GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Desulfacinum infernum DSM 9756

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA

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 (38 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
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase BUB04_RS14925 BUB04_RS10320
ald-dh-CoA acetaldehyde dehydrogenase, acylating BUB04_RS17530
Alternative steps:
ackA acetate kinase BUB04_RS16485 BUB04_RS17570
acs acetyl-CoA synthetase, AMP-forming BUB04_RS16450 BUB04_RS12655
adh acetaldehyde dehydrogenase (not acylating) BUB04_RS17530 BUB04_RS04110
atoB acetyl-CoA C-acetyltransferase BUB04_RS03720 BUB04_RS00235
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BUB04_RS01135 BUB04_RS18395
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BUB04_RS01125 BUB04_RS03725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
bamB class II benzoyl-CoA reductase, BamB subunit BUB04_RS05725 BUB04_RS08160
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BUB04_RS11540
bamE class II benzoyl-CoA reductase, BamE subunit BUB04_RS05165 BUB04_RS20045
bamF class II benzoyl-CoA reductase, BamF subunit BUB04_RS05160 BUB04_RS15995
bamG class II benzoyl-CoA reductase, BamG subunit BUB04_RS10395 BUB04_RS09275
bamH class II benzoyl-CoA reductase, BamH subunit BUB04_RS10400 BUB04_RS09280
bamI class II benzoyl-CoA reductase, BamI subunit BUB04_RS10465 BUB04_RS05180
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit BUB04_RS07265
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit BUB04_RS07265
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 BUB04_RS12135 BUB04_RS03730
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BUB04_RS03725 BUB04_RS07705
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BUB04_RS17405 BUB04_RS00230
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 BUB04_RS15590 BUB04_RS06920
gcdH glutaryl-CoA dehydrogenase BUB04_RS03730 BUB04_RS05240
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BUB04_RS07990
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit
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 BUB04_RS05990
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BUB04_RS01125
paaF 2,3-dehydroadipyl-CoA hydratase BUB04_RS03725 BUB04_RS07705
paaH 3-hydroxyadipyl-CoA dehydrogenase BUB04_RS17405 BUB04_RS00230
paaJ2 3-oxoadipyl-CoA thiolase BUB04_RS03720 BUB04_RS17410
pcaB 3-carboxymuconate cycloisomerase BUB04_RS12330
pcaC 4-carboxymuconolactone decarboxylase BUB04_RS14940
pcaD 3-oxoadipate enol-lactone hydrolase BUB04_RS09605
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BUB04_RS03720 BUB04_RS17410
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 BUB04_RS03720 BUB04_RS00235
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase BUB04_RS16430
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BUB04_RS04110 BUB04_RS05780
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase BUB04_RS17565

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 Apr 09 2024. 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