GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Pseudarthrobacter sulfonivorans Ar51

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa AU252_RS03465 AU252_RS03490
paaK phenylacetate-CoA ligase AU252_RS15070 AU252_RS01265
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A AU252_RS15420
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B AU252_RS15425
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C AU252_RS15430
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E AU252_RS15440
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AU252_RS07800 AU252_RS00885
paaZ1 oxepin-CoA hydrolase AU252_RS15050 AU252_RS00745
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AU252_RS15050
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AU252_RS15005 AU252_RS00310
paaF 2,3-dehydroadipyl-CoA hydratase AU252_RS07800 AU252_RS00745
paaH 3-hydroxyadipyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
paaJ2 3-oxoadipyl-CoA thiolase AU252_RS15005 AU252_RS00310
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AU252_RS12495 AU252_RS01630
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AU252_RS14925 AU252_RS07800
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
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 AU252_RS15050
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AU252_RS01515 AU252_RS00840
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AU252_RS07800 AU252_RS00745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
gcdH glutaryl-CoA dehydrogenase AU252_RS16430 AU252_RS00305
H281DRAFT_04042 phenylacetate:H+ symporter AU252_RS08100 AU252_RS15260
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
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 AU252_RS15005 AU252_RS00785
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AU252_RS00805
pimF 6-carboxyhex-2-enoyl-CoA hydratase

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.

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