Definition of L-isoleucine catabolism

GapMind for catabolism of small carbon sources

Definition of L-isoleucine catabolism

# Isoleucine degradation in GapMind is based on
# MetaCyc pathway L-isoleucine degradation I (metacyc:ILEUDEG-PWY).
# The other pathways are fermentative and do not lead to carbon incorporation
# (metacyc:PWY-5078, metacyc:PWY-8184).

# E. coli livFGHMJ or livFGHMK (livK and livJ are alternate SBPs).
# LivJFGHM from Streptococcus pneumoniae.
# BraCDEFG from Pseudomonas aeruginosa (braC is the SBP).
# BraDEFG/braC3 from R. leguminosarum; braC3 (RL3540; Q1MDE9) is a secondary
#   SBP that transports leucine/isoleucine/valine/alanine (PMID:19597156); the
#   proximal braC might also transport isoleucine, not sure if this is known, so exclude it (Q9L3M3);
#   LivH/BraD = RL3750/Q1MCU0; LivM/BraE = RL3749/Q1MCU1;
#   LivG/BraF = RL3748/Q1MCU2; LivF/BraG = RL3747/Q1MCU3;
# LivFGJHM from Acidovorax sp. GW101-3H11:
#     LivF = Ac3H11_1692 (A0A165KC78), LivG = Ac3H11_1693 (A0A165KC86),
#     LivJ = Ac3H11_2396 (A0A165KTD4; not near the other components, but cofit and has the phenotype on isoleucine),
#     LivH = Ac3H11_1695 (A0A165KC95), LivM = Ac3H11_1694 (A0A165KER0);
# LivKHMGF from Pseudomonas fluorescens FW300-N2E2:
#   LivF = Pf6N2E2_2926 = A0A159ZWL6, LivG = Pf6N2E2_2925 = A0A159ZWS6, LivK = Pf6N2E2_2921 = A0A160A0J6,
#   LivH = Pf6N2E2_2923 = A0A0D9B2B6, LivM = Pf6N2E2_2924 = A0A159ZYE0
livF	L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG)	curated:CharProtDB::CH_003736	curated:TCDB::P21630	curated:TCDB::Q8DQH7	uniprot:Q1MCU3	uniprot:A0A165KC78	uniprot:A0A159ZWL6

livG	L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF)	curated:TCDB::P0A9S7	curated:TCDB::P21629	curated:TCDB::Q8DQH8	uniprot:Q1MCU2	uniprot:A0A165KC86	uniprot:A0A159ZWS6

livJ	L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)	curated:SwissProt::P21175	curated:CharProtDB::CH_107418	curated:TCDB::P0AD96	curated:TCDB::Q8DQI1	uniprot:Q1MDE9	ignore:TCDB::Q9L3M3	uniprot:A0A165KTD4	uniprot:A0A160A0J6

livH	L-isoleucine ABC transporter, permease component 1 (LivH/BraD)	curated:TCDB::P21627	curated:TCDB::Q8DQI0	curated:ecocyc::LIVH-MONOMER	uniprot:Q1MCU0	uniprot:A0A165KC95	uniprot:A0A0D9B2B6

# LivM from Streptococcus pneumoniae lacks an N-terminal domain of unknown
# function (DUF3382) that is found in E.coli and P. aeruginosa
livM	L-isoleucine ABC transporter, permease component 2 (LivM/BraE)	curated:SwissProt::P22729	curated:TCDB::P21628	curated:TCDB::Q8DQH9	uniprot:Q1MCU1	uniprot:A0A165KER0	uniprot:A0A159ZYE0

# Transporters were identified using
# query: transporter:isoleucine:L-isoleucine:ile
# and non-specific large neutral amino acid tranpsorters from mammals were ignored.
isoleucine-transport: livF livG livJ livH livM

# Synechocystis sp. NatABCDE; also a similar system in Anabaena
# (also known as N-I; TC 3.A.1.4.6) is thought to transport isoleucine (PMC4500139).
# A related system from Synechocystis (TC 3.A.1.4.2) transports a range of amino acids, but
# it is not clear that isoleucine is a substrate, so that system is
# marked ignore.
natA	L-isoleucine ABC transporter, ATPase component 1 (NatA)	ignore:TCDB::Q55164	curated:TCDB::Q7A2H0
natB	L-isoleucine ABC transporter, substrate-binding component NatB	ignore:TCDB::Q55387	curated:TCDB::Q8YVY4
natC	L-isoleucine ABC transporter, permease component 1 (NatC)	ignore:TCDB::P74455	curated:TCDB::Q8YY08
natD	L-isoleucine ABC transporter, permease component 2 (NatD)	ignore:TCDB::P74318	curated:TCDB::Q8YXD0
natE	L-isoleucine ABC transporter, ATPase component 2 (NatE)	ignore:TCDB::P73650	curated:TCDB::Q8YT15
isoleucine-transport: natA natB natC natD natE

