GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Neptunomonas antarctica S3-22

Best path

pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase Nant_RS05500
ligA protocatechuate 4,5-dioxygenase, alpha subunit Nant_RS05575
ligB protocatechuate 4,5-dioxygenase, beta subunit Nant_RS05580
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase Nant_RS05545
ligI 2-pyrone-4,6-dicarboxylate hydrolase Nant_RS05570
ligU 4-oxalomesaconate tautomerase Nant_RS05565 Nant_RS14680
ligJ 4-carboxy-2-hydroxymuconate hydratase Nant_RS05555
ligK 4-oxalocitramalate aldolase Nant_RS05560 Nant_RS07385
Alternative steps:
ackA acetate kinase Nant_RS12275 Nant_RS06470
acs acetyl-CoA synthetase, AMP-forming Nant_RS18305 Nant_RS13480
adh acetaldehyde dehydrogenase (not acylating) Nant_RS14835 Nant_RS20560
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Nant_RS07655 Nant_RS01890
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Nant_RS04420 Nant_RS13915
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Nant_RS13960 Nant_RS07340
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Nant_RS13960 Nant_RS07340
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Nant_RS02090
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 Nant_RS13315
bamI class II benzoyl-CoA reductase, BamI subunit Nant_RS13320
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 Nant_RS12630 Nant_RS12590
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Nant_RS13960 Nant_RS07340
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Nant_RS13960 Nant_RS07340
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Nant_RS08070 Nant_RS07350
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 Nant_RS08540 Nant_RS07145
gcdH glutaryl-CoA dehydrogenase Nant_RS10235 Nant_RS12630
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Nant_RS12580 Nant_RS06930
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Nant_RS05640
mhpD 2-hydroxypentadienoate hydratase Nant_RS05460
mhpE 4-hydroxy-2-oxovalerate aldolase Nant_RS05465 Nant_RS18565
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Nant_RS07340 Nant_RS13960
paaH 3-hydroxyadipyl-CoA dehydrogenase Nant_RS08070 Nant_RS07350
paaJ2 3-oxoadipyl-CoA thiolase Nant_RS07360 Nant_RS07655
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Nant_RS02905 Nant_RS09100
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Nant_RS07360 Nant_RS07655
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Nant_RS07520 Nant_RS03905
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Nant_RS07525 Nant_RS03910
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Nant_RS01890 Nant_RS08065
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Nant_RS20195
pimF 6-carboxyhex-2-enoyl-CoA hydratase Nant_RS08070
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Nant_RS05445 Nant_RS19705
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase Nant_RS05460
pta phosphate acetyltransferase Nant_RS06465
xylF 2-hydroxymuconate semialdehyde hydrolase

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