GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Salinicoccus carnicancri Crm

Best path

pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta

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 (29 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 C792_RS0112465 C792_RS0112210
mhpD 2-hydroxypentadienoate hydratase C792_RS0112435 C792_RS0112125
mhpE 4-hydroxy-2-oxovalerate aldolase C792_RS0112230
adh acetaldehyde dehydrogenase (not acylating) C792_RS0112615 C792_RS0110425
ackA acetate kinase C792_RS0108790
pta phosphate acetyltransferase C792_RS0113240 C792_RS0107710
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming C792_RS0109060 C792_RS0110000
ald-dh-CoA acetaldehyde dehydrogenase, acylating C792_RS0112235
atoB acetyl-CoA C-acetyltransferase C792_RS0112545 C792_RS0109325
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase C792_RS0110710 C792_RS0100470
badI 2-ketocyclohexanecarboxyl-CoA hydrolase C792_RS14900
badK cyclohex-1-ene-1-carboxyl-CoA hydratase C792_RS0109005 C792_RS0108985
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
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)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase C792_RS0109005 C792_RS0108985
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase C792_RS0109005 C792_RS0108985
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase C792_RS0109330 C792_RS0108990
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 C792_RS0112135
gcdH glutaryl-CoA dehydrogenase C792_RS0109335
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
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 C792_RS0110855
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase C792_RS14900
paaF 2,3-dehydroadipyl-CoA hydratase C792_RS0109005 C792_RS0108985
paaH 3-hydroxyadipyl-CoA dehydrogenase C792_RS0109330 C792_RS0108990
paaJ2 3-oxoadipyl-CoA thiolase C792_RS0113105 C792_RS0112545
pcaB 3-carboxymuconate cycloisomerase C792_RS0110215
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase C792_RS0113105 C792_RS0112545
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) C792_RS0112540
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) C792_RS0112535
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase C792_RS0113105 C792_RS0109325
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase C792_RS0112325 C792_RS0108995
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase C792_RS0112435

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