GapMind for catabolism of small carbon sources

 

phenylacetate catabolism in Xenophilus azovorans DSM 13620

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 Q392_RS22915
paaK phenylacetate-CoA ligase Q392_RS30150 Q392_RS23115
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A Q392_RS30145
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B Q392_RS30140
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C Q392_RS30135
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Q392_RS30125
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Q392_RS30160 Q392_RS00330
paaZ1 oxepin-CoA hydrolase Q392_RS14950 Q392_RS25260
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Q392_RS20100
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Q392_RS13480 Q392_RS19235
paaF 2,3-dehydroadipyl-CoA hydratase Q392_RS17990 Q392_RS02545
paaH 3-hydroxyadipyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
paaJ2 3-oxoadipyl-CoA thiolase Q392_RS19235 Q392_RS13480
Alternative steps:
atoB acetyl-CoA C-acetyltransferase Q392_RS11095 Q392_RS22590
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Q392_RS13490 Q392_RS01930
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Q392_RS13495 Q392_RS01935
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Q392_RS17990 Q392_RS02545
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 Q392_RS16650 Q392_RS14130
bamI class II benzoyl-CoA reductase, BamI subunit Q392_RS16645
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 Q392_RS20125
boxB benzoyl-CoA epoxidase, subunit B Q392_RS20120
boxC 2,3-epoxybenzoyl-CoA dihydrolase Q392_RS20115
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase Q392_RS20100
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Q392_RS02180 Q392_RS27255
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Q392_RS02515 Q392_RS08845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q392_RS17990 Q392_RS02545
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
gcdH glutaryl-CoA dehydrogenase Q392_RS20240 Q392_RS27255
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
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 Q392_RS27910 Q392_RS25275
pimC pimeloyl-CoA dehydrogenase, small subunit Q392_RS25265 Q392_RS11710
pimD pimeloyl-CoA dehydrogenase, large subunit Q392_RS25270 Q392_RS11705
pimF 6-carboxyhex-2-enoyl-CoA hydratase Q392_RS27900 Q392_RS25280

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.

Links

Downloads

Related tools

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