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
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:
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