GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Sinorhizobium meliloti 1021

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase SM_b20583
pcaH protocatechuate 3,4-dioxygenase, alpha subunit SM_b20576
pcaG protocatechuate 3,4-dioxygenase, beta subunit SM_b20577 SM_b20576
pcaB 3-carboxymuconate cycloisomerase SM_b20575 SMc00508
pcaC 4-carboxymuconolactone decarboxylase SM_b20578 SMc04308
pcaD 3-oxoadipate enol-lactone hydrolase SM_b20579 SMc04308
catI 3-oxoadipate CoA-transferase subunit A (CatI) SM_b20587
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) SM_b20588
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase SM_b20589 SMc03879
Alternative steps:
ackA acetate kinase SM_b21184
acs acetyl-CoA synthetase, AMP-forming SMc04093 SMc04095
adh acetaldehyde dehydrogenase (not acylating) SM_b21301 SM_b21539
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SMc03878 SMc00268
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SMc01669 SMc01153
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SMc01153 SM_b21633
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 SMa1525 SMc02525
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 SM_b21635
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase SMa1400 SM_b21121
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SMc01153 SMc01669
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
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 SMa0151 SM_b20035
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit SMa2037 SM_b20132
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit SM_b20396 SM_b21338
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit SM_b20131 SMa5011
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase SMc02870
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase SMc00503
ligK 4-oxalocitramalate aldolase SMc00502
ligU 4-oxalomesaconate tautomerase SMc00497
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase SMc02778 SMc02546
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase SMc01153 SMc01669
paaH 3-hydroxyadipyl-CoA dehydrogenase SMc02227 SMc00727
paaJ2 3-oxoadipyl-CoA thiolase SM_b20589 SMc03879
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase SM_b20589 SMc03879
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase SM_b21632 SMc02227
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase SMa2213 SMc02689
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase SM_b21532 SMc01126
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