GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Photobacterium gaetbulicola Gung47

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 (31 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 H744_RS25800
ald-dh-CoA acetaldehyde dehydrogenase, acylating H744_RS15310 H744_RS20320
Alternative steps:
ackA acetate kinase H744_RS14130 H744_RS18405
acs acetyl-CoA synthetase, AMP-forming H744_RS09220 H744_RS02130
adh acetaldehyde dehydrogenase (not acylating) H744_RS15310 H744_RS11470
atoB acetyl-CoA C-acetyltransferase H744_RS02875 H744_RS04335
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase H744_RS22030 H744_RS06430
badI 2-ketocyclohexanecarboxyl-CoA hydrolase H744_RS19475
badK cyclohex-1-ene-1-carboxyl-CoA hydratase H744_RS04320 H744_RS10395
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 H744_RS04325 H744_RS04345
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase H744_RS04320
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase H744_RS10395 H744_RS04320
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase H744_RS10395 H744_RS14605
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
gcdH glutaryl-CoA dehydrogenase H744_RS04345 H744_RS04325
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase H744_RS18115 H744_RS15175
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit H744_RS21445
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit H744_RS21450 H744_RS21395
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 H744_RS25230 H744_RS11270
ligU 4-oxalomesaconate tautomerase H744_RS05680
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase H744_RS04320 H744_RS10395
paaH 3-hydroxyadipyl-CoA dehydrogenase H744_RS10395 H744_RS14605
paaJ2 3-oxoadipyl-CoA thiolase H744_RS06715 H744_RS02875
pcaB 3-carboxymuconate cycloisomerase H744_RS06730
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase H744_RS06715 H744_RS02875
pcaG protocatechuate 3,4-dioxygenase, beta subunit H744_RS07650
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) H744_RS02900
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) H744_RS02895
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase H744_RS10390 H744_RS02875
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase H744_RS10395 H744_RS14605
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase H744_RS01660 H744_RS06160
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase H744_RS14125 H744_RS20340

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