GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Derxia gummosa DSM 723

Best path

pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK

Rules

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 (51 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK H566_RS0107035
pobA 4-hydroxybenzoate 3-monooxygenase H566_RS0107020
ligA protocatechuate 4,5-dioxygenase, alpha subunit H566_RS0106745 H566_RS0106695
ligB protocatechuate 4,5-dioxygenase, beta subunit H566_RS0106750 H566_RS0106700
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase H566_RS0106755
ligI 2-pyrone-4,6-dicarboxylate hydrolase H566_RS0106740
ligU 4-oxalomesaconate tautomerase H566_RS0121285
ligJ 4-carboxy-2-hydroxymuconate hydratase H566_RS0106725
ligK 4-oxalocitramalate aldolase H566_RS0106730 H566_RS0120875
Alternative steps:
ackA acetate kinase H566_RS0120655 H566_RS0121200
acs acetyl-CoA synthetase, AMP-forming H566_RS0119605 H566_RS0120475
adh acetaldehyde dehydrogenase (not acylating) H566_RS0101815 H566_RS0108130
ald-dh-CoA acetaldehyde dehydrogenase, acylating H566_RS0111655
atoB acetyl-CoA C-acetyltransferase H566_RS0115455 H566_RS0110200
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase H566_RS0105240 H566_RS0118725
badI 2-ketocyclohexanecarboxyl-CoA hydrolase H566_RS0118410 H566_RS0106825
badK cyclohex-1-ene-1-carboxyl-CoA hydratase H566_RS0118410 H566_RS0111180
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit H566_RS0104880
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 H566_RS0120630 H566_RS27975
bamI class II benzoyl-CoA reductase, BamI subunit H566_RS0120635
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 H566_RS0112930
boxB benzoyl-CoA epoxidase, subunit B H566_RS0112925
boxC 2,3-epoxybenzoyl-CoA dihydrolase H566_RS0112920
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase H566_RS0112825
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase H566_RS0120480 H566_RS0106285
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase H566_RS0118410 H566_RS0111180
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H566_RS0118410 H566_RS0108000
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H566_RS0116335 H566_RS0112415
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 H566_RS0112605 H566_RS0113345
gcdH glutaryl-CoA dehydrogenase H566_RS0120480 H566_RS0116330
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase H566_RS0101475
hcl 4-hydroxybenzoyl-CoA ligase H566_RS0112820
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit H566_RS0104040
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit H566_RS30310
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit H566_RS22110 H566_RS22770
mhpD 2-hydroxypentadienoate hydratase H566_RS0111550 H566_RS0113110
mhpE 4-hydroxy-2-oxovalerate aldolase H566_RS24930 H566_RS0111650
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase H566_RS0111180
paaF 2,3-dehydroadipyl-CoA hydratase H566_RS0118410 H566_RS0111180
paaH 3-hydroxyadipyl-CoA dehydrogenase H566_RS0116335 H566_RS0112415
paaJ2 3-oxoadipyl-CoA thiolase H566_RS0112785 H566_RS0115455
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase H566_RS0119495
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase H566_RS0112785 H566_RS0110200
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) H566_RS0103270
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) H566_RS0103265
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase H566_RS0111165 H566_RS0116340
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase H566_RS0108000
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase H566_RS0111555 H566_RS0113545
praC 2-hydroxymuconate tautomerase H566_RS0111635 H566_RS0112245
praD 2-oxohex-3-enedioate decarboxylase H566_RS0111545 H566_RS0111550
pta phosphate acetyltransferase H566_RS26885 H566_RS0106505
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 Apr 09 2024. 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