GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, 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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK Pf6N2E2_2838 Pf6N2E2_739
pobA 4-hydroxybenzoate 3-monooxygenase Pf6N2E2_2914 Pf6N2E2_227
pcaH protocatechuate 3,4-dioxygenase, alpha subunit Pf6N2E2_2833 Pf6N2E2_2834
pcaG protocatechuate 3,4-dioxygenase, beta subunit Pf6N2E2_2834 Pf6N2E2_2833
pcaB 3-carboxymuconate cycloisomerase Pf6N2E2_2831
pcaC 4-carboxymuconolactone decarboxylase Pf6N2E2_2829 Pf6N2E2_3293
pcaD 3-oxoadipate enol-lactone hydrolase Pf6N2E2_2830 Pf6N2E2_2401
catI 3-oxoadipate CoA-transferase subunit A (CatI) Pf6N2E2_2837
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Pf6N2E2_2836
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Pf6N2E2_2835 Pf6N2E2_2113
Alternative steps:
ackA acetate kinase Pf6N2E2_5444
acs acetyl-CoA synthetase, AMP-forming Pf6N2E2_5659 Pf6N2E2_5149
adh acetaldehyde dehydrogenase (not acylating) Pf6N2E2_1381 Pf6N2E2_4979
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Pf6N2E2_1839 Pf6N2E2_1323
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Pf6N2E2_1934 Pf6N2E2_1147
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1834
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Pf6N2E2_4704
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 Pf6N2E2_1468 Pf6N2E2_273
bamI class II benzoyl-CoA reductase, BamI subunit Pf6N2E2_1467
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf6N2E2_1146 Pf6N2E2_5333
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1922
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
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 Pf6N2E2_4036 Pf6N2E2_2191
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf6N2E2_1522
hcl 4-hydroxybenzoyl-CoA ligase Pf6N2E2_1143 Pf6N2E2_2872
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Pf6N2E2_2336 Pf6N2E2_5938
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 Pf6N2E2_1504
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase Pf6N2E2_2387
ligU 4-oxalomesaconate tautomerase Pf6N2E2_6064
mhpD 2-hydroxypentadienoate hydratase Pf6N2E2_1313
mhpE 4-hydroxy-2-oxovalerate aldolase Pf6N2E2_1314 Pf6N2E2_1103
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Pf6N2E2_1834 Pf6N2E2_1147
paaH 3-hydroxyadipyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
paaJ2 3-oxoadipyl-CoA thiolase Pf6N2E2_2835 Pf6N2E2_2113
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Pf6N2E2_2111
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Pf6N2E2_2112
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Pf6N2E2_2539 Pf6N2E2_2289
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Pf6N2E2_1922 Pf6N2E2_2290
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Pf6N2E2_1309 Pf6N2E2_4679
praC 2-hydroxymuconate tautomerase Pf6N2E2_687
praD 2-oxohex-3-enedioate decarboxylase Pf6N2E2_1313
pta phosphate acetyltransferase Pf6N2E2_5260
xylF 2-hydroxymuconate semialdehyde hydrolase Pf6N2E2_5281 Pf6N2E2_667

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