L-methionine biosynthesis in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

L-methionine biosynthesis in Dinoroseobacter shibae DFL-12

Best path

asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA

Also see fitness data for the top candidates

Rules

Overview: Methionine biosynthesis in GapMind is based on MetaCyc pathways L-methionine biosynthesis I via O-succinylhomoserine and cystathionine (link), II via O-phosphohomoserine and cystathionine (link), III via O-acetylhomoserine (link), or IV with reductive sulfhydrylation of aspartate semialdehyde (link). 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.

all: homocysteine and methionine_synthase
methionine_synthase:

metH * and B12-reactivation
or split_metH_1, split_metH_2, split_metH_3 and B12-reactivation
or metE
or split_metE_1 and split_metE_2
or mesA
or mesB
or mesC
or mesD and mesX
Comment: Besides MetH (with B-12 reactivation) or 3-part MetH as in Phaeobacter (PMC5764234), or MetE, or MetE split into two parts (PMC7857596), GapMind also includes the folate-independent systems MesA, MesB, MesC, and MesD/MesX (PMC7857596). It is possible that the corrinoid-dependent methionine synthases (MesA, MesB, or MesC) would require B12 reactivation, but this is not proven, and some methanogens with MesA seem to lack RamA, so B12 reactivation is not included. The role of split MetE or MesC lacks experimental evidence, and is based on gene neighborhoods and functional residues only (PMC7857596).

B12-reactivation:

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

homocysteine:

aspartate-semialdehyde and asd-sulfhydrylation
or homoserine, metX and metY
or homoserine, metA and metZ
or homoserine and transsulfuration

transsulfuration:

metA, metB and metC
or metX, metB and metC
or hom_kinase, metB and metC
Comment: 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).

homoserine: aspartate-semialdehyde and hom
asd-sulfhydrylation: asd-S-transferase, asd-S-ferredoxin and asd-S-perS

Comment: Reductive sulfhydrylation of aspartate semialdehyde to homocysteine is carried out by a multi-component system (see PMID:25315403 and PMC5764234)

aspartate-semialdehyde: asp-kinase and asd

27 steps (15 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
asp-kinase	aspartate kinase	Dshi_2061
asd	aspartate semi-aldehyde dehydrogenase	Dshi_3240
hom	homoserine dehydrogenase	Dshi_2273	Dshi_2061
metX	homoserine O-acetyltransferase	Dshi_1593
metY	O-acetylhomoserine sulfhydrylase	Dshi_0793	Dshi_2410
split_metH_1	Methionine synthase component, B12 binding and B12-binding cap domains	Dshi_1073
split_metH_2	Methionine synthase component, methyltransferase domain	Dshi_1074
split_metH_3	Methionine synthase component, pterin-binding domain	Dshi_1677
ramA	ATP-dependent reduction of co(II)balamin	Dshi_1680
Alternative steps:
asd-S-ferredoxin	reductive sulfuration of L-aspartate semialdehyde, ferredoxin component
asd-S-perS	putative persulfide forming protein
asd-S-transferase	sulfuration of L-aspartate semialdehyde, persulfide component
B12-reactivation-domain	MetH reactivation domain
hom_kinase	homoserine kinase	Dshi_1609
mesA	Methylcobalamin:homocysteine methyltransferase MesA
mesB	Methylcobalamin:homocysteine methyltransferase MesB
mesC	Methylcobalamin:homocysteine methyltransferase MesC
mesD	oxygen-dependent methionine synthase, methyltransferase component MesD
mesX	oxygen-dependent methionine synthase, putative oxygenase component MesX
metA	homoserine O-succinyltransferase	Dshi_1593
metB	cystathionine gamma-synthase	Dshi_2410	Dshi_1002
metC	cystathionine beta-lyase	Dshi_1002	Dshi_2410
metE	vitamin B12-independent methionine synthase
metH *	vitamin B12-dependent methionine synthase	Dshi_1677 with Dshi_1074
metZ	O-succinylhomoserine sulfhydrylase	Dshi_2410	Dshi_0793
split_metE_1	vitamin B12-independent methionine synthase, folate-binding component
split_metE_2	vitamin B12-independent methionine synthase, catalytic component

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
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

GapMind for Amino acid biosynthesis