GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas benzenivorans DSM 8628

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF

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 (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK BLS63_RS16805 BLS63_RS16340
pobA 4-hydroxybenzoate 3-monooxygenase BLS63_RS16865
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BLS63_RS16845 BLS63_RS16850
pcaG protocatechuate 3,4-dioxygenase, beta subunit BLS63_RS16850 BLS63_RS11020
pcaB 3-carboxymuconate cycloisomerase BLS63_RS16760
pcaC 4-carboxymuconolactone decarboxylase BLS63_RS16750 BLS63_RS22460
pcaD 3-oxoadipate enol-lactone hydrolase BLS63_RS16755 BLS63_RS15525
catI 3-oxoadipate CoA-transferase subunit A (CatI) BLS63_RS16775
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) BLS63_RS16770
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BLS63_RS16765 BLS63_RS22810
Alternative steps:
ackA acetate kinase BLS63_RS09000 BLS63_RS21520
acs acetyl-CoA synthetase, AMP-forming BLS63_RS26090 BLS63_RS23690
adh acetaldehyde dehydrogenase (not acylating) BLS63_RS17270 BLS63_RS19270
ald-dh-CoA acetaldehyde dehydrogenase, acylating BLS63_RS02455 BLS63_RS17010
atoB acetyl-CoA C-acetyltransferase BLS63_RS22810 BLS63_RS21120
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLS63_RS06695 BLS63_RS22805
badI 2-ketocyclohexanecarboxyl-CoA hydrolase
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLS63_RS21705 BLS63_RS21395
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BLS63_RS25245
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit BLS63_RS10705
bamH class II benzoyl-CoA reductase, BamH subunit BLS63_RS10700 BLS63_RS01490
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BLS63_RS26370 BLS63_RS24295
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLS63_RS21705 BLS63_RS06660
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLS63_RS21705 BLS63_RS07890
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2 BLS63_RS12870
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 BLS63_RS12865 BLS63_RS18720
gcdH glutaryl-CoA dehydrogenase BLS63_RS14585 BLS63_RS24330
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BLS63_RS02720 BLS63_RS09790
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit BLS63_RS06640
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BLS63_RS06650 BLS63_RS20940
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 BLS63_RS14170
ligK 4-oxalocitramalate aldolase BLS63_RS14180 BLS63_RS09840
ligU 4-oxalomesaconate tautomerase BLS63_RS13860 BLS63_RS00680
mhpD 2-hydroxypentadienoate hydratase BLS63_RS10105 BLS63_RS02460
mhpE 4-hydroxy-2-oxovalerate aldolase BLS63_RS10115 BLS63_RS17015
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase BLS63_RS18235 BLS63_RS21705
paaH 3-hydroxyadipyl-CoA dehydrogenase BLS63_RS07890 BLS63_RS21115
paaJ2 3-oxoadipyl-CoA thiolase BLS63_RS16765 BLS63_RS22810
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BLS63_RS21205 BLS63_RS25510
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BLS63_RS21195 BLS63_RS25505
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BLS63_RS24670 BLS63_RS12420
pimC pimeloyl-CoA dehydrogenase, small subunit BLS63_RS21710 BLS63_RS07275
pimD pimeloyl-CoA dehydrogenase, large subunit BLS63_RS17700
pimF 6-carboxyhex-2-enoyl-CoA hydratase BLS63_RS10750 BLS63_RS07890
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BLS63_RS10095 BLS63_RS02470
praC 2-hydroxymuconate tautomerase BLS63_RS02440 BLS63_RS10125
praD 2-oxohex-3-enedioate decarboxylase BLS63_RS02445 BLS63_RS10120
pta phosphate acetyltransferase BLS63_RS21525
xylF 2-hydroxymuconate semialdehyde hydrolase BLS63_RS02465 BLS63_RS10100

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