PaperBLAST
PaperBLAST Hits for VIMSS1206623 putative methionine synthase (1209 a.a., MVVAQASRQL...)
Show query sequence
>VIMSS1206623 putative methionine synthase
MVVAQASRQLTNSRFLDHLNGPERPVLVFDGATGTSLQGLDLTAEDFGGPELEGCNENLA
VTKPEAVKAVHRQFLEVGCDVIETDTFGAASIVLAEYGLEDKAFELNKRAAELAREMADE
FSTPDKPRFVAGSMGPTTKLPTLGHIDFDTMRDSFREQAEGLIAGDVDLFIVETCQDVLQ
IKAALQGIEEAFEASGERRALMVSVTMETTGTMLVGTDIAAVVSILEPFPIDILGLNCAT
GPEQMKEHIRYLSEHSPFTVSCIPNAGLPENVGGVAHYRLTPVELKMQLMHFVEDLGVQV
IGGCCGTTPSHIGSLAELAAELKPALRSSRHDAASDANVRPALNYEPAAASIYGVTPYQQ
DNSFLIIGERLNASGSRKVRELLAEEDWDGLVSVARGQVKENAHVLDVNVDYVGRDGEQD
MHQLVSRLVTNVNLPLMLDSTEWQKMEAGLKVAGGKCILNSTNYEDGDERFFKVLELARR
YGAGVVVGTIDEDGMARTAEKKFAIAQRAYRDALEFGIPAHEIFYDPLALPISTGIEEDR
LNGKATVDSIRMIRENLPGVHVVLGVSNVSFGLSPAARITLNSVFLHDCCEAGMDAAIVS
PAKILPLIKITEEHQTVCRDLINDNRRFDDGICVYDPLTELTKLFEGVSAKEARASGPSL
ADLPIEERLKQHIIDGERIGLEPSLDEALQAYPPLQIINTFLLDGMKVVGELFGSGQMQL
PFVLQSAETMKSAVAYLEPHMETAEGESTSKGKFLIATVKGDVHDIGKNLVDIILTNNGY
EVVNLGIKQSCEAIVEAQHEHQADCIAMSGLLVKSTAFMKDNLKAFNDAGIDVPVILGGA
ALTPRFVQKDCREVYNGKVIYGRDAFADLRFMDALMDAKGNDNWNNLEGFITDVPSGVGL
DEETESSTVERSTAEEKSQQDAPSPQLPVTTVRSEAVPAEPTPTAPFLGSVVITEADVDI
EEVFGFLDRNALFAGQWQLRKVQQQSRDEYDAMLKEKAEPVLQQWVDRCLQESLLTPRAA
YGYFPVGRDGNALRVFDASGETELGRFDLPRQRSGNRYCIADFFQDMTADGRPGDVLPMQ
AVTMGDKASEVAQELFKGDQYSDYLYFHGLAVQMAEAMAEWVHARIRRELGFADPDGMPL
RDVLAQRYRGSRYSFGYPACPNVADSRQQLSWLGADRIGLSMDASDQLSPEQSTTALVAL
HSKARYFSA
Running BLASTp...
Found 255 similar proteins in the literature:
SYNW1238 putative methionine synthase from Synechococcus sp. WH 8102
100% identity, 100% coverage
PMT0729 putative methionine synthase from Prochlorococcus marinus str. MIT 9313
74% identity, 99% coverage
SYNPCC7002_A2466 5-methyltetrahydrofolate--homocysteine methyltransferase (methionine synthase) from Synechococcus sp. PCC 7002
65% identity, 99% coverage
- Metagenomic analysis reveals potential interactions in an artificial coculture
Ren, AMB Express 2017 - “...corrinoids transport ( btuBFCD ) SYNPCC7002_A0634/0635/0637 MSTH_03067-03070 Cobalamin-associated enzymes Cobalamin-dependent methionine synthase ( metH ) SYNPCC7002_A2466 MSTH_00354/00815 PSTH_03850 Cobalamin-independent methionine synthase ( metE ) MSTH_01286 PSTH_01866 Methylmalonyl-CoA mutase MSTH_01813/02120 Cobalamin-dependent ribonucleotide reductase (class II) MSTH_00664 PSTH_00904 PSTH_00905 Cobalamin-independent ribonucleotide reductase (class I) SYNPCC7002_A1350 SYNPCC7002_A0382 PSTH_02138 PSTH_02139...”
- Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin Riboswitch In Vivo
Pérez, Journal of bacteriology 2016 - “...fragments of the metH gene (GenBank locus tag SYNPCC7002_A2466) were obtained by PCR with Synechococcus sp. strain PCC 7002 genomic DNA as the template...”
- “...a cobalamin-dependent methionine synthase gene (CyanoBase ID SYNPCC7002_A2466 [metH]), and bioinformatic analyses have suggested that this is probably the only...”
tll1027 5-methyltetrahydrofolate--homocysteine methyltransferase from Thermosynechococcus elongatus BP-1
65% identity, 99% coverage
RGRSB_0352 methionine synthase from cyanobacterium endosymbiont of Rhopalodia gibberula
63% identity, 99% coverage
ETSB_0394 methionine synthase from cyanobacterium endosymbiont of Epithemia turgida isolate EtSB Lake
62% identity, 99% coverage
PMM0877 putative methionine synthase from Prochlorococcus marinus sp. MED4
59% identity, 99% coverage
WP_159536573 methionine synthase from Streptomyces sp. Tu 3180
49% identity, 98% coverage
SCO1657 methionine synthase from Streptomyces coelicolor A3(2)
48% identity, 98% coverage
- Identification of metE as a second target of the sRNA scr5239 in Streptomyces coelicolor
Vockenhuber, PloS one 2015 - “...coelicolor two independent non-homologous enzymes can carry out this reaction: The cobalamin-dependent methionine synthase MetH (SCO1657) and the cobalamin-independent MetE (SCO0985). In the MetH catalysed reaction cobalamin serves as a methyl acceptor and donor giving MetH a roughly 50-fold higher turnover rate then its functional sibling...”
- Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor
Kim, BMC genomics 2015 - “...conditions. In addition, we observed low levels of NdgR binding at the promoters of metH (SCO1657) and leuA (SCO5559) relative to the other binding peaks. Taken together, these results show that binding locations of NdgR were successfully detected in vivo . Sequence analysis of NdgR-binding regions...”
- LAL regulators SCO0877 and SCO7173 as pleiotropic modulators of phosphate starvation response and actinorhodin biosynthesis in Streptomyces coelicolor
Guerra, PloS one 2012 - “...Only three SS genes are common to both mutants, namely aminotransferase SCO1054 , methionine synthase SCO1657 , and the lysyl-tRNA synthetase ( SCO3397 ), and all of them showed increased transcript levels in the mutants ( Table S2 ), which indicates a down-regulation of these genes...”
- ArgR of Streptomyces coelicolor is a versatile regulator
Pérez-Redondo, PloS one 2012 - “...and the B 12 -dependent and the B 12 -independent methionine synthases MetH and MetE (SCO1657 and SCO0985, respectively). Two genes involved in sporulation regulation, and five genes for aerial mycelium formation are also included in this group ( Table S1 ). Type II genes For...”
- Novel genes that influence development in Streptomyces coelicolor
Gehring, Journal of bacteriology 2004 - “...region of metH (Table 1) (36). The metH gene (SCO1657 or SCI46.02c) is inferred to encode the vitamin B12-dependent methionine synthase that catalyzes the final...”
EET03_RS15385 methionine synthase from Mycobacterium innocens
47% identity, 98% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi M.szulgai M. smegmatis...”
SSPN_RS0127935 methionine synthase from Saccharopolyspora spinosa NRRL 18395
47% identity, 100% coverage
CDN37_RS02225 methionine synthase from Mycobacterium persicum
47% identity, 98% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...MSMEG_0969 hemY ChlI component of cobalt chelatase SAMEA4434518_01694 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase CDN37_RS02225 MPHLCCUG_RS15920 A5717_31970 SAMEA4434518_01721 MXEN_01507 AWC27_RS09650 MSMEG_0093 mutB Methylmalonyl-CoA mutase SAMEA4434518_02142 MSMEG_3159 nrdZ Ribonucleotide reductase of class II MKAN_19005 MXEN_17528 We used RNA-Seq data available at ENA Database to estimate gene...”
MXEN_01507 methionine synthase from Mycobacterium xenopi RIVM700367
47% identity, 99% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...of cobalt chelatase SAMEA4434518_01694 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase CDN37_RS02225 MPHLCCUG_RS15920 A5717_31970 SAMEA4434518_01721 MXEN_01507 AWC27_RS09650 MSMEG_0093 mutB Methylmalonyl-CoA mutase SAMEA4434518_02142 MSMEG_3159 nrdZ Ribonucleotide reductase of class II MKAN_19005 MXEN_17528 We used RNA-Seq data available at ENA Database to estimate gene expression through transcripts per...”
O33259 Methionine synthase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Rv2124c Probable 5-methyltetrahydrofolate--homocystein methyltransferase MetH (Methionine synthase, vitamin-B12 dependent isozyme) (MS) from Mycobacterium tuberculosis H37Rv
46% identity, 100% coverage
- The unfoldase ClpC1 of Mycobacterium tuberculosis regulates the expression of a distinct subset of proteins having intrinsically disordered termini
Lunge, The Journal of biological chemistry 2020 (secret) - Diverse protein regulations on PHA formation in Ralstonia eutropha on short chain organic acids
Lee, International journal of biological sciences 2009 - “...tetrahydropteroyltriglutamate--homocysteine methyltransferase 4 28 (25) Q8FQB2 Streptomyces coelicolor Methionine biosynthesis Methionine synthase 6 27 (22) O33259 Mycobacterium tuberclosis Methionine biosynthesis Glutamate 5-kinase 3 35 (34) Q7N7B2 Photorhabdus luminescens subsp. laumondii Proline biosynthesis Putative cystathionine gamma-lyase 2 29 (21) Q59829 Streptomyces coelicolor Cysteine biosynthesis Acetylornitine aminotransferase 2...”
- Vitamin B12 uptake across the mycobacterial outer membrane is influenced by membrane permeability in Mycobacterium marinum
Izquierdo, Microbiology spectrum 2024 - “...(Rv0570) for DNA repair, MutAB proteins (Rv1492-1493) for fatty acid and cholesterol metabolism, and MetH (Rv2124c) involved in methionine synthesis in which B 12 is used as a cofactor for an efficient functionality ( 2 , 3 , 8 10 ). The MetH enzyme operates in...”
- “...we genetically complemented the cobC-metH mutant by expressing the wild-type copy of Mtb metH ( rv2124c ) and observed restored growth on B 12 -containing agar plates (Fig. S3). Vitamin B 12 is available during infection in the zebrafish model Nutrient deprivation is a known strategy...”
- Dependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos, Nature communications 2024 - “...mutant. We followed the procedure described above but starting from BAC Rv73 containing the gene Rv2124c ( metH ). The AES (Supplementary Note 1 ) were obtained using the BAC-knockouts as templates for a PCR using primers described in (Supplementary Table 2 ). Then, M. tuberculosis...”
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...ChlI component of cobalt chelatase Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae...”
- “...chelatase Rv2850c 135.66 6.78823001 38.01666667 3.454488224 81.53333333 115.3055458 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c 155.78 9.823003614 311.4966667 16.31473431 128.15 45.50090622 mutB Methylmalonyl-CoA mutase Rv1493 48.83 1.851323851 139.7433333 70.5155852 38.08333333 53.8579665 nrdZ Ribonucleotide reductase of class II Rv0570 60.79333333 1.360890232 366.2433333 120.7928051 119.6 101.265619 Studies...”
- Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis
Minias, Genome biology and evolution 2018 - “...metZ Rv0391 1,221 2.54 0.90 8 8 cobL Rv2072c 1,173 4.18 0.87 5 5 metH Rv2124c 3,579 2.93 0.84 14 13 hemD Rv0511 1,698 3.47 0.84 5 4 nrdZ Rv0570 2,054 3.65 0.76 11 10 cobK Rv2070c 735 5.85 0.72 5 3 cobB Rv2848c 1,374 1.97...”
- Identification of Mycobacterial Antigens in Human Urine by Use of Immunoglobulin G Isolated from Sera of Patients with Active Pulmonary Tuberculosis
Kim, Journal of clinical microbiology 2016 - “...Membrane transport protein mmpL8 Rv3823c 2 Methionine synthase Rv2124c 2 Molybdenum import ATP-binding protein Rv1859 1 Urine donors Serum donors Identified by...”
- Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs
Guzzo, PLoS pathogens 2016 - “...metH exhibited significantly increased sensitivity to SULFA treatment. In trans expression of H37Rv metH ( rv2124c ) restored SULFA resistance to both Rv metH and CDC1551 ( Fig 3E and 3F ). As previously suggested [ 39 ], the proliferation of CDC1551 in macrophages in the...”
- Phylogenetic analysis of vitamin B12-related metabolism in Mycobacterium tuberculosis
Young, Frontiers in molecular biosciences 2015 - “...B12-independent mechanism. Biosynthesis of methionine B12-dependent methionine synthesis M. tuberculosis has a B12-dependent methionine synthase (Rv2124c) with sequence characteristics matching the predominant form of MetH found in most actinomycetes (MetH a ). MetH catalyzes the B12-dependent synthesis of L-methionine (EC 2.1.1.13), utilizing L-homocysteine and 5-methyltetrahydrofolate (N...”
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AWC07_11205 methionine synthase from Mycobacterium gastri
47% identity, 99% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...cobalt chelatase Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi M.szulgai...”
ML1307 5-methyltetrahydrofolate-homocysteine methyltransferase from Mycobacterium leprae TN
46% identity, 100% coverage
- Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases
Ojo, Frontiers in cellular and infection microbiology 2021 - “...(ML2323c), asd (ML2322c), thrA (ML1129), metB (ML2394c), metA/X (ML0682c), metZ (ML0275c), metE (ML0961c) and metH (ML1307) were transcriptionally active in M. leprae under all conditions tested ( Figure4B ). All the genes of this probable alternate pathway were upregulated under axenic conditions with the exception of...”
SY28_RS08890 methionine synthase from Meiothermus taiwanensis
47% identity, 99% coverage
- Species-specific transcriptomic network inference of interspecies interactions
McClure, The ISME journal 2018 - “...each species. Specifically, the M. ruber metH gene (SY28_RS08890) which encodes methionine synthase, a B12-dependent enzyme, also had a large number of edges...”
- Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership
Bernstein, mSystems 2017 - “...i and pO 2 treatments into opposing clusters D ( tll1027 ) and C ( SY28_RS08890 ), indicating that methionine may be directly exchanged from T. elongatus as growth requirements increase with the specific growth rate. Both strains also expressed vitamin B 12 -independent homocysteine methyltransferase...”
- “...decreased with I i , and they were grouped into cluster C, including metHX ( SY28_RS08890 and SY28_RS05725 ). Genes involved in cysteine biosynthesis shared common transcriptional patterning between species, indicating that while M. ruber may have salvaged cyanobacterium-derived methionine, it likely synthesized its own cysteine...”
metH / Q8NQD1 cobalamin-dependent methionine synthase (EC 2.1.1.13) from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (see paper)
44% identity, 99% coverage
cg1701 homocysteine methyltransferase from Corynebacterium glutamicum ATCC 13032
45% identity, 98% coverage
PFREUD_11340 methionine synthase from Propionibacterium freudenreichii subsp. shermanii CIRM-BIA1
46% identity, 98% coverage
TTH_RS03220 methionine synthase from Thermus thermophilus HB8
45% identity, 98% coverage
NIS_RS03035 methionine synthase from Nitratiruptor sp. SB155-2
42% identity, 98% coverage
MT2183 5-methyltetrahydrofolate-homocysteine methyltransferase from Mycobacterium tuberculosis CDC1551
52% identity, 65% coverage
PPSC2_RS42420 methionine synthase from Paenibacillus polymyxa
39% identity, 98% coverage
PPE_RS12455 methionine synthase from Paenibacillus polymyxa E681
39% identity, 98% coverage
C1A50_RS13320 methionine synthase from Paenibacillus polymyxa
40% identity, 98% coverage
MLD56_13735 methionine synthase from Paenibacillus peoriae
39% identity, 98% coverage
WP_108075232 methionine synthase from Vitiosangium sp. GDMCC 1.1324
39% identity, 99% coverage
- 2-Hydroxysorangiadenosine: Structure and Biosynthesis of a Myxobacterial Sesquiterpene-Nucleoside
Okoth, Molecules (Basel, Switzerland) 2020 - “...Sensory transducer WP_146210122 92/74.69 sora12 509 Eudesmadiene transferase WP_108075230 100/73.80 sora13 1171 Methionine synthase (MetH) WP_108075232 100/97.61 sora14 299 SAM-dependent methyltransferase WP_108075233 100/97.32 sora15 292 Patatin lipid acyl hydrolases WP_108075234 100/98.97 sora16 375 Dehydrogenase WP_052519033 91/82.11 sora17 205 Tet R transcriptional regulator WP_073564266 100/79.62 sora18 147...”
GBAA4478 5-methyltetrahydrofolate--homocysteine methyltransferase from Bacillus anthracis str. 'Ames Ancestor'
39% identity, 98% coverage
- Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains
Zaide, Microorganisms 2020 - “...failure of the htrA strain to respond to oxidative stress. Interestingly, the two genesGBAA2633 and GBAA4478 (belonging to the metal ion binding GO category)downregulated in the WT strain, encode a cysteine dioxygenase and a 5-methyltetrahydrofolate-homocysteine methyltransferase, respectively ( Figure 4 A). Cysteine dioxygenase (GBAA2633), which is...”
- “...cysteine, is downregulated 26-fold upon induction of oxidative stress. The second gene, homocysteine methyl transferase (GBAA4478), downregulated more than 3-fold, participates in the process of converting homocysteine to methionine. The downregulation of these two genes that are part of the biosynthesis of cysteine and methionine may...”
8g3hA / A0A0A2XCD7 Structure of cobalamin-dependent methionine synthase (meth) in a resting state (see paper)
48% identity, 72% coverage
- Ligand: cobalamin (8g3hA)
MSMEG_4185 methionine synthase from Mycobacterium smegmatis str. MC2 155
MSMEG_4185 methionine synthase from Mycolicibacterium smegmatis MC2 155
34% identity, 95% coverage
- The Benefits of Toxicity: M. smegmatis VapBC TA Module Is Induced by Tetracycline Exposure and Promotes Survival
Zamakhaev, Microorganisms 2023 - “...the decrease amidst synthase enzymes, such as tryptophan synthase MSMEG_3220, asparagine synthase MSMEG_2594, methionine synthase MSMEG_4185, carbamoyl phosphate synthase MSMEG_3047, etc. (nine enzymes overall). However, the abundance ratio of glutamine synthetase MSMEG_4290 was 94-fold higher when compared to the control. Moreover, three enzymes of amino acid...”
- De Novo Cobalamin Biosynthesis, Transport, and Assimilation and Cobalamin-Mediated Regulation of Methionine Biosynthesis in Mycobacterium smegmatis
Kipkorir, Journal of bacteriology 2021 - “...Ethanolamine ammonia-lyase, large subunit AdoCbl Isomerization MSMEG_1554 ( eutC ) Ethanolamine ammonia-lyase, light chain AdoCbl MSMEG_4185 ( metH ) Methionine synthase MeCbl Methyl transfer a Annotation is from reference 63 . We postulated that metE would similarly be subject to riboswitch-mediated repression in M. smegmatis ,...”
- “...deleted 120-bp cobK allele. To generate an in-frame, unmarked deletion in M. smegmatis metH ( MSMEG_4185 ), a 1,524-bp amplicon (FR1) of the 5 coding sequence of metH and another 1,480-bp amplicon (FR2) containing 354bp of the 3 end of metH were joined in a three-way...”
- Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs
Guzzo, PLoS pathogens 2016 - “...in this subgroup had Himar1 insertions at three different TA dinucleotides within the same gene, msmeg_4185 (2xTA 499-500 , 1xTA 2881-2882 , and 1xTA 3091-3092 , S1 Fig ), which encodes a homolog of B 12 -dependent methionine synthase. Two other mutants had insertions at TA...”
- “...the intrinsic SULFA resistance, and 5-CH 3 -H 4 PteGlu n metabolism, the encoding genes, msmeg_4185 and msmeg_3873 , respectively, were individually deleted by homologous recombination [ 34 ]. Similar to the transposon mutants, the targeted null mutants, Ms metH and Ms cobIJ , displayed increased...”
V22_33860 methionine synthase from Calycomorphotria hydatis
33% identity, 97% coverage
MPHLCCUG_RS15920 methionine synthase from Mycolicibacterium phlei
33% identity, 94% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...hemY ChlI component of cobalt chelatase SAMEA4434518_01694 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase CDN37_RS02225 MPHLCCUG_RS15920 A5717_31970 SAMEA4434518_01721 MXEN_01507 AWC27_RS09650 MSMEG_0093 mutB Methylmalonyl-CoA mutase SAMEA4434518_02142 MSMEG_3159 nrdZ Ribonucleotide reductase of class II MKAN_19005 MXEN_17528 We used RNA-Seq data available at ENA Database to estimate gene expression...”
Alvin_1622 methionine synthase from Allochromatium vinosum DSM 180
34% identity, 94% coverage
- Metabolomic profiling of the purple sulfur bacterium Allochromatium vinosum during growth on different reduced sulfur compounds and malate
Weissgerber, Metabolomics : Official journal of the Metabolomic Society 2014 - “...O -succinyl- l -homoserine sulfhydrylase (Alvin_1027), MetE cobalamin-independent methionine synthase (Alvin_2262), MetH cobalamin-dependent methionine synthase (Alvin_1622), AhcY adenosylhomocysteinase (Alvin_0320), BchM magnesium protoporphyrin O -methyltransferase (Alvin_2638), MetK S -adenosylmethionine synthetase (Alvin_0318); 0319, methyltransferase type 11 (Alvin_0319). The transcriptomic ( boxes ) (Weissgerber et al. 2013 ), proteomic...”
- “...precursor for methionine by accepting a methyl group from N5-methyl-5,6,7,8-tetrahydrofolate catalyzed by either cobalamin-dependent (MetH: Alvin_1622) or cobalamin-independent (MetE: Alvin_2262) methionine synthase (Pejchal and Ludwig 2005 ). Homocysteine is the most abundant amino acid in A. vinosum (up to five times more abundant than the proteinogenic...”
