GapMind for Amino acid biosynthesis


Definition of L-methionine biosynthesis

As text, or see rules and steps

# Methionine biosynthesis in GapMind is based on MetaCyc pathways
# L-methionine biosynthesis I via O-succinylhomoserine and cystathionine (metacyc:HOMOSER-METSYN-PWY),
# II via O-phosphohomoserine and cystathionine (metacyc:PWY-702),
# III via O-acetylhomoserine (metacyc:HSERMETANA-PWY),
# or IV with reductive sulfhydrylation of aspartate semialdehyde (metacyc:PWY-7977).
# These pathways vary in how aspartate semialdehyde is reduced and sulfhydrylated to homocysteine.
# GapMind does not represent the formation of the methyl donors for methionine synthase,
# such as 5-methyltetrahydrofolate or methyl corrinoid proteins.

# For BRENDA::O63067 -- the paper describes a monofunctional hom but the sequence of uniprot:O63067 is
# much longer and has a close homolog of functional aspartate kinase (due to alternative splicing?)
asp-kinase	aspartate kinase	EC:	ignore:BRENDA::O63067
asd	aspartate semi-aldehyde dehydrogenase	EC:

# Ga0059261_2711 from Sphingomonas koreensis DSMZ 15582 is distant from characterized homoserine dehydrogenases
# and is confirmed by  fitness data. It is identical to uniprot:A0A1L6J6Q3.
# It has been updated in the reannotations so need not be mentioned here.
# BT2403 from Bacteroides thetaiotaomicron (uniprot:Q8A541_BACTN)
# is a fusion of aspartate kinase and homoserine dehydrogenase.
# The homoserine dehydrogenase portion is somewhat diverged. Its role is confirmed by strong cofitness with
# threonine synthase (the defined media for B. thetaiotaomicron included methionine).
# DvMF_1412 from Desulfovibrio vulgaris Miyazaki F (uniprot:B8DRS3_DESVM) is a somewhat
# diverged homoserine dehydrogenase. It has auxotrophic phenotypes.
hom	homoserine dehydrogenase	EC:	uniprot:A0A1L6J6Q3	uniprot:Q8A541_BACTN	uniprot:B8DRS3_DESVM

# As discussed in PMID:28581482, many homologs of MetA family are
# actually homoserine O-acetyltransferases, and many homologs of MetX
# are actually homoserine O-succinyltransferases.  Fortunately, many
# enzymes of both types have been curated in Swiss-Prot.
metA	homoserine O-succinyltransferase	EC:

# MetX is often found alongside a methyltransferase-like protein MetW.
# Because MetW is not consistently required for MetX's activity, it is not included in GapMind.
# Details on MetW: PMID:28581482 briefly mention that
# MetX proteins lacked activity when expressed in E. coli unless MetW
# was cloned along with it. They purified MetX by adding an N-terminal
# hexahistidine tag; MetW would not necessarily be purified along with
# it. Most likely, MetW is either modifying MetX and improving its
# activity, or forming a complex with MetX and stabilizing it.  Mutant
# fitness data for MetW from various Proteobacteria shows that MetW need
# not be required for MetX activity (see Herbaspirillum seropedicae or
# Cupriavidus necator). In other organisms, MetW mutants have milder
# phenotypes than MetX mutants, or MetX mutants do not have a defect
# in some conditions, which suggests that MetW is only sometimes
# required (Burkholderia phytofirmans, Acidovorax 3H11, Dechlorosoma
# suillum PS, Marinobacter adhaerens). This might suggest that any
# modification has a regulatory role. In many other organisms, there
# is tight cofitness between MetX and MetW, suggesting that MetW is
# required for MetX's activity (Paraburkholderia bryophila, many
# Pseudomonas, Caulobacter crescentus, or Sphingomonas koreensis).
metX	homoserine O-acetyltransferase	EC:

hom_kinase	homoserine kinase	EC:

# METI_BACSU (uniprot:O31631) has activity as CGS but is given a more vague EC number.
metB	cystathionine gamma-synthase	curated:SwissProt::O31631	EC:

metC	cystathionine beta-lyase	EC:	

