GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Azospirillum brasilense Sp245

Best path

ppa, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Also see fitness data for the top candidates

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
ppa phenylacetate permease ppa AZOBR_RS02940 AZOBR_RS19235
paaK phenylacetate-CoA ligase AZOBR_RS31155
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 AZOBR_RS29210 AZOBR_RS07775
paaZ1 oxepin-CoA hydrolase AZOBR_RS15730 AZOBR_RS29210
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
paaF 2,3-dehydroadipyl-CoA hydratase AZOBR_RS01260 AZOBR_RS26485
paaH 3-hydroxyadipyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
paaJ2 3-oxoadipyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
Alternative steps:
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AZOBR_RS24695 AZOBR_RS25545
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AZOBR_RS18155 AZOBR_RS26485
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AZOBR_RS01260 AZOBR_RS26485
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 AZOBR_RS14955 AZOBR_RS31940
bamI class II benzoyl-CoA reductase, BamI subunit AZOBR_RS14960
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 AZOBR_RS22300 AZOBR_RS22365
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AZOBR_RS26485 AZOBR_RS01260
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AZOBR_RS18155
paaT phenylacetate transporter Paa
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit AZOBR_RS23550 AZOBR_RS18730
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 AZOBR_RS20220 AZOBR_RS30610
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AZOBR_RS29205 AZOBR_RS17455
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 Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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