GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Shewanella loihica PV-4

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 (30 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) Shew_3574 Shew_1910
ackA acetate kinase Shew_2393
pta phosphate acetyltransferase Shew_2394
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Shew_1533 Shew_2568
ald-dh-CoA acetaldehyde dehydrogenase, acylating Shew_1910
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Shew_1603 Shew_3525
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Shew_3814 Shew_0540
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Shew_2672 Shew_0540
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 Shew_1669 Shew_2570
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Shew_2672 Shew_2864
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shew_0019 Shew_2425
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 Shew_0900 Shew_2570
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Shew_2188
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Shew_2266
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 Shew_2117 Shew_3370
ligU 4-oxalomesaconate tautomerase Shew_1823
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Shew_1670 Shew_2864
paaH 3-hydroxyadipyl-CoA dehydrogenase Shew_0019 Shew_2425
paaJ2 3-oxoadipyl-CoA thiolase Shew_0018 Shew_1667
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Shew_2734 Shew_1860
pcaD* 3-oxoadipate enol-lactone hydrolase Shew_2734 with Shew_1860
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Shew_0018 Shew_1667
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Shew_2575
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Shew_2576
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Shew_2858 Shew_0018
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Shew_2570
pimF 6-carboxyhex-2-enoyl-CoA hydratase Shew_2864 Shew_2425
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Shew_3574 Shew_0967
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