GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Belnapia rosea CPCC 100156

Best path

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


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
pobA 4-hydroxybenzoate 3-monooxygenase BLR02_RS08565
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BLR02_RS16065 BLR02_RS03030
pcaG protocatechuate 3,4-dioxygenase, beta subunit BLR02_RS16060 BLR02_RS03035
pcaB 3-carboxymuconate cycloisomerase BLR02_RS19140 BLR02_RS19925
pcaC 4-carboxymuconolactone decarboxylase BLR02_RS16055 BLR02_RS22510
pcaD 3-oxoadipate enol-lactone hydrolase BLR02_RS16055 BLR02_RS10235
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BLR02_RS16990 BLR02_RS27300
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BLR02_RS27295 BLR02_RS16985
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BLR02_RS13910 BLR02_RS00935
Alternative steps:
ackA acetate kinase BLR02_RS16785
acs acetyl-CoA synthetase, AMP-forming BLR02_RS09295 BLR02_RS17730
adh acetaldehyde dehydrogenase (not acylating) BLR02_RS07320 BLR02_RS18460
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase BLR02_RS13910 BLR02_RS06650
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLR02_RS23080 BLR02_RS06485
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BLR02_RS23085 BLR02_RS23955
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLR02_RS23955 BLR02_RS02380
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 BLR02_RS18705 BLR02_RS23805
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 BLR02_RS23270 BLR02_RS03525
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLR02_RS23955 BLR02_RS04715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR02_RS23955 BLR02_RS03400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
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 BLR02_RS25805 BLR02_RS12990
gcdH glutaryl-CoA dehydrogenase BLR02_RS06730 BLR02_RS03525
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BLR02_RS04745 BLR02_RS03520
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit BLR02_RS02245 BLR02_RS08385
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit BLR02_RS18195 BLR02_RS19270
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BLR02_RS02250 BLR02_RS03445
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 BLR02_RS06440 BLR02_RS03205
ligJ 4-carboxy-2-hydroxymuconate hydratase BLR02_RS14015
ligK 4-oxalocitramalate aldolase BLR02_RS16730 BLR02_RS18525
ligU 4-oxalomesaconate tautomerase BLR02_RS04850
mhpD 2-hydroxypentadienoate hydratase BLR02_RS20705
mhpE 4-hydroxy-2-oxovalerate aldolase BLR02_RS13965 BLR02_RS16825
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BLR02_RS23085
paaF 2,3-dehydroadipyl-CoA hydratase BLR02_RS23955 BLR02_RS09775
paaH 3-hydroxyadipyl-CoA dehydrogenase BLR02_RS03400 BLR02_RS23340
paaJ2 3-oxoadipyl-CoA thiolase BLR02_RS13910 BLR02_RS00935
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BLR02_RS00935 BLR02_RS13910
pimC pimeloyl-CoA dehydrogenase, small subunit BLR02_RS03410 BLR02_RS20985
pimD pimeloyl-CoA dehydrogenase, large subunit BLR02_RS03405 BLR02_RS20980
pimF 6-carboxyhex-2-enoyl-CoA hydratase BLR02_RS03400
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BLR02_RS04250 BLR02_RS07320
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase BLR02_RS11800
pta phosphate acetyltransferase BLR02_RS16780 BLR02_RS20655
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 24 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:

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