Definition of 4-hydroxybenzoate catabolism

GapMind for catabolism of small carbon sources

Definition of 4-hydroxybenzoate catabolism

# 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, metacyc:PHENOLDEG-PWY)

pcaK	4-hydroxybenzoate transporter pcaK	curated:SwissProt::Q43975	curated:SwissProt::Q51955

# Transporters were identified using:
# query: transporter:4-hydroxybenzoate:p-hydroxybenzoate:4-hydroxybenzoic acid:p-hydroxybenzoic acid
4-hydroxybenzoate-transport: pcaK

# The primary substrate for this system is 4-chlorobenzoate, but TCDB
# reports that binding of that substrate to fcbT1 is inhibited by 1 mM
# 4-hydroxybenzoate, suggesting a reasonable affinity for
# 4-hydroxybenzoate as well.
fcbT1	tripartite 4-hydroxybenzoate transporter, substrate-binding component FcbT1	curated:TCDB::Q9RBR1
fcbT2	tripartite 4-hydroxybenzoate transporter, small DctQ-like component FcbT2	curated:TCDB::Q9RBR0
fcbT3	tripartite 4-hydroxybenzoate transporter, large permease subunit FcbT3	curated:TCDB::Q9RBQ9
4-hydroxybenzoate-transport: fcbT1 fcbT2 fcbT3

# Ignore efflux pumps such as aaeB (distantly related to Pf6N2E2_2879).
# Putative NodT/MFP/FUSC type efflux systems are important for utilization --
#	but it is not clear if these are involved in efflux or uptake, so they are also ignored.

# 3-oxoadipate is an intermediate in the ortho-cleavage pathway

# Ignore EC:2.8.3.5, 3-oxoacid CoA-transferase, usually active on shorter substrates but who knows?
pcaI	3-oxoadipate CoA-transferase subunit A (PcaI)	curated:CharProtDB::CH_021928	ignore_other:2.8.3.6	ignore_other:2.8.3.5

pcaJ	3-oxoadipate CoA-transferase subunit B (PcaJ)	curated:BRENDA::P0A102	ignore_other:2.8.3.6	ignore_other:2.8.3.5

# Two different types of 3-oxoadipate CoA-transferases (EC:2.8.3.6) are known.
# They are both heteromeric with each subunit containing a CoA-transferase domain
3-oxodipate-CoA-transferase: pcaI pcaJ

# Ignore EC:2.8.3.5, 3-oxoacid CoA-transferase, usually active on shorter substrates but who knows?
catI	3-oxoadipate CoA-transferase subunit A (CatI)	curated:SwissProt::Q8VPF3	curated:reanno::WCS417:GFF1318	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4592	curated:reanno::pseudo3_N2E3:AO353_17195	ignore_other:2.8.3.6	ignore_other:2.8.3.5

catJ	3-oxoadipate CoA-transferase subunit B (CatJ)	curated:SwissProt::Q8VPF2	curated:reanno::WCS417:GFF1319	curated:reanno::pseudo13_GW456_L13:PfGW456L13_4591	curated:reanno::pseudo3_N2E3:AO353_17200	ignore_other:2.8.3.6	ignore_other:2.8.3.5

3-oxodipate-CoA-transferase: catI catJ

pcaF	succinyl-CoA:acetyl-CoA C-succinyltransferase	EC:2.3.1.174

# MetaCyc pathway 3-oxoadipate degradation (metacyc:PWY-2361)
# involves activation by CoA (using succinyl-CoA) and a thiolase
# (succinyltransferase) reaction that splits it to
# acetyl-CoA and succinyl-CoA.
3-oxoadipate-degradation: 3-oxodipate-CoA-transferase pcaF

mhpD	2-hydroxypentadienoate hydratase	EC:4.2.1.80

# Q2XQZ7 is misannotated in BRENDA
mhpE	4-hydroxy-2-oxovalerate aldolase	EC:4.1.3.39	ignore:BRENDA::Q2XQZ7

import ethanol.steps:acetaldehyde-degradation

# (2Z)-2-hydroxypenta-2,4-dienoate (HPD) is a common intermediate in the aerobic
# degradation of many aromatic compounds.
# In MetaCyc pathway 2-hydroxypenta-2,4-dienoate degradation (metacyc:PWY-5162),
# HPD is hydrated to (S)-4-hydroxy-2-oxopentanoate and an aldolase cleaves it
# to pyruvate and acetaldehyde.
2-hydroxypenta-2,4-dienoate-degradation: mhpD mhpE acetaldehyde-degradation

