GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pseudomonas putida KT2440

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF

Also see fitness data for the top candidates

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK PP_1376 PP_3165
pobA 4-hydroxybenzoate 3-monooxygenase PP_3537
pcaH protocatechuate 3,4-dioxygenase, alpha subunit PP_4655 PP_4656
pcaG protocatechuate 3,4-dioxygenase, beta subunit PP_4656
pcaB 3-carboxymuconate cycloisomerase PP_1379
pcaC 4-carboxymuconolactone decarboxylase PP_1381 PP_3648
pcaD 3-oxoadipate enol-lactone hydrolase PP_1380 PP_4540
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PP_3951 PP_3122
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PP_3952 PP_3123
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PP_1377 PP_3280
Alternative steps:
ackA acetate kinase PP_1457
acs acetyl-CoA synthetase, AMP-forming PP_4487 PP_4702
adh acetaldehyde dehydrogenase (not acylating) PP_2680 PP_0545
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PP_1946 PP_1852
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PP_3283 PP_2217
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PP_2217 PP_3284
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PP_0311
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 PP_2184 PP_4123
bamI class II benzoyl-CoA reductase, BamI subunit PP_2185
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 PP_3270 PP_0708
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PP_2216 PP_4064
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PP_2217 PP_3284
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
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 PP_0158 PP_4064
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase PP_2213 PP_4549
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit PP_3309
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PP_3308 PP_3947
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit PP_2518
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase PP_1699
ligJ 4-carboxy-2-hydroxymuconate hydratase PP_2515
ligK 4-oxalocitramalate aldolase PP_2514 PP_4462
ligU 4-oxalomesaconate tautomerase PP_2513 PP_2055
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase PP_1791
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PP_2217
paaF 2,3-dehydroadipyl-CoA hydratase PP_3284 PP_2217
paaH 3-hydroxyadipyl-CoA dehydrogenase PP_2136 PP_3282
paaJ2 3-oxoadipyl-CoA thiolase PP_1377 PP_3280
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PP_2051 PP_2137
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase PP_2136 PP_2047
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PP_2487 PP_5063
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase PP_0774
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 Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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