GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Dyella japonica UNC79MFTsu3.2

Best path

aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

Also see fitness data for the top candidates

Rules

Overview: Phenylalanine utilization in GapMind is based on MetaCyc pathway L-phenylalanine degradation I (aerobic, via tyrosine, link), pathway II (anaerobic, via phenylacetaldehyde dehydrogenase, link), degradation via phenylpyruvate:ferredoxin oxidoreductase (PMC3346364), or degradation via phenylacetaldehyde:ferredoxin oxidoreductase (PMID:24214948). (MetaCyc describes additional pathways, but they do not result in carbon incorporation or are not reported in prokaryotes, so they are not included in GapMind.)

76 steps (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP N515DRAFT_3653 N515DRAFT_2630
PAH phenylalanine 4-monooxygenase N515DRAFT_3052
PCBD pterin-4-alpha-carbinoalamine dehydratase N515DRAFT_1530
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase N515DRAFT_0360
hmgA homogentisate dioxygenase N515DRAFT_0361
maiA maleylacetoacetate isomerase N515DRAFT_4292 N515DRAFT_3479
fahA fumarylacetoacetate hydrolase N515DRAFT_0362
atoA acetoacetyl-CoA transferase, A subunit N515DRAFT_1736
atoD acetoacetyl-CoA transferase, B subunit N515DRAFT_1736
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
Alternative steps:
aacS acetoacetyl-CoA synthetase N515DRAFT_1417
ARO10 phenylpyruvate decarboxylase N515DRAFT_1617
ARO8 L-phenylalanine transaminase N515DRAFT_3488 N515DRAFT_0006
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase N515DRAFT_2873 N515DRAFT_1104
badI 2-ketocyclohexanecarboxyl-CoA hydrolase N515DRAFT_1164 N515DRAFT_0930
badK cyclohex-1-ene-1-carboxyl-CoA hydratase N515DRAFT_1164 N515DRAFT_0930
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 N515DRAFT_2810
bamI class II benzoyl-CoA reductase, BamI subunit
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase N515DRAFT_0492 N515DRAFT_0941
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase N515DRAFT_1164
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
gcdH glutaryl-CoA dehydrogenase N515DRAFT_0484 N515DRAFT_0492
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) N515DRAFT_3950 N515DRAFT_1248
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) N515DRAFT_3950 N515DRAFT_1248
livH L-phenylalanine ABC transporter, permease component 1 (LivH)
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM)
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
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
paaF 2,3-dehydroadipyl-CoA hydratase N515DRAFT_1164 N515DRAFT_0930
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase N515DRAFT_1164 N515DRAFT_0930
paaH 3-hydroxyadipyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase N515DRAFT_2688 N515DRAFT_0938
paaJ2 3-oxoadipyl-CoA thiolase N515DRAFT_2688 N515DRAFT_0938
paaK phenylacetate-CoA ligase N515DRAFT_1417
paaZ1 oxepin-CoA hydrolase N515DRAFT_1164
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase N515DRAFT_3729 N515DRAFT_4224
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
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase N515DRAFT_2688 N515DRAFT_0938
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit N515DRAFT_0356
PPDCbeta phenylpyruvate decarboxylase, beta subunit N515DRAFT_0355 N515DRAFT_0481

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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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