GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pantoea rwandensis LMG 26275

Best path

pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK HA51_RS09065 HA51_RS13285
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase HA51_RS23475 HA51_RS01965
praC 2-hydroxymuconate tautomerase HA51_RS26870
praD 2-oxohex-3-enedioate decarboxylase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase HA51_RS20315
adh acetaldehyde dehydrogenase (not acylating) HA51_RS23475 HA51_RS08520
ackA acetate kinase HA51_RS11240 HA51_RS10465
pta phosphate acetyltransferase HA51_RS11235 HA51_RS26220
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming
ald-dh-CoA acetaldehyde dehydrogenase, acylating HA51_RS08520
atoB acetyl-CoA C-acetyltransferase HA51_RS19810 HA51_RS26555
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HA51_RS14510 HA51_RS03820
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HA51_RS05000
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HA51_RS04965 HA51_RS11045
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 HA51_RS11290
bamH class II benzoyl-CoA reductase, BamH subunit HA51_RS11295
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HA51_RS08785
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HA51_RS26560 HA51_RS11045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HA51_RS26560 HA51_RS11045
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
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase HA51_RS10660
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit HA51_RS01575 HA51_RS13115
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 HA51_RS13275
ligK 4-oxalocitramalate aldolase HA51_RS13270 HA51_RS16105
ligU 4-oxalomesaconate tautomerase HA51_RS13265
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase HA51_RS04965 HA51_RS26560
paaH 3-hydroxyadipyl-CoA dehydrogenase HA51_RS26560 HA51_RS11045
paaJ2 3-oxoadipyl-CoA thiolase HA51_RS19810 HA51_RS26555
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase HA51_RS03295
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase HA51_RS19810 HA51_RS26555
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) HA51_RS19820
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) HA51_RS19815
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase HA51_RS26555 HA51_RS19810
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase HA51_RS26560 HA51_RS11045
xylF 2-hydroxymuconate semialdehyde hydrolase HA51_RS22045

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