GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase CA265_RS12370
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
adh acetaldehyde dehydrogenase (not acylating) CA265_RS19780 CA265_RS21385
ackA acetate kinase CA265_RS10080
pta phosphate acetyltransferase CA265_RS10075 CA265_RS19000
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming CA265_RS16340
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase CA265_RS06590 CA265_RS17585
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CA265_RS08355 CA265_RS15450
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CA265_RS20005 CA265_RS09125
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CA265_RS20005 CA265_RS09125
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit CA265_RS02450
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 CA265_RS23555
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CA265_RS22715 CA265_RS02820
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CA265_RS20005
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CA265_RS20005 CA265_RS09125
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CA265_RS17590 CA265_RS07715
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 CA265_RS09630 CA265_RS14465
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase CA265_RS16340
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit CA265_RS09865
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit CA265_RS09870 CA265_RS00480
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 CA265_RS13680
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase CA265_RS20005 CA265_RS09125
paaH 3-hydroxyadipyl-CoA dehydrogenase CA265_RS17590 CA265_RS07715
paaJ2 3-oxoadipyl-CoA thiolase CA265_RS17585 CA265_RS06590
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase CA265_RS17585 CA265_RS06590
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) CA265_RS06305
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) CA265_RS06310
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CA265_RS17585 CA265_RS06590
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase CA265_RS14635 CA265_RS24850
praC 2-hydroxymuconate tautomerase CA265_RS13720
praD 2-oxohex-3-enedioate decarboxylase

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