GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Rhizobium grahamii CCGE 502

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase RGCCGE502_RS28020
pcaH protocatechuate 3,4-dioxygenase, alpha subunit RGCCGE502_RS27985
pcaG protocatechuate 3,4-dioxygenase, beta subunit RGCCGE502_RS27990 RGCCGE502_RS15085
pcaB 3-carboxymuconate cycloisomerase RGCCGE502_RS27980 RGCCGE502_RS10390
pcaC 4-carboxymuconolactone decarboxylase RGCCGE502_RS27995 RGCCGE502_RS30975
pcaD 3-oxoadipate enol-lactone hydrolase RGCCGE502_RS28000 RGCCGE502_RS30980
catI 3-oxoadipate CoA-transferase subunit A (CatI) RGCCGE502_RS28035
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) RGCCGE502_RS28040
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase RGCCGE502_RS27680 RGCCGE502_RS28045
Alternative steps:
ackA acetate kinase RGCCGE502_RS11645
acs acetyl-CoA synthetase, AMP-forming RGCCGE502_RS24205 RGCCGE502_RS24215
adh acetaldehyde dehydrogenase (not acylating) RGCCGE502_RS23535 RGCCGE502_RS00735
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase RGCCGE502_RS33960 RGCCGE502_RS23710
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase RGCCGE502_RS23705 RGCCGE502_RS31680
badI 2-ketocyclohexanecarboxyl-CoA hydrolase RGCCGE502_RS01905 RGCCGE502_RS23980
badK cyclohex-1-ene-1-carboxyl-CoA hydratase RGCCGE502_RS01905 RGCCGE502_RS31710
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 RGCCGE502_RS19355
bamH class II benzoyl-CoA reductase, BamH subunit RGCCGE502_RS19360 RGCCGE502_RS22795
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 RGCCGE502_RS27645
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase RGCCGE502_RS27030 RGCCGE502_RS24000
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase RGCCGE502_RS01905 RGCCGE502_RS27610
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RGCCGE502_RS01905 RGCCGE502_RS31710
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RGCCGE502_RS31710 RGCCGE502_RS27610
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 RGCCGE502_RS25205
gcdH glutaryl-CoA dehydrogenase RGCCGE502_RS31695 RGCCGE502_RS28240
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase RGCCGE502_RS21975 RGCCGE502_RS02470
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit RGCCGE502_RS32875 RGCCGE502_RS03805
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit RGCCGE502_RS26525 RGCCGE502_RS19680
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit RGCCGE502_RS32880 RGCCGE502_RS22735
ligA protocatechuate 4,5-dioxygenase, alpha subunit
ligB protocatechuate 4,5-dioxygenase, beta subunit
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase RGCCGE502_RS12680
ligI 2-pyrone-4,6-dicarboxylate hydrolase
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase RGCCGE502_RS33030 RGCCGE502_RS15670
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase RGCCGE502_RS29460 RGCCGE502_RS31565
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase RGCCGE502_RS01905 RGCCGE502_RS31710
paaH 3-hydroxyadipyl-CoA dehydrogenase RGCCGE502_RS31710 RGCCGE502_RS27610
paaJ2 3-oxoadipyl-CoA thiolase RGCCGE502_RS27680 RGCCGE502_RS28045
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) RGCCGE502_RS33970
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) RGCCGE502_RS33965
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase RGCCGE502_RS20895 RGCCGE502_RS33960
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase RGCCGE502_RS27610 RGCCGE502_RS31710
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase RGCCGE502_RS11775 RGCCGE502_RS05285
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase RGCCGE502_RS02115 RGCCGE502_RS10690
xylF 2-hydroxymuconate semialdehyde hydrolase RGCCGE502_RS08825 RGCCGE502_RS25775

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