GapMind for catabolism of small carbon sources


4-hydroxybenzoate catabolism in Klebsiella michiganensis M5al

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 BWI76_RS26970 BWI76_RS06435
pobA 4-hydroxybenzoate 3-monooxygenase BWI76_RS04020
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BWI76_RS13285
pcaG protocatechuate 3,4-dioxygenase, beta subunit BWI76_RS13290 BWI76_RS13285
pcaB 3-carboxymuconate cycloisomerase BWI76_RS16130
pcaC 4-carboxymuconolactone decarboxylase BWI76_RS16120 BWI76_RS14810
pcaD 3-oxoadipate enol-lactone hydrolase BWI76_RS16125
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BWI76_RS16145
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BWI76_RS16140
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BWI76_RS13135 BWI76_RS16135
Alternative steps:
ackA acetate kinase BWI76_RS20235 BWI76_RS23200
acs acetyl-CoA synthetase, AMP-forming BWI76_RS02095 BWI76_RS17800
adh acetaldehyde dehydrogenase (not acylating) BWI76_RS21985 BWI76_RS15205
ald-dh-CoA acetaldehyde dehydrogenase, acylating BWI76_RS17250 BWI76_RS20790
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BWI76_RS11090 BWI76_RS23705
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BWI76_RS20065
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BWI76_RS13115 BWI76_RS13120
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
bamH class II benzoyl-CoA reductase, BamH subunit BWI76_RS20170
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit BWI76_RS03740
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit BWI76_RS03740
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 BWI76_RS13085
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 BWI76_RS13115
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
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 BWI76_RS17800
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BWI76_RS17570
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit BWI76_RS14200
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase BWI76_RS14190
ligK 4-oxalocitramalate aldolase BWI76_RS14185 BWI76_RS00740
ligU 4-oxalomesaconate tautomerase BWI76_RS14180 BWI76_RS04370
mhpD 2-hydroxypentadienoate hydratase BWI76_RS16910 BWI76_RS03850
mhpE 4-hydroxy-2-oxovalerate aldolase BWI76_RS16900 BWI76_RS19980
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BWI76_RS20065
paaF 2,3-dehydroadipyl-CoA hydratase BWI76_RS13115 BWI76_RS13120
paaH 3-hydroxyadipyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
paaJ2 3-oxoadipyl-CoA thiolase BWI76_RS16135 BWI76_RS13135
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BWI76_RS13135 BWI76_RS16135
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase BWI76_RS01365 BWI76_RS20455
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BWI76_RS03865 BWI76_RS07615
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase BWI76_RS03850 BWI76_RS16910
pta phosphate acetyltransferase BWI76_RS20240 BWI76_RS20805
xylF 2-hydroxymuconate semialdehyde hydrolase BWI76_RS16915

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