GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Marinomonas arctica 328

Best path

pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK

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 DK187_RS07420
ligA protocatechuate 4,5-dioxygenase, alpha subunit DK187_RS15735 DK187_RS09710
ligB protocatechuate 4,5-dioxygenase, beta subunit DK187_RS15740 DK187_RS09705
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase DK187_RS09675
ligI 2-pyrone-4,6-dicarboxylate hydrolase DK187_RS09715
ligU 4-oxalomesaconate tautomerase DK187_RS09720 DK187_RS04090
ligJ 4-carboxy-2-hydroxymuconate hydratase DK187_RS09730
ligK 4-oxalocitramalate aldolase DK187_RS09725 DK187_RS13370
Alternative steps:
ackA acetate kinase DK187_RS12110
acs acetyl-CoA synthetase, AMP-forming DK187_RS06350 DK187_RS08760
adh acetaldehyde dehydrogenase (not acylating) DK187_RS00035 DK187_RS07470
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase DK187_RS06190 DK187_RS08790
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase DK187_RS05415 DK187_RS06280
badI 2-ketocyclohexanecarboxyl-CoA hydrolase
badK cyclohex-1-ene-1-carboxyl-CoA hydratase DK187_RS04965 DK187_RS04960
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit DK187_RS18275
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 DK187_RS04910 DK187_RS07470
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase DK187_RS06285 DK187_RS15195
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase DK187_RS08770
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DK187_RS04965 DK187_RS08785
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
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 DK187_RS15895 DK187_RS07355
gcdH glutaryl-CoA dehydrogenase
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit DK187_RS18130
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase DK187_RS15790
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase DK187_RS04960
paaF 2,3-dehydroadipyl-CoA hydratase DK187_RS04965 DK187_RS04960
paaH 3-hydroxyadipyl-CoA dehydrogenase DK187_RS08785 DK187_RS04955
paaJ2 3-oxoadipyl-CoA thiolase DK187_RS04945 DK187_RS08790
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase DK187_RS04945 DK187_RS06190
pcaG protocatechuate 3,4-dioxygenase, beta subunit DK187_RS02315
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) DK187_RS06180
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) DK187_RS06185
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase DK187_RS06190 DK187_RS04945
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase DK187_RS08785
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase DK187_RS17920 DK187_RS01055
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase DK187_RS12115
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 Sep 24 2021. 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