GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Sphingomonas histidinilytica UM2

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ppa phenylacetate permease ppa B5X82_RS16925
paaK phenylacetate-CoA ligase B5X82_RS21515 B5X82_RS14210
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A B5X82_RS23070
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B B5X82_RS23075
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C B5X82_RS23080
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E B5X82_RS23090
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B5X82_RS23050 B5X82_RS16470
paaZ1 oxepin-CoA hydrolase B5X82_RS23045 B5X82_RS23095
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase B5X82_RS23045
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase B5X82_RS23065 B5X82_RS11200
paaF 2,3-dehydroadipyl-CoA hydratase B5X82_RS23095 B5X82_RS19780
paaH 3-hydroxyadipyl-CoA dehydrogenase B5X82_RS23055 B5X82_RS15560
paaJ2 3-oxoadipyl-CoA thiolase B5X82_RS23065 B5X82_RS11200
Alternative steps:
atoB acetyl-CoA C-acetyltransferase B5X82_RS18105 B5X82_RS24295
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase B5X82_RS20980 B5X82_RS14100
badI 2-ketocyclohexanecarboxyl-CoA hydrolase B5X82_RS19870 B5X82_RS19780
badK cyclohex-1-ene-1-carboxyl-CoA hydratase B5X82_RS23095 B5X82_RS23050
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 B5X82_RS21655
bamH class II benzoyl-CoA reductase, BamH subunit B5X82_RS21650 B5X82_RS15110
bamI class II benzoyl-CoA reductase, BamI subunit B5X82_RS21645
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 B5X82_RS23045
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase B5X82_RS24130 B5X82_RS22330
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase B5X82_RS16885 B5X82_RS16345
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B5X82_RS19780 B5X82_RS16280
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B5X82_RS15560 B5X82_RS24290
gcdH glutaryl-CoA dehydrogenase B5X82_RS04280 B5X82_RS20685
H281DRAFT_04042 phenylacetate:H+ symporter B5X82_RS24315
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase B5X82_RS25360
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 B5X82_RS04605 B5X82_RS03015
pimC pimeloyl-CoA dehydrogenase, small subunit B5X82_RS02875 B5X82_RS04520
pimD pimeloyl-CoA dehydrogenase, large subunit B5X82_RS02870 B5X82_RS04515
pimF 6-carboxyhex-2-enoyl-CoA hydratase B5X82_RS02895 B5X82_RS20355

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 24 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:

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