GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Stutzerimonas stutzeri A1501

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK PST_RS08460
pobA 4-hydroxybenzoate 3-monooxygenase PST_RS07570
pcaH protocatechuate 3,4-dioxygenase, alpha subunit PST_RS06360 PST_RS06355
pcaG protocatechuate 3,4-dioxygenase, beta subunit PST_RS06355
pcaB 3-carboxymuconate cycloisomerase PST_RS06395
pcaC 4-carboxymuconolactone decarboxylase PST_RS06405 PST_RS06400
pcaD 3-oxoadipate enol-lactone hydrolase PST_RS06400
catI 3-oxoadipate CoA-transferase subunit A (CatI) PST_RS06380
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PST_RS06385
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PST_RS06390 PST_RS16155
Alternative steps:
ackA acetate kinase PST_RS06035 PST_RS05740
acs acetyl-CoA synthetase, AMP-forming PST_RS08720 PST_RS05700
adh acetaldehyde dehydrogenase (not acylating) PST_RS10485 PST_RS18325
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PST_RS10135 PST_RS03535
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PST_RS09740
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS03120
bamB class II benzoyl-CoA reductase, BamB subunit
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
bamH class II benzoyl-CoA reductase, BamH subunit
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PST_RS16120 PST_RS09700
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS06175
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
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 PST_RS16175 PST_RS08415
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase PST_RS04505
hcl 4-hydroxybenzoyl-CoA ligase PST_RS00545 PST_RS08720
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit PST_RS04730
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PST_RS04725 PST_RS02350
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 PST_RS10335
ligU 4-oxalomesaconate tautomerase PST_RS10320
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase PST_RS09740 PST_RS06175
paaH 3-hydroxyadipyl-CoA dehydrogenase PST_RS08735 PST_RS00510
paaJ2 3-oxoadipyl-CoA thiolase PST_RS06390 PST_RS16155
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PST_RS16145
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PST_RS16150
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PST_RS12565 PST_RS06390
pimC pimeloyl-CoA dehydrogenase, small subunit PST_RS00520
pimD pimeloyl-CoA dehydrogenase, large subunit PST_RS00515 PST_RS08590
pimF 6-carboxyhex-2-enoyl-CoA hydratase PST_RS00510 PST_RS08735
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PST_RS08835 PST_RS00240
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase PST_RS05735 PST_RS03555
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