GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Amycolatopsis halophila YIM 93223

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase AMYHA_RS04470 AMYHA_RS22925
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A AMYHA_RS04455
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B AMYHA_RS04450
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C AMYHA_RS04445
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E AMYHA_RS04435 AMYHA_RS06410
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AMYHA_RS24905 AMYHA_RS15335
paaZ1 oxepin-CoA hydrolase AMYHA_RS04460 AMYHA_RS02120
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AMYHA_RS04460
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AMYHA_RS23855 AMYHA_RS09650
paaF 2,3-dehydroadipyl-CoA hydratase AMYHA_RS20710 AMYHA_RS06590
paaH 3-hydroxyadipyl-CoA dehydrogenase AMYHA_RS03760 AMYHA_RS17210
paaJ2 3-oxoadipyl-CoA thiolase AMYHA_RS23855 AMYHA_RS09650
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AMYHA_RS06490 AMYHA_RS10330
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AMYHA_RS17065 AMYHA_RS23710
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AMYHA_RS01260 AMYHA_RS06465
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AMYHA_RS20710 AMYHA_RS02120
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit AMYHA_RS03345 AMYHA_RS20405
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 AMYHA_RS01210
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 AMYHA_RS04460 AMYHA_RS06610
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AMYHA_RS25070 AMYHA_RS06270
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AMYHA_RS10445 AMYHA_RS06335
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMYHA_RS20710 AMYHA_RS24905
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMYHA_RS03760 AMYHA_RS17210
gcdH glutaryl-CoA dehydrogenase AMYHA_RS24060 AMYHA_RS09585
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit AMYHA_RS04810
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 AMYHA_RS09000 AMYHA_RS23855
pimC pimeloyl-CoA dehydrogenase, small subunit AMYHA_RS06450 AMYHA_RS23685
pimD pimeloyl-CoA dehydrogenase, large subunit AMYHA_RS06475 AMYHA_RS23690
pimF 6-carboxyhex-2-enoyl-CoA hydratase
ppa phenylacetate permease ppa AMYHA_RS10755

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.

Links

Downloads

Related tools

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