GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Nocardioides dokdonensis FR1436

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs


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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase I601_RS04750
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase I601_RS17180 I601_RS02865
mhpD 2-hydroxypentadienoate hydratase I601_RS02755
mhpE 4-hydroxy-2-oxovalerate aldolase I601_RS02745 I601_RS17190
adh acetaldehyde dehydrogenase (not acylating) I601_RS01590 I601_RS05735
acs acetyl-CoA synthetase, AMP-forming I601_RS07695 I601_RS18315
Alternative steps:
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating I601_RS02750 I601_RS17195
atoB acetyl-CoA C-acetyltransferase I601_RS03035 I601_RS19250
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase I601_RS11285 I601_RS16775
badI 2-ketocyclohexanecarboxyl-CoA hydrolase I601_RS07275 I601_RS19165
badK cyclohex-1-ene-1-carboxyl-CoA hydratase I601_RS19165 I601_RS11365
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit I601_RS04875
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 I601_RS03870
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) I601_RS03020
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase I601_RS04215 I601_RS08940
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase I601_RS19165 I601_RS16330
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I601_RS19165 I601_RS05525
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I601_RS04220 I601_RS05790
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 I601_RS02110 I601_RS10230
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase I601_RS07695 I601_RS04470
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit I601_RS06500
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit I601_RS02530 I601_RS06495
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
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase I601_RS19165 I601_RS17105
paaH 3-hydroxyadipyl-CoA dehydrogenase I601_RS04220 I601_RS05790
paaJ2 3-oxoadipyl-CoA thiolase I601_RS17535 I601_RS03035
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase I601_RS07960
pcaD 3-oxoadipate enol-lactone hydrolase I601_RS07960
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase I601_RS17535 I601_RS05865
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) I601_RS13875
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) I601_RS13880
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase I601_RS03035 I601_RS17150
pimC pimeloyl-CoA dehydrogenase, small subunit I601_RS02070 I601_RS02110
pimD pimeloyl-CoA dehydrogenase, large subunit I601_RS02065 I601_RS03050
pimF 6-carboxyhex-2-enoyl-CoA hydratase I601_RS17540
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase I601_RS01130 I601_RS01380
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase I601_RS02755
pta phosphate acetyltransferase

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