GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa HTA01S_RS00870
paaK phenylacetate-CoA ligase HTA01S_RS03875 HTA01S_RS05105
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A HTA01S_RS11330
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B HTA01S_RS11325
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C HTA01S_RS11320
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E HTA01S_RS11310 HTA01S_RS06430
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HTA01S_RS03885 HTA01S_RS05140
paaZ1 oxepin-CoA hydrolase HTA01S_RS08655 HTA01S_RS15600
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase HTA01S_RS15600
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase HTA01S_RS19115 HTA01S_RS24420
paaF 2,3-dehydroadipyl-CoA hydratase HTA01S_RS03890 HTA01S_RS03885
paaH 3-hydroxyadipyl-CoA dehydrogenase HTA01S_RS04710 HTA01S_RS19105
paaJ2 3-oxoadipyl-CoA thiolase HTA01S_RS19115 HTA01S_RS24420
Alternative steps:
atoB acetyl-CoA C-acetyltransferase HTA01S_RS02090 HTA01S_RS06660
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HTA01S_RS18730 HTA01S_RS06665
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HTA01S_RS19095 HTA01S_RS03890
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HTA01S_RS03890 HTA01S_RS03885
bamB class II benzoyl-CoA reductase, BamB subunit HTA01S_RS03165
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit HTA01S_RS06410
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 HTA01S_RS22195 HTA01S_RS09365
bamI class II benzoyl-CoA reductase, BamI subunit HTA01S_RS11210
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 HTA01S_RS24285
boxB benzoyl-CoA epoxidase, subunit B HTA01S_RS24290 HTA01S_RS10345
boxC 2,3-epoxybenzoyl-CoA dihydrolase HTA01S_RS24295
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase HTA01S_RS15600
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase HTA01S_RS11060 HTA01S_RS11035
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HTA01S_RS03890 HTA01S_RS01970
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HTA01S_RS03890 HTA01S_RS13945
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HTA01S_RS04710 HTA01S_RS19105
gcdH glutaryl-CoA dehydrogenase HTA01S_RS14830 HTA01S_RS11035
H281DRAFT_04042 phenylacetate:H+ symporter
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 HTA01S_RS07090 HTA01S_RS16880
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 HTA01S_RS03160
padI phenylglyoxylate dehydrogenase, beta subunit
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase HTA01S_RS13950 HTA01S_RS04705
pimC pimeloyl-CoA dehydrogenase, small subunit HTA01S_RS19795
pimD pimeloyl-CoA dehydrogenase, large subunit HTA01S_RS19790
pimF 6-carboxyhex-2-enoyl-CoA hydratase HTA01S_RS13945 HTA01S_RS19105

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