GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Azospirillum brasilense Sp245

Best path

pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK AZOBR_RS26920
pobA 4-hydroxybenzoate 3-monooxygenase
ligA protocatechuate 4,5-dioxygenase, alpha subunit AZOBR_RS26890
ligB protocatechuate 4,5-dioxygenase, beta subunit AZOBR_RS26885
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase AZOBR_RS26915 AZOBR_RS29845
ligI 2-pyrone-4,6-dicarboxylate hydrolase AZOBR_RS26895
ligU 4-oxalomesaconate tautomerase AZOBR_RS26900 AZOBR_RS28105
ligJ 4-carboxy-2-hydroxymuconate hydratase AZOBR_RS26910
ligK 4-oxalocitramalate aldolase AZOBR_RS26905 AZOBR_RS25265
Alternative steps:
ackA acetate kinase AZOBR_RS12495 AZOBR_RS04605
acs acetyl-CoA synthetase, AMP-forming AZOBR_RS00270 AZOBR_RS06340
adh acetaldehyde dehydrogenase (not acylating) AZOBR_RS22315 AZOBR_RS26825
ald-dh-CoA acetaldehyde dehydrogenase, acylating AZOBR_RS32240 AZOBR_RS32475
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AZOBR_RS24695 AZOBR_RS25545
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AZOBR_RS18155 AZOBR_RS26485
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AZOBR_RS01260 AZOBR_RS26485
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 AZOBR_RS14955 AZOBR_RS31940
bamI class II benzoyl-CoA reductase, BamI subunit AZOBR_RS14960
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AZOBR_RS22300 AZOBR_RS22365
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AZOBR_RS26485 AZOBR_RS01260
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AZOBR_RS01260 AZOBR_RS26485
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
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 AZOBR_RS14700 AZOBR_RS20015
gcdH glutaryl-CoA dehydrogenase AZOBR_RS19670 AZOBR_RS22310
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase AZOBR_RS21705 AZOBR_RS19780
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit AZOBR_RS08560 AZOBR_RS29690
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit AZOBR_RS27480 AZOBR_RS20525
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit AZOBR_RS08565 AZOBR_RS29700
mhpD 2-hydroxypentadienoate hydratase AZOBR_RS15705
mhpE 4-hydroxy-2-oxovalerate aldolase AZOBR_RS05495
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase AZOBR_RS18155
paaF 2,3-dehydroadipyl-CoA hydratase AZOBR_RS01260 AZOBR_RS26485
paaH 3-hydroxyadipyl-CoA dehydrogenase AZOBR_RS20225 AZOBR_RS29225
paaJ2 3-oxoadipyl-CoA thiolase AZOBR_RS30610 AZOBR_RS20220
pcaB 3-carboxymuconate cycloisomerase AZOBR_RS28125 AZOBR_RS04385
pcaC 4-carboxymuconolactone decarboxylase AZOBR_RS05920 AZOBR_RS26370
pcaD 3-oxoadipate enol-lactone hydrolase AZOBR_RS26370 AZOBR_RS05920
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AZOBR_RS30610 AZOBR_RS20220
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 AZOBR_RS20220 AZOBR_RS30610
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AZOBR_RS29205 AZOBR_RS17455
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AZOBR_RS19635 AZOBR_RS26825
praC 2-hydroxymuconate tautomerase AZOBR_RS18455
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase AZOBR_RS04600 AZOBR_RS12500
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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