GapMind for catabolism of small carbon sources


Definition of 4-hydroxybenzoate catabolism

As rules and steps, or see full text


Overview: 4-hydroxybenzoate catabolism in GapMind is based on aerobic oxidation to 3,4-hydroxybenzoate (protocatechuate), followed by meta, ortho, or para cleavage; or reduction to benzoyl-CoA (part of a MetaCyc pathway for phenol degradation, link)


pcaK: 4-hydroxybenzoate transporter pcaK

fcbT1: tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1

fcbT2: tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2

fcbT3: tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3

pcaI: 3-oxoadipate CoA-transferase subunit A (PcaI)

pcaJ: 3-oxoadipate CoA-transferase subunit B (PcaJ)

catI: 3-oxoadipate CoA-transferase subunit A (CatI)

catJ: 3-oxoadipate CoA-transferase subunit B (CatJ)

pcaF: succinyl-CoA:acetyl-CoA C-succinyltransferase

mhpD: 2-hydroxypentadienoate hydratase

mhpE: 4-hydroxy-2-oxovalerate aldolase

ald-dh-CoA: acetaldehyde dehydrogenase, acylating

adh: acetaldehyde dehydrogenase (not acylating)

acs: acetyl-CoA synthetase, AMP-forming

ackA: acetate kinase

pta: phosphate acetyltransferase

atoB: acetyl-CoA C-acetyltransferase

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

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

paaF: 2,3-dehydroadipyl-CoA hydratase

paaH: 3-hydroxyadipyl-CoA dehydrogenase

paaJ2: 3-oxoadipyl-CoA thiolase

pobA: 4-hydroxybenzoate 3-monooxygenase

ligA: protocatechuate 4,5-dioxygenase, alpha subunit

ligB: protocatechuate 4,5-dioxygenase, beta subunit

ligC: 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase

ligI: 2-pyrone-4,6-dicarboxylate hydrolase

ligU: 4-oxalomesaconate tautomerase

ligJ: 4-carboxy-2-hydroxymuconate hydratase

ligK: 4-oxalocitramalate aldolase

praB: 2-hydroxymuconate 6-semialdehyde dehydrogenase

praC: 2-hydroxymuconate tautomerase

praD: 2-oxohex-3-enedioate decarboxylase

xylF: 2-hydroxymuconate semialdehyde hydrolase

pcaH: protocatechuate 3,4-dioxygenase, alpha subunit

pcaG: protocatechuate 3,4-dioxygenase, beta subunit

pcaB: 3-carboxymuconate cycloisomerase

pcaC: 4-carboxymuconolactone decarboxylase

pcaD: 3-oxoadipate enol-lactone hydrolase

praA: protocatechuate 2,3-dioxygenase

hcl: 4-hydroxybenzoyl-CoA ligase

hcrA: 4-hydroxybenzoyl-CoA reductase, alpha subunit

hcrB: 4-hydroxybenzoyl-CoA reductase, beta subunit

hcrC: 4-hydroxybenzoyl-CoA reductase, gamma subunit



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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