GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Pandoraea thiooxydans ATSB16

Best path

pcaK, hcl, hcrA, hcrB, hcrC, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2

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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
hcl 4-hydroxybenzoyl-CoA ligase PATSB16_RS09535 PATSB16_RS13320
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit PATSB16_RS01635
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit PATSB16_RS01630 PATSB16_RS09835
boxA benzoyl-CoA epoxidase, subunit A PATSB16_RS09505
boxB benzoyl-CoA epoxidase, subunit B PATSB16_RS09510
boxC 2,3-epoxybenzoyl-CoA dihydrolase PATSB16_RS09515
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase PATSB16_RS09530 PATSB16_RS19575
paaF 2,3-dehydroadipyl-CoA hydratase PATSB16_RS20735 PATSB16_RS06150
paaH 3-hydroxyadipyl-CoA dehydrogenase PATSB16_RS15750 PATSB16_RS16980
paaJ2 3-oxoadipyl-CoA thiolase PATSB16_RS11260 PATSB16_RS20725
Alternative steps:
ackA acetate kinase PATSB16_RS09135
acs acetyl-CoA synthetase, AMP-forming PATSB16_RS02175 PATSB16_RS15885
adh acetaldehyde dehydrogenase (not acylating) PATSB16_RS15895 PATSB16_RS16135
ald-dh-CoA acetaldehyde dehydrogenase, acylating PATSB16_RS14005
atoB acetyl-CoA C-acetyltransferase PATSB16_RS05650 PATSB16_RS05675
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PATSB16_RS13335 PATSB16_RS07890
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PATSB16_RS20735 PATSB16_RS17655
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PATSB16_RS20735 PATSB16_RS06150
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 PATSB16_RS09730 PATSB16_RS12250
bamI class II benzoyl-CoA reductase, BamI subunit PATSB16_RS12245
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) PATSB16_RS07805
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PATSB16_RS16800 PATSB16_RS16820
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PATSB16_RS20735 PATSB16_RS06150
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PATSB16_RS20735 PATSB16_RS06150
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PATSB16_RS15750 PATSB16_RS16980
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 PATSB16_RS01745 PATSB16_RS16800
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
ligA protocatechuate 4,5-dioxygenase, alpha subunit PATSB16_RS02565
ligB protocatechuate 4,5-dioxygenase, beta subunit PATSB16_RS02570
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase
ligI 2-pyrone-4,6-dicarboxylate hydrolase PATSB16_RS02560 PATSB16_RS17565
ligJ 4-carboxy-2-hydroxymuconate hydratase PATSB16_RS02550 PATSB16_RS17575
ligK 4-oxalocitramalate aldolase PATSB16_RS02555 PATSB16_RS17570
ligU 4-oxalomesaconate tautomerase PATSB16_RS17580 PATSB16_RS02545
mhpD 2-hydroxypentadienoate hydratase PATSB16_RS08690
mhpE 4-hydroxy-2-oxovalerate aldolase PATSB16_RS08695 PATSB16_RS02780
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PATSB16_RS20735
pcaB 3-carboxymuconate cycloisomerase PATSB16_RS03440 PATSB16_RS19025
pcaC 4-carboxymuconolactone decarboxylase PATSB16_RS01790 PATSB16_RS16190
pcaD 3-oxoadipate enol-lactone hydrolase PATSB16_RS01790
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PATSB16_RS11260 PATSB16_RS20725
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PATSB16_RS11255 PATSB16_RS12320
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PATSB16_RS11250 PATSB16_RS12315
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PATSB16_RS08225 PATSB16_RS15745
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit PATSB16_RS04665 PATSB16_RS20515
pimF 6-carboxyhex-2-enoyl-CoA hydratase PATSB16_RS08215
pobA 4-hydroxybenzoate 3-monooxygenase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PATSB16_RS08675 PATSB16_RS15895
praC 2-hydroxymuconate tautomerase PATSB16_RS12560
praD 2-oxohex-3-enedioate decarboxylase PATSB16_RS08690
pta phosphate acetyltransferase PATSB16_RS09130 PATSB16_RS13940
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.

Links

Downloads

Related tools

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