GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Cupriavidus basilensis 4G11

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 (56 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK RR42_RS21935 RR42_RS31660
pobA 4-hydroxybenzoate 3-monooxygenase RR42_RS21940
pcaH protocatechuate 3,4-dioxygenase, alpha subunit RR42_RS32060 RR42_RS32065
pcaG protocatechuate 3,4-dioxygenase, beta subunit RR42_RS32065 RR42_RS32060
pcaB 3-carboxymuconate cycloisomerase RR42_RS32055 RR42_RS25850
pcaC 4-carboxymuconolactone decarboxylase RR42_RS32050 RR42_RS10690
pcaD 3-oxoadipate enol-lactone hydrolase RR42_RS21850 RR42_RS32050
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) RR42_RS35925 RR42_RS10005
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) RR42_RS35920 RR42_RS10010
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase RR42_RS35915 RR42_RS26090
Alternative steps:
ackA acetate kinase RR42_RS03800 RR42_RS22745
acs acetyl-CoA synthetase, AMP-forming RR42_RS13880 RR42_RS10650
adh acetaldehyde dehydrogenase (not acylating) RR42_RS34255 RR42_RS25005
ald-dh-CoA acetaldehyde dehydrogenase, acylating RR42_RS27895 RR42_RS32630
atoB acetyl-CoA C-acetyltransferase RR42_RS07610 RR42_RS25455
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase RR42_RS23690 RR42_RS25125
badI 2-ketocyclohexanecarboxyl-CoA hydrolase RR42_RS23695 RR42_RS18250
badK cyclohex-1-ene-1-carboxyl-CoA hydratase RR42_RS23710 RR42_RS18250
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 RR42_RS03755 RR42_RS05535
bamI class II benzoyl-CoA reductase, BamI subunit RR42_RS05540
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 RR42_RS35120 RR42_RS07500
boxB benzoyl-CoA epoxidase, subunit B RR42_RS35125 RR42_RS07505
boxC 2,3-epoxybenzoyl-CoA dihydrolase RR42_RS07510 RR42_RS35130
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase RR42_RS35145
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) RR42_RS31950
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase RR42_RS00895 RR42_RS28565
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase RR42_RS28050 RR42_RS23710
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RR42_RS18250 RR42_RS23710
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1 RR42_RS24120
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2 RR42_RS24115
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 RR42_RS24110 RR42_RS09080
gcdH glutaryl-CoA dehydrogenase RR42_RS15400 RR42_RS28565
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase RR42_RS34260
hcl 4-hydroxybenzoyl-CoA ligase RR42_RS07520 RR42_RS35150
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit RR42_RS13630 RR42_RS02365
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit RR42_RS13620 RR42_RS02370
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 RR42_RS10620 RR42_RS23430
ligJ 4-carboxy-2-hydroxymuconate hydratase RR42_RS27205 RR42_RS28355
ligK 4-oxalocitramalate aldolase RR42_RS27210 RR42_RS12215
ligU 4-oxalomesaconate tautomerase RR42_RS23050 RR42_RS11275
mhpD 2-hydroxypentadienoate hydratase RR42_RS27885 RR42_RS32645
mhpE 4-hydroxy-2-oxovalerate aldolase RR42_RS27900 RR42_RS32625
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase RR42_RS11095
paaF 2,3-dehydroadipyl-CoA hydratase RR42_RS18250 RR42_RS23710
paaH 3-hydroxyadipyl-CoA dehydrogenase RR42_RS02510 RR42_RS36415
paaJ2 3-oxoadipyl-CoA thiolase RR42_RS35915 RR42_RS26090
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase RR42_RS25210 RR42_RS10260
pimC pimeloyl-CoA dehydrogenase, small subunit RR42_RS36390 RR42_RS36650
pimD pimeloyl-CoA dehydrogenase, large subunit RR42_RS05595 RR42_RS36645
pimF 6-carboxyhex-2-enoyl-CoA hydratase RR42_RS35270 RR42_RS11095
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase RR42_RS05110 RR42_RS32650
praC 2-hydroxymuconate tautomerase RR42_RS32635 RR42_RS15120
praD 2-oxohex-3-enedioate decarboxylase RR42_RS32640 RR42_RS32645
pta phosphate acetyltransferase RR42_RS33690 RR42_RS03805
xylF 2-hydroxymuconate semialdehyde hydrolase RR42_RS27870 RR42_RS31825

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