GapMind for catabolism of small carbon sources

 

Definition of L-phenylalanine catabolism

As rules and steps, or see full text

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.)

Steps

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:

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