GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

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

Also see fitness data for the top candidates


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 (52 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK H281DRAFT_06348 H281DRAFT_03848
pobA 4-hydroxybenzoate 3-monooxygenase H281DRAFT_01166
pcaH protocatechuate 3,4-dioxygenase, alpha subunit H281DRAFT_03864 H281DRAFT_03865
pcaG protocatechuate 3,4-dioxygenase, beta subunit H281DRAFT_03865 H281DRAFT_01051
pcaB 3-carboxymuconate cycloisomerase H281DRAFT_01595 H281DRAFT_02594
pcaC 4-carboxymuconolactone decarboxylase H281DRAFT_01593 H281DRAFT_01594
pcaD 3-oxoadipate enol-lactone hydrolase H281DRAFT_01594 H281DRAFT_02073
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) H281DRAFT_01597 H281DRAFT_04495
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) H281DRAFT_01596 H281DRAFT_04496
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase H281DRAFT_01504 H281DRAFT_05723
Alternative steps:
ackA acetate kinase H281DRAFT_00303 H281DRAFT_01409
acs acetyl-CoA synthetase, AMP-forming H281DRAFT_04953 H281DRAFT_05523
adh acetaldehyde dehydrogenase (not acylating) H281DRAFT_01117 H281DRAFT_02299
ald-dh-CoA acetaldehyde dehydrogenase, acylating H281DRAFT_01665
atoB acetyl-CoA C-acetyltransferase H281DRAFT_00852 H281DRAFT_00857
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase H281DRAFT_00643 H281DRAFT_03703
badI 2-ketocyclohexanecarboxyl-CoA hydrolase H281DRAFT_02741 H281DRAFT_05725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase H281DRAFT_05725 H281DRAFT_02514
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit H281DRAFT_02472
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 H281DRAFT_04572 H281DRAFT_03941
bamI class II benzoyl-CoA reductase, BamI subunit H281DRAFT_03942 H281DRAFT_04573
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 H281DRAFT_00375
boxB benzoyl-CoA epoxidase, subunit B H281DRAFT_00374
boxC 2,3-epoxybenzoyl-CoA dihydrolase H281DRAFT_00373
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase H281DRAFT_00370
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase H281DRAFT_01204 H281DRAFT_06133
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase H281DRAFT_05725 H281DRAFT_01137
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H281DRAFT_05725 H281DRAFT_02514
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
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 H281DRAFT_04737 H281DRAFT_01204
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase H281DRAFT_00369 H281DRAFT_03697
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit H281DRAFT_02182 H281DRAFT_02676
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit H281DRAFT_03033 H281DRAFT_02815
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit H281DRAFT_05973 H281DRAFT_02181
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit H281DRAFT_01373
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase H281DRAFT_01364 H281DRAFT_05953
ligJ 4-carboxy-2-hydroxymuconate hydratase H281DRAFT_03420 H281DRAFT_06355
ligK 4-oxalocitramalate aldolase H281DRAFT_03419 H281DRAFT_06498
ligU 4-oxalomesaconate tautomerase H281DRAFT_01376 H281DRAFT_02982
mhpD 2-hydroxypentadienoate hydratase H281DRAFT_01663 H281DRAFT_05455
mhpE 4-hydroxy-2-oxovalerate aldolase H281DRAFT_01666 H281DRAFT_03252
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase H281DRAFT_05725 H281DRAFT_02514
paaH 3-hydroxyadipyl-CoA dehydrogenase H281DRAFT_00361 H281DRAFT_04625
paaJ2 3-oxoadipyl-CoA thiolase H281DRAFT_05723 H281DRAFT_01504
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase H281DRAFT_00917 H281DRAFT_04626
pimC pimeloyl-CoA dehydrogenase, small subunit H281DRAFT_00359 H281DRAFT_04587
pimD pimeloyl-CoA dehydrogenase, large subunit H281DRAFT_04586 H281DRAFT_00360
pimF 6-carboxyhex-2-enoyl-CoA hydratase H281DRAFT_00916 H281DRAFT_00361
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase H281DRAFT_03256 H281DRAFT_02464
praC 2-hydroxymuconate tautomerase H281DRAFT_01655 H281DRAFT_05328
praD 2-oxohex-3-enedioate decarboxylase H281DRAFT_01664 H281DRAFT_03253
pta phosphate acetyltransferase H281DRAFT_01410 H281DRAFT_06308
xylF 2-hydroxymuconate semialdehyde hydrolase

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 Sep 17 2021. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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