XAUT_RS21625 XAUT_RS11005
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase XAUT_RS04570 XAUT_RS16635
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase XAUT_RS16635 XAUT_RS04570
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase XAUT_RS04535 XAUT_RS04610
gcdH glutaryl-CoA dehydrogenase XAUT_RS23880 XAUT_RS21625
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase XAUT_RS04595 XAUT_RS16635
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 XAUT_RS03990
padI phenylglyoxylate dehydrogenase, beta subunit
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase XAUT_RS03140 XAUT_RS22505
pimC pimeloyl-CoA dehydrogenase, small subunit XAUT_RS08530
pimD pimeloyl-CoA dehydrogenase, large subunit XAUT_RS08535 XAUT_RS06740
pimF 6-carboxyhex-2-enoyl-CoA hydratase XAUT_RS04535 XAUT_RS04610

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