GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3231 Pf1N1B4_4198
pobA 4-hydroxybenzoate 3-monooxygenase Pf1N1B4_703
pcaH protocatechuate 3,4-dioxygenase, alpha subunit Pf1N1B4_5583 Pf1N1B4_3236
pcaG protocatechuate 3,4-dioxygenase, beta subunit Pf1N1B4_5584 Pf1N1B4_3235
pcaB 3-carboxymuconate cycloisomerase Pf1N1B4_3237
pcaC 4-carboxymuconolactone decarboxylase Pf1N1B4_3239 Pf1N1B4_1105
pcaD 3-oxoadipate enol-lactone hydrolase Pf1N1B4_3238 Pf1N1B4_549
catI 3-oxoadipate CoA-transferase subunit A (CatI) Pf1N1B4_3232
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Pf1N1B4_3233
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Pf1N1B4_3234 Pf1N1B4_5835
Alternative steps:
ackA acetate kinase Pf1N1B4_879
acs acetyl-CoA synthetase, AMP-forming Pf1N1B4_3430 Pf1N1B4_2849
adh acetaldehyde dehydrogenase (not acylating) Pf1N1B4_4502 Pf1N1B4_2673
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Pf1N1B4_5039 Pf1N1B4_512
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Pf1N1B4_4788 Pf1N1B4_5593
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_679
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Pf1N1B4_2440
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 Pf1N1B4_2989 Pf1N1B4_4037
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf1N1B4_966 Pf1N1B4_4787
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_3903
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
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 Pf1N1B4_1816 Pf1N1B4_3987
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Pf1N1B4_4784 Pf1N1B4_3430
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Pf1N1B4_4583 Pf1N1B4_3853
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit Pf1N1B4_4199
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase Pf1N1B4_4202
ligK 4-oxalocitramalate aldolase Pf1N1B4_4203 Pf1N1B4_178
ligU 4-oxalomesaconate tautomerase Pf1N1B4_4204 Pf1N1B4_4463
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase Pf1N1B4_5694
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_4777
paaH 3-hydroxyadipyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
paaJ2 3-oxoadipyl-CoA thiolase Pf1N1B4_3234 Pf1N1B4_5835
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Pf1N1B4_5833
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Pf1N1B4_5834
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Pf1N1B4_371 Pf1N1B4_3234
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Pf1N1B4_5610 Pf1N1B4_966
pimF 6-carboxyhex-2-enoyl-CoA hydratase Pf1N1B4_3903 Pf1N1B4_1787
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Pf1N1B4_2417 Pf1N1B4_4355
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase Pf1N1B4_1055
xylF 2-hydroxymuconate semialdehyde hydrolase Pf1N1B4_4192

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 Aug 02 2021. The underlying query database was built on Aug 02 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