GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Dinoroseobacter shibae DFL-12

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase Dshi_3479
pcaH protocatechuate 3,4-dioxygenase, alpha subunit Dshi_3476
pcaG protocatechuate 3,4-dioxygenase, beta subunit Dshi_3477 Dshi_3476
pcaB 3-carboxymuconate cycloisomerase Dshi_3474
pcaC 4-carboxymuconolactone decarboxylase Dshi_3478 Dshi_1007
pcaD 3-oxoadipate enol-lactone hydrolase Dshi_1007
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Dshi_1136
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Dshi_1134
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Dshi_3817 Dshi_3331
Alternative steps:
ackA acetate kinase Dshi_0632 Dshi_5006
acs acetyl-CoA synthetase, AMP-forming Dshi_3553 Dshi_1399
adh acetaldehyde dehydrogenase (not acylating) Dshi_3017 Dshi_1095
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Dshi_2182 Dshi_3067
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Dshi_3370 Dshi_1304
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Dshi_3370 Dshi_3723
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 Dshi_1313
bamH class II benzoyl-CoA reductase, BamH subunit Dshi_1316 Dshi_1281
bamI class II benzoyl-CoA reductase, BamI subunit Dshi_1282
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 Dshi_3827
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Dshi_1297 Dshi_0838
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Dshi_3370 Dshi_3723
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Dshi_3370 Dshi_0835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Dshi_3826 Dshi_0835
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1 Dshi_0697 Dshi_1043
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 Dshi_1041 Dshi_0699
gcdH glutaryl-CoA dehydrogenase Dshi_2357 Dshi_1297
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase Dshi_1078
hcl 4-hydroxybenzoyl-CoA ligase Dshi_1556 Dshi_2999
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit Dshi_2659 Dshi_3719
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Dshi_2660 Dshi_1211
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 Dshi_0604 Dshi_0867
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase Dshi_1647 Dshi_3145
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Dshi_3370 Dshi_1048
paaH 3-hydroxyadipyl-CoA dehydrogenase Dshi_3826 Dshi_0835
paaJ2 3-oxoadipyl-CoA thiolase Dshi_3817 Dshi_3331
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Dshi_3817 Dshi_3331
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Dshi_0838
pimF 6-carboxyhex-2-enoyl-CoA hydratase Dshi_3826
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Dshi_1095 Dshi_3017
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase Dshi_1825 Dshi_0633
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, 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