GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Methylocystis bryophila S285

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs

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)

72 steps (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase B1812_RS07870 B1812_RS18210
adh acetaldehyde dehydrogenase (not acylating) B1812_RS07050 B1812_RS13395
acs acetyl-CoA synthetase, AMP-forming B1812_RS11525 B1812_RS19225
Alternative steps:
ackA acetate kinase B1812_RS12000
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase B1812_RS02620 B1812_RS16320
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase B1812_RS02990 B1812_RS02625
badI 2-ketocyclohexanecarboxyl-CoA hydrolase B1812_RS05255
badK cyclohex-1-ene-1-carboxyl-CoA hydratase B1812_RS05255 B1812_RS16295
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 B1812_RS20065 B1812_RS03685
bamI class II benzoyl-CoA reductase, BamI subunit B1812_RS19285
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase B1812_RS16285 B1812_RS16310
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase B1812_RS05255 B1812_RS17255
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B1812_RS05255 B1812_RS13170
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B1812_RS19300 B1812_RS13170
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
gcdH glutaryl-CoA dehydrogenase B1812_RS16285 B1812_RS14765
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase B1812_RS10600
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit
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
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase B1812_RS05255 B1812_RS16295
paaH 3-hydroxyadipyl-CoA dehydrogenase B1812_RS19300 B1812_RS13170
paaJ2 3-oxoadipyl-CoA thiolase B1812_RS02620 B1812_RS16320
pcaB 3-carboxymuconate cycloisomerase B1812_RS17135
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase B1812_RS02620 B1812_RS16320
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) B1812_RS03940
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) B1812_RS03945
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase B1812_RS02620 B1812_RS13165
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase B1812_RS13170
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase B1812_RS13395 B1812_RS07050
praC 2-hydroxymuconate tautomerase B1812_RS10605
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase B1812_RS05165 B1812_RS11995

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 Apr 09 2024. 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 (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