GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas stutzeri RCH2

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK Psest_2695
pobA 4-hydroxybenzoate 3-monooxygenase
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Psest_3069 Psest_1394
pcaD 3-oxoadipate enol-lactone hydrolase Psest_3069
catI 3-oxoadipate CoA-transferase subunit A (CatI) Psest_3072
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Psest_3071
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Psest_3070 Psest_1076
Alternative steps:
ackA acetate kinase Psest_3137 Psest_3213
acs acetyl-CoA synthetase, AMP-forming Psest_2657 Psest_2220
adh acetaldehyde dehydrogenase (not acylating) Psest_2276 Psest_0671
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Psest_2358 Psest_1147
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Psest_2437
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Psest_2437 Psest_3109
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
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 Psest_1084 Psest_2445
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Psest_2437 Psest_3109
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
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 Psest_1072 Psest_0361
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Psest_2220 Psest_2657
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit Psest_3445
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Psest_3446 Psest_1211
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 Psest_2315
ligU 4-oxalomesaconate tautomerase Psest_2318
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase Psest_1056
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Psest_2437 Psest_3109
paaH 3-hydroxyadipyl-CoA dehydrogenase Psest_2654 Psest_3800
paaJ2 3-oxoadipyl-CoA thiolase Psest_3070 Psest_1076
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Psest_1078
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Psest_1077
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Psest_1829 Psest_3070
pimC pimeloyl-CoA dehydrogenase, small subunit Psest_4233
pimD pimeloyl-CoA dehydrogenase, large subunit Psest_4234 Psest_2669
pimF 6-carboxyhex-2-enoyl-CoA hydratase Psest_4235 Psest_2654
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Psest_0905 Psest_2634
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase Psest_3214
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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