GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Thermovenabulum gondwanense R270

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA

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 (30 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
ald-dh-CoA acetaldehyde dehydrogenase, acylating ATZ99_RS10955
Alternative steps:
ackA acetate kinase ATZ99_RS05055 ATZ99_RS02215
acs acetyl-CoA synthetase, AMP-forming
adh acetaldehyde dehydrogenase (not acylating) ATZ99_RS10955
atoB acetyl-CoA C-acetyltransferase ATZ99_RS10405 ATZ99_RS09740
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase ATZ99_RS08105 ATZ99_RS05100
badI 2-ketocyclohexanecarboxyl-CoA hydrolase
badK cyclohex-1-ene-1-carboxyl-CoA hydratase ATZ99_RS09725
bamB class II benzoyl-CoA reductase, BamB subunit ATZ99_RS04020 ATZ99_RS00670
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 ATZ99_RS04010 ATZ99_RS09330
bamH class II benzoyl-CoA reductase, BamH subunit ATZ99_RS09315 ATZ99_RS04005
bamI class II benzoyl-CoA reductase, BamI subunit ATZ99_RS04000 ATZ99_RS00620
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit ATZ99_RS07110 ATZ99_RS01615
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit ATZ99_RS01615
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) ATZ99_RS01230
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) ATZ99_RS01235 ATZ99_RS06275
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase ATZ99_RS09730
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase ATZ99_RS09725
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ATZ99_RS09725
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ATZ99_RS09735 ATZ99_RS08105
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 ATZ99_RS09730
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit ATZ99_RS05260 ATZ99_RS05200
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit ATZ99_RS05255
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 ATZ99_RS01985
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase ATZ99_RS09725
paaH 3-hydroxyadipyl-CoA dehydrogenase ATZ99_RS09735 ATZ99_RS08105
paaJ2 3-oxoadipyl-CoA thiolase ATZ99_RS10405 ATZ99_RS00630
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase ATZ99_RS10405 ATZ99_RS00630
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) ATZ99_RS00635 ATZ99_RS10410
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) ATZ99_RS10415 ATZ99_RS00640
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase ATZ99_RS10405 ATZ99_RS09740
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
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase ATZ99_RS05050 ATZ99_RS10940

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