GapMind for catabolism of small carbon sources

 

Definition of phenylacetate catabolism

As text, or see rules and steps

# Phenylacetate utilization in GapMind is based on MetaCyc pathway
# phenylacetate degradation I (aerobic via phenylacetyl-CoA dehydrogenase, metacyc:PWY0-321)
# and pathway II (anaerobic via benzoyl-CoA, metacyc:PWY-1341).

# TCDB::B6HIC2 may be a phenylacetate transporter, so it is ignored
paaT	phenylacetate transporter Paa	curated:TCDB::B6H9Q3	curated:TCDB::Q8NKG7	ignore:TCDB::B6HIC2

# Transporters were identified using
# query: transporter:phenylacetate
phenylacetate-transport: paaT

ppa	phenylacetate permease ppa	curated:TCDB::O50471
phenylacetate-transport: ppa

# In Paraburkholderia bryophila 376MFSha3.1, H281DRAFT_04042
# is specifically important for phenylacetate utilization.
# It is similar to E. coli aroP, a proton symporter for aromatic amino acids
H281DRAFT_04042	phenylacetate:H+ symporter	uniprot:A0A2Z5MFR8
phenylacetate-transport: H281DRAFT_04042

# The porin phaK was not included

# phenylglyoxylate dehydrogenase has 5 subunits, padEFGHI, in Aromatoleum evansii
padG	phenylglyoxylate dehydrogenase, alpha subunit	curated:SwissProt::Q8L3B1
padI	phenylglyoxylate dehydrogenase, beta subunit	curated:SwissProt::Q8L3A9
padE	phenylglyoxylate dehydrogenase, gamma subunit	curated:SwissProt::Q8L3B3
padF	phenylglyoxylate dehydrogenase, delta subunit	curated:SwissProt::Q8L3B2
padH	phenylglyoxylate dehydrogenase, epsilon subunit	curated:SwissProt::Q8L3B0

phenylglyoxylate-dehydrogenase: padG padI padE padF padH

import leucine.steps:atoB # acetyl-CoA acetyltransferase 

paaK	phenylacetate-CoA ligase	EC:6.2.1.30

paaA	phenylacetyl-CoA 1,2-epoxidase, subunit A	curated:SwissProt::P76077	curated:metacyc::MONOMER-15947
paaB	phenylacetyl-CoA 1,2-epoxidase, subunit B	curated:SwissProt::P76078	curated:metacyc::MONOMER-15948
paaC	phenylacetyl-CoA 1,2-epoxidase, subunit C	curated:BRENDA::P76079	curated:metacyc::MONOMER-15949
paaE	phenylacetyl-CoA 1,2-epoxidase, subunit E	curated:SwissProt::P76081	curated:metacyc::MONOMER-15950

# In MetaCyc, PaaG is described as a 1,2-epoxyphenylacetyl-CoA isomerase, but
# it is now thought to isomerize  2-(oxepinyl)acetyl-CoA to oxepin-CoA
# as well as cis-3,4-didehydroadiyplCoA to trans-2,3-didehydroadiypl-CoA (see PMID:31689071).
paaG	1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase 	EC:5.3.3.18

# PaaZ is a fusion protein of hydrolase and aldehyde dehydrogenase domains.
# However, in many bacteria that use this pathway, the 3-oxo-5,6-didehydrosuberyl-CoA
# dehydrogenase is a separate protein (PMC3064157).
# That study identified a single-domain protein (CAI08632.1) with oxepin-CoA hydrolase activity, but
# it was ~1,000x more active as a crotonyl-CoA hydrolase; since we are not sure if its
# oxepin-CoA hydrolase activity is physiologically relevant, we did not include it.
# In Paraburkholderia bryophila 376MFSha3.1, which has a single-domain 3-oxo-5,6-didehydrosuberyl-CoA
# dehydrogenase, the putative enoyl-CoA hydrolase H281DRAFT_04594 (A0A2Z5MCI7) is very important for
# phenylacetate utilization, and we predict that it is the missing oxepin-CoA hydrolase.
# (H281DRAFT_04594 is related to enoyl-CoA hydratases that form (S)-3-hydroxylacyl-CoA,
# while the hydrolase domain of PaaZ is related to enoyl-CoA hydratases that form (R)-3-hydroxylacyl-CoA.
# In fact, PaaZ can dehydrate (R)-3-hydroxybutyryl-CoA (PMC3064157).)
paaZ1	oxepin-CoA hydrolase	EC:3.3.2.12	uniprot:A0A2Z5MCI7