AWC27_RS09650 methionine synthase from Mycobacterium szulgai
33% identity, 95% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...cobalt chelatase SAMEA4434518_01694 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase CDN37_RS02225 MPHLCCUG_RS15920 A5717_31970 SAMEA4434518_01721 MXEN_01507 AWC27_RS09650 MSMEG_0093 mutB Methylmalonyl-CoA mutase SAMEA4434518_02142 MSMEG_3159 nrdZ Ribonucleotide reductase of class II MKAN_19005 MXEN_17528 We used RNA-Seq data available at ENA Database to estimate gene expression through transcripts per million...”
ABAYE2822 methionine synthase (B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF) from Acinetobacter baumannii AYE
31% identity, 96% coverage
Q7MHB1 Methionine synthase from Vibrio vulnificus (strain YJ016)
32% identity, 96% coverage
MAB_2129 5-methyltetrahydrofolate--homocysteine methyltransferase MetH from Mycobacterium abscessus ATCC 19977
34% identity, 95% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...component of cobalt chelatase Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M....”
- “...ChlI component of cobalt chelatase MAB_2985c 196.3366667 1.652099674 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase MAB_2129 605.9966667 39.45958101 MSMEG_0093 94.66 39.15167557 mutB Methylmalonyl-CoA mutase MAB_2711c 180.9466667 2.206928484 nrdZ Ribonucleotide reductase of class II Gene name Description M. tuberculosis Locus Rich 7H9 broth Cholesterol Macrophages Average SD...”
MAB_2129 methionine synthase from Mycobacteroides abscessus ATCC 19977
34% identity, 94% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...component of cobalt chelatase Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M....”
- “...ChlI component of cobalt chelatase MAB_2985c 196.3366667 1.652099674 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase MAB_2129 605.9966667 39.45958101 MSMEG_0093 94.66 39.15167557 mutB Methylmalonyl-CoA mutase MAB_2711c 180.9466667 2.206928484 nrdZ Ribonucleotide reductase of class II Gene name Description M. tuberculosis Locus Rich 7H9 broth Cholesterol Macrophages Average SD...”
MAV_2379 methionine synthase from Mycobacterium avium 104
33% identity, 94% coverage
- Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice
Ignatov, Acta naturae 2010 - “...the I/St mice MAV_2015 MbtG; mycobactin lysine-N-oxygenase MAV_1696 Glutamate dehydrogenase MAV_1304 NarH; nitrate reductase, ?-subunit MAV_2379 MetH; vitamin B12-dependent methionine synthase MAV_2385 Mce protein MAV_2063 Mce protein MAV_2386 Mce protein MAV_0118 PPE protein MAV_3109 RifB; polyketide synthase 7 MAV_0880 3-Ketosteroid-?-1-dehydrogenase MAV_3000 Acyl-CoA dehydrogenase MAV_4019 Assumed acyl-CoA...”
- “...important, for example, when the pathogen is in a latent state [ 27 ]. The MAV_2379 gene coding for 12 -dependent methionine synthase MetH is expressed at a high level in M. vium from the I/St mice. This protein is involved in the final stage of...”
A5717_31970 methionine synthase from Mycolicibacterium porcinum
33% identity, 95% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...ChlI component of cobalt chelatase SAMEA4434518_01694 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase CDN37_RS02225 MPHLCCUG_RS15920 A5717_31970 SAMEA4434518_01721 MXEN_01507 AWC27_RS09650 MSMEG_0093 mutB Methylmalonyl-CoA mutase SAMEA4434518_02142 MSMEG_3159 nrdZ Ribonucleotide reductase of class II MKAN_19005 MXEN_17528 We used RNA-Seq data available at ENA Database to estimate gene expression through...”
STY4405 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
32% identity, 96% coverage
Clocel_2896 methionine synthase from Clostridium cellulovorans 743B
32% identity, 97% coverage
- Clostridium cellulovorans Proteomic Responses to Butanol Stress
Costa, Frontiers in microbiology 2021 - “...of amino acids including proline and arginine (Clocel_2734, Clocel_3150, Clocel_1668), lysine (Clocel_1978, Clocel_3115), methionine (Clocel_1764, Clocel_2896, Clocel_3040), and branched chain amino acids (BCAA) (Clocel_1324, Clocel_1325, Clocel_0493) ( Table 1 and Supplementary Table 2 ). In addition, up-regulated proteins include four aminotransferases (Clocel_1948, Clocel_2059, Clocel_2390, Clocel_3812). The...”
MDG893_RS02235 methionine synthase from Marinobacter algicola DG893
32% identity, 97% coverage
VC0390 5-methyltetrahydrofolate--homocysteine methyltransferase from Vibrio cholerae O1 biovar eltor str. N16961
32% identity, 96% coverage
MCNS_30990 methionine synthase from Mycobacterium conspicuum
33% identity, 94% coverage
- Cobalamin is present in cells of non-tuberculous mycobacteria, but not in Mycobacterium tuberculosis
Minias, Scientific reports 2021 - “...of cobalt chelatase Rv2850c MAB_2985c MCNS_17540 Vitamin B12 dependent enzymes metH 5-Methyltetrahydrofolatehomocysteine methyltransferase Rv2124c MAB_2129 MCNS_30990 AWC07_11205 H0P51_RS04340 EET03_RS15385 mutB Methylmalonyl-CoA mutase Rv1493 MAB_2711c MCNS_22010 nrdZ Ribonucleotide reductase of class II Rv0570 AWC07_08365 Species M. kansasii M. persicum M. phlei M. porcinum M. terrae M. xenopi...”
BMEA_RS00885 methionine synthase from Brucella melitensis ATCC 23457
32% identity, 94% coverage
- Genetic Characterization and Comparative Genome Analysis of Brucella melitensis Isolates from India
Azam, International journal of genomics 2016 - “...23457 in the coding region. S. no Gene ID ATCC_23457 Bm IND1 Gene name 1 BMEA_RS00885 GTTTCGCGGAAGCTTTCGCGGAA GTTTCGCGGAA Methionine synthase 2 BMEA_RS00935 CGGG CGGGG Glycerol-3-phosphate dehydrogenase 3 BMEA_RS00980 GCC GCCC ABC transporter permease 4 BMEA_RS01770 ATTTTTT ATTTTT FAD-binding molybdopterin dehydrogenase 5 BMEA_RS02325 ATAT ATATTAT 4-Hydroxy-3-methylbut-2-enyl diphosphate...”
A1S_0971 B12-dependent methionine synthase from Acinetobacter baumannii ATCC 17978
31% identity, 97% coverage
JHW33_RS14885 methionine synthase from Rahnella aceris
32% identity, 96% coverage
STM14_5035 methionine synthase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
32% identity, 96% coverage
BMEI1759 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE from Brucella melitensis 16M
32% identity, 94% coverage
- Transcriptomic Analysis of the Brucella melitensis Rev.1 Vaccine Strain in an Acidic Environment: Insights Into Virulence Attenuation
Salmon-Divon, Frontiers in microbiology 2019 - “...Downregulation BMEI0624 Ketol-acid reductoisomerase Downregulation BMEI0626 PLP-dependent aminotransferase family protein Upregulation BMEI0796 Hypothetical protein Downregulation BMEI1759 Methionine synthase Downregulation BMEI1837 DUF3131 domain-containing protein Downregulation BMEII0056 Magnesium-translocating P-type ATPase Upregulation BMEII0077 Isochorismate synthase Upregulation BMEII0361 Sugar ABC transporter ATP-binding protein Upregulation BMEII0591 Sugar ABC transporter permease Upregulation...”
- “...and degradation ( Eschenbrenner et al., 2002 ). Second, Rev.1 showed a downregulated expression of BMEI1759 ( Table 3 ), which encodes for the vitamin B12-dependent methyltransferase, MetH ( Lestrate et al., 2000 ). As MetH is involved in methionine biosynthesis, its downregulation in Rev.1 may...”
- Genomic analysis of the original Elberg Brucella melitensis Rev.1 vaccine strain reveals insights into virulence attenuation
Salmon-Divon, Virulence 2018 - “...genes involved in amino acid metabolism (Supplementary Table S5). Notably, we found that the ORF BMEI1759 possesses a missense mutation (c.523G>C) in the Rev.1 genome. This ORF encodes the vitamin B12-dependent methyltransferase MetH, which is involved in methionine biosynthesis and was previously screened in a murine...”
- Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M
Brambila-Tapia, PloS one 2014 - “...dipeptide transport protein, partial E 171 [7] BMEI0933 cysK Cysteine synthase A E 212 [17] BMEI1759 metH B12-dependent methionine synthase E 510 [17] BMEII0040 gltB Glutamate synthase [NADPH] large chain E 566 [8] BMEII0136 pheB Homoprotocatechuate 2,3-dioxygenase E 81 [7] BMEII0626 BMEII0626 Membrane dipeptidase E 269...”
- Differential expression of iron acquisition genes by Brucella melitensis and Brucella canis during macrophage infection
Eskra, PloS one 2012 - “...BMEI1757 BCAN_A0196 aminotransferase - NC 2.96 BMEI1758 BCAN_A0195 ttranscriptional activator, LuxR family - 2.36 NC BMEI1759 BCAN_A0193 B12-dependent methionine synthase metH NC 2.17 BMEI1760 BCAN_A0192 hypothetical protein BMEI1760 - NC 2.17 BMEI1764 BCAN_A0188 oxidoreductase - NC 56.25 BMEI1765 BCAN_A0187 phosphoadenosine phosphosulfate reductase cysH NC 45.65 BMEI1766...”
- Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics
He, Frontiers in cellular and infection microbiology 2012 - “...BMEI0451 Macrophages 12438693 20 leuC BMEI0157 Macrophages 12438693 21 lysA BMEI0084 Macrophages 12438693 22 metH BMEI1759 Mice, macrophages, HeLa 14979322 23 nifS BMEI1043 Macrophages 14979322 24 pheB BMEII0136 Mice 14979322 25 serB BMEI0615 Macrophages 12438693 26 thrA BMEI0725 Macrophages 14979322 27 thrC BMEI1450 Macrophages 14979322 F:...”
BAB1_0188 Dihydropteroate synthase, DHPS:Homocysteine S-methyltransferase:Cobalamin-dependent methionine synthase, B12-binding:Vitamin ... from Brucella melitensis biovar Abortus 2308
32% identity, 94% coverage
- Brucella Periplasmic Protein EipB Is a Molecular Determinant of Cell Envelope Integrity and Virulence
Herrou, Journal of bacteriology 2019 - “...and the metabolic genes encoding methionine synthase (bab1_0188) and homoserine dehydrogenase (bab1_1293). (B) Growth on SBA plates containing 2 g/ml of...”
- “...lovHK (bab2_0652) (30), bab1_1293 (homoserine dehydrogenase), and bab1_0188 (methionine synthase) had fewer Tn insertions in the eipB background relative to the...”
- The RNA chaperone Hfq independently coordinates expression of the VirB type IV secretion system and the LuxR-type regulator BabR in Brucella abortus 2308
Caswell, Journal of bacteriology 2012 - “...include metH (B12-dependent methionine synthase; BAB1_0188), hyp (hypothetical protein; BAB1_0189), babR (LuxR-type transcriptional regulator; BAB1_0190), and...”
- “...region are metH (B12dependent methionine synthase; BAB1_0188), hyp (hypothetical protein; BAB1_0189), babR (LuxR-type transcriptional regulator; BAB1_0190), and...”
- Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes
Crasta, PloS one 2008 - “...cysK 42 10 BAB1_1968 7 7 1 Cysteine synthase 97 9 BR0188 metH 42 10 BAB1_0188 1 1 methionine synthase 110 6 BRA1146 fliF 30 3 BAB2_1105 1 1 flagellar M-ring protein FliF 120 8 BR0181 cysI 42 8 BAB1_0181 1 2 1 Hypothetical protein 128...”
BR0188 5-methyltetrahydrofolate--homocysteine methyltransferase from Brucella suis 1330
32% identity, 94% coverage
BCAN_A0193 methionine synthase from Brucella canis ATCC 23365
32% identity, 94% coverage
YPO3722 5-Methyltetrahydrofolate--homocysteine methyltransferase from Yersinia pestis CO92
y0020 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF from Yersinia pestis KIM
31% identity, 96% coverage
- Dynamics of CRISPR loci in microevolutionary process of Yersinia pestis strains
Barros, PloS one 2014 - “...Transcriptional Regulator 2516 AGGTGCAACAGGGACTTTAGGATAGAAAAGTCC fosfolipaseD pMT1 Plasmid Region 2517 ACTTAGGGACATTAGCTTGGGATGTGAAACAG YPO3682 Transcriptional Regulator 2518 GTGTGGGTTTCGACATCCAACAACTGCCAAAT YPO3722 Methyltransferase 2519 AAGCTAAAGGCCCGCCGTTTGTGGTGGTACCA pMT1 pMT1 Plasmid Region 2520 ATGTAGTTCCCGCTGGAACTTGTCCATCCATA YPO2108 Hypothetical Phage Protein 2521 CCTTTCCCAGTAGAGCTGAACCATCTTTATCA YPO2109 Hypothetical Phage Protein 2522 GTTTGCTACCATCACCGCCAGTAGTGTATCCC YPO1270 Protein ABC transporter 2523 CTTGACCCTCAAATTGAGTGTAAAGGGGTTTGG YPO2093 Phage Protein...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...in macrophagesc Annotatione Not applicable YPO3722, methionine synthase Hypothetical protein YPO0256, two-component sensor, spiR/ssrA Defectived Defective...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...95-70 21-29 98-31 100-53 61-22 31-05 75-11 41-48 Unknown 5 to y0020 y0020 y0455b y0513 y0513 y0513 3 to y0564 y0943b 3 to y1820 y1921 y1921 y1921 y2124 3 to...”
- “...in this screen encode hypothetical proteins (e.g., y0020, y2124, Downloaded from http://iai.asm.org/ on February 13, 2017 by University of California, Berkeley...”
LIC20085 methionine synthase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
LB108 B12-dependent methionine synthase from Leptospira interrogans serovar lai str. 56601
LB_108 methionine synthase from Leptospira interrogans serovar Lai str. 56601
32% identity, 96% coverage
- Response of Leptospira interrogans to physiologic osmolarity: relevance in signaling the environment-to-host transition
Matsunaga, Infection and immunity 2007 - “...LIC13430 LIC20149 LIC20079 LIC12233 LIC12331 LIC13353 LIC20085 LIC13321 LIC13194 LIC13202 LIC20132 LIC20171 LIC13208 LIC20041 LIC11143 LIC12322 LIC12323...”
- Response of Leptospira interrogans to physiologic osmolarity: relevance in signaling the environment-to-host transition
Matsunaga, Infection and immunity 2007 - “...LA4275 LA1101 LA4286 LB187 LB102 LA1532 LA1416 LA4200 LB108 LA4164 LA3998 LA4009 LB162 LB215 LA4019 LB055 LA2915 LA1424 LA1423 LB274 LA1430 LA4139 LA0932 LA1161...”
- Synthesis of autoinducer 2 by the lyme disease spirochete, Borrelia burgdorferi
Babb, Journal of bacteriology 2005 - “...salvage enzyme, the ortholog of MetH encoded by ORF LB108. Next, plasmid libraries of B. burgdorferi DNA were used in attempts to complement an E. coli metE...”
- The sigma factor σ54 is required for the long-term survival of Leptospira biflexa in water
Zhang, Molecular microbiology 2018 - “...LEPBI_I2431 2.54 - Hypothetical protein No hit No hit LEPBI_II0183 2.54 COG1410E B12-dependent methionine synthase LB_108 LBL_4107 LEPBI_I3034 2.45 COG3329R Putative permease; putative membrane protein LA_4270 LBL_0122 LEPBI_I2424 2.42 COG1136V ABC-type transport system, ATP binding protein LA_0274, LA_2982, LA_3713 LBL_0572, LBL_0299, LBL_2006, LBL_2140 LEPBI_I3255 2.32 COG0300R...”
SMc03112 PROBABLE 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT ISOZYME) PROTEIN from Sinorhizobium meliloti 1021
32% identity, 94% coverage
GQR50_20625 methionine synthase from Aeromonas hydrophila
31% identity, 96% coverage
VIBHAR_03712 cobalamin-dependent methionine synthase from Vibrio harveyi ATCC BAA-1116
32% identity, 96% coverage
c4976 5-methyltetrahydrofolate--homocysteine methyltransferase from Escherichia coli CFT073
32% identity, 96% coverage
SO1030 5-methyltetrahydrofolate--homocysteine methyltransferase from Shewanella oneidensis MR-1
32% identity, 95% coverage
Cbs_3100 methionine synthase from Clostridium beijerinckii ATCC 35702
32% identity, 98% coverage
W5S_RS19920 methionine synthase from Pectobacterium parmentieri
31% identity, 98% coverage
MMAR_4825 5-methyltetrahydrofolate--homocysteine methyltransferase, MetH from Mycobacterium marinum M
32% identity, 95% coverage
ACIAD1045 methionine synthase (B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase, repressor of metE and metF) from Acinetobacter sp. ADP1
32% identity, 96% coverage
S3645 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase from Shigella flexneri 2a str. 2457T
31% identity, 96% coverage
ECs4937 B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase from Escherichia coli O157:H7 str. Sakai
31% identity, 96% coverage
MetH / b4019 cobalamin-dependent methionine synthase (EC 2.1.1.13) from Escherichia coli K-12 substr. MG1655 (see 60 papers)
metH / P13009 cobalamin-dependent methionine synthase (EC 2.1.1.13) from Escherichia coli (strain K12) (see 58 papers)
METH_ECOLI / P13009 Methionine synthase; 5-methyltetrahydrofolate--homocysteine methyltransferase; Methionine synthase, vitamin-B12-dependent; MS; EC 2.1.1.13 from Escherichia coli (strain K12) (see 4 papers)
metH methionine synthase; EC 2.1.1.13 from Escherichia coli K12 (see 15 papers)
NP_418443 cobalamin-dependent methionine synthase from Escherichia coli str. K-12 substr. MG1655
b4019 B12-dependent methionine synthase from Escherichia coli str. K-12 substr. MG1655
31% identity, 96% coverage
- function: Catalyzes the transfer of a methyl group from methyl- cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate.
catalytic activity: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine (RHEA:11172)
cofactor: methylcob(III)alamin
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.) - Antimalarial target vulnerability of the putative Plasmodium falciparum methionine synthase
Leela, PeerJ 2024 - “...the cobalamin-dependent methionine synthase (MS) enzymes from human (MTR, Q99707-1) and Escherichia coli K12 (metH, P13009), together with Plasmodium spp. candidate MS from orthologous group 1324at5820 encoded by P.falciparum PF3D7_1233700 (Pf, Q8I585), P.knowlesi PKH_145080 (Pk, A0A384KWI2), P.malariae PmUG01_14067900 (Pm, A0A1A8X239), P. ovale wallikeri PowCR01_140053700 (Pow, A0A1C3L5P3),...”
- “...the cobalamin-dependent methionine synthase (MS) enzymes from human (MTR, Q99707-1) and Escherichia coli K12 (metH, P13009), together with Plasmodium candidate MS from orthologous group 1324at5820 encoded by P. falciparum PF3D7_1233700 (Pf, Q8I585), P. knowlesi PKH_145080 (Pk, A0A384KWI2), P. malariae PmUG01_14067900 (Pm, A0A1A8X239), P. ovale wallikeri PowCR01_140053700...”
- Proteomic analyses revealed the antibacterial mechanism of Aronia melanocarpa isolated anthocyanins against Escherichia coli O157: H7
Deng, Current research in food science 2022 - “...related to energy metabolism (P00363), two proteins related to amino acid biosynthesis and metabolism (P00370, P13009), and one protein related to lipid metabolism and transport (P76506). In the MRM experiments, the protein was quantified using peptide segments to draw a box-plot. Fig. 9 shows the box-plot...”
- “...Down P00370 gdhA NADP-specific glutamate dehydrogenase Up Q9S5G5 hisB Histidine biosynthesis bifunctional protein HisB Down P13009 metH Methionine synthase Up P06988 hisD Histidinol dehydrogenase Up B1LRA3 msrA Peptide methionine sulfoxide reductase MsrA Up P0AD97 livJ Leu/Ile/Val-binding protein Up Lipid metabolism and transport P0AEK5 fabI Enoyl-[acyl-carrier-protein] reductase...”
- Study on the Mechanism of the Danggui-Chuanxiong Herb Pair on Treating Thrombus through Network Pharmacology and Zebrafish Models.
Zhang, ACS omega 2021 - “...T54 72kDa type IV collagenase P08253 MMP2 T55 matrix metalloproteinase-9 P14780 MMP9 T56 methionine synthase P13009 MTR T57 NADH dehydrogenase [ubiquinone] 1 subcomplex subunit 4-like2 Q9NRX3 NDUFA4L2 T58 acyl carrier protein, mitochondrial O14561 NDUFAB1 T59 nuclear factor erythroid 2-related factor2 Q14494 NFE2L2 T60 nuclear factor NF-kappa-B...”
- Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels.
Lian, BMC plant biology 2015 - “...(Q2QLY5), METE2 ORYSJ (Q2QLY4), MS1 ARATH (O50008), MS2 ARATH (Q9SRV5), MS3 ARATH (Q0WNZ5), METH ECOLI (P13009), METE YEAST (P05694), METH HUMAN (Q99707), METH RAT (Q9Z2Q4), METH MOUSE (A6H5Y3); FPGS-1 SORBI (C5WWE5), FPGS-2 SORBI (C5WMM8), FPGS-1 SETIT (K4A7H2), FPGS-2 SEITI (K4A839), FPGS-1 ORYSJ (Q337F3), FPGS-2 ORYSJ (Q10SU1),...”
- Uncovering the human methyltransferasome
Petrossian, Molecular & cellular proteomics : MCP 2011 - “...the N-terminal sequence of MetH (UniProtKB accession number P13009 (residues 2-325)) using the PSI-BLAST parameter. These proteins were confirmed by the HHpred...”
