GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas fluorescens FW300-N2C3

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK AO356_04945 AO356_29245
pobA 4-hydroxybenzoate 3-monooxygenase AO356_05295
pcaH protocatechuate 3,4-dioxygenase, alpha subunit AO356_04920 AO356_04925
pcaG protocatechuate 3,4-dioxygenase, beta subunit AO356_04925 AO356_04920
pcaB 3-carboxymuconate cycloisomerase AO356_04910
pcaC 4-carboxymuconolactone decarboxylase AO356_04900 AO356_07160
pcaD 3-oxoadipate enol-lactone hydrolase AO356_04905 AO356_02885
catI 3-oxoadipate CoA-transferase subunit A (CatI) AO356_04940
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) AO356_04935
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AO356_04930 AO356_21640
Alternative steps:
ackA acetate kinase AO356_17605
acs acetyl-CoA synthetase, AMP-forming AO356_18695 AO356_16045
adh acetaldehyde dehydrogenase (not acylating) AO356_28025 AO356_15225
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AO356_25515 AO356_27985
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AO356_30355 AO356_26360
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AO356_26360 AO356_30355
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit AO356_13910
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 AO356_24165 AO356_22050
bamI class II benzoyl-CoA reductase, BamI subunit AO356_24170
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 AO356_26355 AO356_17045
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AO356_26360 AO356_30295
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
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 AO356_10850 AO356_01580
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase AO356_14000
hcl 4-hydroxybenzoyl-CoA ligase AO356_26340 AO356_05100
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit AO356_26665
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit AO356_15625
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit AO356_26655 AO356_15620
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 AO356_23965
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase AO356_25360 AO356_25365
ligU 4-oxalomesaconate tautomerase AO356_28890 AO356_20880
mhpD 2-hydroxypentadienoate hydratase AO356_25565 AO356_28650
mhpE 4-hydroxy-2-oxovalerate aldolase AO356_25560 AO356_26150
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase AO356_26360 AO356_30355
paaH 3-hydroxyadipyl-CoA dehydrogenase AO356_02330 AO356_29995
paaJ2 3-oxoadipyl-CoA thiolase AO356_04930 AO356_21640
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AO356_21650
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AO356_21645
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AO356_03560 AO356_04930
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase AO356_30295 AO356_02330
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AO356_25585 AO356_13795
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase AO356_25565 AO356_28650
pta phosphate acetyltransferase AO356_16680
xylF 2-hydroxymuconate semialdehyde hydrolase AO356_24890

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