GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Marinobacter adhaerens HP15

Best path

pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta

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 (36 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
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase HP15_4032 HP15_1111
praC 2-hydroxymuconate tautomerase HP15_4038 HP15_1117
praD 2-oxohex-3-enedioate decarboxylase HP15_4037 HP15_1116
mhpD 2-hydroxypentadienoate hydratase HP15_4034 HP15_1113
mhpE 4-hydroxy-2-oxovalerate aldolase HP15_1115 HP15_4036
adh acetaldehyde dehydrogenase (not acylating) HP15_3144 HP15_3039
ackA acetate kinase HP15_1245 HP15_1499
pta phosphate acetyltransferase HP15_1498
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming HP15_811 HP15_2053
ald-dh-CoA acetaldehyde dehydrogenase, acylating HP15_4035 HP15_1114
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HP15_4143 HP15_2784
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HP15_4142
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HP15_12 HP15_2692
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 HP15_4173 HP15_1573
bamI class II benzoyl-CoA reductase, BamI subunit HP15_4174
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 HP15_2702
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase HP15_907 HP15_2
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HP15_908 HP15_4142
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HP15_908 HP15_12
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HP15_1512 HP15_3941
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 HP15_3918 HP15_3026
gcdH glutaryl-CoA dehydrogenase HP15_3936 HP15_2
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase HP15_923 HP15_3926
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit HP15_1257 HP15_1561
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 HP15_2228
ligU 4-oxalomesaconate tautomerase HP15_1929
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase HP15_12 HP15_908
paaH 3-hydroxyadipyl-CoA dehydrogenase HP15_1512 HP15_2693
paaJ2 3-oxoadipyl-CoA thiolase HP15_2695 HP15_5
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase HP15_2695 HP15_5
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase HP15_3943 HP15_1513
pimC pimeloyl-CoA dehydrogenase, small subunit HP15_3928
pimD pimeloyl-CoA dehydrogenase, large subunit HP15_3929 HP15_53
pimF 6-carboxyhex-2-enoyl-CoA hydratase HP15_3941 HP15_1512
xylF 2-hydroxymuconate semialdehyde hydrolase HP15_4033 HP15_1112

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