GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Burkholderia vietnamiensis G4

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK WP_011881081.1 WP_011883438.1
pobA 4-hydroxybenzoate 3-monooxygenase WP_011881087.1
pcaH protocatechuate 3,4-dioxygenase, alpha subunit WP_011882025.1 WP_011882026.1
pcaG protocatechuate 3,4-dioxygenase, beta subunit WP_011882026.1
pcaB 3-carboxymuconate cycloisomerase WP_011881084.1
pcaC 4-carboxymuconolactone decarboxylase WP_011881082.1 WP_011881428.1
pcaD 3-oxoadipate enol-lactone hydrolase WP_011881083.1 WP_011882675.1
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) WP_011881086.1 WP_011884535.1
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) WP_011881085.1 WP_011884536.1
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase WP_011883162.1 WP_011880942.1
Alternative steps:
ackA acetate kinase WP_011885604.1 WP_011880246.1
acs acetyl-CoA synthetase, AMP-forming WP_011885480.1 WP_011880617.1
adh acetaldehyde dehydrogenase (not acylating) WP_011881627.1 WP_011880891.1
ald-dh-CoA acetaldehyde dehydrogenase, acylating WP_011875732.1 WP_011882650.1
atoB acetyl-CoA C-acetyltransferase WP_011884947.1 WP_011879792.1
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase WP_011880388.1 WP_011886026.1
badI 2-ketocyclohexanecarboxyl-CoA hydrolase WP_011883164.1 WP_011882343.1
badK cyclohex-1-ene-1-carboxyl-CoA hydratase WP_011883164.1 WP_011881868.1
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit WP_011880772.1
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 WP_011885532.1 WP_011883791.1
bamI class II benzoyl-CoA reductase, BamI subunit WP_011883790.1
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 WP_011880691.1 WP_011880846.1
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase WP_011883164.1 WP_011881868.1
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase WP_011883164.1 WP_011881868.1
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase WP_011885989.1 WP_011886130.1
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 WP_011883419.1 WP_011880846.1
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase WP_011879663.1 WP_011880690.1
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit WP_011886194.1
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit WP_034192514.1 WP_011882245.1
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 WP_011881023.1
mhpD 2-hydroxypentadienoate hydratase WP_011875731.1 WP_011882651.1
mhpE 4-hydroxy-2-oxovalerate aldolase WP_011882649.1 WP_011882092.1
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase WP_011883164.1 WP_011881868.1
paaH 3-hydroxyadipyl-CoA dehydrogenase WP_011885989.1 WP_011886130.1
paaJ2 3-oxoadipyl-CoA thiolase WP_011883162.1 WP_011880942.1
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase WP_011885058.1 WP_011885988.1
pimC pimeloyl-CoA dehydrogenase, small subunit WP_011886128.1 WP_011885519.1
pimD pimeloyl-CoA dehydrogenase, large subunit WP_011885520.1 WP_011886129.1
pimF 6-carboxyhex-2-enoyl-CoA hydratase WP_011885060.1 WP_011886130.1
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase WP_011875730.1 WP_011882088.1
praC 2-hydroxymuconate tautomerase WP_011516083.1 WP_011881613.1
praD 2-oxohex-3-enedioate decarboxylase WP_011875734.1 WP_011875731.1
pta phosphate acetyltransferase WP_011880255.1 WP_011882626.1
xylF 2-hydroxymuconate semialdehyde hydrolase WP_011516071.1 WP_011882647.1

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