GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Flavobacterium glycines Gm-149

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
pcaK 4-hydroxybenzoate transporter pcaK
pobA 4-hydroxybenzoate 3-monooxygenase BLR17_RS09295
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BLR17_RS09310 BLR17_RS09315
pcaG protocatechuate 3,4-dioxygenase, beta subunit BLR17_RS09315
pcaB 3-carboxymuconate cycloisomerase BLR17_RS09305
pcaC 4-carboxymuconolactone decarboxylase BLR17_RS09300 BLR17_RS09065
pcaD 3-oxoadipate enol-lactone hydrolase BLR17_RS09300
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BLR17_RS02660 BLR17_RS09290
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BLR17_RS09290 BLR17_RS02655
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BLR17_RS09285 BLR17_RS15680
Alternative steps:
ackA acetate kinase BLR17_RS10645 BLR17_RS05725
acs acetyl-CoA synthetase, AMP-forming BLR17_RS00555 BLR17_RS13780
adh acetaldehyde dehydrogenase (not acylating) BLR17_RS03500
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoB acetyl-CoA C-acetyltransferase BLR17_RS08645 BLR17_RS15680
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLR17_RS09410 BLR17_RS09120
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BLR17_RS15000 BLR17_RS02485
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLR17_RS02485
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BLR17_RS14460
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 BLR17_RS01425
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
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BLR17_RS11710 BLR17_RS06975
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLR17_RS02485
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLR17_RS02485 BLR17_RS04170
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLR17_RS15685 BLR17_RS09950
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 BLR17_RS01000 BLR17_RS11710
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit
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
ligJ 4-carboxy-2-hydroxymuconate hydratase
ligK 4-oxalocitramalate aldolase
ligU 4-oxalomesaconate tautomerase
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase BLR17_RS02485
paaH 3-hydroxyadipyl-CoA dehydrogenase BLR17_RS15685 BLR17_RS09950
paaJ2 3-oxoadipyl-CoA thiolase BLR17_RS09285 BLR17_RS15680
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BLR17_RS15680 BLR17_RS09285
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BLR17_RS03500
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase BLR17_RS10650 BLR17_RS09275
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.

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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