GapMind for Amino acid biosynthesis

 

Definition of L-isoleucine biosynthesis

As text, or see rules and steps

# Isoleucine biosynthesis in GapMind is based on MetaCyc pathways
# L-isoleucine biosynthesis I (from threonine) (metacyc:ILEUSYN-PWY),
# II via citramalate (metacyc:PWY-5101),
# or IV from propanoate (metacyc:PWY-5104).
# These pathways share a common intermediate, 2-oxobutanoate, but vary
# in how the 2-oxobutanoate is formed.
# Pathway IV is included because propanoate is a common fermentative
# end product and need not be a nutrient requirement, but
# it is not always clear if it could be the main pathway to
# isoleucine.
# Pathway III (metacyc:PWY-5103), via glutamate mutase,
# is not included because the first step (glutamate mutase, EC:5.4.99.1)
# has not been linked to sequence and because no organism has been
# demonstrated to rely on this pathway to form oxobutanoate.
# Pathway V, from 2-methylbutanoate (metacyc:PWY-5108),
# is not included.

# (Ignore some CharProtDB annotations with threonine deaminase but no EC)
ilvA	threonine deaminase	EC:4.3.1.19	ignore_other:threonine deaminase
# ilvIH (or ilvGM) is a two-subunit enzyme that forms acetolactate or acetohydroxybutanoate
# CH_124129 is probably correct but has limited data and vaguer annotations
#
ilvH	acetohydroxybutanoate synthase catalytic subunit	hmm:TIGR00118	term:acetohydroxy-acid synthase%large	term:acetohydroxy acid synthase%large	term:acetohydroxybutanoate synthase, catalytic subunit	term:acetohydroxybutanoate synthase, catalytic subunit	term:acetohydroxyacid synthase subunit B	ignore_other:EC 2.2.1.6	ignore:CharProtDB::CH_124219

# The isolated catalytic subunit has some activity so it's not clear if the regulatory
# subunit should be required.
ilvI	acetohydroxybutanoate synthase regulatory subunit 	hmm:TIGR00119	term:acetohydroxy-acid synthase%small	term:acetohydroxybutanoate synthase, regulatory subunit	term:small subunit of acetolactate synthase	ignore_other:EC 2.2.1.6
# 
# The three EC numbers correspond to different preferences for NAD(P)H as the cofactor;
# the transformations to the carbon skeleton are the same.
ilvC	2-hydroxy-3-ketol-acid reductoisomerase	EC:1.1.1.86	EC:1.1.1.382	EC:1.1.1.383
# The ignored enzyme is involved in salinosporamide A biosynthesis but does a very similar reaction
# and is >50% identical to N515DRAFT_0569, which is confirmed by fitness data to be biosynthetic
ilvD	(R)-2,3-dihydroxy-3-methylpentanoate dehydratase	EC:4.2.1.9	ignore:metacyc::MONOMER-15882
ilvE	isoleucine transaminase	EC:2.6.1.42

# 2-oxobutanoate is formed by deaminating threonine (pathway I, ilvA), via citramalate synthase (pathway II, cimA), or via propionyl-CoA (pathway III, prpE)
oxobutanoate: ilvA

# MetaCyc L-isoleucine biosynthesis II describes the formation of 2-oxobutanoate
# via citramalate. The other steps are the same (although it gives a different
# EC number for ilvC because of different cofactor preference)
# The citramalate synthase from Leptopsira interrogans (LA_2350, NP_712531, or Q8F3Q1_LEPIN) has
# been characterized biochemically but is not in the curated databases, see PMID:18498255
# The putative citramalate synthase HVO_0644 (D4GSQ2) from Haloferax volcanii is required
# for isoleucine biosynthesis, see PMC4300041
cimA	(R)-citramalate synthase	EC:2.3.1.182	uniprot:Q8F3Q1_LEPIN	uniprot:D4GSQ2

