GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Pseudomonas fluorescens GW456-L13

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK PfGW456L13_4593 PfGW456L13_1500
pobA 4-hydroxybenzoate 3-monooxygenase PfGW456L13_1787
pcaH protocatechuate 3,4-dioxygenase, alpha subunit PfGW456L13_4588 PfGW456L13_4589
pcaG protocatechuate 3,4-dioxygenase, beta subunit PfGW456L13_4589 PfGW456L13_4588
pcaB 3-carboxymuconate cycloisomerase PfGW456L13_4586
pcaC 4-carboxymuconolactone decarboxylase PfGW456L13_4584 PfGW456L13_5039
pcaD 3-oxoadipate enol-lactone hydrolase PfGW456L13_4585 PfGW456L13_2295
catI 3-oxoadipate CoA-transferase subunit A (CatI) PfGW456L13_4592
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PfGW456L13_4591 PfGW456L13_2532
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PfGW456L13_4590 PfGW456L13_2430
Alternative steps:
ackA acetate kinase PfGW456L13_4820
acs acetyl-CoA synthetase, AMP-forming PfGW456L13_1963 PfGW456L13_1517
adh acetaldehyde dehydrogenase (not acylating) PfGW456L13_3517 PfGW456L13_1342
ald-dh-CoA acetaldehyde dehydrogenase, acylating PfGW456L13_2505
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PfGW456L13_3458 PfGW456L13_2522
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PfGW456L13_2433 PfGW456L13_2984
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PfGW456L13_1104
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 PfGW456L13_4886 PfGW456L13_2629
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
boxB benzoyl-CoA epoxidase, subunit B
boxC 2,3-epoxybenzoyl-CoA dihydrolase
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase PfGW456L13_2419
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PfGW456L13_2983 PfGW456L13_1630
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
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 PfGW456L13_554 PfGW456L13_2591
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase PfGW456L13_2980 PfGW456L13_1963
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PfGW456L13_3353 PfGW456L13_4084
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 PfGW456L13_2330 PfGW456L13_4110
ligU 4-oxalomesaconate tautomerase PfGW456L13_4115
mhpD 2-hydroxypentadienoate hydratase PfGW456L13_2504
mhpE 4-hydroxy-2-oxovalerate aldolase PfGW456L13_2506 PfGW456L13_3931
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PfGW456L13_2984
paaF 2,3-dehydroadipyl-CoA hydratase PfGW456L13_2434 PfGW456L13_2984
paaH 3-hydroxyadipyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_2432
paaJ2 3-oxoadipyl-CoA thiolase PfGW456L13_4590 PfGW456L13_2430
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PfGW456L13_2498 PfGW456L13_2157
pimC pimeloyl-CoA dehydrogenase, small subunit PfGW456L13_2494
pimD pimeloyl-CoA dehydrogenase, large subunit PfGW456L13_2495 PfGW456L13_2536
pimF 6-carboxyhex-2-enoyl-CoA hydratase PfGW456L13_412 PfGW456L13_4041
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PfGW456L13_1083 PfGW456L13_1397
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PfGW456L13_2504
pta phosphate acetyltransferase PfGW456L13_4990
xylF 2-hydroxymuconate semialdehyde hydrolase PfGW456L13_2503

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:

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