- “...of the C terminus of MetH (UniProtKB accession number P13009 (residues 897-1227)) was used to build its superfamily profile through PSI-BLAST and scan the human...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...P00959 Methionyl-tRNA synthetase 5.56/76,123.54 MetH P13009 Methionine synthase 4.97/135,865.85 4.96/134,153 MetK P0A817 S-Adenosylmethionine synthetase...”
- Synthesis of autoinducer 2 by the lyme disease spirochete, Borrelia burgdorferi
Babb, Journal of bacteriology 2005 - “...accession numbers M87625, AAK45422, X92082, AF082893, P13009, AAN51667, CAE07753, AAC73364, and U50929, respectively). Each BORRELIA BURGDORFERI AI-2 3082...”
- Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication
Pejchal, PLoS biology 2005 - “...(SwissProt P25665), S. cerevisiae MetE (SwissProt P05694), T. maritima MetE/TM1286 (SwissProt Q9X112), and MetH (SwissProt P13009). This research was supported by grants from the National Institutes of Health (NIH) GM16429 (to MLL) and the Michigan NIH Molecular Biophysics Training Grant GM08270 (to RP). The authors would...”
- More
- A disulfide-stabilized conformer of methionine synthase reveals an unexpected role for the histidine ligand of the cobalamin cofactor.
Datta, Proceedings of the National Academy of Sciences of the United States of America 2008 - GeneRIF: describe an x-ray structure of the mutant fragment in the reactivation conformation
- Cloning and sequence analysis of the Escherichia coli metH gene encoding cobalamin-dependent methionine synthase and isolation of a tryptic fragment containing the cobalamin-binding domain.
Banerjee, The Journal of biological chemistry 1989 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs
Guzzo, PLoS pathogens 2016 - “..., b1710 , and b1709 , respectively) triple mutant remained SULFA resistant, whereas metH ( b4019 ), btuB ( b3966 ), and a btuB CED quadruple mutant all became hypersusceptible ( Fig 4A , Table 1 ). In serial dilution-spot tests using 125 g/ml SMZ, these...”
- Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Orth, BMC systems biology 2012 - “...(b3708) or malY (b1622) aroE (b3281) ydiB (b1692) ilvA (b3772) tdcB (b3117) metE (b3829) metH (b4019) ubiB (b3835) alternate reaction: OPHHX3 glnA (b3870) ycjK (b1297) metL (b3940) thrL (b0002) or malY (b1622) ppa (b4226) ppx (b2502) or surE (b2744) serB (b4388) alternate reaction: GHMT2r Table 4...”
- Genome-scale gene/reaction essentiality and synthetic lethality analysis
Suthers, Molecular systems biology 2009 - “...YadF (b0126) Disjoint pair Hashimoto and Kato (2003) High CO 2 concentration metE (b3829), metH (b4019) Disjoint pair Ahmed (1973) and Urbanowski et al (1987) Methionine cysK (b2414), cysM (b2421) Disjoint pair Saito et al (1993) Cysteine argF (b0273), argI (b4254) Disjoint pair Lee and Cho...”
- “...Cannot complement folA (b0048); Hypothesis Suppress cynT (b0339) Cannot complement yadF (b0126); Hypothesis Suppress metH (b4019) Cannot complement metE (b3829); Hypothesis Change HSDy GPR a relationship from OR to AND thrA (b0002) and metL (b3940) cannot complement each other; both essential; Hypothesis Suppress puuA (b1297) cannot...”
SAMCFNEI73_Ch3399 methionine synthase from Sinorhizobium americanum
32% identity, 94% coverage
LBL_4107 Methionine synthase from Leptospira borgpetersenii serovar Hardjo-bovis L550
31% identity, 96% coverage
- The sigma factor σ54 is required for the long-term survival of Leptospira biflexa in water
Zhang, Molecular microbiology 2018 - “...2.54 - Hypothetical protein No hit No hit LEPBI_II0183 2.54 COG1410E B12-dependent methionine synthase LB_108 LBL_4107 LEPBI_I3034 2.45 COG3329R Putative permease; putative membrane protein LA_4270 LBL_0122 LEPBI_I2424 2.42 COG1136V ABC-type transport system, ATP binding protein LA_0274, LA_2982, LA_3713 LBL_0572, LBL_0299, LBL_2006, LBL_2140 LEPBI_I3255 2.32 COG0300R SDR...”
BP3594 5-methyltetrahydrofolate--homocysteine methyltransferase from Bordetella pertussis Tohama I
32% identity, 94% coverage
LEPBI_II0183 Methionine synthase from Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
32% identity, 95% coverage
- The sigma factor σ54 is required for the long-term survival of Leptospira biflexa in water
Zhang, Molecular microbiology 2018 - “...signal peptide No hit No hit LEPBI_I2431 2.54 - Hypothetical protein No hit No hit LEPBI_II0183 2.54 COG1410E B12-dependent methionine synthase LB_108 LBL_4107 LEPBI_I3034 2.45 COG3329R Putative permease; putative membrane protein LA_4270 LBL_0122 LEPBI_I2424 2.42 COG1136V ABC-type transport system, ATP binding protein LA_0274, LA_2982, LA_3713 LBL_0572,...”
Avin_29240 5-methyltetrahydrofolate--homocysteine methyltransferase, MetH from Azotobacter vinelandii AvOP
31% identity, 93% coverage
- Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)
Robson, PloS one 2015 - “...-independent ribonucleoside reductase (discussed earlier: Achr_570; Avin_00800); met H for the B12-dependent methionine synthase (Achr_18530; Avin_29240); and eut BC for ethanolamine ammonia lyase (Achr_32230, 32220; Avin_09920, 09930). However, neither obviously requires B12 for growth because they also carry genes for B12-independent counterparts/pathways: an O 2 -dependent...”
BF638R_RS14560, BF9343_2953 methionine synthase from Bacteroides fragilis 638R
35% identity, 71% coverage
- Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R
Neal, PLoS computational biology 2023 - “...Identifier Function Metabolites Blocked BF638R_RS02825 Aminotransferase All 8 NTPs and dNTPs; NADH/NADPH; Several amino acids BF638R_RS14560 Methionine synthase 6 amino acids BF638R_RS19065 Methylenetetrahydrofolate reductase Arginine, histidine, proline BF638R_RS02840 Homoserine O-succinyltransferase Arginine, histidine, proline Each row in Table 3 corresponds to a gene in the model that...”
- Breed differences in the expression levels of gga-miR-222a in laying hens influenced H2S production by regulating methionine synthase genes in gut bacteria
Xing, Microbiome 2021 - “...microbial genes related to H 2 S production identified two methionine synthase genes, Odosp_3416 and BF9343_2953 , that are targeted by gga-miR-222a. Interestingly, in vitro fermentation results showed that gga-miR-222a upregulates the expression of these genes, which increased methionine concentrations but decreased H 2 S production...”
- “...Selenomonas ruminantium Bache_0784 (2.36) Bacteroides helcogenes MetH Odosp_3416 (8.48) Odoribacter splanchnicus Bacsa_0021 (5.67) Bacteroides salanitronis BF9343_2953 (5.31) Bacteroides fragilis NCTC9343 AspB BVU_0144 ( 5.37) Bacteroides vulgatus Bache_2087 ( 4.20) Bacteroides helcogenes PRU_1300 ( 3.66) Prevotella ruminicola OBV_25710 ( 3.27) Oscillibacter valericigenes MGL GFO_2175 ( 5.68) Gramella...”
PP_2375 5-methyltetrahydrofolate--homocysteine methyltransferase from Pseudomonas putida KT2440
32% identity, 96% coverage
CAC0578 Cobalamine-dependent methionine synthase I (methyltransferase and cobalamine-binding domain) from Clostridium acetobutylicum ATCC 824
31% identity, 99% coverage
- Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum
Venkataramanan, Biotechnology for biofuels 2015 - “...stress. Similarly, among the 12 proteins identified under butanol stress, three (CAC2229 - pyruvate:ferredoxin oxidoreductase, CAC0578 - MetH, CAC3392 - Bdh) and five (CAC2709 - EtfA, CAC0022 - aspartate semialdehyde dehydrogenase, CAP0165 - Adc, CAC2333 - SpsI, CAC3146 - RplJ) were identified under medium and high...”
- Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
Nölling, Journal of bacteriology 2001 - “...2017 by University of California, Berkeley CAC0039, CAC0408 CAC0578 a Commentb B.s. gene product 4834 NOLLING ET AL. J. BACTERIOL. TABLE 4. Specific expansion...”
Achr_18530 methionine synthase from Azotobacter chroococcum NCIMB 8003
31% identity, 96% coverage
- Azotobacter Genomes: The Genome of Azotobacter chroococcum NCIMB 8003 (ATCC 4412)
Robson, PloS one 2015 - “...2 -independent ribonucleoside reductase (discussed earlier: Achr_570; Avin_00800); met H for the B12-dependent methionine synthase (Achr_18530; Avin_29240); and eut BC for ethanolamine ammonia lyase (Achr_32230, 32220; Avin_09920, 09930). However, neither obviously requires B12 for growth because they also carry genes for B12-independent counterparts/pathways: an O 2...”
BT_0180 methionine synthase from Bacteroides thetaiotaomicron VPI-5482
BT0180 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron VPI-5482
35% identity, 71% coverage
- Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam, mBio 2022 - “...2 fold change in peptide abundance a Comments Source or reference Screen 1 Screen 2 BT_0180 MetH, 5-methyltetrahydrofolate-homocysteine methyltransferase 3.37037206 5.10351237 Requires methylcobalamin as a cofactor 16 BT_0418 Outer membrane porin F precursor 0.67090931 0.56612023 BT_0640 Fe-S oxidoreductase family 2 3.11646725 5.56040882 Contains a B 12...”
- “...vitamin B 12 -binding proteins or protein complexes, including MetH (B 12 -dependent methionine synthase; BT_0180), Mta (methylamine/trimethylamine methyltransferase corrinoid proteins; BT_0340, BT_0342, BT_0343), HpnR / Hyp (B 12 -binding domain/radical SAM domain protein; BT_0640), MutAB (methylmalonyl-CoA mutase; BT_2090 and BT_2091), and NrdJ (B 12 -dependent...”
- GapMind: Automated Annotation of Amino Acid Biosynthesis
Price, mSystems 2020 - “...the reactivation domain in one protein (BT0249) and the other four domains in another protein (BT0180) ( Fig.2B ). GapMind automatically joins these proteins together based on the nonoverlapping alignments of two pieces to the same characterized protein ( Fig.2B ). However, GapMind cannot detect more...”
XP_010818713 methionine synthase isoform X1 from Bos taurus
32% identity, 94% coverage
NP_250534 B12-dependent methionine synthase from Pseudomonas aeruginosa PAO1
PA1843 methionine synthase from Pseudomonas aeruginosa PAO1
31% identity, 96% coverage
- Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR.
Yeung, Journal of bacteriology 2009 - GeneRIF: Downregulation of the putative methionine synthase gene metH (PA1843) and the putative ABC transporter gene PA4223 might explain the swarming defect of the metR mutant.
- Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs
Guzzo, PLoS pathogens 2016 - “...also importing B 12 from the environment. Transposon mutants with insertions in genes encoding metH (PA1843), cobI (PA2904), cobJ (PA2903), cobH (PA2905) and btuB (PA1271) were obtained from the Pseudomonas Transposon Mutant Collection (Manoil Laboratory, University of Washington Genome Sciences) [ 46 ] ( S2 Table...”
- Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains
Kwon, Journal of proteome research 2014 - “...and PA4557), nucleotide excision repair (PA1529 and PA4234), and one carbon (folate) metabolism (PA0944 and PA1843) showed low protein-to-mRNA ratios. Genes involved in oxidative phosphorylation (PA1582| sdhD , PA2643| nuoH , PA2645| nuoJ , PA2646| nuoK , PA2648| nuiM , and PA4430) had reasonably high mRNA...”
- Swarming of Pseudomonas aeruginosa is controlled by a broad spectrum of transcriptional regulators, including MetR
Yeung, Journal of bacteriology 2009 - “...Downregulation of the putative methionine synthase gene metH (PA1843) and the putative ABC transporter gene PA4223 might explain the swarming defect of the metR...”
- “...with the genes required for swarming motility revealed PA1843 (metH), PA2399 (pvdD), PA2413 (pvdH), PA2891, PA4144, and PA4223. Conversely, PA0633, PA0848, and...”
NP_110491 methionine synthase from Rattus norvegicus
G3V8A4 Methionine synthase from Rattus norvegicus
31% identity, 95% coverage
- Effects of zinc deficiency and zinc supplementation on homocysteine levels and related enzyme expression in rats.
Jing, Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS) 2015 (PubMed)- GeneRIF: The objective of this study was to investigate the effects of dietary Zn supply on homocysteine levels and expression of Methionine synthase and betaine-homocysteine methyltransferase in growing rats.
- Bioactive constituents of Salvia przewalskii and the molecular mechanism of its antihypoxia effects determined using quantitative proteomics.
Wang, Pharmaceutical biology 2020 - “...D4AAP6 Mn1 Transcriptional regulator 1.40 .028 Q5RJS2 Rhoj Ras homologue family member J 1.28 .005 G3V8A4 Mtr Methyltransferase 1.27 .026 P35444 Comp Cartilage oligomeric matrix protein 1.27 .038 G3V7D0 Mmp8 Matrix metalloproteinase 1.26 .027 P10959 Ces1c Carboxylesterase 1C 1.23 .023 F1LVC4 Tigd2 Tigger transposable element-derived 2...”
- Peptidomic Analysis of Rat Plasma: Proteolysis in Hemorrhagic Shock.
Aletti, Shock (Augusta, Ga.) 2016 - “...P05545 Serpina3k chymotrypsin-like DIISNILHNF D3ZY96 Ngp chymotrypsin-like DIVLTQSPVL F1LYU4 chymotrypsin-like EAHKSEIAHRFKDLGEQHFKGL P02770 Alb chymotrypsin-like ELVEAYQEQAKGLLDGGVDILL G3V8A4 Mtr chymotrypsin-like EMLKGMIMSGMNVAHL D3ZH80 LOC689343 chymotrypsin-like EMQQQELAQMRQRDANL M0R4D8 Taf4a chymotrypsin-like ETLKDDTEKLKQLNTEQNIL Q5FVG2 Epb41l5 chymotrypsin-like FAQVPQAPPVLVFKL P13221 Got1 chymotrypsin-like FGSPLGKDLLFKDSAFGL Q7TMC7 Tf chymotrypsin-like FIGGDAGDAFDGYDFGDDPSDKF P02680 Fgg chymotrypsin-like FILKHTGPGILSMANAGPNTNGSQF M0RCZ9 Ppia chymotrypsin-like...”
- “...Maml2 F1M3B2 Maml2 x Mannan-binding lectin serine protease 1 Q8CHN8-2 Masp1 x x Methionine synthase G3V8A4 Mtr x x Murinoglobulin-1 Q03626 Mug1 x Murinoglobulin-2 Q6IE52 Mug2 x Nicotinamide phosphoribosyltransferase Q80Z29 Nampt x x Nucleosome assembly protein 1-like 4 Q5U2Z3 Nap1l4 x x Neutrophilic granule protein (P...”
METH_RAT / Q9Z2Q4 Methionine synthase; MS; 5-methyltetrahydrofolate--homocysteine methyltransferase; Cobalamin-dependent methionine synthase; Vitamin-B12 dependent methionine synthase; EC 2.1.1.13 from Rattus norvegicus (Rat) (see 2 papers)
Q9Z2Q4 methionine synthase (EC 2.1.1.13) from Rattus norvegicus (see paper)
31% identity, 95% coverage
- function: Catalyzes the transfer of a methyl group from methylcob(III)alamin (MeCbl) to homocysteine, yielding enzyme-bound cob(I)alamin and methionine in the cytosol (PubMed:9219091, PubMed:9972236). MeCbl is an active form of cobalamin (vitamin B12) used as a cofactor for methionine biosynthesis (PubMed:9219091, PubMed:9972236). Cob(I)alamin form is regenerated to MeCbl by a transfer of a methyl group from 5-methyltetrahydrofolate (By similarity). The processing of cobalamin in the cytosol occurs in a multiprotein complex composed of at least MMACHC, MMADHC, MTRR (methionine synthase reductase) and MTR which may contribute to shuttle safely and efficiently cobalamin towards MTR in order to produce methionine (By similarity).
catalytic activity: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine (RHEA:11172)
cofactor: methylcob(III)alamin
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Monomer (PubMed:9219091). Dimer. Forms a multiprotein complex with MMACHC, MMADHC and MTRR. - TMT-based quantitative proteomics analysis of the effects of Jiawei Danshen decoction myocardial ischemia-reperfusion injury.
Zhu, Proteome science 2022 - “...3.60 1 0.03 0.73 1.23 A0A0H2UI07 Pklr Pyruvate kinase L/R 3.58 2 0.01 0.67 1.73 Q9Z2Q4 Mtr Methionine synthase 0.72 1 0.02 1.36 0.79 Bioinformatics analysis of DEPs and JWDSD To investigate the biological role of DEPs screened to prevent and treat MIRI in JWDSD. GO...”
- Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels.
Lian, BMC plant biology 2015 - “...(Q9SRV5), MS3 ARATH (Q0WNZ5), METH ECOLI (P13009), METE YEAST (P05694), METH HUMAN (Q99707), METH RAT (Q9Z2Q4), METH MOUSE (A6H5Y3); FPGS-1 SORBI (C5WWE5), FPGS-2 SORBI (C5WMM8), FPGS-1 SETIT (K4A7H2), FPGS-2 SEITI (K4A839), FPGS-1 ORYSJ (Q337F3), FPGS-2 ORYSJ (Q10SU1), FPGS-3 ORYSJ (B9G6I2), FPGS1 ARATH (F4K2A1), FPGS2 ARATH (F4J2K2),...”
MTR / Q99707 cobalamin-dependent methionine synthase (EC 2.1.1.13) from Homo sapiens (see 5 papers)
METH_HUMAN / Q99707 Methionine synthase; MS; 5-methyltetrahydrofolate--homocysteine methyltransferase; Cobalamin-dependent methionine synthase; Vitamin-B12 dependent methionine synthase; EC 2.1.1.13 from Homo sapiens (Human) (see 7 papers)
Q99707 methionine synthase (EC 2.1.1.13) from Homo sapiens (see paper)
31% identity, 94% coverage
- function: Catalyzes the transfer of a methyl group from methylcob(III)alamin (MeCbl) to homocysteine, yielding enzyme-bound cob(I)alamin and methionine in the cytosol (PubMed:16769880, PubMed:17288554, PubMed:27771510). MeCbl is an active form of cobalamin (vitamin B12) used as a cofactor for methionine biosynthesis. Cob(I)alamin form is regenerated to MeCbl by a transfer of a methyl group from 5-methyltetrahydrofolate (PubMed:16769880, PubMed:17288554, PubMed:27771510). The processing of cobalamin in the cytosol occurs in a multiprotein complex composed of at least MMACHC, MMADHC, MTRR (methionine synthase reductase) and MTR which may contribute to shuttle safely and efficiently cobalamin towards MTR in order to produce methionine (PubMed:16769880, PubMed:27771510).
catalytic activity: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine (RHEA:11172)
cofactor: methylcob(III)alamin
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Monomer (PubMed:17288554). Dimer (PubMed:17288554). Forms a multiprotein complex with MMACHC, MMADHC and MTRR (PubMed:16769880, PubMed:17288554, PubMed:27771510). - A novel nanobody as therapeutics target for EGFR-positive colorectal cancer therapy: exploring the effects of the nanobody on SW480 cells using proteomics approach
Lamtha, Proteome science 2022 - “...5.28E 01 0.01 1.51E 16 Q9HD67 Unconventional myosin-X 0 1.321 2.79E 01 0.01 1.51E 16 Q99707 Methionine synthase 0.002 1.307 4.10E 01 0.01 1.51E 16 Q9NX05 Constitutive coactivator of PPAR-gamma-like protein 2 0 1.305 7.79E 01 0.01 1.51E 16 Q969X5 Endoplasmic reticulum-Golgi intermediate compartment protein 1...”
- “...Comparison between R9VH36 and control dominant proteins, there were 8 proteins (P02042, Q13315, P54802, Q9HD67, Q99707, Q9NX05, Q969X5, and A6NED2) in R9VH36 exhibited opposite expression direction when comparing to gefitinib. These proteins are involved in DNA-damage checkpoint processes. This information could lead us to a broader...”
- Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions.
Sharma, mSystems 2020 - “...significantly higher in gorillas during the wet season. In contrast, abundance of methionine synthase ( Q99707 ) was higher in the BaAka and tended to be higher when gorillas consumed more leaves ( Fig.3d ). Abundance of aconitate hydratase ( Q99798 ) was also higher in...”
- “...of Bacteroides ovatus and an unknown Prevotella were also associated with both XDEs Q99798 and Q99707 (methionine synthase) ( Fig.4d and Data Set S1 , tab 13). Carbohydrate utilization capabilities of shared taxonomic traits between humans and gorillas. Given the associations detected between specific marker taxa...”
- Brain Proteomic Profiling in Intractable Epilepsy Caused by TSC1 Truncating Mutations: A Small Sample Study.
Liu, Frontiers in neurology 2020 - “...(KCNA2) 0.045913807 1.71 Cell membrane/Cell projection/Cell junction Q96D05 Uncharacterized protein FAM241B (FAM241B) 0.027804687 1.7 Membrane Q99707 Methionine synthase (MTR) 0.01578569 1.7 Cytoplasm O94817 Ubiquitin-like protein ATG12 (ATG12) 0.012333544 1.66 Cytoplasm/Preautophagosomal structure membrane Q9Y6D5 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (ARFGEF2) 0.030295761 1.65 Cytoplasm/Membrane/Golgi apparatus Q9BZL4 Protein...”
- Peptidome analysis of umbilical cord mesenchymal stem cell (hUC-MSC) conditioned medium from preterm and term infants.
Wang, Stem cell research & therapy 2020 - “...PLPVKSPA 1.01 2.97 22.11 Q9Y6R1 SLC4A4 Electrogenic sodium bicarbonate cotransporter 1 HHTIYIGVHVPKSYR 0.78 2.99 8.24 Q99707 MTR Methionine synthase KSARVMKKAVG 1.66 3.12 21.33 Q8WXG9 ADGRV1 Adhesion G-protein coupled receptor V1 RFLQSIYLVPEEDHILIIPVVRGKDN 1.97 3.13 8.73 P43243-2 MATR3 Matrin-3 HLILN 0.67 3.21 8.71 O75970-3 MPDZ Multiple PDZ domain...”