# In leucine synthesis, LeuCD allows the dehydration of 2-isopropylmalate and hydration to 3-isopropylmalate.
# Similarly, many of these enzymes allow the isomerization of citramalate to 3-methylmalate via citraconate.
# Citramalate isomerase is usually given as  EC 4.2.1.35, as opposed to 4.2.1.33 for traditional leuCD.
# However, in initial testing, all of the bacteria with the citramalate pathway appeared to have "typical" leuBCD
# (Desulfovibrio vulgaris Hildenborough, Desulfovibrio vulgaris Miyazaki F,
# Bacteroides thetaiotaomicron, Magnetospirillum magneticum AMB-1, and
# Synechococcus elongatus PCC 7942).
# Ignore a 2,3-methylmalate dehydratase (Q0QLE2,Q0QLE1) which is >50% identical to
# leuCD from DvH (DVU2982,DVU2983)
# Ignore some BRENDA annotations without subunit information,
# and ignore CharProtDB::CH_122621 (leuCD fusion) which is not actually characterized
# DvH leuC (DVU2982) has similarity to both LeuC and to homoaconitase, and fitness data confirms
# its role in amino acid biosynthesis, so explicitly include it
leuC	citramalate isomerase large subunit	term:citramalate isomerase large subunit	term:3-isopropylmalate dehydratase large subunit	term:3-isopropylmalate dehydratase%LeuC	hmm:TIGR00170	hmm:TIGR02083	hmm:TIGR02086	ignore:SwissProt::Q0QLE2	ignore_other:EC 4.2.1.33	ignore_other:EC 4.2.1.35	uniprot:LEUC_DESVH	ignore:CharProtDB::CH_122621
leuD	citramalate isomerase small subunit	term:citramalate isomerase small subunit	term:3-isopropylmalate dehydratase small subunit	term:3-isopropylmalate dehydratase%LeuD	hmm:TIGR00171	hmm:TIGR02084	hmm:TIGR02087	ignore:SwissProt::Q0QLE1	ignore_other:EC 4.2.1.33	ignore_other:EC 4.2.1.35	ignore:CharProtDB::CH_122621
# The dehydrogenase is encoded by a leuB-type enzyme.
# Similarly as for leuCD, any 3-isopropylmalate dehydrogenase should be assumed to be capable of this reaction
leuB	3-methylmalate dehydrogenase	EC:1.1.1.85	EC:1.1.1.n5

oxobutanoate: cimA leuC leuD leuB



prpE	propionyl-CoA synthetase	term:propionyl-CoA synthetase	term:propionate--CoA ligase	EC:6.2.1.17
# The key reaction is alpha-ketobutyrate synthase or
# 2-oxobutanoate:ferredoxin oxidoreductase (in reverse)
# These are heterodimeric enzymes and the only one mentioned by MetaCyc is
# an enzyme from Sulfolobus tokodaii 7 that includes ST2300 (alpha subunit, OFOA_SULSP).
# The beta subunit is OFOB_SULSP (but metacyc seems not to know this).
# Some related enzymes also are believed to do this
ofoa	2-oxobutanoate:ferredoxin oxidoreductase, alpha subunit	uniprot:OFOA1_SULTO	uniprot:OFOA_SULSP	uniprot:OFOA_SACSO	uniprot:OFOA2_SULTO	uniprot:OFOA1_AERPE	uniprot:OFOA2_AERPE
ofob	2-oxobutanoate:ferredoxin oxidoreductase, beta subunit	uniprot:OFOB1_SULTO	uniprot:OFOB_SULSP	uniprot:OFOB_SACSO	uniprot:OFOB2_SULTO	uniprot:OFOB1_AERPE	uniprot:OFOB2_AERPE

oxobutanoate: prpE ofoa ofob

# MetaCyc L-isoleucine biosynthesis V describes biosynthesis from 2-methylbutanoate, which
# is a fermentation end product in the rumen. This is an anusual precursor
# so I did not include it.

all: oxobutanoate ilvI ilvH ilvC ilvD ilvE

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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 preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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