GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas simiae WCS417

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK PS417_06695 PS417_05030
pobA 4-hydroxybenzoate 3-monooxygenase PS417_07330
pcaH protocatechuate 3,4-dioxygenase, alpha subunit PS417_06720 PS417_06715
pcaG protocatechuate 3,4-dioxygenase, beta subunit PS417_06715 PS417_06720
pcaB 3-carboxymuconate cycloisomerase PS417_06730 PS417_11635
pcaC 4-carboxymuconolactone decarboxylase PS417_06740 PS417_04220
pcaD 3-oxoadipate enol-lactone hydrolase PS417_06735 PS417_06740 with PS417_20530
catI 3-oxoadipate CoA-transferase subunit A (CatI) PS417_06700
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PS417_06705
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PS417_06710 PS417_10515
Alternative steps:
ackA acetate kinase PS417_22945
acs acetyl-CoA synthetase, AMP-forming PS417_21750 PS417_23925
adh acetaldehyde dehydrogenase (not acylating) PS417_17430 PS417_24810
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PS417_11520 PS417_09065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PS417_13845 PS417_13835
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PS417_13845 PS417_10680
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PS417_26235
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 PS417_16595
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 PS417_13850 PS417_04135
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PS417_13845 PS417_07575
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
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 PS417_14900
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase PS417_10895 PS417_18255
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit PS417_24365
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PS417_13030 PS417_20885
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 PS417_21010 PS417_19020
ligU 4-oxalomesaconate tautomerase PS417_21065
mhpD 2-hydroxypentadienoate hydratase PS417_17860
mhpE 4-hydroxy-2-oxovalerate aldolase PS417_17865
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase PS417_13845 PS417_10680
paaH 3-hydroxyadipyl-CoA dehydrogenase PS417_07575 PS417_21215
paaJ2 3-oxoadipyl-CoA thiolase PS417_06710 PS417_10515
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PS417_10525
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PS417_10520
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PS417_19210 PS417_07580
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit PS417_14930
pimF 6-carboxyhex-2-enoyl-CoA hydratase PS417_07575 PS417_21215
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PS417_17840 PS417_26340
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PS417_17860
pta phosphate acetyltransferase PS417_03730
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