- Synthetic combinations of missense polymorphic genetic changes underlying Down syndrome susceptibility.
Jackson, Cellular and molecular life sciences : CMLS 2016 - Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels.
Lian, BMC plant biology 2015 - “...(O50008), MS2 ARATH (Q9SRV5), MS3 ARATH (Q0WNZ5), METH ECOLI (P13009), METE YEAST (P05694), METH HUMAN (Q99707), METH RAT (Q9Z2Q4), METH MOUSE (A6H5Y3); FPGS-1 SORBI (C5WWE5), FPGS-2 SORBI (C5WMM8), FPGS-1 SETIT (K4A7H2), FPGS-2 SEITI (K4A839), FPGS-1 ORYSJ (Q337F3), FPGS-2 ORYSJ (Q10SU1), FPGS-3 ORYSJ (B9G6I2), FPGS1 ARATH (F4K2A1),...”
- A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors.
Larocque, BMC systems biology 2014 - “...(folD | fhs | fchA) d P24182 [53%] Q96RQ3 [48%] CNC , THL , I2A (Q99707 [31%]) scoB (folD | fhs | fchA) d E9YQ86 [56%] B7Z609 [51%] SIN , EMT (P55809 [52%]) scoA (folD | fhs | fchA) d G1YD51 [53%] Q6IAV5 [42%] SIN ,...”
- Differentiation of mesenchymal stem cells derived from pancreatic islets and bone marrow into islet-like cell phenotype
Zanini, PloS one 2011 - “...Q9UPN3 MACF1 Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 623626 5,27 16 3 56 _ _ Q99707 METH Methionine synthase 141749 5,39 9 9 56 _ _ Q9Y623 MYH4 Myosin-4 223902 5,65 11 7 56 _ _ Q99497 PARK7 Protein DJ-1 20050 6,33 7 28 70 _...”
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XP_011960415 methionine synthase isoform X3 from Ovis aries
32% identity, 94% coverage
A6H5Y3 Methionine synthase from Mus musculus
31% identity, 95% coverage
- Genome-wide identification and transcriptional analysis of folate metabolism-related genes in maize kernels.
Lian, BMC plant biology 2015 - “...(Q0WNZ5), METH ECOLI (P13009), METE YEAST (P05694), METH HUMAN (Q99707), METH RAT (Q9Z2Q4), METH MOUSE (A6H5Y3); FPGS-1 SORBI (C5WWE5), FPGS-2 SORBI (C5WMM8), FPGS-1 SETIT (K4A7H2), FPGS-2 SEITI (K4A839), FPGS-1 ORYSJ (Q337F3), FPGS-2 ORYSJ (Q10SU1), FPGS-3 ORYSJ (B9G6I2), FPGS1 ARATH (F4K2A1), FPGS2 ARATH (F4J2K2), FPGS3 ARATH (Q8W035),...”
- In vivo substrates of the lens molecular chaperones αA-crystallin and αB-crystallin.
Andley, PloS one 2014 - “...8 A-crystallin Q569M7 20 5 Serrate RNA effector molecule homolog Q99MR6 100 2 Methionine synthase A6H5Y3 139 2 2296 Filensin A2AMT1 74 43 1.07 5.61 5.19 Gelsolin P13020 86 5 Calpain 3 A2AVV5 85 4 3001 60 kDa Heat shock protein, mitochondrial P63038 61 16 1.11...”
PSPPH_2620 5-methyltetrahydrofolate--homocysteine methyltransferase from Pseudomonas syringae pv. phaseolicola 1448A
31% identity, 97% coverage
Q54P92 Methionine synthase from Dictyostelium discoideum
30% identity, 94% coverage
- AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods.
Niemyska, Nucleic acids research 2022 - “...not all homological structures deposited in the AlpahFold possess it. Figure 4. Protein (UniProtKB ID: Q54P92) with very high pLDDT value, but whose topology (knot with 10 crossings K10 146 , shown with schematic) suggests that the prediction is not reliable. Other potential applications include in...”
- “...can provide critical insights in such cases. Figure 4 shows a protein structure (UniProtKB ID: Q54P92) with a high pLDDT reliability which is certainly not a realistic model from the topological perspective. The knot formed is 10 146 , which is much more complicated than any...”
XP_011542496 methionine synthase isoform X1 from Homo sapiens
31% identity, 87% coverage
- Genetic Association between the Risk of Dental Caries and MTR Gene Polymorphism in Chinese Children.
Du, The Tohoku journal of experimental medicine 2024 (PubMed)- GeneRIF: Genetic Association between the Risk of Dental Caries and MTR Gene Polymorphism in Chinese Children.
- Association of MTR gene polymorphisms with the occurrence of non-syndromic congenital heart disease: a case-control study.
Liu, Scientific reports 2023 - GeneRIF: Association of MTR gene polymorphisms with the occurrence of non-syndromic congenital heart disease: a case-control study.
- Association of MTR and MTRR genes and oral health-related quality of life in children with dental caries.
Antunes, Brazilian oral research 2023 (PubMed)- GeneRIF: Association of MTR and MTRR genes and oral health-related quality of life in children with dental caries.
- Common Variants in One-Carbon Metabolism Genes (MTHFR, MTR, MTHFD1) and Depression in Gynecologic Cancers.
Pawlik, International journal of molecular sciences 2023 - GeneRIF: Common Variants in One-Carbon Metabolism Genes (MTHFR, MTR, MTHFD1) and Depression in Gynecologic Cancers.
- MTR-G is a high-risk allele for lower-extremity arteriosclerotic occlusion.
Wen, The International journal of neuroscience 2022 (PubMed)- GeneRIF: MTR-G is a high-risk allele for lower-extremity arteriosclerotic occlusion.
- Folate metabolism abnormalities in infertile patients with endometriosis.
Guedes, Biomarkers in medicine 2022 (PubMed)- GeneRIF: Folate metabolism abnormalities in infertile patients with endometriosis.
- "Association of MTHFR and MS/MTR gene polymorphisms with congenital heart defects in North Indian population (Jammu and Kashmir): a case-control study encompassing meta-analysis and trial sequential analysis".
Raina, BMC pediatrics 2022 - GeneRIF: ""Association of MTHFR and MS/MTR gene polymorphisms with congenital heart defects in North Indian population (Jammu and Kashmir): a case-control study encompassing meta-analysis and trial sequential analysis"".
- Investigation of the relationship between MTRR A66G, MTR A2756G gene variations and cell anomalies in early diagnosis and progression of bladder cancer.
Alkanli, Molecular biology reports 2022 (PubMed)- GeneRIF: Investigation of the relationship between MTRR A66G, MTR A2756G gene variations and cell anomalies in early diagnosis and progression of bladder cancer.
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SPRG_02541 methionine synthase from Saprolegnia parasitica CBS 223.65
31% identity, 92% coverage
- Analysis of Saprolegnia parasitica Transcriptome following Treatment with Copper Sulfate
Hu, PloS one 2016 - “...and SPRG_01617) were upregulated, while SPRG_11730, SPRG_04491, SPRG_10490, SPRG_12259, SPRG_04186, SPRG_18377, SPRG_18063, SPRG_06771, SPRG_16261, and SPRG_02541 genes were downregulated after copper sulfate treatment. These findings were consistent with the GO enrichment analysis, which indicated that copper sulfate mostly prevented the growth of S. parasitica by affecting...”
Odosp_3416 methionine synthase from Odoribacter splanchnicus DSM 20712
30% identity, 98% coverage
- Breed differences in the expression levels of gga-miR-222a in laying hens influenced H2S production by regulating methionine synthase genes in gut bacteria
Xing, Microbiome 2021 - “...differentially expressed microbial genes related to H 2 S production identified two methionine synthase genes, Odosp_3416 and BF9343_2953 , that are targeted by gga-miR-222a. Interestingly, in vitro fermentation results showed that gga-miR-222a upregulates the expression of these genes, which increased methionine concentrations but decreased H 2...”
- “...Desulfovibrio desulfuricans CK3_01000 (5.31) Unclassified Clostridiales SELR_06150 (4.94) Selenomonas ruminantium Bache_0784 (2.36) Bacteroides helcogenes MetH Odosp_3416 (8.48) Odoribacter splanchnicus Bacsa_0021 (5.67) Bacteroides salanitronis BF9343_2953 (5.31) Bacteroides fragilis NCTC9343 AspB BVU_0144 ( 5.37) Bacteroides vulgatus Bache_2087 ( 4.20) Bacteroides helcogenes PRU_1300 ( 3.66) Prevotella ruminicola OBV_25710 (...”
Nmar_1267 Methionine synthase from Nitrosopumilus maritimus SCM1
34% identity, 71% coverage
- Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production
Doxey, The ISME journal 2015 - “...maritimus and other Thaumarchaeota were also found to encode cobalamin-dependent enzymes such as methionine synthase (Nmar_1267), ribonucleotide reductase (Nmar_1627), and methylmalonyl CoA mutase (B 12 binding domain, Nmar_0958), as well as probable cobalt transporters (Nmar_0878). As further support for cobalamin biosynthetic potential, we identified dual cob/cbi...”
8sseA / Q5SKM5 Methionine synthase, c-terminal fragment, cobalamin and reactivation domains from thermus thermophilus hb8 (see paper)
43% identity, 45% coverage
- Ligand: cobalamin (8sseA)
RSP_3346 5-methyltetrahydrofolate--homocysteine methyltransferase from Rhodobacter sphaeroides 2.4.1
32% identity, 71% coverage
XP_006516724 methionine synthase isoform X1 from Mus musculus
30% identity, 80% coverage
PSHAa2222 putative B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase (C terminal) from Pseudoalteromonas haloplanktis TAC125
30% identity, 70% coverage
- Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments
Perrin, Nature communications 2020 - “...Aromatic amino acids metabolism 0.11 Concerning MetJ regulon, we noticed a group of genes (including PSHAa2222, PSHAa2223, PSHAa0287 and PSHAa2292) whose expression values are negatively correlated with those of genes PSHAa2274-76 and PSHAa1226 (Fig. 3d ). This group of co-regulated genes include those involved in the...”
- “...(upstream the main product methionine), whereas members the other one are in its close proximity (PSHAa2222) or involved in the methionine salvage pathway (PSHAa2292), the set of reactions responsible for the recycle of the thiomethyl group of S-adenosylmethionine from methylthioadenosine (Fig. 3j ). In a previous...”
M0M57_09420 methionine synthase from Flavobacterium azooxidireducens
31% identity, 71% coverage
CC2137, CC_2137 5-methyltetrahydrofolate--homocysteine methyltransferase from Caulobacter crescentus CB15
CCNA_02221 methionine synthase I metH from Caulobacter crescentus NA1000
31% identity, 70% coverage
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...by iron limitation there are many involved in methionine biosynthesis, such as methionine synthases (CC0482, CC2137, CC2138), adenosylmethionine synthtase (CC0050), S-adenosyl-L-homocysteine hydrolase (CC0257) and methylenetetrahydrofolate reductase (CC2140), which is required to produce 5-methyltetrahydrofolate as methyl-group donor for methionine synthesis. Pathways of protein catabolism were also repressed...”
- “...CCNA_00515 Cobalamin-independent methionine synthase (Zinc) 2.49 CC_0984 CCNA_01035 Gamma-glutamyltranspeptidase 2.68 CC_1048 CCNA_01100 Acylamino-acid-releasing enzyme 2.73 CC_2137 CCNA_02221 Methionine synthase I metH (Zinc) 2.52 CC_2138 CCNA_02222 5-methyltetrahydrofolate 2.72 CC_2139 CCNA_02223 Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid...”
- Use of the Caulobacter crescentus genome sequence to develop a method for systematic genetic mapping
West, Journal of bacteriology 2002 - “...domain of 5-methyltetrahydrofolate-homocysteine methyltransferase, while CC2137 encodes a 900-amino-acid polypeptide homologous to the C-terminal domain of...”
- CAU-1, a subclass B3 metallo-beta-lactamase of low substrate affinity encoded by an ortholog present in the Caulobacter crescentus chromosome
Docquier, Antimicrobial agents and chemotherapy 2002 - “...imperfect palindrome, after which there is another ORF (CC2137) that encodes a homolog to the carboxy-terminal cobalamin-binding domain of the MetH family (27)....”
- Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging
Aretakis, mSystems 2019 - “...colored. (B) Pathway of methionine biosynthesis, MetX1 (CCNA_03309), MetX2 (CCNA_00559), MetZ (CCNA_02321), MetE (CCNA_00515), MetH (CCNA_02221), and CCNA_02222. Pathway for B 12 utilization, BtuB (CCNA_01826) and BtuR (CCNA_02321). Pathway for tRNA modification, MtaB (CCNA_03798). Pathway for nucleotide reduction, NrdJ (CCNA_01966), NrdE (CCNA_03607), and NrdB (CCNA_00261). Pathway...”
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...Cobalamin-independent methionine synthase (Zinc) 2.49 CC_0984 CCNA_01035 Gamma-glutamyltranspeptidase 2.68 CC_1048 CCNA_01100 Acylamino-acid-releasing enzyme 2.73 CC_2137 CCNA_02221 Methionine synthase I metH (Zinc) 2.52 CC_2138 CCNA_02222 5-methyltetrahydrofolate 2.72 CC_2139 CCNA_02223 Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid dehydratase...”
Dde_2115 homocysteine S-methyltransferase family protein from Oleidesulfovibrio alaskensis G20
33% identity, 71% coverage
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
Saxena, Frontiers in microbiology 2023 - “...genes was observed (shown in Figure 4A ). The enriched genes (dde_0276, dde_0528, dde_1112, dde_1258, dde_2115, dde_2271, dde_3081, dde_3604, cysQ , and sucD ) were not only unconstrained to sulfate metabolism but a strong network to three other pathways- cysteine and methionine metabolism, selenocompound metabolism, and...”
- “...metabolite for the formation of methionine ( Gamrasni et al., 2020 ). Parallelly, methionine synthase (dde_2115) was also enriched, which is a vital enzyme in the intermediate step of methionine synthesis ( Ekstrom et al., 2003 ). Serine O-acetyltransferase (dde_3081) shares its role with the Seleno-compound...”
Dde_2115 5-methyltetrahydrofolate-homocysteine methyltransferase, putative from Desulfovibrio desulfuricans G20
33% identity, 71% coverage
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
Saxena, Frontiers in microbiology 2023 - “...genes was observed (shown in Figure 4A ). The enriched genes (dde_0276, dde_0528, dde_1112, dde_1258, dde_2115, dde_2271, dde_3081, dde_3604, cysQ , and sucD ) were not only unconstrained to sulfate metabolism but a strong network to three other pathways- cysteine and methionine metabolism, selenocompound metabolism, and...”
- “...metabolite for the formation of methionine ( Gamrasni et al., 2020 ). Parallelly, methionine synthase (dde_2115) was also enriched, which is a vital enzyme in the intermediate step of methionine synthesis ( Ekstrom et al., 2003 ). Serine O-acetyltransferase (dde_3081) shares its role with the Seleno-compound...”
- Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20
Kuehl, mBio 2014 - “...In addition to the expected methionine biosynthesis genes hom ( Dde_2731 ) and metH ( Dde_2115 ), supplementation of minimal medium with methionine also rescued the fitness defects of the uncharacterized genes Dde_2711 and Dde_3007 ( Fig.4B ). The D.alaskensis G20 MetH is missing the N-terminal...”
- “...metE ( Dde_2328 ) and a vitamin B 12 -dependent enzyme encoded by metH ( Dde_2115 ). metE does not have a significant phenotype in minimal medium and is probably not the predominant methionine synthase in D.alaskensis G20 under our growth conditions. In contrast, metH mutants...”
BPHYT_RS02305 methionine synthase from Paraburkholderia phytofirmans PsJN
32% identity, 71% coverage
- GapMind: Automated Annotation of Amino Acid Biosynthesis
Price, mSystems 2020 - “...-dependent methionine synthase MetH is a single protein with five domains. In Burkholderia phytofirmans PsJN, BPHYT_RS02305 contains the pterin-binding domain, the two domains involved in binding vitamin B12, and the domain for the reactivation of vitamin B12, while BPHYT_RS02310 contains the S -methyltransferase domain ( Fig.2B...”
XC_RS13715 methionine synthase from Xanthomonas campestris pv. campestris str. 8004
30% identity, 72% coverage
Swit_2399 methionine synthase (B12-dependent) from Sphingomonas wittichii RW1
32% identity, 70% coverage
CD3596 putative homocysteine S-methyltransferase from Clostridium difficile 630
30% identity, 68% coverage
- The current riboswitch landscape in <i>Clostridioides difficile</i>
Badilla, Microbiology (Reading, England) 2024 - “...-Methionine-binding lipoprotein CD1825-26 ( metY, A ) O-Acetylhomoserine sulfhydrylase, homoserine O-succinyltransferase CD3598 ( luxS ) -CD3596 Methionine biosynthesis, includes LuxS Purine CD0198 ( guaA ) -0198.1 Glutamine-hydrolysing guanosine monophosphate (GMP) synthase; hypothetical protein CD2107 Xanthine/uracil/vitamin C permease of AgzA family CD2704 Xanthine/uracil/vitamin C permease of AgzA...”
- Control of Clostridium difficile Physiopathology in Response to Cysteine Availability
Dubois, Infection and immunity 2016 - “...(CD3029); metH, cobalamin-dependent methionine synthase (CD3596); metK, SAM synthetase (CD0130); mtnN, adenosylhomocysteine nucleosidase (CD2611); luxS,...”
CDR20291_3434 putative homocysteine S-methyltransferase from Clostridium difficile R20291
CDR20291_3434 homocysteine S-methyltransferase family protein from Clostridioides difficile R20291
30% identity, 68% coverage
- Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms
Slater, Scientific reports 2019 - “...hydrolase 17 CDR20291_3075 1.3649687 osmoprotectant ABC transporter substrate-binding/permease 18 CDR20291_3104 0.8099098 sigma-54-dependent transcriptional activator 19 CDR20291_3434 1.4402419 homocysteine S-methyltransferase 20 CDR20291_0025 1.32053 acetoin:2%2C6-dichlorophenolindophenol oxidoreductase subunit alpha 21 CDR20291_0615 0.86915 nucleotide phosphodiesterase 22 CDR20291_0802 2.260047 ABC transporter substrate-binding protein 23 CDR20291_0911 1.24181 electron transfer flavoprotein subunit beta...”
F7O84_RS02745 homocysteine S-methyltransferase family protein from Candidatus Galacturonibacter soehngenii
29% identity, 72% coverage
- "Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex
Valk, Frontiers in microbiology 2020 - “...reductase 1.5.1.20 metF 1 e 87 F7O84_RS08335 5-Methyl-tetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 2.1.1.258 acsE 5 e 37 F7O84_RS02745 CO-Methylating acetyl-CoA synthase 2.3.1.169 acsBCD >10 Carbon-monoxide dehydrogenase 1.2.7.4 cooS >10 CO dehydrogenases contain highly conserved amino-acid motifs (Pfam or protein-family domains) associated with their nickel-iron-sulfur clusters ( Eggen et...”
- “...and 1.5.1.5 F7O84_RS05385 236 9 Methyltetrahydrofolate reductase 1.5.1.20 F7O84_RS08335 126 13 5-methyl-tetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 2.1.1.258 F7O84_RS02745 144 19 CO-methylating acetyl-CoA synthase 2.3.1.169 n.d. CO dehydrogenase 1.2.7.4 n.d. Prismane/CO dehydrogenase family 1.7.99.1 F7O84_RS02405 40 8 Prismane/CO dehydrogenase family 1.7.99.1 F7O84_RS11645 315 51 Energy-metabolism associated genes Electron transport...”
VARPA_RS01000 methionine synthase from Variovorax paradoxus EPS
30% identity, 70% coverage
- Rhizospheric miRNAs affect the plant microbiota
Middleton, ISME communications 2024 - “...gene was differentially expressed at both time points, a gene coding for a methionine synthase (VARPA_RS01000), which was overexpressed in response to the plant miRNA treatment. Figure 3 Plant miRNAs affect the transcriptome of a rhizosphere bacterium. Gene expression of Variovorax paradoxus after (A) 20min and...”
BTH_I0357 5-methyltetrahydrofolate--homocysteine methyltransferase from Burkholderia thailandensis E264
32% identity, 71% coverage
bglu_1g32290 Methionine synthase from Burkholderia glumae BGR1
31% identity, 71% coverage
- Unraveling the role of quorum sensing-dependent metabolic homeostasis of the activated methyl cycle in a cooperative population of Burkholderia glumae
Kang, Scientific reports 2019 - “...in B . glumae : metE1 (bglu_1g08430) and metE2 (bglu_2g04930), and metH1 (bglu_1g32280) and metH2 (bglu_1g32290). MetE1 and MetE2 share 53% identity (Supplementary Fig. 1 ). The proteins produced by the two respective MetH genes (MetH1; 38.2 KDa and MetH2; 99.6 KDa) aligned to the N-terminus...”
- “...BGR1 a bglu_1g01990 bglu_1g02010 - metE1 (bglu_1g08430) - metE2 (bglu_2g04930) - metH1 (bglu_1g32280) - metH2 (bglu_1g32290) bglu_1g33680 - bglu_2g06400 - bglu_1g23220 - bglu_2g17510 Burkholderia thailandensis E264 b BTH_I3165 BTH_I3163 BTH_I1606 - metH1 (BTH_I0358) - metH2 (BTH_I0357) BTH_I0174 - BTH_II1307 - BTH_II1338 - BTH_I2673 Burkholderia pseudomallei 1026b...”
Cenrod_2368 methionine synthase from Candidatus Symbiobacter mobilis CR
30% identity, 70% coverage
BP1026B_I3121 methionine synthase from Burkholderia pseudomallei 1026b
31% identity, 71% coverage
GM661_16185 homocysteine S-methyltransferase family protein from Iocasia fonsfrigidae
30% identity, 73% coverage
DVU1585 Methionine synthase (cobalamin-dependent) (EC 2.1.1.13) from Desulfovibrio vulgaris Hildenborough JW710
DVU1585 vitamin B12-dependent methionine synthase family protein from Desulfovibrio vulgaris Hildenborough
31% identity, 70% coverage
- mutant phenotype: # Important for fitness in most defined media experiments and cofit with metF (DVU0997)
- Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome
Chhabra, Applied and environmental microbiology 2011 - “...enabling chromosomal modifications in D. vulgaris Hildenborough using DVU1585 as the target gene. A set of reusable parts (color coded) were employed for...”
