GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Sinorhizobium fredii NGR234

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, 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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase NGR_RS05995
pcaH protocatechuate 3,4-dioxygenase, alpha subunit NGR_RS10180
pcaG protocatechuate 3,4-dioxygenase, beta subunit NGR_RS10185 NGR_RS10180
pcaB 3-carboxymuconate cycloisomerase NGR_RS10175 NGR_RS24325
pcaC 4-carboxymuconolactone decarboxylase NGR_RS10190 NGR_RS06900
pcaD 3-oxoadipate enol-lactone hydrolase NGR_RS10195 NGR_RS08195
catI 3-oxoadipate CoA-transferase subunit A (CatI) NGR_RS10280
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) NGR_RS10285
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase NGR_RS10290 NGR_RS27475
Alternative steps:
ackA acetate kinase NGR_RS06510
acs acetyl-CoA synthetase, AMP-forming NGR_RS27780 NGR_RS27800
adh acetaldehyde dehydrogenase (not acylating) NGR_RS06135 NGR_RS22740
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase NGR_RS27475 NGR_RS26100
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase NGR_RS14355 NGR_RS26200
badI 2-ketocyclohexanecarboxyl-CoA hydrolase NGR_RS29675 NGR_RS05550
badK cyclohex-1-ene-1-carboxyl-CoA hydratase NGR_RS29675 NGR_RS24180
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 NGR_RS22210 NGR_RS26580
bamI class II benzoyl-CoA reductase, BamI subunit NGR_RS22205
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 NGR_RS24200
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase NGR_RS10015 NGR_RS05525
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase NGR_RS29675 NGR_RS21990
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase NGR_RS29675 NGR_RS12210
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
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 NGR_RS14505
gcdH glutaryl-CoA dehydrogenase NGR_RS06370 NGR_RS05525
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase NGR_RS24520 NGR_RS14360
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit NGR_RS14300 NGR_RS26490
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit NGR_RS02330
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit NGR_RS14310 NGR_RS01010
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 NGR_RS24065
ligJ 4-carboxy-2-hydroxymuconate hydratase NGR_RS07815 NGR_RS07090
ligK 4-oxalocitramalate aldolase NGR_RS07045 NGR_RS07860
ligU 4-oxalomesaconate tautomerase NGR_RS02985
mhpD 2-hydroxypentadienoate hydratase NGR_RS09670 NGR_RS02865
mhpE 4-hydroxy-2-oxovalerate aldolase NGR_RS02860 NGR_RS09675
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase NGR_RS29675 NGR_RS24180
paaH 3-hydroxyadipyl-CoA dehydrogenase NGR_RS24175 NGR_RS12210
paaJ2 3-oxoadipyl-CoA thiolase NGR_RS10290 NGR_RS27475
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase NGR_RS13865 NGR_RS27475
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase NGR_RS24175 NGR_RS12210
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase NGR_RS09650 NGR_RS26215
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase NGR_RS02865 NGR_RS09670
pta phosphate acetyltransferase NGR_RS06505 NGR_RS11510
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 Apr 09 2024. 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