GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Shewanella sp. ANA-3

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta

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 (29 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
adh acetaldehyde dehydrogenase (not acylating) Shewana3_0250 Shewana3_1788
ackA acetate kinase Shewana3_1552 Shewana3_3197
pta phosphate acetyltransferase Shewana3_1551
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Shewana3_2523 Shewana3_1675
ald-dh-CoA acetaldehyde dehydrogenase, acylating Shewana3_1788
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Shewana3_2558 Shewana3_0327
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Shewana3_4123
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Shewana3_2768 Shewana3_0721
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Shewana3_2769 Shewana3_1672
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Shewana3_0024
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shewana3_2768 Shewana3_0024
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
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 Shewana3_1414
gcdH glutaryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Shewana3_2386
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Shewana3_1496
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 Shewana3_2373 Shewana3_3723
ligU 4-oxalomesaconate tautomerase Shewana3_3828
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Shewana3_2768 Shewana3_0721
paaH 3-hydroxyadipyl-CoA dehydrogenase Shewana3_0024 Shewana3_1461
paaJ2 3-oxoadipyl-CoA thiolase Shewana3_0023 Shewana3_2771
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Shewana3_3552
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Shewana3_0023 Shewana3_2771
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Shewana3_1667 Shewana3_3467
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Shewana3_3468 Shewana3_1666
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Shewana3_0023 Shewana3_2771
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Shewana3_1461 Shewana3_0024
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Shewana3_0250 Shewana3_3105
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase

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