GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Escherichia coli BW25113

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 (38 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 b0349
mhpD 2-hydroxypentadienoate hydratase b0350
mhpE 4-hydroxy-2-oxovalerate aldolase b0352 b2245
adh acetaldehyde dehydrogenase (not acylating) b1746 b1241
ackA acetate kinase b3115 b2296
pta phosphate acetyltransferase b2297 b2458
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming b4069 b0335
ald-dh-CoA acetaldehyde dehydrogenase, acylating b1241 b2455
atoB acetyl-CoA C-acetyltransferase b2224 b2844
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase b1093 b2426
badI 2-ketocyclohexanecarboxyl-CoA hydrolase b2262
badK cyclohex-1-ene-1-carboxyl-CoA hydratase b1393 b1394
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 b2284
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit b4334
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit b4334
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 b1387
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase b1695
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase b1393 b2341
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase b1393 b3846
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase b3846 b2341
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 b3578
gcdH glutaryl-CoA dehydrogenase
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase b1805
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit b2866
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit b0285
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit b0286 b2868
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 b3929
ligU 4-oxalomesaconate tautomerase b0769
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase b2262
paaF 2,3-dehydroadipyl-CoA hydratase b1393 b1394
paaH 3-hydroxyadipyl-CoA dehydrogenase b3846 b2341
paaJ2 3-oxoadipyl-CoA thiolase b1397 b2224
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase b1397 b2224
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) b2221
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) b2222
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase b1397 b2224
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase b3846 b2341
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase b0312 b1300
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase b0350

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, 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