Bap2	L-isoleucine permease Bap2	curated:CharProtDB::CH_091448	curated:SwissProt::P38084	curated:TCDB::Q2VQZ4
isoleucine-transport: Bap2

brnQ	L-isoleucine:cation symporter BrnQ/BraZ/BraB	curated:TCDB::P0AD99	curated:TCDB::P25185	curated:TCDB::P19072
isoleucine-transport: brnQ

bcaP	L-isoleucine uptake transporter BcaP/CitA	curated:TCDB::S6EX81
isoleucine-transport: bcaP

# Amino acid efflux pumps were ignored

import propionate.steps:propionyl-CoA-degradation

import leucine.steps:BKD # branched-chain alpha-ketoacid dehydrogenases

# EC:1.3.8.5 includes (2S)-2-methylbutanoyl-CoA dehydrogenases and also
# isobutyryl-CoA dehydrogenases (involved in valine degradation)
# or sometimes 3-methylbutanoyl-CoA
# dehydrogenases (involved in leucine degradation, usually given
# EC:1.3.8.4). Some enzymes act on all three methylacyl-CoA
# substrates. Other genes are required only for valine degradation and
# their activity on 2-methylbutanoyl-CoA uncertain, so they are marked
# ignore.
#
# PfGW456L13_2983 and Shewana3_2769 (VIMSS 7025618) and PP_2216 (MONOMER-17424)
# were annotated with other EC numbers (implying other acyl-CoA substrates)
# but are involved in isoleucine utilization, so are included.
#
# Various isobutyryl-CoA dehydrogenases are ignored (they may well act on 2-methylbutanoyl-CoA as well).
#
# uniprot:P45857 (mmgC from B. subtilis) is part of an operon with methylcitrate cycle genes, and
# could be involved in isoleucine catabolism, but its biochemical activity is uncertain,
# so it is ignored, as is the nearly-identical CH_091788.
acdH	(2S)-2-methylbutanoyl-CoA dehydrogenase	EC:1.3.8.5	curated:reanno::pseudo13_GW456_L13:PfGW456L13_2983	curated:reanno::ANA3:7025618	curated:metacyc::MONOMER-17424	ignore:reanno::psRCH2:GFF2392	ignore:reanno::WCS417:GFF2713	ignore:reanno::pseudo13_GW456_L13:PfGW456L13_2985	ignore:reanno::pseudo3_N2E3:AO353_25670	ignore:SwissProt::P45857	ignore:CharProtDB::CH_091788

# Psest_2437 (GFF2389) is the enoyl-CoA hydrotase for both isoleucine and valine degradation.
# A paper claiming that uniprot:Q9SE41 (PMID:23809632) is ech relies on
# homology modeling, and it could well be a hydrolase instead; it is
# 69% identical to the hydrolase from Arabidopsis (uniprot:Q9LKJ1).  And
# MetaCyc linked uniprot:Q51969 (MONOMER-11695) from P. putida to ech, but the
# sequence shown in the paper (PMID:12115060, Fig. 3) is different.
# And PP_3358 (hydroxycinnamoyl-CoA hydratase-lyase) was incorrectly given this EC number.
ech	2-methyl-3-hydroxybutyryl-CoA hydro-lyase	EC:4.2.1.17	curated:reanno::psRCH2:GFF2389	ignore_other:4.2.1.150	ignore:BRENDA::Q9SE41	ignore:metacyc::MONOMER-11695	ignore:reanno::Putida:PP_3358

# SO1683 (Q8EGC1) was proposed to have this activity (PMC2612455; PMC3219624) and is important for
# isoleucine utilization.
ivdG	3-hydroxy-2-methylbutyryl-CoA dehydrogenase	EC:1.1.1.178	uniprot:Q8EGC1

# 2.3.1.9 is a similar reaction, acetoacetyl-CoA thiolase
fadA	2-methylacetoacetyl-CoA thiolase	EC:2.3.1.16	ignore_other:2.3.1.9

# A transaminase (which is not represented) converts isoleucine to (3S)-3-methyl-2-oxopentanoate,
# the decarboxylating dehydrogenase BKD forms
# (2S)-2-methylbutanoyl-CoA, dehydrogenase acdH forms
# (E)-2-methylcrotonyl-CoA, hydratase ech forms
# (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA, dehydrogenase ivdG forms
# 2-methylacetoacetyl-CoA, and a thiolase forms propanioyl-CoA and
# acetyl-CoA.
# (The initial transaminase is not represented because
# amino-acid aminotransferases are often non-specific.)
all: isoleucine-transport BKD acdH ech ivdG fadA propionyl-CoA-degradation

# MetaCyc Pathway: L-isoleucine degradation II
# is a fermentative pathway, to 2-methylbutanol. It does not yield any
# fixed carbon and is not described here.

# MetaCyc Pathway: L-isoleucine degradation III (oxidative Stickland reaction)
# is a fermentative pathway, to 2-methylbutanoate. It does not yield
# any fixed carbon and is not described here.

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Protein sequences (fasta format)
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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