GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Phaeobacter inhibens BS107

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, 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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase PGA1_c02810
pcaH protocatechuate 3,4-dioxygenase, alpha subunit PGA1_c02550
pcaG protocatechuate 3,4-dioxygenase, beta subunit PGA1_c02560
pcaB 3-carboxymuconate cycloisomerase PGA1_c04560
pcaC 4-carboxymuconolactone decarboxylase PGA1_c02570 PGA1_c21140
pcaD 3-oxoadipate enol-lactone hydrolase PGA1_c04570
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PGA1_c06210
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PGA1_c06200
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PGA1_c04090 PGA1_c34350
Alternative steps:
ackA acetate kinase PGA1_c28840
acs acetyl-CoA synthetase, AMP-forming PGA1_c12950 PGA1_c11900
adh acetaldehyde dehydrogenase (not acylating) PGA1_c32800 PGA1_c29650
ald-dh-CoA acetaldehyde dehydrogenase, acylating PGA1_c19350
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PGA1_c17930 PGA1_c03390
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PGA1_262p01980 PGA1_c26820
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
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 PGA1_c10430 PGA1_c25750
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 PGA1_c26830 PGA1_262p00800
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PGA1_c10280 PGA1_c17340
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
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 PGA1_c12980
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase PGA1_c23440 PGA1_c34070
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit PGA1_c16220 PGA1_c20870
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PGA1_c20880 PGA1_c16210
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
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase PGA1_c32190
mhpE 4-hydroxy-2-oxovalerate aldolase PGA1_c31400 PGA1_c19370
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PGA1_c36500
paaF 2,3-dehydroadipyl-CoA hydratase PGA1_c36500 PGA1_262p01980
paaH 3-hydroxyadipyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
paaJ2 3-oxoadipyl-CoA thiolase PGA1_c04090 PGA1_c34350
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PGA1_c22730 PGA1_c04120
pimC pimeloyl-CoA dehydrogenase, small subunit PGA1_c04140
pimD pimeloyl-CoA dehydrogenase, large subunit PGA1_c04130 PGA1_c12060
pimF 6-carboxyhex-2-enoyl-CoA hydratase PGA1_c22740 PGA1_c04110
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PGA1_c32220 PGA1_c21670
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PGA1_c32190
pta phosphate acetyltransferase PGA1_c28850
xylF 2-hydroxymuconate semialdehyde hydrolase

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