GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Sedimenticola selenatireducens DSM 17993

Best path

pcaK, hcl, hcrA, hcrB, hcrC, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2

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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
hcl 4-hydroxybenzoyl-CoA ligase A3GO_RS0109310 A3GO_RS24835
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit A3GO_RS0111500
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit A3GO_RS0111505
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit A3GO_RS0111495
boxA benzoyl-CoA epoxidase, subunit A A3GO_RS0113935
boxB benzoyl-CoA epoxidase, subunit B A3GO_RS0118600
boxC 2,3-epoxybenzoyl-CoA dihydrolase A3GO_RS0118595
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase A3GO_RS0115405
paaF 2,3-dehydroadipyl-CoA hydratase A3GO_RS0115400 A3GO_RS0104130
paaH 3-hydroxyadipyl-CoA dehydrogenase A3GO_RS0115390 A3GO_RS0108695
paaJ2 3-oxoadipyl-CoA thiolase A3GO_RS0115675 A3GO_RS0115385
Alternative steps:
ackA acetate kinase A3GO_RS0105460
acs acetyl-CoA synthetase, AMP-forming A3GO_RS0111360 A3GO_RS0103965
adh acetaldehyde dehydrogenase (not acylating) A3GO_RS0105360 A3GO_RS0115130
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase A3GO_RS0108835 A3GO_RS0107785
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase A3GO_RS0104110 A3GO_RS0109385
badI 2-ketocyclohexanecarboxyl-CoA hydrolase A3GO_RS0109460 A3GO_RS0105700
badK cyclohex-1-ene-1-carboxyl-CoA hydratase A3GO_RS0104130 A3GO_RS0115400
bamB class II benzoyl-CoA reductase, BamB subunit A3GO_RS0107855
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 A3GO_RS0120600 A3GO_RS0108155
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit A3GO_RS0115785
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit A3GO_RS0115780
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit A3GO_RS0115775
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit A3GO_RS0115790 A3GO_RS0115785
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase A3GO_RS0114370 A3GO_RS0114380
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase A3GO_RS0115770 A3GO_RS0114405
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3GO_RS0114405 A3GO_RS0115400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3GO_RS0108695 A3GO_RS0114400
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 A3GO_RS0112650 A3GO_RS0106065
gcdH glutaryl-CoA dehydrogenase A3GO_RS0115815 A3GO_RS0114380
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase A3GO_RS0115760
ligA protocatechuate 4,5-dioxygenase, alpha subunit A3GO_RS0100130
ligB protocatechuate 4,5-dioxygenase, beta subunit A3GO_RS0100135
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase A3GO_RS0100165
ligI 2-pyrone-4,6-dicarboxylate hydrolase A3GO_RS0100140
ligJ 4-carboxy-2-hydroxymuconate hydratase A3GO_RS0100155
ligK 4-oxalocitramalate aldolase A3GO_RS0100150 A3GO_RS0109305
ligU 4-oxalomesaconate tautomerase A3GO_RS0100145
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase A3GO_RS0115765
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase A3GO_RS0115675 A3GO_RS0115385
pcaG protocatechuate 3,4-dioxygenase, beta subunit A3GO_RS0107195
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 A3GO_RS0108690 A3GO_RS0107785
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
pobA 4-hydroxybenzoate 3-monooxygenase A3GO_RS0100110
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase A3GO_RS0117140 A3GO_RS0120300
praC 2-hydroxymuconate tautomerase A3GO_RS0109480 A3GO_RS0104085
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase A3GO_RS0105465 A3GO_RS0103715
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 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