# Anaerobic degradation of 4-hydroxybenzoate is via benzoyl-CoA.
# Our rules also allow for the aerobic pathway for degradation of
# benzoyl-CoA.  (We don't know if this actually occurs.)

import leucine.steps:atoB # acetyl-CoA acetyltransferase 
import phenylacetate.steps:benzoyl-CoA-degradation

pobA	4-hydroxybenzoate 3-monooxygenase	EC:1.14.13.2	EC:1.14.13.33

ligA	protocatechuate 4,5-dioxygenase, alpha subunit	curated:metacyc::MONOMER-15116	curated:metacyc::MONOMER-3165	ignore_other:1.13.11.8

ligB	protocatechuate 4,5-dioxygenase, beta subunit	curated:BRENDA::G2IQQ3	curated:metacyc::MONOMER-15117	curated:metacyc::MONOMER-3166	ignore_other:1.13.11.8

ligC	2-hydroxy-4-carboxymuconate-6-semialdehyde dehydrogenase	EC:1.1.1.312

ligI	2-pyrone-4,6-dicarboxylate hydrolase	EC:3.1.1.57

# This isomerization can occur spontaneously, but the enzyme is probably required for good growth
# (i.e., fitness data for utilization of 4-vinylphenol or gallic acid).
# This enzyme is named gllD in MetaCyc.
# Note that ligU = uniprot:Q0KJL4 is reported to carry out a different isomerization of 4-oxalomesaconate
# as part of this pathway. I believe this is just a question of whether to treat the product
# as the enol form (in UniProt) or the keto form (in MetaCyc).
ligU	4-oxalomesaconate tautomerase	EC:5.3.2.8	curated:SwissProt::Q0KJL4

# SwissProt G2IQQ5 = ligJ is described as using the enol form,
# (3Z)-2-oxo-4-carboxy-3-hexenedioate, of the substrate, but it yields the same product
ligJ	4-carboxy-2-hydroxymuconate hydratase	EC:4.2.1.83	curated:SwissProt::G2IQQ5

ligK	4-oxalocitramalate aldolase	EC:4.1.3.17

# EC:1.2.1.32 is 2-aminomuconate 6-semialdehyde dehydrogenase, but it is also reported
# to act on 2-hydroxymuconate-6-semialdehyde; many of these proteins
# are very similar to EC:1.2.1.85
praB	2-hydroxymuconate 6-semialdehyde dehydrogenase	EC:1.2.1.85	EC:1.2.1.32

praC	2-hydroxymuconate tautomerase	EC:5.3.2.6

praD	2-oxohex-3-enedioate decarboxylase	EC:4.1.1.77

# Dehydrogenase praB forms 2-hydroxymuconate, tautomerase praC forms
# (3E)-2-oxohex-3-enedioate (2-oxalocrotonate), and decarboxylase praD yields
# 2-hydroxypenta-2,4-dienoate (HPD).
# (This series of steps is part of protocatechuate para-cleavage, metacyc:PWY-6336,
#  or catechol degradation II, metacyc:PWY-5419.)
2-hydroxymuconate-6-semialdehyde-degradation: praB praC praD 2-hydroxypenta-2,4-dienoate-degradation

xylF	2-hydroxymuconate semialdehyde hydrolase	EC:3.7.1.9

# Or, hydrolase xylF forms HPD and formate.
# (This is part of a MetaCyc pathway for catechol degradation, metacyc:P183-PWY.)
2-hydroxymuconate-6-semialdehyde-degradation: xylF 2-hydroxypenta-2,4-dienoate-degradation

# In the meta-cleavage pathway (metacyc:P184-PWY), the 4,5-dioxygenase
# ligAB splits protocatechuate to
# 4-carboxy-2-hydroxymuconate-6-semialdehyde. (In solution, this is in
# the hemiacetal form.) The semialdehyde is oxidized to
# 2-pyrone-4,6-dicarboxylate, hydrolyzed to
# (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate, tautomerized to
# (1E,3E)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylate, hydrated to
# 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate (4-oxalocitramalate), and
# split by an aldolase to pyruvate and oxaloacetate.
protocatechuate-degradation: ligA ligB ligC ligI ligU ligJ ligK

