GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Marivita geojedonensis DPG-138

Best path

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

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 MGEO_RS04675 MGEO_RS15970
pcaH protocatechuate 3,4-dioxygenase, alpha subunit MGEO_RS15945 MGEO_RS15950
pcaG protocatechuate 3,4-dioxygenase, beta subunit MGEO_RS15950
pcaB 3-carboxymuconate cycloisomerase MGEO_RS15940 MGEO_RS16165
pcaC 4-carboxymuconolactone decarboxylase MGEO_RS15955 MGEO_RS04800
pcaD 3-oxoadipate enol-lactone hydrolase MGEO_RS08365 MGEO_RS15960
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) MGEO_RS03530 MGEO_RS07025
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) MGEO_RS03535 MGEO_RS07035
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase MGEO_RS17560 MGEO_RS09905
Alternative steps:
ackA acetate kinase MGEO_RS02500
acs acetyl-CoA synthetase, AMP-forming MGEO_RS21005 MGEO_RS10460
adh acetaldehyde dehydrogenase (not acylating) MGEO_RS02095 MGEO_RS02570
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase MGEO_RS09905 MGEO_RS17560
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase MGEO_RS02740 MGEO_RS09910
badI 2-ketocyclohexanecarboxyl-CoA hydrolase MGEO_RS17480 MGEO_RS05775
badK cyclohex-1-ene-1-carboxyl-CoA hydratase MGEO_RS17480 MGEO_RS11285
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 MGEO_RS05845 MGEO_RS15620
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 MGEO_RS06815
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase MGEO_RS05735 MGEO_RS13880
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase MGEO_RS17480 MGEO_RS14005
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MGEO_RS17480 MGEO_RS15835
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MGEO_RS15835 MGEO_RS14675
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1 MGEO_RS11895
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 MGEO_RS11885 MGEO_RS11995
gcdH glutaryl-CoA dehydrogenase MGEO_RS11945 MGEO_RS05735
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase MGEO_RS05745
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit MGEO_RS14085
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit MGEO_RS14090 MGEO_RS10380
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 MGEO_RS06765
ligK 4-oxalocitramalate aldolase MGEO_RS06770
ligU 4-oxalomesaconate tautomerase MGEO_RS06775
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase MGEO_RS00820 MGEO_RS04965
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase MGEO_RS17480 MGEO_RS14005
paaH 3-hydroxyadipyl-CoA dehydrogenase MGEO_RS15835 MGEO_RS14675
paaJ2 3-oxoadipyl-CoA thiolase MGEO_RS17560 MGEO_RS09905
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase MGEO_RS15830 MGEO_RS09905
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase MGEO_RS15835
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase MGEO_RS07470 MGEO_RS17260
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase MGEO_RS02495
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 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