# METI_BACSU (uniprot:O31631) has activity as OAS but is given a more vague EC number.
metY	O-acetylhomoserine sulfhydrylase	EC:	curated:SwissProt::O31631	ignore_other:O-succinylhomoserine sulfhydrylase

# No EC number for metZ, so use "O-succinylhomoserine sulfhydrylase", which matches
# uniprot:METZ_PSEAE and uniprot:METZ_MYCTU.
# Two related proteins, Ac3H11_2452 (uniprot:A0A165KUI5_9BURK) and HSERO_RS16440 (uniprot:D8J1Y3_HERSS)
# are diverged metZ -- strongly cofit with homoserine succinyltransferases and similar to either
# sulfhydrylases or methionine gamma-lyases (but the latter function would not explain their phenotype).
metZ	O-succinylhomoserine sulfhydrylase	term:O-succinylhomoserine sulfhydrylase	ignore_other:EC	uniprot:A0A165KUI5_9BURK	uniprot:D8J1Y3_HERSS

metE	vitamin B12-independent methionine synthase	EC:

# Desulfovibrio have a somewhat diverged MetH, without the activation domain, but confirmed by
# cofitness (DVU1585 = uniprot:Q72BP9_DESVH is cofit with MetF; DvMF_0476 = uniprot:B8DKK4_DESVM is cofit with a RamA-
# like activation protein).
# 3-part split MetH proteins from Phaeobacter are ignored.
metH	vitamin B12-dependent methionine synthase	EC:	ignore:reanno::Phaeo:GFF1501	ignore:reanno::Phaeo:GFF1318	ignore:reanno::Phaeo:GFF1321	ignore:reanno::Phaeo:GFF1319	ignore:reanno::Phaeo:GFF1582	uniprot:Q72BP9_DESVH	uniprot:B8DKK4_DESVM

# In Phaeobacter and some related bacteria, MetH is split into 3 parts (PMC5764234)
split_metH_1	Methionine synthase component, B12 binding and B12-binding cap domains	curated:reanno::Phaeo:GFF1319
split_metH_2	Methionine synthase component, methyltransferase domain	curated:reanno::Phaeo:GFF1321
split_metH_3	Methionine synthase component, pterin-binding domain	curated:reanno::Phaeo:GFF1582

# In E. coli and many other bacteria, the MetH protein includes a reactivation domain (pfam:PF02965),
# but other ATP-dependent (ramA-like) activation proteins are also thought to exist.
# Ignore MetH proteins, as they often contain the reactivation domain and this
# creates confusion when checking for reverse hits.
B12-reactivation-domain	MetH reactivation domain	hmm:PF02965	ignore_other:EC

# As of April 2019, all characterized members of the RamA family or PF14574 are involved in the reactivation
# of co(II)balamin. This includes RamA (uniprot:B8Y445), DvMF_1398, PGA1_c15200, and ELI_0370 (part of a O-demethylase).
# Many bacteria contain MetH and probably rely on a distant homolog of RamA for reactivation of B-12.
# pfam:PF14574 describes only the C-terminal putative ATPase domain of RamA, but no other functions are known.
ramA	ATP-dependent reduction of co(II)balamin	hmm:PF14574	term:ATP-dependent reduction of co(II)balamin

# reductive sulfuration of aspartate semi-aldehyde

# MA1821 or DvMF_1464 (see PMID:25315403 and PMC5764234)
asd-S-transferase	sulfuration of L-aspartate semialdehyde, persulfide component	uniprot:Q8TPT4_METAC	curated:reanno::Miya:8500721
# MA1822 or DvMF_0262 (see PMID:25315403 and PMC5764234)
asd-S-ferredoxin	reductive sulfuration of L-aspartate semialdehyde, ferredoxin component	uniprot:Q8TPT3_METAC	curated:reanno::Miya:8499492
# MA1715 or DvMF_0044 (see PMID:25315403 and PMC5764234)
# This putative persulfide forming component is not 100% required in Methanosarcina acetivorans (possible redundancy).
asd-S-perS	putative persulfide forming protein	uniprot:Y1715_METAC	curated:reanno::Miya:8499265

