GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Desulfobacter vibrioformis DSM 8776

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 (35 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 Q366_RS10695
adh acetaldehyde dehydrogenase (not acylating) Q366_RS11495 Q366_RS17050
ackA acetate kinase Q366_RS12110
pta phosphate acetyltransferase Q366_RS09670 Q366_RS07670
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Q366_RS12130 Q366_RS06190
ald-dh-CoA acetaldehyde dehydrogenase, acylating Q366_RS10690
atoB acetyl-CoA C-acetyltransferase Q366_RS09305 Q366_RS02505
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Q366_RS09470 Q366_RS02355
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Q366_RS13010 Q366_RS18135
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Q366_RS18135 Q366_RS13010
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Q366_RS10555
bamE class II benzoyl-CoA reductase, BamE subunit Q366_RS03515 Q366_RS02775
bamF class II benzoyl-CoA reductase, BamF subunit Q366_RS03510
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit Q366_RS04805
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit Q366_RS02065 Q366_RS05275
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit Q366_RS02070
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit Q366_RS02075
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit Q366_RS02060 Q366_RS05275
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)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Q366_RS11450 Q366_RS06780
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Q366_RS18135 Q366_RS07650
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
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 Q366_RS12825 Q366_RS00125
gcdH glutaryl-CoA dehydrogenase Q366_RS06780 Q366_RS11450
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Q366_RS02090 Q366_RS02045
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Q366_RS02010
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase Q366_RS04385
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase
ligU 4-oxalomesaconate tautomerase Q366_RS12885
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Q366_RS18135 Q366_RS07650
paaH 3-hydroxyadipyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
paaJ2 3-oxoadipyl-CoA thiolase Q366_RS02505 Q366_RS00870
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase Q366_RS15225
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Q366_RS02505 Q366_RS00870
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Q366_RS00870 Q366_RS09305
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 Q366_RS10385 Q366_RS13505
praC 2-hydroxymuconate tautomerase
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.

Links

Downloads

Related tools

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