- “...into D. vulgaris to examine the role of DVU1585 in this sulfate reducer. Results for gene essentiality, protein-protein interactions, and protein localization...”
- Response of Desulfovibrio vulgaris to alkaline stress
Stolyar, Journal of bacteriology 2007 - “...DVU0468 DVU0469 DVU0470 DVU0471 DVU0663 DVU0890 DVU1466 DVU1585 DVU1609 DVU1610 DVU2981 DVU2982 DVU2983 DVU2984 DVU3048 DVU3371 Expression change (log2 ratio)...”
RSc0294 PROBABLE 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT ISOZYME) PROTEIN from Ralstonia solanacearum GMI1000
30% identity, 71% coverage
PITG_01804 methionine synthase from Phytophthora infestans T30-4
36% identity, 45% coverage
4cczA / Q99707 Crystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains
33% identity, 50% coverage
- Ligand: (6s)-5,6,7,8-tetrahydrofolate (4cczA)
TEL01S_RS06970 homocysteine S-methyltransferase family protein from Pseudothermotoga elfii DSM 9442 = NBRC 107921
27% identity, 70% coverage
- Adaptation Strategies to High Hydrostatic Pressures in Pseudothermotoga species Revealed by Transcriptional Analyses
Fenouil, Microorganisms 2023 - “..., Table 1 ), while genes metB , metH , mtnK , and mtnA (TEL01S_RS05650, TEL01S_RS06970, TEL01S_RS08685, and TEL01S_RS08690), which are involved in methionine metabolism, were over-expressed at 20 and 30 MPa. The gene cluster TEL01S_RS01770TEL01S_RS01785, which encodes ArgGHCJ, was over-expressed at 30 and 40 MPa...”
- “...1 0 0 TEL01S_RS05650 ko00270:Cysteine and methionine metabolism|ko00260:Glycine, serine, and threonine metabolism 0 1 0 TEL01S_RS06970 metH ko00270:Cysteine and methionine metabolism 0 1 1 TEL01S_RS03640 dapB ko00300:Lysine biosynthesis 0 1 1 TEL01S_RS00130 dapA ko00300:Lysine biosynthesis 0 1 0 TEL01S_RS09220 murF ko00300:Lysine biosynthesis 0 1 0 TEL01S_RS10080...”
Q9WYA5 methionine synthase (EC 2.1.1.13) from Thermotoga maritima (see paper)
TM0268 5-methyltetrahydrofolate S-homocysteine methyltransferase from Thermotoga maritima MSB8
29% identity, 70% coverage
- Four families of folate-independent methionine synthases
Price, PLoS genetics 2021 - “...], but it scores below the trusted cutoff of TIGR02082. We used protein BLAST with Q9WYA5 as the query to identify additional MetH proteins, with E < 0.001 and at least 80% coverage of the query. The identification of MetF and split MetE proteins are more...”
- Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269
Huang, Protein science : a publication of the Protein Society 2007 - “...(TM0268) requires the downstream gene product TM0269 SHA HUANG,1 GAIL ROMANCHUK,2 KATHERINE PATTRIDGE,2 SCOTT A. LESLEY,4 2,5 IAN A. WILSON,4 ROWENA G. MATTHEWS,1,3...”
- “...specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module...”
DvMF_0476 vitamin B12-dependent methionine synthase without a reactivation domain (EC 2.1.1.13) from Desulfovibrio vulgaris Miyazaki F
DvMF_0476 homocysteine S-methyltransferase from Desulfovibrio vulgaris str. Miyazaki F
30% identity, 69% coverage
- mutant phenotype: Important for fitness in most defined media and strongly cofit with the ATP-dependent co(II)balamin reductase (DvMF_1398). This lacks the usual reactivation domain for converting co(II)balamin to co(I)balamin; that activity is instead provided by DvMF_1398.
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...the reactivation of B12 in D . vulgaris , which encodes a B12-dependent methionine synthase (DvMF_0476) that lacks the standard B12 activation domain. This methionine synthase has a very similar fitness pattern as DvMF_1398, which contains two DUF4445 domains (r = 0.92 across 170 experiments; also...”
B4DST3 Methionine synthase from Homo sapiens
34% identity, 44% coverage
5vooA / Q5SKM5 Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus hb8 (see paper)
46% identity, 24% coverage
- Ligand: 5-methyl-5,6,7,8-tetrahydrofolic acid (5vooA)
BPHYT_RS02310 homocysteine S-methyltransferase family protein from Paraburkholderia phytofirmans PsJN
41% identity, 25% coverage
- GapMind: Automated Annotation of Amino Acid Biosynthesis
Price, mSystems 2020 - “...involved in binding vitamin B12, and the domain for the reactivation of vitamin B12, while BPHYT_RS02310 contains the S -methyltransferase domain ( Fig.2B ). In Bacteroides thetaiotaomicron VPI-5482, methionine synthase is split in a different way, with the reactivation domain in one protein (BT0249) and the...”
bglu_1g32280 Methionine synthase I (cobalamin-dependent), methyltransferase domain protein from Burkholderia glumae BGR1
39% identity, 26% coverage
- Unraveling the role of quorum sensing-dependent metabolic homeostasis of the activated methyl cycle in a cooperative population of Burkholderia glumae
Kang, Scientific reports 2019 - “...and metH genes in B . glumae : metE1 (bglu_1g08430) and metE2 (bglu_2g04930), and metH1 (bglu_1g32280) and metH2 (bglu_1g32290). MetE1 and MetE2 share 53% identity (Supplementary Fig. 1 ). The proteins produced by the two respective MetH genes (MetH1; 38.2 KDa and MetH2; 99.6 KDa) aligned...”
- “...SAM-MTases Burkholderia glumae BGR1 a bglu_1g01990 bglu_1g02010 - metE1 (bglu_1g08430) - metE2 (bglu_2g04930) - metH1 (bglu_1g32280) - metH2 (bglu_1g32290) bglu_1g33680 - bglu_2g06400 - bglu_1g23220 - bglu_2g17510 Burkholderia thailandensis E264 b BTH_I3165 BTH_I3163 BTH_I1606 - metH1 (BTH_I0358) - metH2 (BTH_I0357) BTH_I0174 - BTH_II1307 - BTH_II1338 - BTH_I2673...”
BTH_I0358 Homocysteine S-methyltransferase, putative from Burkholderia thailandensis E264
40% identity, 26% coverage
RSc0295 PROBABLE 5-METHYLTETRAHYDROFOLATE--HOMOCYSTEINE METHYLTRANSFERASE (METHIONINE SYNTHASE, VITAMIN-B12 DEPENDENT ISOZYME) PROTEIN from Ralstonia solanacearum GMI1000
41% identity, 25% coverage
Pnuc_1980 methionine synthase from Polynucleobacter sp. QLW-P1DMWA-1
40% identity, 25% coverage
- Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes
Srivastava, Frontiers in microbiology 2020 - “...HscB homolog 2.19 0.001331 Pnuc_1637 NAD-dependent epimerase/dehydratase 2.17 0.009716 Pnuc_1224 GTP-binding protein TypA 2.11 0.000017 Pnuc_1980 Methionine synthase (B12-dependent) 2.11 0.000110 Pnuc_1453 Metal dependent phosphohydrolase 1.99 0.002009 Pnuc_1869 Chaperone SurA 1.98 0.000033 Pnuc_0657 Uroporphyrinogen-III synthase (EC 4.2.1.75) 1.96 0.011631 Pnuc_1708 3-Mercaptopyruvate sulfurtransferase 1.94 0.000033 Pnuc_0196 GTPase...”
- “...0.000224 Pnuc_1453 Metal dependent phosphohydrolase 1.99 0.001607 Pnuc_2008 Exodeoxyribonuclease III Xth (EC 4.2.99.18) 1.95 0.000799 Pnuc_1980 Methionine synthase (B12-dependent) 1.93 0.000120 Pnuc_0644 Pantothenate synthetase (PS) (EC 6.3.2.1) 1.92 0.003478 Pnuc_1324 Haloacid dehalogenase, type II 1.89 0.022058 Pnuc_0217 Shikimate dehydrogenase [NADP(+)] 1.83 0.000209 Pnuc_1131 Phage transcriptional regulator,...”
3bofA / Q9WYA5 Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima complexed with zn2+ and homocysteine (see paper)
30% identity, 48% coverage
BP1026B_I3120 homocysteine S-methyltransferase family protein from Burkholderia pseudomallei 1026b
38% identity, 26% coverage
PXO_RS13400 homocysteine S-methyltransferase family protein from Xanthomonas oryzae pv. oryzae PXO99A
39% identity, 25% coverage
XC_2724 5-methyltetrahydrofolate-homocysteine methyl transferase from Xanthomonas campestris pv. campestris str. 8004
38% identity, 25% coverage
- Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence
An, PLoS pathogens 2014 - “...XC_0026 (cellulase), XC_0027 (endoglucanase), XC_1058 (pilin), XC_1165 (TonB receptor) XC_1732 (glycosyltransferase), XC_2013 (MASE1 domain-containing protein), XC_2724 (methyltransferase), and XC_3591 (pectate lyase). The qRTPCR data were normalised to 16S rRNA and is presented as the fold change with respect to the wild-type for each gene. Data (means...”
3bulA / P13009 E. Coli i690c/g743c meth c-terminal fragment (649-1227) (see paper)
29% identity, 45% coverage
- Ligand: cobalamin (3bulA)
Cenrod_2596 homocysteine S-methyltransferase family protein from Candidatus Symbiobacter mobilis CR
40% identity, 25% coverage
PSHAa2223 putativeB12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase (N terminal) from Pseudoalteromonas haloplanktis TAC125
36% identity, 25% coverage
HWN72_14090 homocysteine S-methyltransferase family protein from Novosphingobium sp. HR1a
35% identity, 25% coverage
- LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes
Segura, Frontiers in microbiology 2023 - “...phosphotransferase 2 ( ptsP ) HWN72_14810 4.69 Hypothetical protein HWN72_14815 1.82 Polysaccharide biosynthesis tyrosine autokinase HWN72_14090 3.45 homocysteine S-methyltransferase family protein HWN72_14095 3.25 GNAT family N-acetyltransferase Novel00673 2.10 Vitamin B12 dependent methionine synthase, activation domain HWN72_01945 2.99 Bacterial regulatory proteins, luxR family (l uxR402 ) HWN72_23475...”
3k13C / Q8ABD0 Structure of the pterin-binding domain metr of 5- methyltetrahydrofolate-homocysteine methyltransferase from bacteroides thetaiotaomicron
39% identity, 20% coverage
- Ligand: n-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid (3k13C)
CC2138, CC_2138 5-methyltetrahydrofolate--homocysteine methyltransferase from Caulobacter crescentus CB15
CCNA_02222 5-methyltetrahydrofolate--homocysteine methyltransferase homocysteine-binding subunit from Caulobacter crescentus NA1000
32% identity, 26% coverage
- Asymmetric cellular memory in bacteria exposed to antibiotics
Mathis, BMC evolutionary biology 2017 - “...suggests that blaA (CC2139) is part of an operon with three other genes (CC2141, CC2140, CC2138) [ 22 ]. We amplified the promoter region of CC2141 and fused it with e gfp (green fluorescent protein). The amplified region was inserted into pMR10 background. The resulting plasmid...”
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...iron limitation there are many involved in methionine biosynthesis, such as methionine synthases (CC0482, CC2137, CC2138), adenosylmethionine synthtase (CC0050), S-adenosyl-L-homocysteine hydrolase (CC0257) and methylenetetrahydrofolate reductase (CC2140), which is required to produce 5-methyltetrahydrofolate as methyl-group donor for methionine synthesis. Pathways of protein catabolism were also repressed by...”
- “...Gamma-glutamyltranspeptidase 2.68 CC_1048 CCNA_01100 Acylamino-acid-releasing enzyme 2.73 CC_2137 CCNA_02221 Methionine synthase I metH (Zinc) 2.52 CC_2138 CCNA_02222 5-methyltetrahydrofolate 2.72 CC_2139 CCNA_02223 Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid dehydratase (Fe-S cluster) 3.35 CC_3246 CCNA_03355 Acylamino-acid-releasing enzyme...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, metF CC2138, 5-methyltetrahydrofolate-homocysteine methyltransferase 0.56 0.23 0.29 0.58...”
- “...could be relevant, including CC2138 (5-methyltetrahydrofolate-homocysteine methyltransferase), CC2140 (5,10-methylenetetrahydrofolate reductase), and CC3630...”
- CAU-1, a subclass B3 metallo-beta-lactamase of low substrate affinity encoded by an ortholog present in the Caulobacter crescentus chromosome
Docquier, Antimicrobial agents and chemotherapy 2002 - “...the putative metallo-lactamase gene (CC2139) and the downstream CC2138 open reading frame (ORF) was amplified with primers BLA-CAU/F and OP-CAU/R (Fig. 1) and...”
- “...was generated from pFG2002 following partial removal of the CC2138 ORF as described in Materials and Methods. VOL. 46, 2002 1825 same as those described...”
- Use of the Caulobacter crescentus genome sequence to develop a method for systematic genetic mapping
West, Journal of bacteriology 2002 - “...codon overlaps the start codon of the subsequent ORF (CC2138) (Fig. 3b). A PCR product containing the upstream genes of the putative operon and the intergenic...”
- “...reductase, while the gene immediately 3 to blaA (CC2138) is homologous to the 5 portion of the E. coli metH gene, encoding the N-terminal...”
- Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging
Aretakis, mSystems 2019 - “...Pathway of methionine biosynthesis, MetX1 (CCNA_03309), MetX2 (CCNA_00559), MetZ (CCNA_02321), MetE (CCNA_00515), MetH (CCNA_02221), and CCNA_02222. Pathway for B 12 utilization, BtuB (CCNA_01826) and BtuR (CCNA_02321). Pathway for tRNA modification, MtaB (CCNA_03798). Pathway for nucleotide reduction, NrdJ (CCNA_01966), NrdE (CCNA_03607), and NrdB (CCNA_00261). Pathway for succinyl-CoA...”
- Global transcriptional response of Caulobacter crescentus to iron availability
da, BMC genomics 2013 - “...2.68 CC_1048 CCNA_01100 Acylamino-acid-releasing enzyme 2.73 CC_2137 CCNA_02221 Methionine synthase I metH (Zinc) 2.52 CC_2138 CCNA_02222 5-methyltetrahydrofolate 2.72 CC_2139 CCNA_02223 Beta-lactamase, type II (Zinc) 2.83 CC_2140 CCNA_02224 Methylenetetrahydrofolate reductase 2.39 CC_2840 CCNA_02933 Aminopeptidase 2.14 CC_3044 CCNA_03139 Dihydroxy-acid dehydratase (Fe-S cluster) 3.35 CC_3246 CCNA_03355 Acylamino-acid-releasing enzyme 2.20...”
Swit_2400 methionine synthase (B12-dependent) from Sphingomonas wittichii RW1
34% identity, 25% coverage
GSU2974 methylenetetrahydrofolate reductase family protein from Geobacter sulfurreducens PCA
34% identity, 27% coverage
YITJ_BACSU / O06745 Bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase; EC 2.1.1.10; EC 1.5.1.20 from Bacillus subtilis (strain 168) (see paper)
30% identity, 25% coverage
- catalytic activity: S-methyl-L-methionine + L-homocysteine = 2 L-methionine + H(+) (RHEA:26337)
catalytic activity: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + NADP(+) = (6R)-5,10- methylene-5,6,7,8-tetrahydrofolate + NADPH + H(+) (RHEA:19817)
catalytic activity: (6S)-5-methyl-5,6,7,8-tetrahydrofolate + NAD(+) = (6R)-5,10- methylene-5,6,7,8-tetrahydrofolate + NADH + H(+) (RHEA:19821)
cofactor: FAD
cofactor: Zn(2+) - A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study
Albaum, Proteome science 2011 - “...<0.000001 <0.000001 1257 P25994 0.000001 0.755894 0.006728 0.000072 1641 O32243 0.000003 0.599332 >0.99 0.000505 404 O06745 0.000005 >0.99 0.013199 0.011193 485 P37527 0.000013 >0.99 >0.99 0.051621 181 P04969 0.000016 >0.99 >0.99 0.708837 745 O32167 0.000020 >0.99 0.001374 0.000021 2891 O32157 0.000035 0.016583 <0.000001 0.000796 957 O31501...”
- “...<0.000001 0.004345 471 P71070 0.417433 >0.99 0.000001 0.009605 314 Q9KWU4 0.280189 >0.99 0.000448 0.009979 807 O06745 0.000005 >0.99 0.013199 0.011193 485 O35007 0.002474 >0.99 >0.99 0.011411 410 O05252 0.111360 0.104107 0.601796 0.017767 835 O32218 0.009165 >0.99 >0.99 0.018027 567 O34633 0.000185 >0.99 >0.99 0.025892 433 P94421...”
SAMCFNEI73_Ch2207 betaine--homocysteine S-methyltransferase from Sinorhizobium americanum
34% identity, 24% coverage
BC_4251 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase from Bacillus cereus ATCC 14579
30% identity, 26% coverage
- Bacillus cereus Response to a Proanthocyanidin Trimer, a Transcriptional and Functional Analysis
Tamura, Current microbiology 2016 - “...response BC_2984 21.2 Immune inhibitor A precursor BC_1419 20.2 Diaminopimelate decarboxylase BC_4775 20.0 Phosphoglycerol transferase BC_4251 17.5 Bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein BC_3410 17.4 D-Threo-aldose 1-dehydrogenase BC_2603 17.3 Putative uncharacterized protein BC_1461 16.5 DNA integration/recombination/invertion protein BC_1779 16.3 Ketol-acid reductoisomerase BC_2496 15.9 D-Alanyl- d -alanine carboxypeptidase...”
R1CGJ7 Methionine synthase from Emiliania huxleyi
38% identity, 16% coverage
- How haptophytes microalgae mitigate vitamin B12 limitation.
Nef, Scientific reports 2019 - “...with following entries (Uniprot): Chlamydomonas reinhardtii METH (A8HYR2) and METE (A8JH37), E . huxleyi METH (R1CGJ7), MAT from Escherichia coli (P0A817) and Arabidopsis thaliana (Q9SJL8), Homo sapiens and A . thaliana SAHH (P23526; O23255), Rattus norvegicus CBLA (D3ZNY3), Homo sapiens CBLB (Q96EY8) and MMCM (P22033), Propionibacterium...”
gbs2004 unknown from Streptococcus agalactiae NEM316
31% identity, 26% coverage
PGA1_c16040 Methionine synthase component, pterin-binding domain (EC:2.1.1.13) from Phaeobacter inhibens DSM 17395
PGA1_c16040 methyltetrahydrofolate cobalamin methyltransferase from Phaeobacter inhibens DSM 17395
35% identity, 21% coverage
- mutant phenotype: Its auxotrophic phenotype is rescued by methionine. PGA1_c16040 has the pterin-binding domain (auxotroph)
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...vitamin B12 binding domain (PF02310). In P . inhibens , PGA1_c13370 has the methyltransferase domain, PGA1_c16040 has the pterin-binding domain, and MtbC (PGA1_c13350) was originally annotated as "putative dimethylamine corrinoid protein" and contains the vitamin B12-binding cap and vitamin B12-binding domains. Thole and colleagues [ 28...”
SMc04325 CONSERVED HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
WP_003530700 betaine--homocysteine S-methyltransferase from Sinorhizobium meliloti MVII-I
33% identity, 24% coverage
- Glycine Betaine Monooxygenase, an Unusual Rieske-Type Oxygenase System, Catalyzes the Oxidative N-Demethylation of Glycine Betaine in Chromohalobacter salexigens DSM 3043
Shao, Applied and environmental microbiology 2018 - “...(16). In addition, Barra and colleagues identified the SMc04325 open reading frame (ORF) from Sinorhizobium meliloti strain 102F34 as the BHMT-encoding gene...”
- An orphan LuxR homolog of Sinorhizobium meliloti affects stress adaptation and competition for nodulation
Patankar, Applied and environmental microbiology 2009 - “...California, Berkeley SMc03112 (metH) CCCAATCTATCCGA AAGG SMc04325 (bmt) GCCCTTTCCGATCT CCTC SMc01109 (metK) GGGCATCATGTTCG GCTATG SMc02755 (ahcY) CGGACCCTGCTGCT...”
- “...102F43, the betaine methyltransferase enzyme encoded by bmt (SMc04325) can also serve as a methionine synthase by methylating homocysteine to methionine using...”
- Interrelations between glycine betaine catabolism and methionine biosynthesis in Sinorhizobium meliloti strain 102F34
Barra, Journal of bacteriology 2006 - “...BHMT sequence revealed that the protein encoded by the SMc04325 open reading frame showed 24% identity with the human BHMT (9). BLAST scanning of the SMc04325...”
- “...of alphaproteobacteria carried an apparent ortholog of the Smc04325 protein. Although none of the Smc04325-related proteins have known functions, all of them...”
- Interrelations between glycine betaine catabolism and methionine biosynthesis in Sinorhizobium meliloti strain 102F34.
Barra, Journal of bacteriology 2006 - GeneRIF: An S. meliloti gene whose product is related to the human betaine-homocysteine methyl transferase enzyme has been identified and named bmt
LMOf2365_1702 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein from Listeria monocytogenes str. 4b F2365
lmo1678 similar to 5-methyltetrahydrofolate-homocysteine methyltransferase (metH) from Listeria monocytogenes EGD-e
29% identity, 27% coverage
- Transcriptomic Analysis of Listeria monocytogenes in Response to Bile Under Aerobic and Anaerobic Conditions
Chakravarty, Frontiers in microbiology 2021 - “...LMOf2365_1386 Phosphate butyryltransferase 5.7 thiI LMOf2365_1614 tRNA uracil 4-sulfurtransferase 5.7 galU LMOf2365_1099 UTPglucose-1-phosphate uridylyltransferase 5.6 LMOf2365_1702 Methionine synthase/methylenetetrahydrofolate reductase (NADPH) 5.6 LMOf2365_2609 FAD:protein FMN transferase 5.6 eno LMOf2365_2428 Enolase 5.5 LMOf2365_2670 N-acetylmuramoyl-L-alanine amidase, family 4 5.3 fabI LMOf2365_0990 Enoyl-[acyl-carrier-protein] reductase I 5.2 LMOf2365_1880 Copper chaperone; heavy...”
