GapMind for catabolism of small carbon sources


Definition of L-phenylalanine catabolism

As rules and steps, or see full text


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.)


livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF)

livG: L-phenylalanine ABC transporter, ATPase component 2 (LivG)

livH: L-phenylalanine ABC transporter, permease component 1 (LivH)

livM: L-phenylalanine ABC transporter, permease component 2 (LivM)

livJ: L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK

aroP: L-phenylalanine:H+ symporter AroP

atoA: acetoacetyl-CoA transferase, A subunit

atoD: acetoacetyl-CoA transferase, B subunit

aacS: acetoacetyl-CoA synthetase

atoB: acetyl-CoA C-acetyltransferase

HPD: 4-hydroxyphenylpyruvate dioxygenase

hmgA: homogentisate dioxygenase

maiA: maleylacetoacetate isomerase

fahA: fumarylacetoacetate hydrolase

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

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

gcdH: glutaryl-CoA dehydrogenase

ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase

padB: phenylacetyl-CoA dehydrogenase, PadB subunit

padC: phenylacetyl-CoA dehydrogenase, PadC subunit

padD: phenylacetyl-CoA dehydrogenase, PadD subunit

padG: phenylglyoxylate dehydrogenase, alpha subunit

padI: phenylglyoxylate dehydrogenase, beta subunit

padE: phenylglyoxylate dehydrogenase, gamma subunit

padF: phenylglyoxylate dehydrogenase, delta subunit

padH: phenylglyoxylate dehydrogenase, epsilon subunit

dch: cyclohexa-1,5-diene-1-carboxyl-CoA hydratase

had: 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase

oah: 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase

pimB: 3-oxopimeloyl-CoA:CoA acetyltransferase

Ch1CoA: cyclohex-1-ene-1-carbonyl-CoA dehydrogenase

badK: cyclohex-1-ene-1-carboxyl-CoA hydratase

badH: 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase

badI: 2-ketocyclohexanecarboxyl-CoA hydrolase

pimD: pimeloyl-CoA dehydrogenase, large subunit

pimC: pimeloyl-CoA dehydrogenase, small subunit

pimF: 6-carboxyhex-2-enoyl-CoA hydratase

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

paaK: phenylacetate-CoA ligase

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

paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase

paaZ1: oxepin-CoA hydrolase

paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase

paaJ1: 3-oxo-5,6-dehydrosuberyl-CoA thiolase

paaF: 2,3-dehydroadipyl-CoA hydratase

paaH: 3-hydroxyadipyl-CoA dehydrogenase

paaJ2: 3-oxoadipyl-CoA thiolase

ARO8: L-phenylalanine transaminase

ARO10: phenylpyruvate decarboxylase

PPDCalpha: phenylpyruvate decarboxylase, alpha subunit

PPDCbeta: phenylpyruvate decarboxylase, beta subunit

iorA: phenylpyruvate:ferredoxin oxidoreductase, IorA subunit

iorB: phenylpyruvate:ferredoxin oxidoreductase, IorB subunit

iorAB: phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB

pad-dh: phenylacetaldehyde dehydrogenase

pfor: phenylacetaldeyde:ferredoxin oxidoreductase

PAH: phenylalanine 4-monooxygenase

PCBD: pterin-4-alpha-carbinoalamine dehydratase

QDPR: 6,7-dihydropteridine reductase



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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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