GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Aquimarina macrocephali JAMB N27

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 (29 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 Z054_RS0105015 Z054_RS0121900
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase Z054_RS0121885
mhpD 2-hydroxypentadienoate hydratase Z054_RS0121885
mhpE 4-hydroxy-2-oxovalerate aldolase Z054_RS0121890
adh acetaldehyde dehydrogenase (not acylating) Z054_RS0109000 Z054_RS0110935
ackA acetate kinase Z054_RS0124325
pta phosphate acetyltransferase Z054_RS0124320 Z054_RS0118930
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming Z054_RS0124460
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase Z054_RS0106210 Z054_RS0115825
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Z054_RS0106690 Z054_RS0120995
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Z054_RS0106490 Z054_RS0108580
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Z054_RS0105210
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 Z054_RS0106365
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 Z054_RS0124770
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Z054_RS0106865 Z054_RS0108580
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0112885
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 Z054_RS0123520 Z054_RS0121070
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Z054_RS0105510
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
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
paaH 3-hydroxyadipyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0124785
paaJ2 3-oxoadipyl-CoA thiolase Z054_RS0124775 Z054_RS0115825
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Z054_RS0124775 Z054_RS0115825
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Z054_RS0108630
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Z054_RS0108615
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Z054_RS0115825 Z054_RS0124775
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Z054_RS0124785
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