GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism in Burkholderia phytofirmans PsJN

Best path

pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF

Also see fitness data for the top candidates

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 BPHYT_RS30250 BPHYT_RS03795
pobA 4-hydroxybenzoate 3-monooxygenase BPHYT_RS11060
pcaH protocatechuate 3,4-dioxygenase, alpha subunit BPHYT_RS33460 BPHYT_RS33455
pcaG protocatechuate 3,4-dioxygenase, beta subunit BPHYT_RS33455
pcaB 3-carboxymuconate cycloisomerase BPHYT_RS21425 BPHYT_RS14615
pcaC 4-carboxymuconolactone decarboxylase BPHYT_RS21435 BPHYT_RS21430
pcaD 3-oxoadipate enol-lactone hydrolase BPHYT_RS21430 BPHYT_RS02320
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BPHYT_RS21415 BPHYT_RS13675
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BPHYT_RS21420 BPHYT_RS13670
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BPHYT_RS29385 BPHYT_RS17345
Alternative steps:
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BPHYT_RS30440 BPHYT_RS04770
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BPHYT_RS28620 BPHYT_RS17335
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BPHYT_RS17335 BPHYT_RS17350
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BPHYT_RS25200
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 BPHYT_RS06650 BPHYT_RS14990
bamI class II benzoyl-CoA reductase, BamI subunit BPHYT_RS14995 BPHYT_RS06655
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 BPHYT_RS13335
boxB benzoyl-CoA epoxidase, subunit B BPHYT_RS13340
boxC 2,3-epoxybenzoyl-CoA dihydrolase BPHYT_RS13345
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase BPHYT_RS13360
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase BPHYT_RS20780 BPHYT_RS28040
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BPHYT_RS17335 BPHYT_RS10815
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BPHYT_RS17335 BPHYT_RS28020
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
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 BPHYT_RS30450
gcdH glutaryl-CoA dehydrogenase BPHYT_RS03780 BPHYT_RS23260
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hcl 4-hydroxybenzoyl-CoA ligase BPHYT_RS13365 BPHYT_RS35445
hcrA 4-hydroxybenzoyl-CoA reductase, alpha subunit BPHYT_RS01765 BPHYT_RS10835
hcrB 4-hydroxybenzoyl-CoA reductase, beta subunit BPHYT_RS29710 BPHYT_RS20915
hcrC 4-hydroxybenzoyl-CoA reductase, gamma subunit BPHYT_RS01770 BPHYT_RS10825
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 BPHYT_RS35395 BPHYT_RS00910
ligJ 4-carboxy-2-hydroxymuconate hydratase BPHYT_RS30325
ligK 4-oxalocitramalate aldolase BPHYT_RS12315 BPHYT_RS30330
ligU 4-oxalomesaconate tautomerase BPHYT_RS30140
mhpD 2-hydroxypentadienoate hydratase BPHYT_RS07240 BPHYT_RS28900
mhpE 4-hydroxy-2-oxovalerate aldolase BPHYT_RS07250 BPHYT_RS28905
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaF 2,3-dehydroadipyl-CoA hydratase BPHYT_RS17335 BPHYT_RS25360
paaH 3-hydroxyadipyl-CoA dehydrogenase BPHYT_RS13545 BPHYT_RS03225
paaJ2 3-oxoadipyl-CoA thiolase BPHYT_RS17345 BPHYT_RS29385
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BPHYT_RS09565 BPHYT_RS03230
pimC pimeloyl-CoA dehydrogenase, small subunit BPHYT_RS13555 BPHYT_RS25385
pimD pimeloyl-CoA dehydrogenase, large subunit BPHYT_RS06715 BPHYT_RS13550
pimF 6-carboxyhex-2-enoyl-CoA hydratase BPHYT_RS09560 BPHYT_RS13545
praA protocatechuate 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BPHYT_RS07235 BPHYT_RS28885
praC 2-hydroxymuconate tautomerase BPHYT_RS24200 BPHYT_RS10700
praD 2-oxohex-3-enedioate decarboxylase BPHYT_RS07255 BPHYT_RS28900
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
xylF 2-hydroxymuconate semialdehyde hydrolase BPHYT_RS23610

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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