GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Caulobacter crescentus NA1000

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK CCNA_02495
pobA 4-hydroxybenzoate 3-monooxygenase CCNA_02487
pcaH protocatechuate 3,4-dioxygenase, alpha subunit CCNA_02492 CCNA_02491
pcaG protocatechuate 3,4-dioxygenase, beta subunit CCNA_02491 CCNA_02492
pcaB 3-carboxymuconate cycloisomerase CCNA_02493 CCNA_02572
pcaC 4-carboxymuconolactone decarboxylase CCNA_02494
pcaD 3-oxoadipate enol-lactone hydrolase CCNA_02494
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) CCNA_00206 CCNA_02488
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) CCNA_02489 CCNA_00207
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase CCNA_02490 CCNA_01168
Alternative steps:
ackA acetate kinase
acs acetyl-CoA synthetase, AMP-forming CCNA_03696 CCNA_01889
adh acetaldehyde dehydrogenase (not acylating) CCNA_03695 CCNA_03242
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CCNA_00545 CCNA_01885
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CCNA_00006 CCNA_01794
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CCNA_00006 CCNA_02658
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 CCNA_02024
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CCNA_01412 CCNA_02254
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CCNA_00006 CCNA_01891
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CCNA_00006 CCNA_01794
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CCNA_00123 CCNA_03293
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 CCNA_01515
gcdH glutaryl-CoA dehydrogenase CCNA_02254 CCNA_01412
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase CCNA_02483
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit CCNA_00022 CCNA_02353
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
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase CCNA_01610
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase CCNA_00006 CCNA_02658
paaH 3-hydroxyadipyl-CoA dehydrogenase CCNA_00123 CCNA_03293
paaJ2 3-oxoadipyl-CoA thiolase CCNA_02490 CCNA_01168
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CCNA_03575 CCNA_00544
pimC pimeloyl-CoA dehydrogenase, small subunit CCNA_01369 CCNA_01884
pimD pimeloyl-CoA dehydrogenase, large subunit CCNA_01368 CCNA_02215
pimF 6-carboxyhex-2-enoyl-CoA hydratase CCNA_03293 CCNA_00074
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase CCNA_03243 CCNA_03695
praC 2-hydroxymuconate tautomerase CCNA_03070
praD 2-oxohex-3-enedioate decarboxylase CCNA_01577
pta phosphate acetyltransferase CCNA_03663 CCNA_02704
xylF 2-hydroxymuconate semialdehyde hydrolase CCNA_02478

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