GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Ruegeria conchae TW15

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta


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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase
mhpD 2-hydroxypentadienoate hydratase G7G_RS0111655 G7G_RS0121215
mhpE 4-hydroxy-2-oxovalerate aldolase G7G_RS0111660 G7G_RS0100625
adh acetaldehyde dehydrogenase (not acylating) G7G_RS0104060 G7G_RS0111065
ackA acetate kinase G7G_RS0109955
pta phosphate acetyltransferase G7G_RS0111665 G7G_RS0104460
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming G7G_RS0105955 G7G_RS0104455
ald-dh-CoA acetaldehyde dehydrogenase, acylating G7G_RS0121370 G7G_RS0107180
atoB acetyl-CoA C-acetyltransferase G7G_RS0122070 G7G_RS0116445
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase G7G_RS0114145 G7G_RS0122065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase G7G_RS0116465
badK cyclohex-1-ene-1-carboxyl-CoA hydratase G7G_RS0116465 G7G_RS0122460
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 G7G_RS0117610 G7G_RS0102730
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 G7G_RS0102290
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase G7G_RS0117695 G7G_RS0106645
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase G7G_RS0116465 G7G_RS0111395
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase G7G_RS0116465 G7G_RS0104515
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2 G7G_RS0105965
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 G7G_RS0111790 G7G_RS0112980
gcdH glutaryl-CoA dehydrogenase G7G_RS0107335 G7G_RS0117695
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase G7G_RS0117685
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit G7G_RS0110060 G7G_RS0116990
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit G7G_RS0106430 G7G_RS0110055
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 G7G_RS0100615
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase G7G_RS0100460
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase G7G_RS0116465 G7G_RS0122460
paaH 3-hydroxyadipyl-CoA dehydrogenase G7G_RS0102205 G7G_RS0108810
paaJ2 3-oxoadipyl-CoA thiolase G7G_RS0102215 G7G_RS0116445
pcaB 3-carboxymuconate cycloisomerase G7G_RS0114000
pcaC 4-carboxymuconolactone decarboxylase G7G_RS0112310 G7G_RS0102510
pcaD 3-oxoadipate enol-lactone hydrolase G7G_RS0102510 G7G_RS0122440
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase G7G_RS0102215 G7G_RS0116445
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) G7G_RS0111965
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) G7G_RS0111960
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase G7G_RS0102215 G7G_RS0122070
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit G7G_RS0110000
pimF 6-carboxyhex-2-enoyl-CoA hydratase G7G_RS0102205
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase G7G_RS0111640 G7G_RS0120200
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase G7G_RS0121215 G7G_RS0111655

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