GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Marinobacter guineae M3B

Best path

pcaK, pobA, praA, praB, praC, praD, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase CLH62_RS03080
praA protocatechuate 2,3-dioxygenase CLH62_RS03075
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase CLH62_RS09600 CLH62_RS09710
praC 2-hydroxymuconate tautomerase CLH62_RS09570 CLH62_RS09695
praD 2-oxohex-3-enedioate decarboxylase CLH62_RS09575 CLH62_RS09700
mhpD 2-hydroxypentadienoate hydratase CLH62_RS09590 CLH62_RS09705
mhpE 4-hydroxy-2-oxovalerate aldolase CLH62_RS09580 CLH62_RS09685
adh acetaldehyde dehydrogenase (not acylating) CLH62_RS14090 CLH62_RS07755
ackA acetate kinase CLH62_RS14355 CLH62_RS18460
pta phosphate acetyltransferase CLH62_RS18455
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming CLH62_RS16445 CLH62_RS02220
ald-dh-CoA acetaldehyde dehydrogenase, acylating CLH62_RS09585 CLH62_RS09690
atoB acetyl-CoA C-acetyltransferase CLH62_RS07455 CLH62_RS15420
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CLH62_RS11700 CLH62_RS00510
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CLH62_RS11695 CLH62_RS05465
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CLH62_RS05465 CLH62_RS00910
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 CLH62_RS10835 CLH62_RS00205
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 CLH62_RS05515 CLH62_RS10190
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CLH62_RS15975 CLH62_RS15440
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CLH62_RS15970 CLH62_RS00910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLH62_RS15970 CLH62_RS10205
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS10205
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 CLH62_RS10300 CLH62_RS07690
gcdH glutaryl-CoA dehydrogenase CLH62_RS10225 CLH62_RS15440
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase CLH62_RS15945
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit CLH62_RS20055 CLH62_RS00130
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 CLH62_RS03210
ligU 4-oxalomesaconate tautomerase CLH62_RS01910
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase CLH62_RS15970 CLH62_RS05465
paaH 3-hydroxyadipyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS05470
paaJ2 3-oxoadipyl-CoA thiolase CLH62_RS05480 CLH62_RS07455
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase CLH62_RS05480 CLH62_RS07455
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) CLH62_RS11885 CLH62_RS15680
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) CLH62_RS15675 CLH62_RS11890
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CLH62_RS10200 CLH62_RS18535
pimC pimeloyl-CoA dehydrogenase, small subunit CLH62_RS10235
pimD pimeloyl-CoA dehydrogenase, large subunit CLH62_RS10230 CLH62_RS04855
pimF 6-carboxyhex-2-enoyl-CoA hydratase CLH62_RS10205 CLH62_RS18530
xylF 2-hydroxymuconate semialdehyde hydrolase CLH62_RS09595

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