GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Desulfoscipio geothermicus DSM 3669

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
paaT phenylacetate transporter Paa
paaK phenylacetate-CoA ligase BM299_RS14430 BM299_RS02760
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 BM299_RS00960 BM299_RS00245
paaZ1 oxepin-CoA hydrolase BM299_RS00245 BM299_RS10405
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BM299_RS17115 BM299_RS00890
paaF 2,3-dehydroadipyl-CoA hydratase BM299_RS07795 BM299_RS18360
paaH 3-hydroxyadipyl-CoA dehydrogenase BM299_RS08140 BM299_RS17110
paaJ2 3-oxoadipyl-CoA thiolase BM299_RS17115 BM299_RS00890
Alternative steps:
atoB acetyl-CoA C-acetyltransferase BM299_RS18350 BM299_RS11340
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BM299_RS17970 BM299_RS05100
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BM299_RS18360 BM299_RS07900
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BM299_RS07795 BM299_RS00820
bamB class II benzoyl-CoA reductase, BamB subunit BM299_RS10290 BM299_RS04745
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BM299_RS04395 BM299_RS18345
bamE class II benzoyl-CoA reductase, BamE subunit BM299_RS14930 BM299_RS09510
bamF class II benzoyl-CoA reductase, BamF subunit BM299_RS14935 BM299_RS09475
bamG class II benzoyl-CoA reductase, BamG subunit BM299_RS05480 BM299_RS05505
bamH class II benzoyl-CoA reductase, BamH subunit BM299_RS14790 BM299_RS14450
bamI class II benzoyl-CoA reductase, BamI subunit BM299_RS14460 BM299_RS14785
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit BM299_RS00975 BM299_RS04845
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit BM299_RS04840
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit BM299_RS00975 BM299_RS04845
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 BM299_RS17105 BM299_RS11335
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BM299_RS10405 BM299_RS07795
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BM299_RS00820 BM299_RS18360
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BM299_RS08140 BM299_RS17110
gcdH glutaryl-CoA dehydrogenase BM299_RS11335 BM299_RS06045
H281DRAFT_04042 phenylacetate:H+ symporter
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BM299_RS10405
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit BM299_RS17000
padD phenylacetyl-CoA dehydrogenase, PadD subunit
padE phenylglyoxylate dehydrogenase, gamma subunit
padF phenylglyoxylate dehydrogenase, delta subunit BM299_RS09480
padG phenylglyoxylate dehydrogenase, alpha subunit
padH phenylglyoxylate dehydrogenase, epsilon subunit BM299_RS10000 BM299_RS11455
padI phenylglyoxylate dehydrogenase, beta subunit
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BM299_RS08135 BM299_RS18350
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit BM299_RS12590
pimF 6-carboxyhex-2-enoyl-CoA hydratase
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 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