GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Acidovorax sp. GW101-3H11

Best path

pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK

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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase Ac3H11_3418 Ac3H11_3993
ligA protocatechuate 4,5-dioxygenase, alpha subunit Ac3H11_1187 Ac3H11_1164
ligB protocatechuate 4,5-dioxygenase, beta subunit Ac3H11_1188 Ac3H11_1163
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase Ac3H11_1189
ligI 2-pyrone-4,6-dicarboxylate hydrolase Ac3H11_1186 Ac3H11_139
ligU 4-oxalomesaconate tautomerase Ac3H11_4370 Ac3H11_2325
ligJ 4-carboxy-2-hydroxymuconate hydratase Ac3H11_1183
ligK 4-oxalocitramalate aldolase Ac3H11_1184 Ac3H11_2834
Alternative steps:
ackA acetate kinase Ac3H11_4666
acs acetyl-CoA synthetase, AMP-forming Ac3H11_951 Ac3H11_191
adh acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Ac3H11_2074 Ac3H11_2257
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Ac3H11_4006 Ac3H11_2775
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Ac3H11_4006 Ac3H11_2775
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 Ac3H11_1447 Ac3H11_3809
bamI class II benzoyl-CoA reductase, BamI subunit
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 Ac3H11_3083
boxB benzoyl-CoA epoxidase, subunit B Ac3H11_3084
boxC 2,3-epoxybenzoyl-CoA dihydrolase Ac3H11_3085
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase Ac3H11_3089
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Ac3H11_2996 Ac3H11_2359
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Ac3H11_4006 Ac3H11_3192
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ac3H11_4006 Ac3H11_2775
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
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 Ac3H11_155 Ac3H11_2592
gcdH glutaryl-CoA dehydrogenase Ac3H11_3533 Ac3H11_2991
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Ac3H11_3090 Ac3H11_4556
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit Ac3H11_3591
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Ac3H11_3590 Ac3H11_3428
mhpD 2-hydroxypentadienoate hydratase Ac3H11_1483 Ac3H11_4809
mhpE 4-hydroxy-2-oxovalerate aldolase Ac3H11_1482 Ac3H11_3372
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Ac3H11_4006 Ac3H11_2775
paaH 3-hydroxyadipyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
paaJ2 3-oxoadipyl-CoA thiolase Ac3H11_3920 Ac3H11_178
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Ac3H11_134
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Ac3H11_3920 Ac3H11_178
pcaG protocatechuate 3,4-dioxygenase, beta subunit Ac3H11_545
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Ac3H11_3922 Ac3H11_132
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Ac3H11_3921 Ac3H11_131
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Ac3H11_2522 Ac3H11_1916
pimC pimeloyl-CoA dehydrogenase, small subunit Ac3H11_1712
pimD pimeloyl-CoA dehydrogenase, large subunit Ac3H11_1711 Ac3H11_2717
pimF 6-carboxyhex-2-enoyl-CoA hydratase Ac3H11_2523 Ac3H11_1931
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Ac3H11_4805 Ac3H11_1486
praC 2-hydroxymuconate tautomerase Ac3H11_4833 Ac3H11_2374
praD 2-oxohex-3-enedioate decarboxylase Ac3H11_1483 Ac3H11_4809
pta phosphate acetyltransferase Ac3H11_1079 Ac3H11_4331
xylF 2-hydroxymuconate semialdehyde hydrolase Ac3H11_413

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.



Related tools

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