GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Xenophilus azovorans DSM 13620

Best path

pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs

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 (53 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK Q392_RS24240 Q392_RS02605
pobA 4-hydroxybenzoate 3-monooxygenase Q392_RS26760 Q392_RS15650
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Q392_RS08470 Q392_RS02760
praC 2-hydroxymuconate tautomerase Q392_RS02725 Q392_RS03825
praD 2-oxohex-3-enedioate decarboxylase Q392_RS03820 Q392_RS08495
mhpD 2-hydroxypentadienoate hydratase Q392_RS03805 Q392_RS02755
mhpE 4-hydroxy-2-oxovalerate aldolase Q392_RS03815 Q392_RS24255
adh acetaldehyde dehydrogenase (not acylating) Q392_RS11065 Q392_RS04025
acs acetyl-CoA synthetase, AMP-forming Q392_RS08265 Q392_RS22940
Alternative steps:
ackA acetate kinase Q392_RS16085 Q392_RS19465
ald-dh-CoA acetaldehyde dehydrogenase, acylating Q392_RS02740 Q392_RS08485
atoB acetyl-CoA C-acetyltransferase Q392_RS11095 Q392_RS22590
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Q392_RS13490 Q392_RS01930
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Q392_RS13495 Q392_RS01935
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Q392_RS17990 Q392_RS02545
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 Q392_RS16650 Q392_RS14130
bamI class II benzoyl-CoA reductase, BamI subunit Q392_RS16645
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 Q392_RS20125
boxB benzoyl-CoA epoxidase, subunit B Q392_RS20120
boxC 2,3-epoxybenzoyl-CoA dihydrolase Q392_RS20115
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase Q392_RS20100
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Q392_RS30240
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Q392_RS02180 Q392_RS27255
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Q392_RS02515 Q392_RS08845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q392_RS17990 Q392_RS02545
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
fcbT1 tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1
fcbT2 tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2 Q392_RS09630
fcbT3 tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3 Q392_RS00275 Q392_RS09635
gcdH glutaryl-CoA dehydrogenase Q392_RS20240 Q392_RS27255
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase Q392_RS20095 Q392_RS30335
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit Q392_RS06705 Q392_RS09700
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit Q392_RS30305
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit Q392_RS06715 Q392_RS29780
ligA protocatechuate 4,5-dioxygenase, alpha subunit Q392_RS13415 Q392_RS04085
ligB protocatechuate 4,5-dioxygenase, beta subunit Q392_RS13410 Q392_RS04080
ligC 2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase Q392_RS04075 Q392_RS13405
ligI 2-pyrone-4,6-dicarboxylate hydrolase Q392_RS04090 Q392_RS13420
ligJ 4-carboxy-2-hydroxymuconate hydratase Q392_RS13435 Q392_RS04100
ligK 4-oxalocitramalate aldolase Q392_RS04095 Q392_RS13430
ligU 4-oxalomesaconate tautomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase Q392_RS17990 Q392_RS02545
paaH 3-hydroxyadipyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
paaJ2 3-oxoadipyl-CoA thiolase Q392_RS19235 Q392_RS13480
pcaB 3-carboxymuconate cycloisomerase
pcaC 4-carboxymuconolactone decarboxylase Q392_RS08970 Q392_RS12085
pcaD 3-oxoadipate enol-lactone hydrolase Q392_RS23540
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Q392_RS19235 Q392_RS13480
pcaG protocatechuate 3,4-dioxygenase, beta subunit
pcaH protocatechuate 3,4-dioxygenase, alpha subunit
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Q392_RS29045 Q392_RS06750
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Q392_RS29040 Q392_RS06755
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Q392_RS27910 Q392_RS25275
pimC pimeloyl-CoA dehydrogenase, small subunit Q392_RS25265 Q392_RS11710
pimD pimeloyl-CoA dehydrogenase, large subunit Q392_RS25270 Q392_RS11705
pimF 6-carboxyhex-2-enoyl-CoA hydratase Q392_RS27900 Q392_RS25280
pta phosphate acetyltransferase Q392_RS16090 Q392_RS06055
xylF 2-hydroxymuconate semialdehyde hydrolase Q392_RS02780 Q392_RS08475

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