GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Geobacter lovleyi SZ

Best path

pcaK, pobA, praA, xylF, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK GLOV_RS04610
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
adh acetaldehyde dehydrogenase (not acylating) GLOV_RS08400 GLOV_RS13735
ackA acetate kinase GLOV_RS08705 GLOV_RS02085
pta phosphate acetyltransferase GLOV_RS05950 GLOV_RS06215
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming GLOV_RS16915 GLOV_RS06850
ald-dh-CoA acetaldehyde dehydrogenase, acylating GLOV_RS14220
atoB acetyl-CoA C-acetyltransferase
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase GLOV_RS09625 GLOV_RS10875
badI 2-ketocyclohexanecarboxyl-CoA hydrolase GLOV_RS14360
badK cyclohex-1-ene-1-carboxyl-CoA hydratase GLOV_RS14360
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit GLOV_RS02765
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit GLOV_RS04255
bamG class II benzoyl-CoA reductase, BamG subunit GLOV_RS15495
bamH class II benzoyl-CoA reductase, BamH subunit GLOV_RS15490 GLOV_RS13835
bamI class II benzoyl-CoA reductase, BamI subunit GLOV_RS15485 GLOV_RS03220
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit GLOV_RS11895 GLOV_RS00435
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit GLOV_RS11905
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit GLOV_RS00435 GLOV_RS11895
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 GLOV_RS14360
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GLOV_RS14360
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GLOV_RS11935 GLOV_RS09625
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 GLOV_RS14850
hcl 4-hydroxybenzoyl-CoA ligase GLOV_RS11885
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit GLOV_RS12050
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit GLOV_RS11970
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
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase GLOV_RS14360
paaH 3-hydroxyadipyl-CoA dehydrogenase GLOV_RS11935 GLOV_RS09625
paaJ2 3-oxoadipyl-CoA thiolase
pcaB 3-carboxymuconate cycloisomerase GLOV_RS13345
pcaC 4-carboxymuconolactone decarboxylase GLOV_RS04935
pcaD 3-oxoadipate enol-lactone hydrolase GLOV_RS04935
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase GLOV_RS13735 GLOV_RS08400
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase

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