# PaaZ is a fusion protein of hydrolase and aldehyde dehydrogenase domains.
# However, a single-domain dehydrogenase has also been characterized
# (PacL = CAI08120 = Q5P3J4; see PMC3064157).
# Some of these dehydrogenases are closely related to
# 3,4-dehydroadipyl-CoA semialdehyde dehydrogenases (EC:1.2.1.77),
# which perform a similar reaction, so similarity to those are ignored.
paaZ2	3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase	EC:1.2.1.91	uniprot:Q5P3J4	ignore_other:1.2.1.77

# PaaJ is a thiolase with two activities that are linked to two different EC numbers, so it is
# listed twice, as paaJ1 and paaJ2.
# The product of the first thiolase reaction should be 3,4-dehydroadipyl-CoA, not 2,3-dehydro-,
# so there is probably a second isomerization step, which might be catalyzed by paaG or by paaJ itself.
# In Burkholderia phytofirmans PsJN, this enzyme is BPHYT_RS17345 (uniprot:B2SYZ2).
# In Paraburkholderia bryophila 376MFSha3.1, it is H281DRAFT_05723 (uniprot:A0A2Z5MFE9).
# In Herbaspirillum seropedicae, it is HSERO_RS20660 (uniprot:D8ITH5).
# In Marinobacter adhaerens, it is HP15_2695 (GFF2751).
# In BRENDA, Q845J3 is misannotated as paaJ; it is probably an accessory protein for assembly of the epoxidase
#	(paaD, not included here).
paaJ1	3-oxo-5,6-dehydrosuberyl-CoA thiolase	EC:2.3.1.223	ignore_other:2.3.1.174	ignore:BRENDA::Q845J3	uniprot:B2SYZ2	uniprot:A0A2Z5MFE9	uniprot:D8ITH5	curated:reanno::Marino:GFF2751

# This reaction is associated with EC:4.2.1.17, which is very broad (enoyl-CoA hydratase).
# P76081 is E. coli paaF and MONOMER-15953 is the characterized enzyme from Pseudomonas sp. Y2.
# BPHYT_RS17335 from Burkholderia phytofirmans and H281DRAFT_05725 (A0A2Z5MEB0) from Paraburkholderia bryophila 376MFSha3.1
# are required for phenylacetate utilization and are distantly related to E. coli paaF.
paaF	2,3-dehydroadipyl-CoA hydratase	curated:BRENDA::P76082	curated:metacyc::MONOMER-15953	curated:reanno::BFirm:BPHYT_RS17335	uniprot:A0A2Z5MEB0

# This step is described by 1.1.1.35, a broader term for 3-hydroxyacyl-CoA dehydrogenases.
# HP15_2693 (GFF2749) is involved in phenylalanine degradation via phenylacetyl-CoA and
# likely has this activity.
# HP15_1512 (GFF1550) is annotated as enoyl-CoA hydratase but likely has 3-hydroxyacyl-CoA dehydrogenase
# activity as well.
paaH	3-hydroxyadipyl-CoA dehydrogenase	EC:1.1.1.35	curated:reanno::Marino:GFF2749	ignore:reanno::Marino:GFF1550

# Enzymes from B. phytofirmans and P. bryophila and H. seropedicae
# and M. adhaerens are included, as for paaJ1 above
paaJ2	3-oxoadipyl-CoA thiolase	EC:2.3.1.174	ignore_other:2.3.1.223	uniprot:B2SYZ2	uniprot:A0A2Z5MFE9	uniprot:D8ITH5	curated:reanno::Marino:GFF2751

