GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Dyella japonica UNC79MFTsu3.2

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs

Also see fitness data for the top candidates

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 (26 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 N515DRAFT_0574
adh acetaldehyde dehydrogenase (not acylating) N515DRAFT_0465 N515DRAFT_3729
acs acetyl-CoA synthetase, AMP-forming N515DRAFT_3075 N515DRAFT_0016
Alternative steps:
ackA acetate kinase N515DRAFT_2456
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase N515DRAFT_0938 N515DRAFT_2688
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase N515DRAFT_2873 N515DRAFT_1104
badI 2-ketocyclohexanecarboxyl-CoA hydrolase N515DRAFT_1164 N515DRAFT_0930
badK cyclohex-1-ene-1-carboxyl-CoA hydratase N515DRAFT_1164 N515DRAFT_0930
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 N515DRAFT_2810
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase N515DRAFT_0492 N515DRAFT_0941
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase N515DRAFT_1164
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase N515DRAFT_1164 N515DRAFT_0416
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
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 N515DRAFT_0484 N515DRAFT_0492
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 N515DRAFT_2295 N515DRAFT_4010
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
ligU 4-oxalomesaconate tautomerase N515DRAFT_0030
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase N515DRAFT_1164 N515DRAFT_0930
paaH 3-hydroxyadipyl-CoA dehydrogenase N515DRAFT_2687 N515DRAFT_0416
paaJ2 3-oxoadipyl-CoA thiolase N515DRAFT_2688 N515DRAFT_0938
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase N515DRAFT_2628
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase N515DRAFT_2688 N515DRAFT_0938
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) N515DRAFT_1736
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) N515DRAFT_1736
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase N515DRAFT_2688 N515DRAFT_0938
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 N515DRAFT_3729 N515DRAFT_0379
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase N515DRAFT_2182

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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