GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Geotalea uraniireducens Rf4

Best path

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

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 (37 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
mhpE 4-hydroxy-2-oxovalerate aldolase
adh acetaldehyde dehydrogenase (not acylating) GURA_RS00565 GURA_RS16875
ackA acetate kinase GURA_RS17300 GURA_RS13515
pta phosphate acetyltransferase GURA_RS17295 GURA_RS10515
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming GURA_RS08185 GURA_RS08015
ald-dh-CoA acetaldehyde dehydrogenase, acylating GURA_RS18035
atoB acetyl-CoA C-acetyltransferase GURA_RS15490 GURA_RS08100
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase GURA_RS09505 GURA_RS18385
badI 2-ketocyclohexanecarboxyl-CoA hydrolase GURA_RS15480
badK cyclohex-1-ene-1-carboxyl-CoA hydratase GURA_RS15480 GURA_RS08130
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit GURA_RS12275 GURA_RS06195
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit GURA_RS18270
bamG class II benzoyl-CoA reductase, BamG subunit GURA_RS21560
bamH class II benzoyl-CoA reductase, BamH subunit GURA_RS21555 GURA_RS01690
bamI class II benzoyl-CoA reductase, BamI subunit GURA_RS21550 GURA_RS18545
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit GURA_RS19745
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit GURA_RS19745
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) GURA_RS15445
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase GURA_RS15475 GURA_RS15455
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase GURA_RS15480
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GURA_RS15480 GURA_RS08130
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GURA_RS08095 GURA_RS15485
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 GURA_RS14175
gcdH glutaryl-CoA dehydrogenase GURA_RS16870 GURA_RS15475
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase GURA_RS08185
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit GURA_RS05055
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 GURA_RS15480 GURA_RS08130
paaH 3-hydroxyadipyl-CoA dehydrogenase GURA_RS08095 GURA_RS15485
paaJ2 3-oxoadipyl-CoA thiolase GURA_RS08100 GURA_RS15490
pcaB 3-carboxymuconate cycloisomerase GURA_RS10470
pcaC 4-carboxymuconolactone decarboxylase GURA_RS02920
pcaD 3-oxoadipate enol-lactone hydrolase GURA_RS02920
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase GURA_RS08100 GURA_RS15490
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) GURA_RS22155
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) GURA_RS22150
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase GURA_RS08100 GURA_RS15490
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase GURA_RS00565 GURA_RS08035
praC 2-hydroxymuconate tautomerase GURA_RS12550
praD 2-oxohex-3-enedioate decarboxylase

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