# phenylacetyl-CoA oxidoreductase has three subunits, padBCD.
# The system from Thauera aromatica includes
# 93 kDa protein: TTPNxPtGVtKVAtY = padB = Tharo_1297 = uniprot:A0A2R4BLL6;
# 27 kDa protein: TRYAMVADLRRxVGxQTxTAAxKHTNATPP = padC = Tharo_1296 = uniprot:A0A2R4BLY8;
# 26 kDa protein: kRGVQPELQPFtDAr = padD = Tharo_1295 = uniprot:A0A2R4BLZ0
# (see N-terminal sequences in PMID:10336636).
# TCDB 5.A.3.11.1 / Q5P037 describes a related system, not the system from T. aromatica,
# and I'm not sure if those sequences are actually characterized.
padB	phenylacetyl-CoA dehydrogenase, PadB subunit	uniprot:A0A2R4BLL6
padC	phenylacetyl-CoA dehydrogenase, PadC subunit	uniprot:A0A2R4BLY8	ignore:TCDB::Q5P036
padD	phenylacetyl-CoA dehydrogenase, PadD subunit	uniprot:A0A2R4BLZ0	ignore:TCDB::Q5P0H8
phenylacetyl-CoA-dehydrogenase: padB padC padD

# Thauera aromatica has BrcABCD; a similar system in Rhodopseudomonas palustris is known as badFEDG;
# and a similar system in Azoarcus is known as BzdQONP (see PMC516837 and Genbank AF521665).
# [The curated entries for Azoarcus, in BRENDA, are from another strain and are not
#  quite identical to the protein sequences in AF521665]
bcrA	ATP-dependent benzoyl-CoA reductase, alpha subunit	curated:SwissProt::O87876	curated:BRENDA::O07462	curated:BRENDA::Q8VUG0	ignore_other:1.3.7.8
bcrB	ATP-dependent benzoyl-CoA reductase, beta subunit	curated:SwissProt::O87875	curated:BRENDA::O07461	curated:BRENDA::Q8VUG2	ignore_other:1.3.7.8
bcrC	ATP-dependent benzoyl-CoA reductase, gamma subunit	curated:SwissProt::O87874	curated:BRENDA::O07460	curated:BRENDA::Q8VUG3	ignore_other:1.3.7.8
bcrD	ATP-dependent benzoyl-CoA reductase, delta subunit	curated:SwissProt::O87877	curated:BRENDA::O07463	curated:BRENDA::Q8VUG1	ignore_other:1.3.7.8

# Benzoyl-CoA reduction is energetically unfavorable. There are two
# classes of reductases: class I enzymes (bcrABCD) use ATP to drive
# the reaction, while class II enzymes (bamBCDEFGHI) are thought to us
# an electron bifurcation. SYN_02587 (uniprot:Q2LQN9) from Syntrophus
# aciditrophicus, which can oxidize cyclohex-1,5-diene-1-carbonyl-CoA
# to benzoyl-CoA, is not included because it seems to lack a mechanism to
# drive benzoyl-CoA reduction.
benzoyl-CoA-reductase: bcrA bcrB bcrC bcrD

# bamBCDEFGHI has been described in Geobacter metallireducens (PMID:30674680).
# There is also a paper about the enzyme from Desulfocarcina cetonica but
# I could not find those sequences.
# bamB = Gmet_2087
bamB	class II benzoyl-CoA reductase, BamB subunit	uniprot:Q39TV8
# bamC = Gmet_2086
bamC	class II benzoyl-CoA reductase, BamC subunit	uniprot:Q39TV9
# bamD = Gmet_2085
bamD	class II benzoyl-CoA reductase, BamD subunit	uniprot:Q39TW0
# bamE = Gmet_2084
bamE	class II benzoyl-CoA reductase, BamE subunit	uniprot:Q39TW1
# bamF = Gmet_2083
bamF	class II benzoyl-CoA reductase, BamF subunit	uniprot:Q39TW2
# bamG = Gmet_2081
bamG	class II benzoyl-CoA reductase, BamG subunit	uniprot:Q39TW4
# bamH = Gmet_2080
bamH	class II benzoyl-CoA reductase, BamH subunit	uniprot:Q39TW5
# bamI = Gmet_2079
bamI	class II benzoyl-CoA reductase, BamI subunit	uniprot:Q39TW6
benzoyl-CoA-reductase: bamB bamC bamD bamE bamF bamG bamH bamI

dch	cyclohexa-1,5-diene-1-carboxyl-CoA hydratase	EC:4.2.1.100
had	6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase	EC:1.1.1.368
oah	6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase	EC:3.7.1.21
pimB	3-oxopimeloyl-CoA:CoA acetyltransferase	curated:metacyc::MONOMER-20679

