GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Nocardioides daejeonensis MJ31

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase DNK54_RS01780 DNK54_RS20170
mhpD 2-hydroxypentadienoate hydratase DNK54_RS16745
mhpE 4-hydroxy-2-oxovalerate aldolase DNK54_RS02760 DNK54_RS05865
adh acetaldehyde dehydrogenase (not acylating) DNK54_RS10870 DNK54_RS07665
acs acetyl-CoA synthetase, AMP-forming DNK54_RS14895 DNK54_RS12540
Alternative steps:
ackA acetate kinase
ald-dh-CoA acetaldehyde dehydrogenase, acylating DNK54_RS02755
atoB acetyl-CoA C-acetyltransferase DNK54_RS13705 DNK54_RS12220
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase DNK54_RS06790 DNK54_RS03880
badI 2-ketocyclohexanecarboxyl-CoA hydrolase DNK54_RS14555 DNK54_RS13680
badK cyclohex-1-ene-1-carboxyl-CoA hydratase DNK54_RS00105 DNK54_RS19555
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit DNK54_RS10730
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 DNK54_RS10940
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) DNK54_RS05155
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase DNK54_RS19595 DNK54_RS20105
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase DNK54_RS18345 DNK54_RS06420
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase DNK54_RS00105 DNK54_RS12945
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase DNK54_RS19600 DNK54_RS12225
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 DNK54_RS13625
gcdH glutaryl-CoA dehydrogenase DNK54_RS12090 DNK54_RS20105
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase DNK54_RS20110 DNK54_RS20210
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit DNK54_RS12175 DNK54_RS17005
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit DNK54_RS12180
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit DNK54_RS08415 DNK54_RS18825
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 DNK54_RS13680
paaF 2,3-dehydroadipyl-CoA hydratase DNK54_RS00105 DNK54_RS19555
paaH 3-hydroxyadipyl-CoA dehydrogenase DNK54_RS19600 DNK54_RS12225
paaJ2 3-oxoadipyl-CoA thiolase DNK54_RS09450 DNK54_RS09790
pcaB 3-carboxymuconate cycloisomerase DNK54_RS11290
pcaC* 4-carboxymuconolactone decarboxylase DNK54_RS09795 with DNK54_RS16605
pcaD 3-oxoadipate enol-lactone hydrolase DNK54_RS09795
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase DNK54_RS09450 DNK54_RS09790
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) DNK54_RS09445 DNK54_RS16900
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) DNK54_RS09440 DNK54_RS16905
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase DNK54_RS09790 DNK54_RS08955
pimC pimeloyl-CoA dehydrogenase, small subunit DNK54_RS08750 DNK54_RS10005
pimD pimeloyl-CoA dehydrogenase, large subunit DNK54_RS08745 DNK54_RS02820
pimF 6-carboxyhex-2-enoyl-CoA hydratase DNK54_RS14955
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase DNK54_RS17595 DNK54_RS07665
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase DNK54_RS16745
pta phosphate acetyltransferase

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