- Transcriptomic and phenotypic analyses identify coregulated, overlapping regulons among PrfA, CtsR, HrcA, and the alternative sigma factors sigmaB, sigmaC, sigmaH, and sigmaL in Listeria monocytogenes
Chaturongakul, Applied and environmental microbiology 2011 - “...(i.e., lmo0850, lmo1293, lmo1335, lmo1473, lmo1539, lmo1678, lmo1849, lmo1993, lmo2040, lmo2159, lmo2161, lmo2163, lmo2193, lmo2335, lmo2557, lmo2597, and...”
A8FBU4 Homocysteine methyltransferase from Bacillus pumilus (strain SAFR-032)
30% identity, 25% coverage
CAETHG_0145 methyltetrahydrofolate cobalamin methyltransferase from Clostridium autoethanogenum DSM 10061
34% identity, 20% coverage
SAR0354 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
31% identity, 26% coverage
SPO1884 betaine--homocysteine S-methyltransferase from Ruegeria pomeroyi DSS-3
31% identity, 24% coverage
- A mutant fitness assay identifies bacterial interactions in a model ocean hot spot
Schreier, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...O-succinylhomoserine sulfhydrylase ( metZ ) Homocysteine 3 SPO1734 homoserine dehydrogenase ( hom ) Homoserine 5 SPO1884 S-methyltransferase component of split metH Methionine 3.9 SPO1973 3-dehydroquinate dehydratase, type II ( aroQ ) Aromatic amino acids 3.9 SPO2150 anthranilate phosphoribosyltransferase ( trpD ) Tryptophan 3.6 2.3 SPO2151 indole-3-glycerol...”
- Experimental Identification of Small Non-Coding RNAs in the Model Marine Bacterium Ruegeria pomeroyi DSS-3
Rivers, Frontiers in microbiology 2016 - “...Amino acid metabolism 0.002 SPO3390 Hypothetical protein 0.003 SPO2630 C4-dicarboxylate transport sensor protein Transport 0.006 SPO1884 Methionine synthase I Amino acid metabolism 0.009 SPO3077 TldD/PmbA family protein 0.009 SPO1050 Phage integrase family site specific recombinase Phage 0.001 SPO0323 Hypothetical protein 0.001 trans54 207 N/A trans56 146...”
ELI_2004 B12-binding domain-containing protein from Eubacterium callanderi
36% identity, 15% coverage
SSCH_1000016 methyltetrahydrofolate cobalamin methyltransferase from Syntrophaceticus schinkii
33% identity, 20% coverage
SE2381 conserved hypothetical protein from Staphylococcus epidermidis ATCC 12228
28% identity, 25% coverage
SMc04342 PUTATIVE METHYLTRANSFERASE PROTEIN from Sinorhizobium meliloti 1021
32% identity, 20% coverage
NWMN_0349 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein from Staphylococcus aureus subsp. aureus str. Newman
SAUSA300_0358 putative 5-methyltetrahydrofolate--homocysteine methyltransferase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL0429 5-methyltetrahydrofolate--homocysteine methyltransferase, putative from Staphylococcus aureus subsp. aureus COL
30% identity, 26% coverage
- CodY in Staphylococcus aureus: a regulatory link between metabolism and virulence gene expression
Pohl, Journal of bacteriology 2009 - “...on April 16, 2019 by guest NWMN_0349 NWMN_0350 NWMN_0351 NWMN_0425 NWMN_0436 NWMN_0437 NWMN_0516 NWMN_0831 NWMN_0855 NWMN_0858 NWMN_0860 NWMN_0883...”
- The ClpXP protease is dispensable for degradation of unfolded proteins in Staphylococcus aureus
Stahlhut, Scientific reports 2017 - “...3,7 1,2E-07 SAUSA300_0797 ABC transporter permease protein 3,7 9,0E-15 SAUSA300_0846 Na+/H+antiporter family protein 3,7 1,5E-14 SAUSA300_0358 putative 5-methyltetrahydrofolatehomocysteine methyltransferase 3,6 6,0E-15 sak staphylokinase precursor 3,6 7,5E-22 ear Ear protein 3,6 4,7E-11 ilvD dihydroxy-acid dehydratase 3,6 2,0E-09 ilvC ketol-acid reductoisomerase 3,5 6,6E-22 ilvB acetolactate synthase, large subunit...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_2520 SAUSA300_0488 SAUSA300_1816 SAUSA300_2173 SAUSA300_2408 SAUSA300_1259 SAUSA300_2623 SAUSA300_0358 1.8 1.8 1.8 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7...”
- Nutrient limitation governs Staphylococcus aureus metabolism and niche adaptation in the human nose
Krismer, PLoS pathogens 2014 - “...in SNM3. Among the methionine-biosynthetic genes those for MetE (5-methyltetrahydropteroyltriglutamate-homocysteine S-methyl-transferase) and its homologue MetF SAUSA300_0358 (bifunctional homocysteine S-methyltransferase), responsible for the conversion of L-homocysteine to L-methionine, were 13 to 14-fold up-regulated. The strong up-regulation of two L-methionine ABC-transport systems (SAUSA300_0435-0437 and SAUSA300_0796-0798) underscored the importance...”
- In vitro and in vivo models of Staphylococcus aureus endophthalmitis implicate specific nutrients in ocular infection
Sadaka, PloS one 2014 - “...NupC 7.2 (2.0) SACOL0427 Hypothetical protein 7.5 (1.1) SACOL0428 metE 5-methyltetrahydropteroyltriglutamate/homocysteineS-methyltransferase 19.7 (1.2) 9.2 (1.6) SACOL0429 Bifunctional homocysteineS-methyltransferase/5,10-methylenetetrahydrofolate reductase 28.3 (1.2) 11.5 (1.4) SACOL0430 Trans-sulfuration enzyme family protein 36.1 (1.1) 12.8 (1.1) SACOL0431 Trans-sulfuration enzyme family protein 30.9 (1.1) 10.4 (1.1) SACOL0431 rev comp Reverse complement...”
- Global analysis of the Staphylococcus aureus response to mupirocin
Reiss, Antimicrobial agents and chemotherapy 2012 - “...PurH SACOL1074 SACOL1080 SACOL1077 SACOL1216 SACOL2213 SACOL1274 SACOL2057 SACOL0429 PurK PurM PurQ PyrF RpoA RpsB RsbU 0.97 1.13 0.87 0.95 1.36 0.72 1.22 1.49...”
PGA1_c13370 Methionine synthase component, methyltransferase domain (EC:2.1.1.13) from Phaeobacter inhibens DSM 17395
PGA1_c13370 betaine--homocysteine S-methyltransferase from Phaeobacter inhibens DSM 17395
31% identity, 24% coverage
- mutant phenotype: PGA1_c13370 has a methyltransferase domain and its auxotrophic phenotype is rescued by added methionine. Also, S. Thole et al. (ISME J. 2012) proposed that PGA1_c13360, which contains a radical SAM domain (PF04055), might be involved in B12 activation, but it lacks phenotypes in our data. (auxotroph)
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “...binding cap (PF02607), and a vitamin B12 binding domain (PF02310). In P . inhibens , PGA1_c13370 has the methyltransferase domain, PGA1_c16040 has the pterin-binding domain, and MtbC (PGA1_c13350) was originally annotated as "putative dimethylamine corrinoid protein" and contains the vitamin B12-binding cap and vitamin B12-binding domains....”
BT_0340 trimethylamine corrinoid protein 2 (TCP 2) from Bacteroides thetaiotaomicron VPI-5482
40% identity, 14% coverage
- Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam, mBio 2022 - “...protein complexes, including MetH (B 12 -dependent methionine synthase; BT_0180), Mta (methylamine/trimethylamine methyltransferase corrinoid proteins; BT_0340, BT_0342, BT_0343), HpnR / Hyp (B 12 -binding domain/radical SAM domain protein; BT_0640), MutAB (methylmalonyl-CoA mutase; BT_2090 and BT_2091), and NrdJ (B 12 -dependent ribonucleotide reductase; BT_2145) ( 12 ,...”
Tph_c05860 B12-binding domain-containing protein from Thermacetogenium phaeum DSM 12270
42% identity, 13% coverage
H6NQX3 Bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein from Paenibacillus mucilaginosus 3016
30% identity, 25% coverage
SpAn4DRAFT_2140 B12-binding domain-containing protein from Sporomusa ovata
40% identity, 14% coverage
- Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by 'Candidatus Formimonas warabiya' strain DCMF
Holland, Frontiers in microbiology 2022 - “...Ga0180325_114742, Ca. Frackibacter sp. T328-2 AWU54_1980 AWU54_1975, Sporomusa ovata DSM 2662 SOV_3c09370SOV_3c09310, S. ovata An4 SpAn4DRAFT_2140 SpAn4DRAFT_2133. CoP, corrinoid protein; MTI, methyltransferase I; HydA, hydantoinase; MTII, methyltransferase II; BCCT, betaine/carnitine/choline family transporter; RACE, reductive activator of corrinoid-dependent enzymes; ProX, extracellular glycine betaine ligand binding protein. Asterisks...”
SXYL_02643 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase from Staphylococcus xylosus
26% identity, 26% coverage
PGA1_c13350 Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) from Phaeobacter inhibens DSM 17395
PGA1_c13350 corrinoid protein from Phaeobacter inhibens DSM 17395
37% identity, 15% coverage
- mutant phenotype: PGA1_c13350 is annotated as putative dimethylamine corrinoid protein. Its auxotrophic phenotype is rescued by added methionine. Compared to MetH from E. cli, it has the B12-binding cap (PF02607) and B12 binding (PF02310) domains but lacks methyltransferase (PF02574) or pterin-binding (PF00809) domains or the B12 activation domain (PF02965). (auxotroph)
- Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics
Price, PLoS genetics 2018 - “.... inhibens , PGA1_c13370 has the methyltransferase domain, PGA1_c16040 has the pterin-binding domain, and MtbC (PGA1_c13350) was originally annotated as "putative dimethylamine corrinoid protein" and contains the vitamin B12-binding cap and vitamin B12-binding domains. Thole and colleagues [ 28 ] previously suggested that two of these...”
ELI_2005 methyltetrahydrofolate cobalamin methyltransferase from Eubacterium callanderi
31% identity, 20% coverage
2yckX / Q3ACR9 Methyltransferase bound with tetrahydrofolate (see paper)
33% identity, 20% coverage
- Ligand: (6s)-5,6,7,8-tetrahydrofolate (2yckX)
Tph_c03600 B12-binding domain-containing protein from Thermacetogenium phaeum DSM 12270
37% identity, 15% coverage
LGS26_08025 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase from Dissulfurimicrobium hydrothermale
32% identity, 26% coverage
Tph_c15130 methyltetrahydrofolate cobalamin methyltransferase from Thermacetogenium phaeum DSM 12270
30% identity, 20% coverage
- Energy-Conserving Enzyme Systems Active During Syntrophic Acetate Oxidation in the Thermophilic Bacterium Thermacetogenium phaeum
Keller, Frontiers in microbiology 2019 - “...encoding CODH/ACS (structural precursor genes and their maturation factors; Tph_c15140- Tph_c15190), methyl-tetrahydrofolate-corrinoid iron-sulfur protein Co-methyltransferase (Tph_c15130) and MTHFR (Tph_c15100- Tph_c15110). MTHFR subunits of T. phaeum show high similarity to the MetF (Tph_c15100, 39% identity) and MetV (Tph_c15110 34% identity) of A. woodii ( Table 1 ;...”
- Alternative Pathways of Acetogenic Ethanol and Methanol Degradation in the Thermophilic Anaerobe Thermacetogenium phaeum
Keller, Frontiers in microbiology 2019 - “...2 ). The CODH/ACS precursors and their maturation factors (Tph_c15140Tph_c15190), the methyltetrahydrofolate-corrinoid ironsulfur protein Co-methyltransferase (Tph_c15130) and the methylene-tetrahydrofolate (THF) reductase (Tph_c15100Tph_c15110) are encoded in one gene cluster, whereas the methylene-THF dehydrogenase (Tph_c16310Tph_c16320) is encoded further upstream. All these genes are expressed during growth with all...”
- Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum
Oehler, BMC genomics 2012 - “...pathway. It is located in the acs operon which contains in addition a methyltetrahydrofolate:corrinoid/iron-sulfur methyltransferase (Tph_c15130), a corrinoid/iron-sulfur protein (Tph_c15140), and the methylenetetrahydrofolate reductase (Tph_c15100). An interesting feature of the acs operon is the presence of two genes resembling heterodisulfide reductase genes (Tph_c15090, Tph_c15120). There are...”
CDR20291_0654 putative carbon monoxide dehydrogenase/acetyl-CoA synthase complex, methyltransferase subunit from Clostridium difficile R20291
CD0727 putative carbon monoxide dehydrogenase/acetyl-CoA synthase complex,methyltransferase subunit from Clostridium difficile 630
CDR20291_0654 carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit from Clostridioides difficile R20291
33% identity, 20% coverage
- Identification of Clostridium difficile Immunoreactive Spore Proteins of the Epidemic Strain R20291
Pizarro-Guajardo, Proteomics. Clinical applications 2018 - “...immunoreactive in the surface of epidemic R20291 spores. Among these proteins we identified a methyltransferase (CDR20291_0654). As previously suggested, it is likely that these proteins are derived from vegetative contaminants that could not be removed by the spore purification procedures [ 9 ] . Nevertheless, these...”
- “...35209 3.98 8 17.2 2 CDR20291_1282 C9YL30 Peroxiredoxin (CotE) 838 81612 5.25 40 33.9 3 CDR20291_0654 C9YJA5 Putative carbon monoxide dehydrogenase/acetyl-CoA synthase complex, methyltransferase subunit 288 29762 4.78 25 71.3 4 CDR20291_0926 C9YK25 Uncharacterized protein (CdeC) 330 46958 4.84 27 40 5 CDR20291_2291 C9YNX8 Putative spore-coat...”
- Vegetative Cell and Spore Proteomes of Clostridioides difficile Show Finite Differences and Reveal Potential Protein Markers
Abhyankar, Journal of proteome research 2019 - “...of life of C.difficile requires specific enzymes, such as acetyl-CoA synthases/CO dehydrogenases (CD0174, CD0176, and CD0727), formate dehydrogenases (CD2179), and iron-only hydrogenases (CD0893, CD3258, and CD3406). Enzymes CD0174 and CD0176 synthesize the key metabolite acetyl-CoA from CO, methyl corrinoid, and CoASH. The formate dehydrogenases can be...”
- “...to formate, which is further metabolized to acetyl-CoA through enzymatic reactions. One of these enzymes, CD0727, is a unique acetyl-CoA synthase/CO dehydrogenase with a methyltransferase subunit and is reported to be essential for sporulation. 50 The acetogens lacking cytochromes use the Rnf complex (encoded by CD113742)...”
- "One-Pot" Sample Processing Method for Proteome-Wide Analysis of Microbial Cells and Spores
Swarge, Proteomics. Clinical applications 2018 - “...previously. 17 In addition, from P. difficile spores, we identified proteins GerG (CD0311), CD3298, and CD0727 that were the focus of recent functional studies. 34 , 35 , 36 In a previous study, domain prediction approach identified proteins with domains predicted to be pathogenically critical and...”
- A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors
Larocque, BMC systems biology 2014 - “...(P34896 [44%]) CD2834 (glyA) - B7ZLW7 [31%] PLP , THL (P34897 [41%]); Mimosine (Pr4896 [40%]) CD0727 (folD | fhs | fchA) d P24182 [53%] Q96RQ3 [48%] CNC , THL , I2A (Q99707 [31%]) scoB (folD | fhs | fchA) d E9YQ86 [56%] B7Z609 [51%] SIN ,...”
- Clostridium difficile is an autotrophic bacterial pathogen
Köpke, PloS one 2013 - “...have been shown to be expressed. In addition, the methyltransferase of strain 630 (encoded by CD0727) has been purified in recombinant E. coli and its activity been confirmed [40] . Acetogens are known for their energy efficiency, the use of a wide range of electron acceptors,...”
acsE / Q46389 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase subunit (EC 2.1.1.258) from Moorella thermoacetica (see 4 papers)
ACSE_MOOTH / Q46389 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase; 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase; MeTr; EC 2.1.1.258 from Moorella thermoacetica (Clostridium thermoaceticum) (see 3 papers)
Q46389 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein Co-methyltransferase (EC 2.1.1.258) from Moorella thermoacetica (see 3 papers)
4djdA / Q46389 Crystal structure of folate-free corrinoid iron-sulfur protein (cfesp) in complex with its methyltransferase (metr) (see paper)
33% identity, 19% coverage
- function: Methyltransferase that mediates the transfer of a N5-methyl group of (6S)-methyltetrahydrofolate to the 5- methoxybenzimidazolylcobamide cofactor of a corrinoid/Fe-S protein (AcsC/AcsD) in the anaerobic acetyl-CoA pathway (Wood-Ljungdahl pathway) of carbon monoxide and carbon dioxide fixation.
catalytic activity: methyl-Co(III)-[corrinoid Fe-S protein] + (6S)-5,6,7,8- tetrahydrofolate = Co(I)-[corrinoid Fe-S protein] + (6S)-5-methyl- 5,6,7,8-tetrahydrofolate + H(+) (RHEA:45200)
cofactor: Ca(2+)
subunit: Heterohexamer composed of 2 subunits of AcsC, 2 subunits of AcsD and 2 subunits of AcsE. - Ligand: calcium ion (4djdA)
DSY1647 hypothetical protein from Desulfitobacterium hafniense Y51
34% identity, 20% coverage
CAETHG_2844, CAETHG_2849 corrinoid protein from Clostridium autoethanogenum DSM 10061
34% identity, 15% coverage
mtvA1 / Q2RLH0 [methyl-Co(III) methoxylated-aromatic-compound-specific corrinoid protein]--tetrahydrofolate methyltransferase monomer (EC 2.1.1.385) from Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (see 2 papers)
31% identity, 22% coverage
AF_0006 corrinoid protein from Archaeoglobus fulgidus DSM 4304
38% identity, 11% coverage
- A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
Welte, Environmental microbiology 2021 - “...demethoxylation pathway of A. fulgidus . Genomic and transcriptomic analysis revealed cobalamin binding protein MtoC (AF_0006) and its activator MtoD (AF_0010), Odemethylase MtoB (AF_0007) and methyl transferase MtoA (AF_0009) to be essential for growth of A. fulgidus on methoxylated aromatic compounds. CoM: coenzyme M, H 4...”
- “...ribosomal protein (gene AF_1919) RPKM under growth on lactate or 2methoxyphenol (MP). RPKM values for AF_0006 and AF_0007 are depicted with a different scale (green shades) than the other genes (blue shades). Log 2 fold change values are shown for MP versus lactate (this study), H...”
Dhaf_4611 cobalamin B12-binding domain protein from Desulfitobacterium hafniense DCB-2
38% identity, 14% coverage
- Characterization of an O-demethylase of Desulfitobacterium hafniense DCB-2
Studenik, Journal of bacteriology 2012 - “...Dhaf_2573, Dhaf_2795, Dhaf_3310, Dhaf_3879, Dhaf_4322, Dhaf_4610, Dhaf_4611, and Dhaf_4612 (GenBank accession no. CP001336.1) as Strep tag fusions (at...”
- “...min at 95C, 45 s at 55C, and 1 min (Dhaf_4610, Dhaf_4611, and Dhaf_4612) or 3 min (all other genes) at 72C were performed. After the last cycle, a final...”
Cbei_1828 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein from Clostridium beijerincki NCIMB 8052
26% identity, 24% coverage
- Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii
Sandoval-Espinola, Scientific reports 2017 - “...and accessory genes (Cbei_3798 to Cbei_3801), formyl-THF ligase (Cbei_0101), methylene-THF dehydrogenase/cyclohydrolase (Cbei_1702) and methylene-THF reductase (Cbei_1828). The putative proteins encoded by these genes have high sequence identity to those of Clostridium ljungdahlii , the species most often utilized for ethanol generation from synthesis gas 5 ,...”
- “...assembled reads, we found the putative genes required for C1-assimilation being expressed, either constitutively (Cbei_5054, Cbei_1828 and Cbei_4318) or differentially over time (Cbei_1702, Cbei_0101, Cbei_3801, Cbei_3794, Cbei_3798, Cbei_3799, Cbei_3800, Cbei_3020, Cbei_1010 and Cbei_1011) (Figs 3 and S3 ). After mapping this transcriptomic response to our gas...”
CA_C0291 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase from Clostridium acetobutylicum ATCC 824
25% identity, 25% coverage
WP_052718253 corrinoid protein from Methanosarcina sp. MTP4
33% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240...”
mtgC / Q24SP8 glycine betaine-specific corrinoid protein from Desulfitobacterium hafniense (strain Y51) (see paper)
DSY3155 hypothetical protein from Desulfitobacterium hafniense Y51
36% identity, 14% coverage
FKV42_RS08550, WP_154809803 corrinoid protein from Methanolobus vulcani
31% identity, 16% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting hydrogen-dependent methylotrophic the enzymes important for energy conversion/recycling of reducing equivalents are shown as those play an...”
- “...(Creighbaum et al. 2019 ). Further, proteomic analysis revealed that MtgB, a corrinoid binding protein (FKV42_RS08550), a corrinoid reductive activation enzyme (FKV42_RS10455) and a methylcorrinoid:CoM methyltransferase (FKV42_RS10480) were highly abundant when M. vulcani B1d was grown on betaine relative to growth on trimethylamine. Energy conservation presumably...”
- “...amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455 WP_154810143 CoM methyltransferase FKV42_RS10480 WP_154810148 For the organisms conducting hydrogen-dependent methylotrophic the enzymes important for energy conversion/recycling of reducing equivalents are shown as those play an important...”
