GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas litoralis 2SM5

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 (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
adh acetaldehyde dehydrogenase (not acylating) BLU11_RS01865 BLU11_RS14925
ackA acetate kinase BLU11_RS01770 BLU11_RS12900
pta phosphate acetyltransferase BLU11_RS12905
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BLU11_RS00320 BLU11_RS01910
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase BLU11_RS15740 BLU11_RS15515
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLU11_RS08870 BLU11_RS12680
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BLU11_RS12290 BLU11_RS17725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLU11_RS12290 BLU11_RS15435
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) BLU11_RS14180
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) BLU11_RS14175
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BLU11_RS15705 BLU11_RS02525
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLU11_RS12290 BLU11_RS02050
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLU11_RS12290 BLU11_RS02050
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLU11_RS06160 BLU11_RS15910
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 BLU11_RS09895
gcdH glutaryl-CoA dehydrogenase BLU11_RS13665 BLU11_RS12305
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 BLU11_RS08235
ligU 4-oxalomesaconate tautomerase BLU11_RS05830
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase BLU11_RS12290 BLU11_RS15435
paaH 3-hydroxyadipyl-CoA dehydrogenase BLU11_RS06160 BLU11_RS15865
paaJ2 3-oxoadipyl-CoA thiolase BLU11_RS14170 BLU11_RS15870
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase BLU11_RS15575
pcaD 3-oxoadipate enol-lactone hydrolase BLU11_RS14120
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BLU11_RS15870 BLU11_RS14170
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BLU11_RS15730 BLU11_RS15505
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BLU11_RS15735 BLU11_RS15510
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BLU11_RS04500 BLU11_RS14170
pimC pimeloyl-CoA dehydrogenase, small subunit BLU11_RS15920
pimD pimeloyl-CoA dehydrogenase, large subunit BLU11_RS15915 BLU11_RS15115
pimF 6-carboxyhex-2-enoyl-CoA hydratase BLU11_RS15910 BLU11_RS06160
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BLU11_RS01865 BLU11_RS14925
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase

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