GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Herbaspirillum aquaticum IEH 4430

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, 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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK CEJ45_RS07610 CEJ45_RS21550
pobA 4-hydroxybenzoate 3-monooxygenase CEJ45_RS16110
pcaH protocatechuate 3,4-dioxygenase, alpha subunit CEJ45_RS16095
pcaG protocatechuate 3,4-dioxygenase, beta subunit CEJ45_RS16095
pcaB 3-carboxymuconate cycloisomerase CEJ45_RS16085
pcaC 4-carboxymuconolactone decarboxylase CEJ45_RS16080 CEJ45_RS21340
pcaD 3-oxoadipate enol-lactone hydrolase CEJ45_RS21340 CEJ45_RS16080
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) CEJ45_RS16020 CEJ45_RS12845
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) CEJ45_RS16025 CEJ45_RS12850
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase CEJ45_RS16030 CEJ45_RS20030
Alternative steps:
ackA acetate kinase CEJ45_RS14515 CEJ45_RS03830
acs acetyl-CoA synthetase, AMP-forming CEJ45_RS19345 CEJ45_RS12485
adh acetaldehyde dehydrogenase (not acylating) CEJ45_RS12165 CEJ45_RS06185
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase CEJ45_RS14415 CEJ45_RS09425
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CEJ45_RS11695 CEJ45_RS09675
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CEJ45_RS16530 CEJ45_RS00250
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CEJ45_RS16530 CEJ45_RS20050
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 CEJ45_RS23980
bamH class II benzoyl-CoA reductase, BamH subunit CEJ45_RS23985 CEJ45_RS05500
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 CEJ45_RS20095
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CEJ45_RS06405 CEJ45_RS12595
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CEJ45_RS06410 CEJ45_RS16530
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEJ45_RS16530 CEJ45_RS06410
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEJ45_RS14455 CEJ45_RS11470
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 CEJ45_RS01835 CEJ45_RS11705
gcdH glutaryl-CoA dehydrogenase CEJ45_RS11500 CEJ45_RS12595
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase CEJ45_RS14175
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit CEJ45_RS09995 CEJ45_RS18930
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit CEJ45_RS21545 CEJ45_RS18705
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase CEJ45_RS18735 CEJ45_RS18765
ligJ 4-carboxy-2-hydroxymuconate hydratase CEJ45_RS21565
ligK 4-oxalocitramalate aldolase CEJ45_RS21570 CEJ45_RS03340
ligU 4-oxalomesaconate tautomerase CEJ45_RS21560 CEJ45_RS04210
mhpD 2-hydroxypentadienoate hydratase CEJ45_RS01895
mhpE 4-hydroxy-2-oxovalerate aldolase CEJ45_RS14805
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase CEJ45_RS16530 CEJ45_RS06410
paaH 3-hydroxyadipyl-CoA dehydrogenase CEJ45_RS14455 CEJ45_RS11470
paaJ2 3-oxoadipyl-CoA thiolase CEJ45_RS20030 CEJ45_RS16030
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CEJ45_RS11475 CEJ45_RS14460
pimC pimeloyl-CoA dehydrogenase, small subunit CEJ45_RS11485
pimD pimeloyl-CoA dehydrogenase, large subunit CEJ45_RS11480 CEJ45_RS01415
pimF 6-carboxyhex-2-enoyl-CoA hydratase CEJ45_RS11470
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase CEJ45_RS06185 CEJ45_RS01340
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase CEJ45_RS14510 CEJ45_RS09385
xylF 2-hydroxymuconate semialdehyde hydrolase CEJ45_RS05220

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