GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK AO353_17190 AO353_14270
pobA 4-hydroxybenzoate 3-monooxygenase AO353_03895
pcaH protocatechuate 3,4-dioxygenase, alpha subunit AO353_17215 AO353_17210
pcaG protocatechuate 3,4-dioxygenase, beta subunit AO353_17210 AO353_17215
pcaB 3-carboxymuconate cycloisomerase AO353_17225
pcaC 4-carboxymuconolactone decarboxylase AO353_17235 AO353_05280
pcaD 3-oxoadipate enol-lactone hydrolase AO353_17230 AO353_19350
catI 3-oxoadipate CoA-transferase subunit A (CatI) AO353_17195
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) AO353_17200
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AO353_17205 AO353_01065
Alternative steps:
ackA acetate kinase AO353_04410
acs acetyl-CoA synthetase, AMP-forming AO353_03060 AO353_14365
adh acetaldehyde dehydrogenase (not acylating) AO353_22390 AO353_06560
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AO353_04045 AO353_01660
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AO353_25675 AO353_25665
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AO353_25675 AO353_03780
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit AO353_07705
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 AO353_15695 AO353_27760
bamI class II benzoyl-CoA reductase, BamI subunit AO353_15690
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AO353_25680 AO353_20350
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AO353_25675 AO353_00510
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO353_25675 AO353_00510
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO353_00510 AO353_27535
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 AO353_11100 AO353_20350
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase AO353_19865 AO353_07635
hcl 4-hydroxybenzoyl-CoA ligase AO353_19945 AO353_25695
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit AO353_23430 AO353_01425
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 AO353_28370
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase AO353_00850 AO353_07830
ligU 4-oxalomesaconate tautomerase AO353_00885
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AO353_25675
paaF 2,3-dehydroadipyl-CoA hydratase AO353_25675 AO353_24830
paaH 3-hydroxyadipyl-CoA dehydrogenase AO353_00510 AO353_27535
paaJ2 3-oxoadipyl-CoA thiolase AO353_17205 AO353_01065
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AO353_27935
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AO353_27940
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AO353_17205 AO353_01065
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase AO353_00510
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AO353_07805 AO353_09195
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase AO353_05065
xylF 2-hydroxymuconate semialdehyde hydrolase AO353_04920 AO353_25150

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