GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Mesorhizobium ciceri WSM1271

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF

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 Mesci_5210
pcaH protocatechuate 3,4-dioxygenase, alpha subunit Mesci_5212
pcaG protocatechuate 3,4-dioxygenase, beta subunit Mesci_5213 Mesci_5212
pcaB 3-carboxymuconate cycloisomerase Mesci_5211 Mesci_4348
pcaC 4-carboxymuconolactone decarboxylase Mesci_5214 Mesci_6253
pcaD 3-oxoadipate enol-lactone hydrolase Mesci_5215 Mesci_2298
catI 3-oxoadipate CoA-transferase subunit A (CatI) Mesci_1093
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Mesci_1094
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Mesci_1095 Mesci_1329
Alternative steps:
ackA acetate kinase Mesci_3747
acs acetyl-CoA synthetase, AMP-forming Mesci_1162 Mesci_0223
adh acetaldehyde dehydrogenase (not acylating) Mesci_0701 Mesci_5289
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Mesci_2838 Mesci_2477
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Mesci_6037 Mesci_4665
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Mesci_6037 Mesci_4665
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 Mesci_0140 Mesci_3289
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 Mesci_3403 Mesci_4845
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Mesci_6037 Mesci_1071
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Mesci_6037 Mesci_4665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Mesci_1071 Mesci_6001
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 Mesci_1983 Mesci_4845
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Mesci_3963
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit Mesci_2831 Mesci_0582
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit Mesci_3779 Mesci_2890
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Mesci_2832 Mesci_3039
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase Mesci_2062
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase Mesci_6234
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase Mesci_0681
mhpE 4-hydroxy-2-oxovalerate aldolase Mesci_2590 Mesci_0112
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Mesci_6037 Mesci_4665
paaH 3-hydroxyadipyl-CoA dehydrogenase Mesci_1071 Mesci_6001
paaJ2 3-oxoadipyl-CoA thiolase Mesci_1095 Mesci_1329
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Mesci_1329 Mesci_1095
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Mesci_6214 Mesci_6003
pimF 6-carboxyhex-2-enoyl-CoA hydratase Mesci_1071 Mesci_6001
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Mesci_0678 Mesci_2633
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase Mesci_0681
pta phosphate acetyltransferase Mesci_0182 Mesci_4113
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 24 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:

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