GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, 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 AU252_RS04970 AU252_RS22885
pobA 4-hydroxybenzoate 3-monooxygenase AU252_RS11900 AU252_RS10020
pcaH protocatechuate 3,4-dioxygenase, alpha subunit AU252_RS10745 AU252_RS10740
pcaG protocatechuate 3,4-dioxygenase, beta subunit AU252_RS10740
pcaB 3-carboxymuconate cycloisomerase AU252_RS10750
pcaC 4-carboxymuconolactone decarboxylase AU252_RS10760 AU252_RS10755
pcaD 3-oxoadipate enol-lactone hydrolase AU252_RS16275 AU252_RS10755
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AU252_RS10770 AU252_RS07725
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AU252_RS10775 AU252_RS03410
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AU252_RS15005 AU252_RS00310
Alternative steps:
ackA acetate kinase AU252_RS15110
acs acetyl-CoA synthetase, AMP-forming AU252_RS14440 AU252_RS07515
adh acetaldehyde dehydrogenase (not acylating) AU252_RS16200 AU252_RS12650
ald-dh-CoA acetaldehyde dehydrogenase, acylating AU252_RS17310
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AU252_RS12495 AU252_RS01630
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AU252_RS14925 AU252_RS07800
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
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 AU252_RS15050
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AU252_RS01515 AU252_RS00840
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AU252_RS07800 AU252_RS00745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
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 AU252_RS16430 AU252_RS00305
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase AU252_RS00120 AU252_RS00800
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit AU252_RS13745
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit AU252_RS20565 AU252_RS13745
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase AU252_RS10155
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase AU252_RS11025 AU252_RS13825
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase AU252_RS17315 AU252_RS22420
mhpE 4-hydroxy-2-oxovalerate aldolase AU252_RS17305 AU252_RS22425
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase AU252_RS07800 AU252_RS00745
paaH 3-hydroxyadipyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
paaJ2 3-oxoadipyl-CoA thiolase AU252_RS15005 AU252_RS00310
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AU252_RS15005 AU252_RS00785
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AU252_RS00805
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AU252_RS22410 AU252_RS11515
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase AU252_RS22420 AU252_RS17315
pta phosphate acetyltransferase AU252_RS15080
xylF 2-hydroxymuconate semialdehyde hydrolase AU252_RS17320 AU252_RS22250

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