GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Magnetospirillum magneticum AMB-1

Best path

pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB


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 (52 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK AMB_RS01320 AMB_RS22655
hcl 4-hydroxybenzoyl-CoA ligase AMB_RS14445 AMB_RS07835
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit AMB_RS10200 AMB_RS07490
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit AMB_RS10205
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit AMB_RS10195 AMB_RS14510
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit AMB_RS10810
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit AMB_RS10815
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit AMB_RS10820
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit AMB_RS10805 AMB_RS10810
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AMB_RS10825 AMB_RS03265
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase AMB_RS10835
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AMB_RS10830
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AMB_RS13850 AMB_RS04295
gcdH glutaryl-CoA dehydrogenase AMB_RS16315 AMB_RS03480
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AMB_RS03265 AMB_RS13070
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
atoB acetyl-CoA C-acetyltransferase AMB_RS18210 AMB_RS04295
Alternative steps:
ackA acetate kinase AMB_RS12860
acs acetyl-CoA synthetase, AMP-forming AMB_RS21140 AMB_RS11645
adh acetaldehyde dehydrogenase (not acylating) AMB_RS18195 AMB_RS06710
ald-dh-CoA acetaldehyde dehydrogenase, acylating
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AMB_RS13035 AMB_RS13020
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AMB_RS03265 AMB_RS13070
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AMB_RS03265 AMB_RS13070
bamB class II benzoyl-CoA reductase, BamB subunit AMB_RS14710
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 AMB_RS13985 AMB_RS17165
bamI class II benzoyl-CoA reductase, BamI subunit AMB_RS00865 AMB_RS13980
boxA benzoyl-CoA epoxidase, subunit A AMB_RS00895
boxB benzoyl-CoA epoxidase, subunit B AMB_RS00890
boxC 2,3-epoxybenzoyl-CoA dihydrolase AMB_RS00885
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase AMB_RS00880
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AMB_RS18215 AMB_RS18150
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 AMB_RS04130 AMB_RS02190
ligA protocatechuate 4,5-dioxygenase, alpha subunit AMB_RS01305
ligB protocatechuate 4,5-dioxygenase, beta subunit AMB_RS01310
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase AMB_RS01295
ligI 2-pyrone-4,6-dicarboxylate hydrolase AMB_RS01290
ligJ 4-carboxy-2-hydroxymuconate hydratase AMB_RS01275
ligK 4-oxalocitramalate aldolase AMB_RS01280
ligU 4-oxalomesaconate tautomerase AMB_RS01270
mhpD 2-hydroxypentadienoate hydratase AMB_RS04100
mhpE 4-hydroxy-2-oxovalerate aldolase AMB_RS04095
paaF 2,3-dehydroadipyl-CoA hydratase AMB_RS03265 AMB_RS13070
paaH 3-hydroxyadipyl-CoA dehydrogenase AMB_RS15050 AMB_RS19750
paaJ2 3-oxoadipyl-CoA thiolase AMB_RS13850 AMB_RS13060
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase AMB_RS20060
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AMB_RS13850 AMB_RS13060
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)
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AMB_RS03480
pimF 6-carboxyhex-2-enoyl-CoA hydratase AMB_RS15050
pobA 4-hydroxybenzoate 3-monooxygenase AMB_RS01315
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AMB_RS04115 AMB_RS18195
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase AMB_RS04100
pta phosphate acetyltransferase AMB_RS12865 AMB_RS01465
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 17 2021. The underlying query database was built on Sep 17 2021.



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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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