GapMind for catabolism of small carbon sources

 

Definition of 4-hydroxybenzoate catabolism

As rules and steps, or see full text

Rules

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)

Steps

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 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