GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Herbaspirillum seropedicae SmR1

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF

Also see fitness data for the top candidates


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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK HSERO_RS05600 HSERO_RS06575
pobA 4-hydroxybenzoate 3-monooxygenase HSERO_RS19905
pcaH protocatechuate 3,4-dioxygenase, alpha subunit HSERO_RS19925 HSERO_RS19920
pcaG protocatechuate 3,4-dioxygenase, beta subunit HSERO_RS19920
pcaB 3-carboxymuconate cycloisomerase HSERO_RS19930
pcaC 4-carboxymuconolactone decarboxylase HSERO_RS19935 HSERO_RS06525
pcaD 3-oxoadipate enol-lactone hydrolase HSERO_RS06525 HSERO_RS19935
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) HSERO_RS20000 HSERO_RS23190
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) HSERO_RS19995 HSERO_RS23185
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase HSERO_RS19990 HSERO_RS20660
Alternative steps:
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HSERO_RS05565 HSERO_RS02535
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HSERO_RS19405 HSERO_RS18840
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HSERO_RS19405 HSERO_RS20665
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 HSERO_RS07420
bamH class II benzoyl-CoA reductase, BamH subunit HSERO_RS07425 HSERO_RS08845
bamI class II benzoyl-CoA reductase, BamI subunit HSERO_RS08850
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 HSERO_RS20590
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase HSERO_RS04640 HSERO_RS12750
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HSERO_RS19405 HSERO_RS12745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS04630
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 HSERO_RS13470 HSERO_RS05555
gcdH glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase HSERO_RS00095 HSERO_RS04625
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit HSERO_RS06620 HSERO_RS16320
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase HSERO_RS12100
ligI 2-pyrone-4,6-dicarboxylate hydrolase HSERO_RS22245 HSERO_RS22275
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase HSERO_RS10555 HSERO_RS22295
ligU 4-oxalomesaconate tautomerase HSERO_RS11420
mhpD 2-hydroxypentadienoate hydratase HSERO_RS16775 HSERO_RS13395
mhpE 4-hydroxy-2-oxovalerate aldolase HSERO_RS01600 HSERO_RS14210
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase HSERO_RS19405 HSERO_RS20665
paaH 3-hydroxyadipyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS20645
paaJ2 3-oxoadipyl-CoA thiolase HSERO_RS20660 HSERO_RS19990
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase HSERO_RS01265 HSERO_RS01180
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit HSERO_RS14055
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase HSERO_RS09465 HSERO_RS19755
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300
xylF 2-hydroxymuconate semialdehyde hydrolase HSERO_RS08570

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 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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