# Methanogens have a short homolog of MetE that transfers methyl groups from methylcobalamin
# (not 5-methyltetrahydrofolates) to homocysteine to form methionine (PMID:10469143).
# We named this family of "core" methioine synthases MesA and proposed
# that MtrA (the corrinoid subunit of methyltetrahydromethanopterin:coenzyme M methyltransferase)
# is the physiological methyl donor (PMC7857596).
mesA	Methylcobalamin:homocysteine methyltransferase MesA	curated:SwissProt::P55299

# Another core methionine synthase (distantly related to MesA) has been characterized
# in Dehalococcoides (PMC7005905).
# It probably obtains methyl groups from the iron-sulfur corrinoid protein of the
# Wood-Ljungdahl pathway (CoFeSP), but this is not proven.
# We named this family MesB (PMID:33534785).
mesB	Methylcobalamin:homocysteine methyltransferase MesB	uniprot:A0A0V8M4G6

# Genetic evidence shows that ACIAD3523 and Ga0059261_2929 are methionine synthases,
# see PMC2290942 and PMID:33534785.
# They require mesX (ACIAD3524 or Ga0059261_2928) and oxygen for activity, but not
# 5-methyltetrahydrofolates or cobalamin.
mesD	oxygen-dependent methionine synthase, methyltransferase component MesD	uniprot:Q6F6Z8	uniprot:A0A2M8WFA5
# MesX is required for the activity of MesD, see PMC2290942.
mesX	oxygen-dependent methionine synthase, putative oxygenase component MesX	uniprot:Q6F6Z7	uniprot:A0A2M8WFB3

aspartate-semialdehyde: asp-kinase asd

# Reductive sulfhydrylation of aspartate semialdehyde to homocysteine is carried out by
# a multi-component system (see PMID:25315403 and PMC5764234)
asd-sulfhydrylation: asd-S-transferase asd-S-ferredoxin asd-S-perS

homoserine: aspartate-semialdehyde hom

# Transsulfuration is the conversion of homoserine to homocysteine, with the sulfur being obtained from cysteine.
# It is thought to occur with any
# of the activated forms of homoserine (O-acetyl-, O-succinyl-, or O-phospho-homoserine).
transsulfuration: metA metB metC
transsulfuration: metX metB metC
transsulfuration: hom_kinase metB metC

# Homocysteine can be formed by reduction of aspartate semialdehyde, direct sulfurylation of activated homoserine,
# or transsulfuration of (activated) homoserine.
# Activated forms of homoserine include O-acetylhomoserine, O-succinylhomoserine, or O-phospho-homoserine.

homocysteine: aspartate-semialdehyde asd-sulfhydrylation
homocysteine: homoserine metX metY
homocysteine: homoserine metA metZ
homocysteine: homoserine transsulfuration

# MetH occasionally oxidizes the vitamin B12 cofactor from Co(I) to Co(II), so
# a reductase is needed to maintain its activity.
B12-reactivation: B12-reactivation-domain
B12-reactivation: ramA

# Besides MetH (with B-12 reactivation) or 3-part MetH as in Phaeobacter (PMC5764234), or MetE,
# GapMind also includes the folate-independent systems MesA, MesB, and MesD/MesX (PMC7857596).
# It is possible that the corrinoid-dependent methionine synthases (MesA or MesB) would require B12 reactivation,
# but this is not proven, and some methanogens with MesA seem to lack RamA, so
# B12 reactivation is not included.
# Also, we proposed that many archaea use split MetE-like methionine synthases or another
# corrinoid-dependent methionine synthase (MesC), but there is no experimental evidence, so
# these are not included in GapMind.
methionine_synthase: metH B12-reactivation
methionine_synthase: split_metH_1 split_metH_2 split_metH_3 B12-reactivation
methionine_synthase: metE
methionine_synthase: mesA
methionine_synthase: mesB
methionine_synthase: mesD mesX

all: homocysteine methionine_synthase 



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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, 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