# This reaction runs in reverse (1,5-diene to cyclohex-1-ene-1-carbonyl-CoA)
Ch1CoA	cyclohex-1-ene-1-carbonyl-CoA dehydrogenase	EC:1.3.8.10

badK	cyclohex-1-ene-1-carboxyl-CoA hydratase	curated:metacyc::MONOMER-943

badH	2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase	curated:metacyc::MONOMER-893

badI	2-ketocyclohexanecarboxyl-CoA hydrolase	curated:metacyc::MONOMER-892

# EC:1.3.1.62
pimD	pimeloyl-CoA dehydrogenase, large subunit	curated:metacyc::MONOMER-20676
pimC	pimeloyl-CoA dehydrogenase, small subunit	curated:metacyc::MONOMER-20677

# 6-carboxyhex-2-enoyl-CoA is another name for 2,3-didehydropimeloyl-CoA
pimF	6-carboxyhex-2-enoyl-CoA hydratase	curated:metacyc::MONOMER-20678

# From EC:1.14.13.208
boxA	benzoyl-CoA epoxidase, subunit A	curated:SwissProt::Q9AIX6
boxB	benzoyl-CoA epoxidase, subunit B	curated:SwissProt::Q9AIX7

boxC	2,3-epoxybenzoyl-CoA dihydrolase	EC:4.1.2.44

# This reaction is similar to that of 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC:1.2.1.91)
boxD	3,4-dehydroadipyl-CoA semialdehyde dehydrogenase	EC:1.2.1.77	ignore_other:1.2.1.91

# The gene for 3,4-dehydroadipyl-CoA isomerase is not known

# glutaryl-CoA degradation

gcdH	glutaryl-CoA dehydrogenase	EC:1.3.8.6

# Psest_2437 (GFF2389) is the enoyl-CoA hydrotase for both isoleucine and valine degradation,
# which implies that (S)-3-hydroxybutanoyl-CoA is a substrate.
# Q97MS7 is misannotated in BRENDA.
# BPHYT_RS17335 was misannotated as paaF; it is very similar to the ech H16_A3307, which
# is a different explanation for its role in phenylacetate utilization.
# Short-chain enoyl-CoA hydratases are sometimes given EC:4.2.1.17 instead, so those are ignored.
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	EC:4.2.1.150	ignore:BRENDA::Q97MS7	curated:reanno::BFirm:BPHYT_RS17335	curated:reanno::psRCH2:GFF2389	ignore_other:4.2.1.17

# HP15_1512 (GFF1550) is annotated as enoyl-CoA hydratase but likely does this as well
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	EC:1.1.1.35	ignore:reanno::Marino:GFF1550

# In MetaCyc pathway glutaryl-CoA degradation (metacyc:PWY-5177), glutaryl-CoA is
# oxidized to (E)-glutaconyl-CoA and oxidatively decarboxylated to
# crotonyl-CoA (both by the same enzyme), hydrated to
# 3-hydroxybutanoyl-CoA, oxidized to acetoacetyl-CoA, and cleaved to
# two acetyl-CoA.
glutaryl-CoA-degradation: gcdH ech fadB atoB

