GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Streptacidiphilus oryzae TH49

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 (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK BS73_RS06270
pobA 4-hydroxybenzoate 3-monooxygenase BS73_RS09990 BS73_RS10270
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BS73_RS10010 BS73_RS10015
pcaG protocatechuate 3,4-dioxygenase, beta subunit BS73_RS10015
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase BS73_RS09995 BS73_RS15110
pcaD 3-oxoadipate enol-lactone hydrolase BS73_RS09995 BS73_RS15110
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BS73_RS10025
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BS73_RS10020
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BS73_RS12600 BS73_RS30630
Alternative steps:
ackA acetate kinase BS73_RS15005
acs acetyl-CoA synthetase, AMP-forming BS73_RS20690 BS73_RS01530
adh acetaldehyde dehydrogenase (not acylating) BS73_RS04090 BS73_RS01745
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase BS73_RS10365 BS73_RS08675
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BS73_RS03225 BS73_RS09090
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BS73_RS32220 BS73_RS07070
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BS73_RS14910 BS73_RS05650
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BS73_RS19015
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit BS73_RS32425
bamH class II benzoyl-CoA reductase, BamH subunit BS73_RS32420 BS73_RS21765
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 BS73_RS07420
boxC 2,3-epoxybenzoyl-CoA dihydrolase BS73_RS07415
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) BS73_RS10355
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BS73_RS23895 BS73_RS08225
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BS73_RS00915 BS73_RS14910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BS73_RS14910 BS73_RS05650
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BS73_RS08975 BS73_RS07230
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 BS73_RS32915 BS73_RS25270
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BS73_RS00385 BS73_RS27680
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit BS73_RS29680 BS73_RS33760
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit BS73_RS05105 BS73_RS06285
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BS73_RS24330 BS73_RS08345
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase BS73_RS09795 BS73_RS01145
ligI 2-pyrone-4,6-dicarboxylate hydrolase BS73_RS27585
ligJ 4-carboxy-2-hydroxymuconate hydratase BS73_RS27580 BS73_RS32535
ligK 4-oxalocitramalate aldolase BS73_RS32540 BS73_RS31825
ligU 4-oxalomesaconate tautomerase BS73_RS31830 BS73_RS10825
mhpD 2-hydroxypentadienoate hydratase BS73_RS04080 BS73_RS37045
mhpE 4-hydroxy-2-oxovalerate aldolase BS73_RS11375
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BS73_RS32220
paaF 2,3-dehydroadipyl-CoA hydratase BS73_RS14910 BS73_RS20300
paaH 3-hydroxyadipyl-CoA dehydrogenase BS73_RS08975 BS73_RS07230
paaJ2 3-oxoadipyl-CoA thiolase BS73_RS30630 BS73_RS12600
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BS73_RS15085 BS73_RS30630
pimC pimeloyl-CoA dehydrogenase, small subunit BS73_RS07080 BS73_RS00880
pimD pimeloyl-CoA dehydrogenase, large subunit BS73_RS07085 BS73_RS33675
pimF 6-carboxyhex-2-enoyl-CoA hydratase BS73_RS06375 BS73_RS32280
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BS73_RS01225 BS73_RS23595
praC 2-hydroxymuconate tautomerase BS73_RS17890 BS73_RS04070
praD 2-oxohex-3-enedioate decarboxylase BS73_RS04080 BS73_RS37045
pta phosphate acetyltransferase
xylF 2-hydroxymuconate semialdehyde hydrolase BS73_RS00370

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