WP_026394334 corrinoid protein from Acetobacterium dehalogenans DSM 11527
35% identity, 15% coverage
CBO1494 dimethylamine corrinoid protein from Clostridium botulinum A str. ATCC 3502
33% identity, 14% coverage
7xcnP / O93659 Crystal structure of the mttb-mttc complex at 2.7 a resolution (see paper)
32% identity, 16% coverage
- Ligand: 5-hydroxybenzimidazolylcobamide (7xcnP)
AMET1_0748 cobalamin-dependent protein from Methanonatronarchaeum thermophilum
32% identity, 14% coverage
- Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia"
Ferrer, Genes 2018 - “...). In addition, FeS causes downregulation of both methanogenic corrinoid protein MtaC paralogs AMET1_1049 and AMET1_0748, which are likely involved in methanol reduction. Both proteins, especially AMET1_1049, are abundant at normal conditions. Both FeS and H 2 conditions, as expected, affect iron uptake and formation of...”
- “...(4.4) FeS AMET1_1049 Methanogenic corrinoid protein MtaC DOWN (11.8) AMET1_0222 (2R,3R)-3-methylornithine synthase PylB DOWN (10/8) AMET1_0748 Methanogenic corrinoid protein MtaC DOWN (7.0) AMET1_0462 Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain UP (13.7) AMET1_1183 Energy-coupling factor transporter ATP-binding protein EcfA2 UP (5.5) AMET1_0093 ABC-type cobalamin/Fe3+-siderophores transport system,...”
MA2971 monomethylamine corrinoid protein from Methanosarcina acetivorans C2A
30% identity, 16% coverage
METHO_RS06035, WP_015324657 uroporphyrinogen decarboxylase family protein from Methanomethylovorans hollandica DSM 15978
29% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...MtsH MA_4558 AAM07897 Methylmercaptopropionate MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ?...”
- “...MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis...”
mttC / O93659 trimethylamine-specific corrinoid protein from Methanosarcina barkeri (see paper)
MTTC_METBA / O93659 Trimethylamine corrinoid protein; TCP from Methanosarcina barkeri (see paper)
32% identity, 16% coverage
- function: Acts probably as a methyl group carrier between MttB and either MtbA or MtaA
subunit: Can form a complex with MttB
METHO_RS01750, WP_015323796 corrinoid protein from Methanomethylovorans hollandica DSM 15978
32% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...MA_4558 AAM07897 Methylmercaptopropionate MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ?...”
- “...MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1...”
MSMTP_RS14200, WP_048180685 methyltransferase cognate corrinoid protein from Methanosarcina sp. MTP4
31% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515...”
- “...WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521...”
MSMTP_RS00505, WP_048177073 uroporphyrinogen decarboxylase family protein from Methanosarcina sp. MTP4
31% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein...”
- “...WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase...”
MM2047 dimethylamine corrinoid protein from Methanosarcina mazei Goe1
32% identity, 13% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mtb C 1 encoding dimethylamine corrinoid protein; MM1690, mtt C 1 encoding dimethylamine corrinoid protein; MM2047, mtt C 2 encoding trimethylamine corrinoid protein; MM2052, mtb C 2 encoding dimethylamine corrinoid protein; MM2961, mtb C 3 encoding dimethylamine corrinoid protein; MM3334, monomethylamine corrinoid protein; MM2440, hypothetical protein;...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...MM1692; mtbB1, MM1693/MM1694; mttP2, MM2045/MM2046; mttC2, MM2047; mttB2, MM2048/MM2049; mtbB2, MM2050/2051; mtbC2, MM2052; mtbC3, MM2961; mtbB3, MM2962/MM2963;...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...MM1687 to pRS252 ..............................orfs MM2047 to pRS254 ..............................orfs MM1693 to pRS255 ..............................orfs...”
HUE98_15605 methyltetrahydrofolate cobalamin methyltransferase from Candidatus Contubernalis alkalaceticus
29% identity, 19% coverage
AMET1_0105 cobalamin-dependent protein from Methanonatronarchaeum thermophilum
35% identity, 13% coverage
MA0456 methanol-5-hydroxybenzimidazolylcobamide co-methyltransferase, isozyme 1 from Methanosarcina acetivorans C2A
33% identity, 15% coverage
- A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer
Holmes, mBio 2019 - “...isozyme 1 mtaA1 1.68 0.01 0.02 MA0455 Methanol:5-hydroxybenzimidazolyl-cobamide methyltransferase, isozyme 1 mtaB1 6.84 0.02 0.04 MA0456 Corrinoid-containing methyl-accepting protein, isozyme 1 mtaC1 7.95 0.01 0.03 MA4392 Methanol:5-hydroxybenzimidazolylcobamide methyltransferase, isozyme 2 mtaB2 68.55 5.70 10 11 2.56 10 7 MA4391 Corrinoid-containing methyl-accepting protein, isozyme 2 mtaC2 48.28...”
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...cyanogen bromide-like cleavage at the observed position. The N -terminal peptide of M. acetivorans C2A MA0456 (MtaC1, methanol-5-hydroxybenzimidazolyl cobamide co-methyl transferase) was previously recovered as MLDFTEASLK and in its methionine sulfoxide form. Methionines are often oxidized under experimental conditions. A related peptide 58-Da heavier than the...”
- “...annotated position) (Deppenmeier et al., 2002 ). Figure 2 N -terminal peptides of M. acetivorans MA0456 (MtaC1). (A) Unmodified MLDFTEASLK, (B) Low abundance variant Ac-M ox LDFTEASLK. Intense 190-Da ions correspond to the b 1 product from the N -terminally acetylated peptide. Larger b -ions show...”
- Development of β -lactamase as a tool for monitoring conditional gene expression by a tetracycline-riboswitch in Methanosarcina acetivorans
Demolli, Archaea (Vancouver, B.C.) 2014 - “...constructed by replacing mcrB P in pBlaNFSP by the ca. one kb sequence preceding mtaC1 (MA0456), which encodes the corrinoid protein of the methanol-specific methyltransferase MT1 [ 35 , 36 ]. To obtain plasmid pP0145NFSP, mcrB P in pBlaNFSP was replaced by the ca. one kb...”
- S-layer, surface-accessible, and concanavalin A binding proteins of Methanosarcina acetivorans and Methanosarcina mazei
Francoleon, Journal of proteome research 2009 - “...ID with multiple peptides Band 11 MA3895 nitrogenase (iron protein) 134 29.2 8 yes 0 MA0456 methanol--5-hydroxybenzimidazolylcobamideco-methyltransferase (methanol-specific corrinoid-binding protein) 55 27.7 2 no 0 Band 12 MA3895 nitrogenase (iron protein) 53 29.2 3 no 0 Band 13 None streptavidin background only a NCBI protein accession...”
- Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
Li, Journal of proteome research 2007 - “...MA0308 MA0309 MA0368 MA0406 MA0455 NIH-PA Author Manuscript MA0456 MA0490 MA0619 MA0620 MA0630 MA0659 MA0660 MA0661 MA0662 MA0663 MA0664 MA0887 MA0889 MA0891...”
mtmC / O30641 monomethylamine corrinoid protein from Methanosarcina barkeri (see 2 papers)
MTMC1_METBA / O30641 Monomethylamine corrinoid protein 1; MMCP 1 from Methanosarcina barkeri (see paper)
29% identity, 16% coverage
- function: Acts as a methyl group carrier between MtmB and MtbA
subunit: Can form a complex with MtmB - A corrinoid-dependent catabolic pathway for growth of a Methylobacterium strain with chloromethane
Vannelli, Proceedings of the National Academy of Sciences of the United States of America 1999 - “...tuberculosis) (P72042) MtbA (M. barkeri) (O30640) MtmC (M. barkeri) (O30641) 47 31 (143 aa) 24y32 ND 34.2 24.9 34.3 ,1 2,275 3,345 3,507 1,275 1,283 2,686 4,469...”
- “...from CmuA, MtmC of M. barkeri (SwissProt accession no. O30641), MetH of E. coli (P13009), and MutA the human methylmalonyl-CoA mutase (P22033), in the conserved...”
CAETHG_1609, CLAU_1567, CLJU_c37560 carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit from Clostridium autoethanogenum DSM 10061
29% identity, 20% coverage
- Clostridium autoethanogenum alters cofactor synthesis, redox metabolism, and lysine-acetylation in response to elevated H2:CO feedstock ratios for enhancing carbon capture efficiency
Davin, Biotechnology for biofuels and bioproducts 2024 - “...p value Log2 fold change WoodLjungdahl pathway/fermentation end products CAETHG_1608 CO-methylating acetyl-CoA synthase 0.268 0.08 CAETHG_1609 Dihydropteroate synthase DHPS 0.321 0.08 CAETHG_1610 CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel 0.136 0.15 CAETHG_1611 CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel 0.018* 0.29 CAETHG_1614 Methylenetetrahydrofolate reductase 0.139 0.15...”
- Required Gene Set for Autotrophic Growth of Clostridium autoethanogenum
Woods, Applied and environmental microbiology 2022 - “...CLAU_1566 to -1570, in which CLAU_1566, CLAU_1568, and CLAU_1569 were only required on CO, whereas CLAU_1567 and CLAU_1570 were required on CO and on YTF. Essentiality in the metabolism from acetyl-CoA. There are four main carbon compounds at the endpoints of metabolism for C. autoethanogenum :...”
- Energy Conservation and Carbon Flux Distribution During Fermentation of CO or H2/CO2 by Clostridium ljungdahlii
Zhu, Frontiers in microbiology 2020 - “...of the CODH and hydrogenase genes. There are four putative genes/gene clusters, i.e., CLJU_c01650, CLJU_c09110, CLJU_c37560 and CLJU_c37660-70 encoding CODH, among which only the transcriptional level of CLJU_c09110 was induced during CO fermentation, in comparison with H 2 fermentation ( Supplementary Table S1 ; Kpke et...”
- Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii
Philipps, Biotechnology for biofuels 2019 - “...internal controls: DFEPVLER (CODH/ACS, CO dehydrogenase/acetyl-CoA synthase complex beta subunit, CLJU_c37550), AIEAGLK (MeTr, methyltetrahydrofolate:corrinoid/iron-sulfur protein, CLJU_c37560), and IVVGYTR (F-THFL, formate-tetrahydrofolate ligase, CLJU_c37650). Peptide FDGTVEVK (glyceraldehyde 3-phosphate dehydrogenase) was used to exclude potential E. coli contamination. GCMS analysis The concentrations of acetone, isopropanol, ethanol, and acetate were...”
- Functional Expression of the Clostridium ljungdahlii Acetyl-Coenzyme A Synthase in Clostridium acetobutylicum as Demonstrated by a Novel In Vivo CO Exchange Activity En Route to Heterologous Installation of a Functional Wood-Ljungdahl Pathway
Fast, Applied and environmental microbiology 2018 - “...Ni-insertase (CLJU_c37660), the acetogenic methyltransferase (CLJU_c37560), and the codon-optimized E. coli methylenetetrahydrofolate reductase (metF). The...”
- “...protein levels. (A) sq-RT-PCR of metF, CLJU_c37550, CLJU_c37560, CLJU_c37660, and CLJU_c37670 for C. ljungdahlii (CLJ), C. acetobutylicum p95ACS_MetF (ACS), and...”
Desti_5447 MtaA/CmuA family methyltransferase from Desulfomonile tiedjei DSM 6799
33% identity, 15% coverage
MM1690 dimethylamine corrinoid protein from Methanosarcina mazei Goe1
32% identity, 13% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mtm C 1 encoding monomethylamine corrinoid protein; MM1687, mtb C 1 encoding dimethylamine corrinoid protein; MM1690, mtt C 1 encoding dimethylamine corrinoid protein; MM2047, mtt C 2 encoding trimethylamine corrinoid protein; MM2052, mtb C 2 encoding dimethylamine corrinoid protein; MM2961, mtb C 3 encoding dimethylamine corrinoid...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...for M. mazei, since the transcript levels of mttC1 (MM1690) and mtbC1 (MM1687) were essentially the same under all growth conditions tested, indicating that the...”
- “...MM0176; mtbC1, MM1687; mttB1, MM1688/MM1689; mttC1, MM1690; mttP1, MM1691/ MM1692; mtbB1, MM1693/MM1694; mttP2, MM2045/MM2046; mttC2, MM2047; mttB2,...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...MM2961 to vector (QIAGEN) MM1438 cloned in MM3336 cloned in MM1690 cloned in MM2049 cloned in MM1694 cloned in MM2052 cloned in MM2963 cloned in a Sequence (5 3...”
BP07_RS03260, WP_042685521 B12-binding domain-containing protein from Methermicoccus shengliensis DSM 18856
34% identity, 14% coverage
- Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
Kurth, The ISME journal 2021 - “...34%. Heterologous protein production of MtoC and MtoD The gene encoding the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) were amplified from genomic M. shengliensis DNA with primers 3235fw/3235Srev (CTCATATGAGCGTCAGAGTAACGTTCGAGC, CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCTGAAGAGAGTTTTTCTCC) and 3260fw/3260Srev (CTCATATGACGGACGTAAGAGAAGAGCTC/CTGCGGCCGCTTATTTTTCGAACTGCGGGTGGCTCCAGCTAGCCTCCACCCCCACCAGAGC) for cloning in expression vector pET-30a inserting an N-terminal...”
- “...coli DH5 (NEB) was used for plasmid transformation. For production of the corrinoid protein MtoC (BP07_RS03260) and the corrinoid activating enzyme (BP07_RS03235) the plasmids pET-30a_BP07_RS03260 and pET-30a_BP07_RS03235 were used for transformation into E. coli Bl21 (DE3). For protein overexpression, one colony was inoculated in 600ml LB-medium...”
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator...”
- “...ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like methyltransferase BP07_RS03240 WP_042685937 Corrinoid activation protein BP07_RS03235 WP_042685513 Methanococcoides Tertiary amines ? ? ? Methanolobus vulcani Quaternary amines MtgB methyltransferase FKV42_RS08545 WP_154809802 Corrinoid protein FKV42_RS08550 WP_154809803 Corrinoid activator FKV42_RS10455...”
Desac_1969 dihydropteroate synthase from Desulfobacca acetoxidans DSM 11109
29% identity, 19% coverage
MM2052 dimethylamine corrinoid protein from Methanosarcina mazei Goe1
32% identity, 15% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mtt C 1 encoding dimethylamine corrinoid protein; MM2047, mtt C 2 encoding trimethylamine corrinoid protein; MM2052, mtb C 2 encoding dimethylamine corrinoid protein; MM2961, mtb C 3 encoding dimethylamine corrinoid protein; MM3334, monomethylamine corrinoid protein; MM2440, hypothetical protein; MM2441, : transcriptional regulator, ArsR family; MM2442, hypothetical...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...mttC2, MM2047; mttB2, MM2048/MM2049; mtbB2, MM2050/2051; mtbC2, MM2052; mtbC3, MM2961; mtbB3, MM2962/MM2963; mtbP, MM2964; mtmC2, MM3334; mtmB2, MM3335; mtmP,...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...in MM1690 cloned in MM2049 cloned in MM1694 cloned in MM2052 cloned in MM2963 cloned in a Sequence (5 3 3) ORFs, open reading frames. pDrive pDrive pDrive...”
- “...MM1438 for.rt MM1438 rev.rt MM3334 for.rt MM3334 rev.rt MM2052 for.rt MM2052 rev.rt MM1688 for.rt MM1688 rev.rt MM2049 for.rt MM2049 rev.rt MM505 for.rt MM505...”
MA4164 corrinoid protein from Methanosarcina acetivorans C2A
MA_4164, WP_011024052 corrinoid protein from Methanosarcina acetivorans C2A
30% identity, 15% coverage
- Transcriptional response of <i>Methanosarcina acetivorans</i> to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Buan, Microbiology spectrum 2024 - “...genes (MA4389, MA4391, MA4393, MA4394), mtaCB3 methanol corrinoid methyltransferases (MA1617, MA1616), methylsulfide corrinoid protein mtaC MA4164, iron-sulfur flavoprotein MA1773, and coenzyme B biosynthesis gene 2-isopropyl malate synthase MA4615. In addition to hdrD MA0688, transcripts with decreased abundance when averaged across all five time points were hypothetical...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
Fu, Journal of bacteriology 2015 - “...use of these substrates. Here, we show that the MA4164 to MA4166 locus (which we designated the mtpCAP operon) is specifically required for MMPA metabolism and...”
- “...The results of bioinformatics analyses suggested that the MA4164 to MA4167 locus, which we designated mtpCAP-msrH, is involved in the metabolism of an unknown...”
- Transcriptional response of <i>Methanosarcina acetivorans</i> to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Buan, Microbiology spectrum 2024 - “...are shown. A complete list of genes can be found in Table S2 . Note MA_4164 is included in all panels as it met both statistical criteria. Bar charts depict unique mean log2 fold changes and unique log2 FC per hour for hdrED genes, with individual...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species.
Fu, Journal of bacteriology 2015 - GeneRIF: MtpC; required for growth on methylmercaptopropionate
AMET1_1049 cobalamin-dependent protein from Methanonatronarchaeum thermophilum
28% identity, 14% coverage
- Proteomic Analysis of Methanonatronarchaeum thermophilum AMET1, a Representative of a Putative New Class of Euryarchaeota, "Methanonatronarchaeia"
Ferrer, Genes 2018 - “...in the medium causes several predictable changes in the methyl-reduction pathways. The methylated-thiol corrinoid protein AMET1_1049 that is likely specific for methanol (MtaC) is downregulated, whereas several methylamine utilization proteins are upregulated, including one that is specific for TMA (MttC) and shows the largest fold change...”
- “...Table 3 ). In addition, FeS causes downregulation of both methanogenic corrinoid protein MtaC paralogs AMET1_1049 and AMET1_0748, which are likely involved in methanol reduction. Both proteins, especially AMET1_1049, are abundant at normal conditions. Both FeS and H 2 conditions, as expected, affect iron uptake and...”
WP_049796371 methyltransferase cognate corrinoid protein from Methanomassiliicoccus luminyensis B10
32% identity, 13% coverage
- Growth Characteristics of Methanomassiliicoccus luminyensis and Expression of Methyltransferase Encoding Genes
Kröninger, Archaea (Vancouver, B.C.) 2017 - “...WP_026068679.1; mtmB2 -N-term, WP_019176314.1; mtmB2 -C-term, WP_019176315.1; mtmB3 -C-term, WP_019178553; mtmB3 -N-term, WP_019178554; mtmC3 , WP_049796371. Not shown: putative MMA transporter with low homology to the corresponding enzyme from Ms. mazei [ 16 ], WP_01976434 (contig 5, 35060-37315). Table 1 Sequences of primer used for quantitative...”
- “...Rev: TCCCCTTTCAAAACGAGT mtmC1 WP_026068678.1 For: TGATGAAATGTTAGGACG Rev: CCCTTCCCGAGACCATTC mtmC2 WP_026068679.1 For: AGAAGAAGTGCTGGCGT Rev: CCTTGGCTCAATCCGCTC mtmC3 WP_049796371 For: ACAAGCTATATTGGCAGA Rev: CCCTTTCCCAGGCCTTGG mtmC4 WP_019178518 For: GGACGAGATTCTAGCCAC Rev: CCCTTTCCCAGGCCGTTC Ribosomal S15 WP_026068997 For: CTCATTCTCAGGGACCAGCA Rev: TGCATGTTCCTCTTGTTGGC Table 2 Comparison of growth yields. Organism Substrate Y CH4 (g cells/mol CH...”
Q8THX4 tetrahydromethanopterin S-methyltransferase (EC 2.1.1.86) from Methanosarcina acetivorans (see paper)
MA4384 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
MA_4384, WP_011024263 uroporphyrinogen decarboxylase family protein from Methanosarcina acetivorans C2A
29% identity, 17% coverage
- Transcriptional response of <i>Methanosarcina acetivorans</i> to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Buan, Microbiology spectrum 2024 - “...became apparent that the longest contiguous cluster of genes regulated by HdrED repression ranged from MA4384 to MA4394 ( Fig. 8a ). This region is directly downstream of the gene for the methylotrophic m ethanogenesi s r egulator msrC and encompasses genes for the fused c...”
- Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments
Tebbe, The ISME journal 2023 - “...million (rpkm). The methylthiol:coenzyme M methyltransferase MtsAB and methyl transferases MtsDFH (homologs of loci MA0859, MA4384, MA4558 of Methanosarcina acetivorans ) [ 42 ] were identified with DIAMOND BLASTp [ 63 ] with Q48924, Q8PUA8, and Q48925 (UniProtKB/Swiss-Prot), as well as WP_048064984.1, WP_011024263.1, and WP_011024431.1 (NCBI)...”
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...synthesized at elevated levels in response to CO (Rother et al. 2007 ). Further, CmtA (MA4384) is a soluble CH 3 -tetrahydrosarcinapterin:HS-CoM methyltransferase postulated to supplement the membrane-bound CH 3 -tetrahydrosarcinapterin:HS-CoM methyltransferase during CO-dependent growth of M. acetivorans (Vepachedu and Ferry 2012 ). Tetrahydrosarcinopterin is an...”
- “...DMS as the sole energy source and specific methyltransferases, called MtsD, MtsF, and MtsH (MA0859, MA4384, and MA4558) could be associated with the ability to grow on methyl sulfides (Oelgeschlger and Rother 2009a , b ). Further analysis of those methyltransferases revealed that the preferred substrate...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
Fu, Journal of bacteriology 2015 - “...MtmB MtmC MtbA MeSH MPA Co Co(I) MtsB MA0859 (MtsD) MA4384 (MtsF) MA4558 (MtsH) CH3-S-CoM D Co(III) MtsA DMS MMPA HS-CoM Co(III) HS-CoM H4MPT CH 3 Co(I) MtsA...”
- “...of single-subunit CoM methyltransferases, encoded by the MA0859, MA4384, and MA4558 loci of M. acetivorans, has also been characterized. These proteins are...”
- Reducing the genetic code induces massive rearrangement of the proteome
O'Donoghue, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...the composition of the proteome. Mr (kDa) 100 75 MA0859 MA4384 MA0857 MA4392 MA0455 50 MA4391 MA0855 MA2718 37 MA2813 25 MA4547 MA0456 MA1091 MA2699 MA1108 pH 3...”
