Definition of L-methionine biosynthesis
As rules and steps, or see full text
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 mesA
- or mesB
- or mesD and mesX
- Comment: 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.
- 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
Steps
asp-kinase: aspartate kinase
- Curated proteins or TIGRFams with EC 2.7.2.4
- Ignore hits to O63067 when looking for 'other' hits (homoserine dehydrogenase (EC 1.1.1.3))
- Comment: For BRENDA::O63067 -- the paper describes a monofunctional hom but the sequence of O63067 is much longer and has a close homolog of functional aspartate kinase (due to alternative splicing?)
- Total: 3 HMMs and 29 characterized proteins
asd: aspartate semi-aldehyde dehydrogenase
hom: homoserine dehydrogenase
- Curated proteins or TIGRFams with EC 1.1.1.3
- UniProt sequence A0A1L6J6Q3: RecName: Full=Homoserine dehydrogenase {ECO:0000256|ARBA:ARBA00013376, ECO:0000256|RuleBase:RU000579}; EC=1.1.1.3 {ECO:0000256|ARBA:ARBA00013213, ECO:0000256|RuleBase:RU000579};
- UniProt sequence Q8A541_BACTN: RecName: Full=Aspartokinase {ECO:0000256|ARBA:ARBA00016273}; EC=1.1.1.3 {ECO:0000256|ARBA:ARBA00013213}; EC=2.7.2.4 {ECO:0000256|ARBA:ARBA00013059}; AltName: Full=Homoserine dehydrogenase {ECO:0000256|ARBA:ARBA00013376};
- UniProt sequence B8DRS3_DESVM: RecName: Full=Homoserine dehydrogenase {ECO:0000256|ARBA:ARBA00013376, ECO:0000256|RuleBase:RU000579}; EC=1.1.1.3 {ECO:0000256|ARBA:ARBA00013213, ECO:0000256|RuleBase:RU000579};
- Comment: Ga0059261_2711 from Sphingomonas koreensis DSMZ 15582 is distant from characterized homoserine dehydrogenases and is confirmed by fitness data. It is identical to A0A1L6J6Q3. It has been updated in the reannotations so need not be mentioned here. BT2403 from Bacteroides thetaiotaomicron (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 (B8DRS3_DESVM) is a somewhat diverged homoserine dehydrogenase. It has auxotrophic phenotypes.
- Total: 21 characterized proteins
metA: homoserine O-succinyltransferase
- Curated proteins or TIGRFams with EC 2.3.1.46
- Comment: 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.
- Total: 1 HMMs and 33 characterized proteins
metX: homoserine O-acetyltransferase
- Curated proteins or TIGRFams with EC 2.3.1.31
- Comment: 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).
- Total: 1 HMMs and 65 characterized proteins
hom_kinase: homoserine kinase
metB: cystathionine gamma-synthase
- Curated sequence O31631: Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.-
- Curated proteins or TIGRFams with EC 2.5.1.48
- Comment: METI_BACSU (O31631) has activity as CGS but is given a more vague EC number.
- Total: 1 HMMs and 13 characterized proteins
metC: cystathionine beta-lyase
metY: O-acetylhomoserine sulfhydrylase
- Curated proteins or TIGRFams with EC 2.5.1.49
- Curated sequence O31631: Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.-
- Ignore hits to items matching O-succinylhomoserine sulfhydrylase when looking for 'other' hits
- Comment: METI_BACSU (O31631) has activity as OAS but is given a more vague EC number.
- Total: 12 characterized proteins
metZ: O-succinylhomoserine sulfhydrylase
- Curated proteins matching O-succinylhomoserine sulfhydrylase
- Ignore hits to items matching EC 2.5.1.49 when looking for 'other' hits
- UniProt sequence A0A165KUI5_9BURK: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:KZT16112.1};
- UniProt sequence D8J1Y3_HERSS: SubName: Full=O-acetylhomoserine sulfhydrylase protein {ECO:0000313|EMBL:ADJ64766.1}; EC=2.3.1.31 {ECO:0000313|EMBL:ADJ64766.1};
- Comment: No EC number for metZ, so use "O-succinylhomoserine sulfhydrylase", which matches METZ_PSEAE and METZ_MYCTU. Two related proteins, Ac3H11_2452 (A0A165KUI5_9BURK) and HSERO_RS16440 (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).