# Benzoyl-CoA can be degraded anaerobically (metacyc:CENTBENZCOA-PWY)
# by reduction to cyclohex-1,5-diene-1-carbonyl-CoA,
# followed by hydratase (dch) to 6-hydroxycyclohex-1-ene-1-carbonyl-CoA, a dehydrogenase
# to 6-oxocyclohex-1-ene-1-carbonyl-CoA, a hydrolase to
# 2-hydroxy-6-oxocycloheane-1-carbonyl-CoA, a ring-opening hydrolase
# to 3-hydroxypimeloyl-CoA [the last two steps are both catalyzed by
# oah], a dehydrogenase to 3-oxopimeloyl-CoA [not linked to sequence and omitted],
# and an acetyltransferase to glutaryl-CoA and acetyl-CoA.
benzoyl-CoA-degradation: benzoyl-CoA-reductase dch had oah pimB glutaryl-CoA-degradation

# Alternatively, after reduction to cyclohex-1,5-diene-1-carbonyl-CoA,
# Ch1CoA can further reduce it to cyclohex-1-ene-1-carboxyl-CoA (metacyc:P321-PWY),
# followed by hydration to 2-hydroxy-cyclohexane-1-carbonyl-CoA, oxidation to
# 2-ketocyclohexane-1-carbonyl-CoA, cleavage by a ring-opening
# hydrolase to pimeloyl-CoA, oxidation to
# 2,3-didehydropimeloyl-CoA, hydration to 3-hydroxypimeloyl-C,
# oxidation to 3-oxopimeloyl-CoA and cleavage by a thiolase to glutaryl-CoA and acetyl-CoA.
benzoyl-CoA-degradation: benzoyl-CoA-reductase Ch1CoA badK badH badI pimD pimC pimF glutaryl-CoA-degradation

# Benzoyl-CoA degradation can be degraded aerobically (metacyc:PWY-1361)
# by an epoxidase (boxAB) that forms 2,3-epoxy-2-3-dihydrobenzoyl-CoA; a
# dihydrolase forms cis-3,4-dihydroadipyl-CoA semialdehyde and
# formate; a dehydrogenase forms cis-3,4-dehydroadipyl-CoA; and an
# unknown isomerase forms trans-2,3-dehydroadipyl-CoA. This is
# converted to succinyl-CoA as in the anaerobic pathway (paaF,
# paaH, and paaJ2).
benzoyl-CoA-degradation: boxA boxB boxC boxD paaF paaH paaJ2

# In the aerobic pathway, oxygen-dependent 1,2-epoxidase (PaaABCE) converts
# phenylacetyl-CoA to 1,2-epoxyphenylacetyl-CoA, which spontaenously
# rearranges to 2-(oxepinyl)acetyl-CoA; isomerase PaaG forms
# 2-oxepin-2(3H)-ylideneacetyl-CoA ("oxepin-CoA"); a ring-opening hydrolase forms
# 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde; a dehydrogenase forms
# 3-oxo-5,6-didehydrosuberyl-CoA; thiolase PaaJ forms
# cis-3,4-didehydroadipyl-CoA (and acetyl-CoA); isomerase PaaG forms
# trans-2,3-didehydroadipyl-CoA; hydratase PaaF forms
# (3S)-hydroxyadipyl-CoA; dehydrogenase PaaH forms 3-oxoadipyl-CoA, and
# thiolase PaaJ forms succinyl-CoA and acetyl-CoA.
# (The role of PaaG is described in PMID:31689071 and differs slightly from
# MetaCyc.)
phenylacetyl-CoA-degradation: paaA paaB paaC paaE paaG paaZ1 paaZ2 paaJ1 paaF paaH paaJ2

# In the anaerobic pathway, a dehydrogenase forms
# phenylglyoxyl-CoA, a hydrolase forms phenylglyoxylate (this step is
# not linked to sequence but is likely provided by the phenylglyoxylyl-CoA dehydrogenase,
# see PMID:10336636), and another dehydrogenase forms benzoyl-CoA and
# CO2. In principle, this pathway could occur aerobically, so GapMind
# includes aerobic pathways for degrading the benzoyl-CoA.
phenylacetyl-CoA-degradation: phenylacetyl-CoA-dehydrogenase phenylglyoxylate-dehydrogenase benzoyl-CoA-degradation

# Phenylacetate is activated to phenylacetyl-CoA by paaK
phenylacetate-degradation: paaK phenylacetyl-CoA-degradation

all: phenylacetate-transport phenylacetate-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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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