pcaH	protocatechuate 3,4-dioxygenase, alpha subunit	curated:BRENDA::A0A193DXA9	curated:BRENDA::A8I4B7	curated:BRENDA::I0DHJ0	curated:BRENDA::Q0SH26	curated:CharProtDB::CH_121294	curated:metacyc::MONOMER-14209	curated:metacyc::MONOMER-3186	ignore_other:1.13.11.3

pcaG	protocatechuate 3,4-dioxygenase, beta subunit	curated:BRENDA::A0A193DXP2	curated:BRENDA::A8I4B3	curated:BRENDA::I0DHJ1	curated:BRENDA::Q0SH27	curated:CharProtDB::CH_121290	curated:metacyc::MONOMER-14210	curated:metacyc::MONOMER-3185	ignore_other:1.13.11.3

# RR42_RS32055 (A0A0C4YE08) is a somewhat diverged pcaB, confirmed by fitness data
pcaB	3-carboxymuconate cycloisomerase	EC:5.5.1.2	uniprot:A0A0C4YE08

pcaC	4-carboxymuconolactone decarboxylase	EC:4.1.1.44

pcaD	3-oxoadipate enol-lactone hydrolase	EC:3.1.1.24

# In the ortho-cleavage pathway (metacyc:PROTOCATECHUATE-ORTHO-CLEAVAGE-PWY),
# the 3,4-oxygenase pcaHG cleaves the ring to 3-carboxy-cis,cis-muconate, a
# cycloisomerase forms 4-carboxymuconolactone
# (2-carboxy-2,5-dihydro-5-oxofuran-2-yl)-acetate), a decarboxylase
# forms 3-oxoadipate enol lactone
# ((4,5-dihydro-5-oxofuran-2-yl)-acetate), and a hydrolase forms
# 3-oxoadipate.
protocatechuate-degradation: pcaH pcaG pcaB pcaC pcaD 3-oxoadipate-degradation

praA	protocatechuate 2,3-dioxygenase	curated:metacyc::MONOMER-15106

# In the para-cleavage pathway (metacyc:PWY-6336),
# the 2,3-dioxygenase praA forms
# (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde, which spontaneously decarboxylates to
# (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate, also known as 2-hydroxymuconate 6-semialdehyde.
protocatechuate-degradation: praA 2-hydroxymuconate-6-semialdehyde-degradation

# An aerobic route for degradation of 4-hydroxybenzoate involves
# 4-hydroxybenzoate 3-monooxygenase pobA, which forms protocatechuate
# (3,4-dihydroxybenzoate).
all: 4-hydroxybenzoate-transport pobA protocatechuate-degradation

# benzoyl-CoA ligases (EC:6.2.1.25) may have this activity as well, i.e. see PMID:12897012
# (discussing uniprot:Q8GQN9).
# Q8VUF1 (probably a benzoyl-CoA ligase) is misannotated in BRENDA as benzoyl-CoA reductase.
hcl	4-hydroxybenzoyl-CoA ligase	EC:6.2.1.27	curated:SwissProt::Q8GQN9	ignore_other:6.2.1.25	ignore:BRENDA::Q8VUF1

# EC:1.3.7.9 has been transferred to EC:1.1.7.1, but currently the annotations still use 1.3.7.9
hcrA	4-hydroxybenzoyl-CoA reductase, alpha subunit	curated:SwissProt::O33819	curated:metacyc::MONOMER-14376	curated:metacyc::MONOMER-17404	ignore_other:1.1.7.1	ignore_other:1.3.7.9

hcrB	4-hydroxybenzoyl-CoA reductase, beta subunit	curated:SwissProt::O33820	curated:metacyc::MONOMER-14377	curated:metacyc::MONOMER-17405	ignore_other:1.1.7.1	ignore_other:1.3.7.9

hcrC	4-hydroxybenzoyl-CoA reductase, gamma subunit	curated:SwissProt::O33818	curated:metacyc::MONOMER-14378	curated:metacyc::MONOMER-17403	ignore_other:1.1.7.1	ignore_other:1.3.7.9

# Alternatively, 4-hydroxybenzoate can be activated to 4-hydroxybenzoyl-CoA by hcl
# and reduced to benzoyl-CoA by hcrABC (metacyc:PHENOLDEG-PWY).
all: 4-hydroxybenzoate-transport hcl hcrA hcrB hcrC benzoyl-CoA-degradation

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources