GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Shewanella sp. ANA-3

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase Shewana3_2781
PCBD pterin-4-alpha-carbinoalamine dehydratase Shewana3_2780
QDPR 6,7-dihydropteridine reductase Shewana3_3174 Shewana3_3507
HPD 4-hydroxyphenylpyruvate dioxygenase Shewana3_2482
hmgA homogentisate dioxygenase Shewana3_2481
maiA maleylacetoacetate isomerase Shewana3_2777 Shewana3_0013
fahA fumarylacetoacetate hydrolase Shewana3_2778
atoA acetoacetyl-CoA transferase, A subunit Shewana3_3467 Shewana3_1667
atoD acetoacetyl-CoA transferase, B subunit Shewana3_1666 Shewana3_3468
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
Alternative steps:
aacS acetoacetyl-CoA synthetase Shewana3_2475 Shewana3_2386
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Shewana3_2121 Shewana3_1974
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Shewana3_2558 Shewana3_0327
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Shewana3_4123
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Shewana3_2768 Shewana3_0721
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
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 Shewana3_2769 Shewana3_1672
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Shewana3_0024
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
gcdH glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
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) Shewana3_0673 Shewana3_2074
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Shewana3_0673 Shewana3_3192
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 Shewana3_3010
paaF 2,3-dehydroadipyl-CoA hydratase Shewana3_2768 Shewana3_0721
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Shewana3_0721 Shewana3_4123
paaH 3-hydroxyadipyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Shewana3_0023 Shewana3_2771
paaJ2 3-oxoadipyl-CoA thiolase Shewana3_0023 Shewana3_2771
paaK phenylacetate-CoA ligase Shewana3_2386
paaZ1 oxepin-CoA hydrolase Shewana3_2768 Shewana3_1461
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Shewana3_3105 Shewana3_0250
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Shewana3_0635 Shewana3_3618
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 Shewana3_0023 Shewana3_2771
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Shewana3_1461 Shewana3_0024
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Shewana3_2131
PPDCbeta phenylpyruvate decarboxylase, beta subunit Shewana3_2130

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.

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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 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