- Total: 4 characterized proteins
metE: vitamin B12-independent methionine synthase
metH: vitamin B12-dependent methionine synthase
- Curated proteins or TIGRFams with EC 2.1.1.13
- Ignore hits to GFF1501 when looking for 'other' hits (ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13))
- Ignore hits to GFF1318 when looking for 'other' hits (Accessory protein for co(II)balamin reduction (DUF1638) (EC:2.1.1.13))
- Ignore hits to GFF1321 when looking for 'other' hits (Methionine synthase component, methyltransferase domain (EC:2.1.1.13))
- Ignore hits to GFF1319 when looking for 'other' hits (Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13))
- Ignore hits to GFF1582 when looking for 'other' hits (Methionine synthase component, pterin-binding domain (EC:2.1.1.13))
- UniProt sequence Q72BP9_DESVH: RecName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00014139}; EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032}; AltName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998};
- UniProt sequence B8DKK4_DESVM: RecName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00014139}; EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032}; AltName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998};
- Comment: Desulfovibrio have a somewhat diverged MetH, without the activation domain, but confirmed by cofitness (DVU1585 = Q72BP9_DESVH is cofit with MetF; DvMF_0476 = B8DKK4_DESVM is cofit with a RamA- like activation protein). 3-part split MetH proteins from Phaeobacter are ignored.
- Total: 1 HMMs and 7 characterized proteins
split_metH_1: Methionine synthase component, B12 binding and B12-binding cap domains
- Curated sequence GFF1319: Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13)
- Comment: In Phaeobacter and some related bacteria, MetH is split into 3 parts (PMC5764234)
- Total: 1 characterized proteins
split_metH_2: Methionine synthase component, methyltransferase domain
split_metH_3: Methionine synthase component, pterin-binding domain
B12-reactivation-domain: MetH reactivation domain
- HMM PF02965
- Ignore hits to items matching EC 2.1.1.13 when looking for 'other' hits
- Comment: In E. coli and many other bacteria, the MetH protein includes a reactivation domain (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.
- Total: 1 HMMs
ramA: ATP-dependent reduction of co(II)balamin
- HMM PF14574
- Curated proteins matching ATP-dependent reduction of co(II)balamin
- Comment: 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 (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. PF14574 describes only the C-terminal putative ATPase domain of RamA, but no other functions are known.
- Total: 1 HMMs and 2 characterized proteins
asd-S-transferase: sulfuration of L-aspartate semialdehyde, persulfide component
- UniProt sequence Q8TPT4_METAC: RecName: Full=L-aspartate semialdehyde sulfurtransferase {ECO:0000305}; EC=2.8.1.16 {ECO:0000305|PubMed:25938369};
- Curated sequence 8500721: Homocysteine formation from aspartate semialdehyde (DUF39 component)
- Comment: MA1821 or DvMF_1464 (see PMID:25315403 and PMC5764234)
- Total: 2 characterized proteins
asd-S-ferredoxin: reductive sulfuration of L-aspartate semialdehyde, ferredoxin component
asd-S-perS: putative persulfide forming protein
- UniProt sequence Y1715_METAC: RecName: Full=UPF0280 protein MA_1715 {ECO:0000255|HAMAP-Rule:MF_01079};
- Curated sequence 8499265: Homocysteine formation from aspartate semialdehyde (COG2122 or apbE like component)
- Comment: MA1715 or DvMF_0044 (see PMID:25315403 and PMC5764234) This putative persulfide forming component is not 100% required in Methanosarcina acetivorans (possible redundancy).
- Total: 2 characterized proteins
mesA: Methylcobalamin:homocysteine methyltransferase MesA
- Curated sequence P55299: Methionine synthase; Homocysteine methyltransferase; Methylcobalamin:homocysteine methyltransferase; EC 2.1.1.-
- Comment: 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).
- Total: 1 characterized proteins
mesB: Methylcobalamin:homocysteine methyltransferase MesB
- UniProt sequence A0A0V8M4G6: SubName: Full=Methionine synthase {ECO:0000313|EMBL:KSV18675.1};
- Comment: 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).
- Total: 1 characterized proteins
mesD: oxygen-dependent methionine synthase, methyltransferase component MesD
- UniProt sequence Q6F6Z8: SubName: Full=5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase {ECO:0000313|EMBL:CAG70167.1}; EC=2.1.1.14 {ECO:0000313|EMBL:CAG70167.1};
- UniProt sequence A0A2M8WFA5: SubName: Full=Methionine synthase {ECO:0000313|EMBL:RSU61740.1}; EC=2.1.1.13 {ECO:0000313|EMBL:RSU61740.1}; SubName: Full=Methionine synthase (B12-independent) {ECO:0000313|EMBL:PJI89611.1};
- Comment: 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.
- Total: 2 characterized proteins
mesX: oxygen-dependent methionine synthase, putative oxygenase component MesX
- UniProt sequence Q6F6Z7: SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:CAG70168.1};
- UniProt sequence A0A2M8WFB3: SubName: Full=DUF1852 domain-containing protein {ECO:0000313|EMBL:RSU61739.1};
- Comment: MesX is required for the activity of MesD, see PMC2290942.
- Total: 2 characterized proteins
Links
Downloads
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, 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