GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Dinoroseobacter shibae DFL-12

Best path

paaT, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase Dshi_3824 Dshi_0253
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A Dshi_3818
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B Dshi_3819
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C Dshi_3820
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Dshi_3822
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Dshi_1753 Dshi_3370
paaZ1 oxepin-CoA hydrolase Dshi_3827 Dshi_1304
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Dshi_3827
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Dshi_3817 Dshi_3331
paaF 2,3-dehydroadipyl-CoA hydratase Dshi_3370 Dshi_1048
paaH 3-hydroxyadipyl-CoA dehydrogenase Dshi_3826 Dshi_0835
paaJ2 3-oxoadipyl-CoA thiolase Dshi_3817 Dshi_3331
Alternative steps:
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Dshi_2182 Dshi_3067
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Dshi_3370 Dshi_1304
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Dshi_3370 Dshi_3723
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 Dshi_1313
bamH class II benzoyl-CoA reductase, BamH subunit Dshi_1316 Dshi_1281
bamI class II benzoyl-CoA reductase, BamI subunit Dshi_1282
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 Dshi_3827
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Dshi_1297 Dshi_0838
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Dshi_3370 Dshi_3723
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase Dshi_1078
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Dshi_1237
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 Dshi_3817 Dshi_3331
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Dshi_0838
pimF 6-carboxyhex-2-enoyl-CoA hydratase Dshi_3826
ppa phenylacetate permease ppa

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