- “...MA4127 MA1317 MA1275 MA3564 MA4386 MA0857 MA1091 MA1108 MA4384 MA0859 MA4558 Gene name Function x-Fold change ilvC S-layer domain pgi Exosome eif2b valS eif2B1...”
- A heme-based redox sensor in the methanogenic archaeon Methanosarcina acetivorans
Molitor, The Journal of biological chemistry 2013 - “...in M. acetivorans, MtsD (MA0859) and MtsF (MA4384), which are also regulated individually by vicinally encoded transcriptional regulators. MtsD transcription is...”
- “...sites of pE4384tetO1 (1) to exchange the ma4384 coding region against the ma4561 coding region resulting in pE4561tetO1. The constructed PmcrB(tetO1)-ma4561...”
- Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans
Vepachedu, Journal of bacteriology 2012 - “...50-fold elevated levels of proteins encoded by loci MA0859, MA4384, and MA4558 in cells grown with CO versus methanol or acetate (18). These proteins were first...”
- “...propose that the name of the enzyme encoded by MA4384 be CmtA (for cytoplasmic methyltransferase). Vepachedu and Ferry TABLE 1 Reactions and free energy yields...”
- MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans
Reichlen, mBio 2012 - “...MA2424MA2425 ( mtbBC-3 ) 0.780.95 MA2971MA2972 ( mtmBC-2 ) 1.371.44 MA4379 ( mtaA-1 ) 7.83 MA4384 ( mtsF ) 1.00 MA4558 ( mtsH ) 0.93 Oxidative branch MA0010 ( ftr ) 4.98 (7.07 1.52) b MA0304MA0309 ( fmdEFADCB ) 7.8110.09 MA0304 ( fmdE ) 14.8 4.0...”
- More
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...WP_143406895, WP_086637820, WP_086637822, WP_161490830, WP_086637824-25, WP_086637860, WP_086637826-32 Methanosarcina acetivorans Methyl sulfides MtsD MA_0859 AAM04298 MtsF MA_4384 AAM07726 MtsH MA_4558 AAM07897 Methylmercaptopropionate MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF...”
- In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans.
Oelgeschläger, Molecular microbiology 2009 (PubMed)- GeneRIF: The corrinoid/methyl transfer proteins MA0859, MA4384 and MA4558 are methyltransferases specific for methylsulfides.
Q8PWE1 Methanol corrinoid protein MtaC from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MM1648 Methanol corrinoid protein MtaC from Methanosarcina mazei Goe1
32% identity, 15% coverage
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...MM1589 Surface layer protein B 3 128 1 Y Y Q8PWE2 MM1647 MtaB1 14 357 Q8PWE1 MM1648 MtaC1 10 533 Q8PWA1 MM1695 Hypothetical protein 10 425 2 Y Y Y Q8PW83 MM1713 Hypothetical protein 2 173 Y Q8PW41 MM1760 Rps2p 30S ribosomal protein S2 3 104...”
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...Surface layer protein B 3 128 1 Y Y Q8PWE2 MM1647 MtaB1 14 357 Q8PWE1 MM1648 MtaC1 10 533 Q8PWA1 MM1695 Hypothetical protein 10 425 2 Y Y Y Q8PW83 MM1713 Hypothetical protein 2 173 Y Q8PW41 MM1760 Rps2p 30S ribosomal protein S2 3 104 Y...”
- “...et al., 2006 ). Interestingly, we observed only non-acetylated MLDFTEASLK from the M. mazei ortholog, MM1648, despite the larger protein quantity available for analysis. Note that M. mazei initiates translation 10 residues downstream of the originally annotated position) (Deppenmeier et al., 2002 ). Figure 2 N...”
- Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15
Cao, Applied and environmental microbiology 2014 - “...(MM0176), mtaB1 (MM1647), mtaB2 (MM1074), mtaB3 (MM0175), mtaC1 (MM1648), mtaC2 (MM1073), mtaC3 (MM0174), pta (MM0496), and ackA (MM0495). Cao et al. and...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...MM1075 MM1112 MM1271 MM1272 MM1273 MM1274 MM1275 MM1647 MM1648 MM1761 MM1762 MM1977 MM2882 MM2933 MM3197 MM0011 MM0093 MM0496 MM0583 MM0671 MM0772 MM0869 MM0870...”
MM2961 dimethylamine corrinoid protein from Methanosarcina mazei Goe1
32% identity, 15% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mtt C 2 encoding trimethylamine corrinoid protein; MM2052, mtb C 2 encoding dimethylamine corrinoid protein; MM2961, mtb C 3 encoding dimethylamine corrinoid protein; MM3334, monomethylamine corrinoid protein; MM2440, hypothetical protein; MM2441, : transcriptional regulator, ArsR family; MM2442, hypothetical protein; MM2446, conserved protein. On the basis of...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...MM2048/MM2049; mtbB2, MM2050/2051; mtbC2, MM2052; mtbC3, MM2961; mtbB3, MM2962/MM2963; mtbP, MM2964; mtmC2, MM3334; mtmB2, MM3335; mtmP, MM1434/MM1435; mtmB1,...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...pRS255 ..............................orfs MM2050 to pRS256 ..............................orfs MM2961 to vector (QIAGEN) MM1438 cloned in MM3336 cloned in MM1690...”
LOC107451377 betaine--homocysteine S-methyltransferase 1 from Parasteatoda tepidariorum
30% identity, 23% coverage
F7O84_RS08335 bifunctional homocysteine S-methyltransferase/methylenetetrahydrofolate reductase from Candidatus Galacturonibacter soehngenii
26% identity, 25% coverage
- "Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex
Valk, Frontiers in microbiology 2020 - “...3.5.4.9 and 1.5.1.5 folD 5 e 152 F7O84_RS05380 Methyltetrahydrofolate reductase 1.5.1.20 metF 1 e 87 F7O84_RS08335 5-Methyl-tetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 2.1.1.258 acsE 5 e 37 F7O84_RS02745 CO-Methylating acetyl-CoA synthase 2.3.1.169 acsBCD >10 Carbon-monoxide dehydrogenase 1.2.7.4 cooS >10 CO dehydrogenases contain highly conserved amino-acid motifs (Pfam or protein-family...”
- “...F7O84_RS05385 256 58 Methenyl-tetrahydrofolate cyclohydrolase/methylenetetrahydrofolate dehydrogenase 3.5.4.9 and 1.5.1.5 F7O84_RS05385 236 9 Methyltetrahydrofolate reductase 1.5.1.20 F7O84_RS08335 126 13 5-methyl-tetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase 2.1.1.258 F7O84_RS02745 144 19 CO-methylating acetyl-CoA synthase 2.3.1.169 n.d. CO dehydrogenase 1.2.7.4 n.d. Prismane/CO dehydrogenase family 1.7.99.1 F7O84_RS02405 40 8 Prismane/CO dehydrogenase family 1.7.99.1 F7O84_RS11645...”
WP_019178518 B12-binding domain-containing protein from Methanomassiliicoccus luminyensis B10
33% identity, 14% coverage
- Growth Characteristics of Methanomassiliicoccus luminyensis and Expression of Methyltransferase Encoding Genes
Kröninger, Archaea (Vancouver, B.C.) 2017 - “...WP_019178088.1; mtaA , WP_026068914.1; mtbA , WP_019176765.1; mtmB4 -C-term, WP_019178516; mtmB4 -N-term, WP_026069098; mtmC4 , WP_019178518; mttB -N-term, WP_026069099.1; mttB -C-term, WP_049796374.1; mttC , WP_026069100.1; mttP -N-term, WP_049796368.1; mttP -C-term, WP_019178523.1; mtbC , WP_026069102.1; mtbB -N-term, WP_026069103.1; mtbB -C-term, WP_026069104.1; mtbP , WP_049796369.1; mtmB1 -C-term, WP_019176305.1;...”
- “...Rev: CCCTTCCCGAGACCATTC mtmC2 WP_026068679.1 For: AGAAGAAGTGCTGGCGT Rev: CCTTGGCTCAATCCGCTC mtmC3 WP_049796371 For: ACAAGCTATATTGGCAGA Rev: CCCTTTCCCAGGCCTTGG mtmC4 WP_019178518 For: GGACGAGATTCTAGCCAC Rev: CCCTTTCCCAGGCCGTTC Ribosomal S15 WP_026068997 For: CTCATTCTCAGGGACCAGCA Rev: TGCATGTTCCTCTTGTTGGC Table 2 Comparison of growth yields. Organism Substrate Y CH4 (g cells/mol CH 4 ) Reference Methanogens without cytochromes...”
MA0527 dimethylamine corrinoid protein from Methanosarcina acetivorans C2A
32% identity, 15% coverage
Ccar_18790 carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit from Clostridium carboxidivorans P7
28% identity, 20% coverage
MA4558 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
MA_4558, WP_011024431 uroporphyrinogen decarboxylase family protein from Methanosarcina acetivorans C2A
28% identity, 19% coverage
- Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments
Tebbe, The ISME journal 2023 - “...(rpkm). The methylthiol:coenzyme M methyltransferase MtsAB and methyl transferases MtsDFH (homologs of loci MA0859, MA4384, MA4558 of Methanosarcina acetivorans ) [ 42 ] were identified with DIAMOND BLASTp [ 63 ] with Q48924, Q8PUA8, and Q48925 (UniProtKB/Swiss-Prot), as well as WP_048064984.1, WP_011024263.1, and WP_011024431.1 (NCBI) as...”
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...the sole energy source and specific methyltransferases, called MtsD, MtsF, and MtsH (MA0859, MA4384, and MA4558) could be associated with the ability to grow on methyl sulfides (Oelgeschlger and Rother 2009a , b ). Further analysis of those methyltransferases revealed that the preferred substrate for MtsD...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
Fu, Journal of bacteriology 2015 - “...MeSH MPA Co Co(I) MtsB MA0859 (MtsD) MA4384 (MtsF) MA4558 (MtsH) CH3-S-CoM D Co(III) MtsA DMS MMPA HS-CoM Co(III) HS-CoM H4MPT CH 3 Co(I) MtsA CH3-S-CoM HS-CoM...”
- “...CoM methyltransferases, encoded by the MA0859, MA4384, and MA4558 loci of M. acetivorans, has also been characterized. These proteins are comprised of an...”
- Reducing the genetic code induces massive rearrangement of the proteome
O'Donoghue, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...MA1275 MA3564 MA4386 MA0857 MA1091 MA1108 MA4384 MA0859 MA4558 Gene name Function x-Fold change ilvC S-layer domain pgi Exosome eif2b valS eif2B1 mtaC2 mtaA...”
- A heme-based redox sensor in the methanogenic archaeon Methanosarcina acetivorans
Molitor, The Journal of biological chemistry 2013 - “...direct transcriptional activator of the protein MtsH (MA4558), which is one of three highly similar corrinoid/methyltransferase fusion protein isoforms required...”
- Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans
Vepachedu, Journal of bacteriology 2012 - “...levels of proteins encoded by loci MA0859, MA4384, and MA4558 in cells grown with CO versus methanol or acetate (18). These proteins were first named fused...”
- “...mutants, for which combinations of MA0859, MA4384, and MA4558 were deleted or disrupted, fail to produce DMS or utilize it for methanogenesis or growth...”
- MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans
Reichlen, mBio 2012 - “...MA2971MA2972 ( mtmBC-2 ) 1.371.44 MA4379 ( mtaA-1 ) 7.83 MA4384 ( mtsF ) 1.00 MA4558 ( mtsH ) 0.93 Oxidative branch MA0010 ( ftr ) 4.98 (7.07 1.52) b MA0304MA0309 ( fmdEFADCB ) 7.8110.09 MA0304 ( fmdE ) 14.8 4.0 b MA0309 ( fmdB )...”
- In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans
Oelgeschläger, Molecular microbiology 2009 (PubMed)- “...to both corrinoid proteins and methyltransferases (MA0859, MA4384 and MA4558) are highly abundant. To address their role in M. acetivorans, a set of single and...”
- “...energy source, which demonstrates that MA0859, MA4384 and MA4558 are involved in, and required for, methylsulphide metabolism of M. acetivorans. Based on these...”
- More
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...WP_161490830, WP_086637824-25, WP_086637860, WP_086637826-32 Methanosarcina acetivorans Methyl sulfides MtsD MA_0859 AAM04298 MtsF MA_4384 AAM07726 MtsH MA_4558 AAM07897 Methylmercaptopropionate MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200...”
- In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans.
Oelgeschläger, Molecular microbiology 2009 (PubMed)- GeneRIF: The corrinoid/methyl transfer proteins MA0859, MA4384 and MA4558 are methyltransferases specific for methylsulfides.
MA0859 hypothetical protein (multi-domain) from Methanosarcina acetivorans C2A
31% identity, 15% coverage
- Physiological and transcriptomic response to methyl-coenzyme M reductase limitation in Methanosarcina acetivorans
Chadwick, Applied and environmental microbiology 2024 - “...dramatic increase in expression occurs in two of the methylsulfide-specific methyltransferases, mtpCAP (MA4164MA4166) and mtsD (MA0859), which increase in expression to approximately 100-fold ( Fig. 4B and C ). Notably, the gene encoding tetR does not significantly change in expression level under any of our experimental...”
- Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments
Tebbe, The ISME journal 2023 - “...one million (rpkm). The methylthiol:coenzyme M methyltransferase MtsAB and methyl transferases MtsDFH (homologs of loci MA0859, MA4384, MA4558 of Methanosarcina acetivorans ) [ 42 ] were identified with DIAMOND BLASTp [ 63 ] with Q48924, Q8PUA8, and Q48925 (UniProtKB/Swiss-Prot), as well as WP_048064984.1, WP_011024263.1, and WP_011024431.1...”
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...use DMS as the sole energy source and specific methyltransferases, called MtsD, MtsF, and MtsH (MA0859, MA4384, and MA4558) could be associated with the ability to grow on methyl sulfides (Oelgeschlger and Rother 2009a , b ). Further analysis of those methyltransferases revealed that the preferred...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
Fu, Journal of bacteriology 2015 - “...MtbA MMA MtmB MtmC MtbA MeSH MPA Co Co(I) MtsB MA0859 (MtsD) MA4384 (MtsF) MA4558 (MtsH) CH3-S-CoM D Co(III) MtsA DMS MMPA HS-CoM Co(III) HS-CoM H4MPT CH 3...”
- “...family of single-subunit CoM methyltransferases, encoded by the MA0859, MA4384, and MA4558 loci of M. acetivorans, has also been characterized. These proteins...”
- Reducing the genetic code induces massive rearrangement of the proteome
O'Donoghue, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...the composition of the proteome. Mr (kDa) 100 75 MA0859 MA4384 MA0857 MA4392 MA0455 50 MA4391 MA0855 MA2718 37 MA2813 25 MA4547 MA0456 MA1091 MA2699 MA1108 pH...”
- “...MA1317 MA1275 MA3564 MA4386 MA0857 MA1091 MA1108 MA4384 MA0859 MA4558 Gene name Function x-Fold change ilvC S-layer domain pgi Exosome eif2b valS eif2B1 mtaC2...”
- A heme-based redox sensor in the methanogenic archaeon Methanosarcina acetivorans
Molitor, The Journal of biological chemistry 2013 - “...Mts isoforms present in M. acetivorans, MtsD (MA0859) and MtsF (MA4384), which are also regulated individually by vicinally encoded transcriptional regulators....”
- Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans
Vepachedu, Journal of bacteriology 2012 - “...revealed 50-fold elevated levels of proteins encoded by loci MA0859, MA4384, and MA4558 in cells grown with CO versus methanol or acetate (18). These proteins...”
- “...(18). However, M. acetivorans mutants, for which combinations of MA0859, MA4384, and MA4558 were deleted or disrupted, fail to produce DMS or utilize it for...”
- MreA functions in the global regulation of methanogenic pathways in Methanosarcina acetivorans
Reichlen, mBio 2012 - “...( mtaBC-1 ) 0.880.49 MA0527, MA0532 ( mtbBC-1 ) 0.681.70 MA0528MA0529 ( mttBC-1 ) 0.530.57 MA0859 ( mtsD ) 1.36 MA0931MA0932 ( mttBC-2 ) 6.129.27 MA0933MA0934 ( mtbBC-2 ) 8.210.60 MA1615 ( mtaA2 ) 0.92 MA1616MA1617 ( mtaBC-3 ) 1.211.22 MA2424MA2425 ( mtbBC-3 ) 0.780.95 MA2971MA2972...”
- More
MA_0859, WP_048064984 methyltransferase cognate corrinoid protein from Methanosarcina acetivorans C2A
31% identity, 15% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...WP_086636543, WP_161490715, WP_086636999, WP_143406895, WP_086637820, WP_086637822, WP_161490830, WP_086637824-25, WP_086637860, WP_086637826-32 Methanosarcina acetivorans Methyl sulfides MtsD MA_0859 AAM04298 MtsF MA_4384 AAM07726 MtsH MA_4558 AAM07897 Methylmercaptopropionate MtpCAP MA_416466 AAM0751214 Methanomethylovorans hollandica Methyl sulfides MtsD, MtsF, MtsH, MtpCAP METHO_RS06035 METHO_RS01750 METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl...”
- In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans.
Oelgeschläger, Molecular microbiology 2009 (PubMed)- GeneRIF: The corrinoid/methyl transfer proteins MA0859, MA4384 and MA4558 are methyltransferases specific for methylsulfides.
3ezxA / O30641 Structure of methanosarcina barkeri monomethylamine corrinoid protein
29% identity, 16% coverage
- Ligand: 5-hydroxybenzimidazolylcobamide (3ezxA)
LGS26_01905 dihydropteroate synthase from Dissulfurimicrobium hydrothermale
31% identity, 19% coverage
- Genetic Potential of Dissulfurimicrobium hydrothermale, an Obligate Sulfur-Disproportionating Thermophilic Microorganism
Yvenou, Microorganisms 2021 - “...LGS26_01380), a formate-tetrahydrofolate ligase (LGS26_01960), a bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase (LGS26_01955), a 5-methyltetrahydrofolate corrinoid/iron-sulfur protein methyltransferase (LGS26_01905), a carbon-monoxide dehydrogenase (LGS26_01950), a 5,10-methylenetetrahydrofolate reductase (LGS26_08700; LGS26_08025) and a CO-methylating acetyl-CoA synthase (LGS26_01915). Acetyl-CoA molecules formed by this carbon fixation pathway can then be used as precursor metabolites...”
mtsB / Q48925 methanethiol corrinoid protein from Methanosarcina barkeri (see 3 papers)
MTSB_METBA / Q48925 Methylated-thiol--corrinoid protein MtsB; Methylthiol:coenzyme M methyltransferase 30 kDa subunit from Methanosarcina barkeri (see paper)
30% identity, 16% coverage
- function: Harbors a corrinoid prosthetic group and acts as a methyl group carrier in methanogenesis from methylated-thiols.
- Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments
Tebbe, The ISME journal 2023 - “...[ 42 ] were identified with DIAMOND BLASTp [ 63 ] with Q48924, Q8PUA8, and Q48925 (UniProtKB/Swiss-Prot), as well as WP_048064984.1, WP_011024263.1, and WP_011024431.1 (NCBI) as references (>70% amino acid identity, e -value<110 29 ). Metagenome binning and functional classification Contig coverage was determined using SAMtools...”
mtaC / Q46EH4 Co(I) methanol-specific corrinoid protein from Methanosarcina barkeri (strain Fusaro / DSM 804) (see 6 papers)
MTAC_METBF / Q46EH4 Methanol--corrinoid protein; Methanol:corrinoid methyltransferase 1 subunit of 27 kDa; MT1 subunit 27 kDa from Methanosarcina barkeri (strain Fusaro / DSM 804) (see 2 papers)
Q46EH4 methanol-corrinoid protein Co-methyltransferase (subunit 1/3) (EC 2.1.1.90) from Methanosarcina barkeri (see paper)
2i2xB / Q46EH4 Crystal structure of methanol:cobalamin methyltransferase complex mtabc from methanosarcina barkeri (see paper)
31% identity, 15% coverage
- function: Harbors a corrinoid prosthetic group and acts as a methyl group carrier in methanogenesis in the methanol pathway. The methyl group of methanol is first transferred to the corrinoid prosthetic group of MtaC in the cob(I)amide oxidation state. This reaction is mediated by MtaB. The methyl group from MtaC is then transferred to coenzyme M by MtaA.
subunit: Heterotetramer, composed of 2 MtaB and 2 MtaC subunits. - Ligand: 5-hydroxybenzimidazolylcob(iii)amide (2i2xB)
MA4391 methanol-5-hydroxybenzimidazolylcobamide co-methyltransferase, isozyme 2 from Methanosarcina acetivorans C2A
31% identity, 18% coverage
- Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Buan, Microbiology spectrum 2024 - “...were hypothetical proteins (MA4565, MA2945, MA2324, MA1757), mtaCB2 methanol corrinoid methyltransferases and nearby genes (MA4389, MA4391, MA4393, MA4394), mtaCB3 methanol corrinoid methyltransferases (MA1617, MA1616), methylsulfide corrinoid protein mtaC MA4164, iron-sulfur flavoprotein MA1773, and coenzyme B biosynthesis gene 2-isopropyl malate synthase MA4615. In addition to hdrD MA0688,...”
- A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer
Holmes, mBio 2019 - “...0.01 0.03 MA4392 Methanol:5-hydroxybenzimidazolylcobamide methyltransferase, isozyme 2 mtaB2 68.55 5.70 10 11 2.56 10 7 MA4391 Corrinoid-containing methyl-accepting protein, isozyme 2 mtaC2 48.28 3.27 10 10 5.54 10 7 MA1615 Co-methyl-5-hydroxybenzimidazolylcobamide:2- mercapto-ethanesulphonic acid methyltransferase, isozyme 2 mtaA2 5.39 1.77 10 7 8.04 10 6 MA1616 Methanol:5-hydroxybenzimidazolylcobamide...”
- Reducing the genetic code induces massive rearrangement of the proteome
O'Donoghue, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...The most striking examples are the MtaB2 (MA1616) and MtaC2 (MA4391) proteins, which each make up 6% of the soluble proteome in WT cells and 0.4% of the...”
- “...Mr (kDa) 100 75 MA0859 MA4384 MA0857 MA4392 MA0455 50 MA4391 MA0855 MA2718 37 MA2813 25 MA4547 MA0456 MA1091 MA2699 MA1108 pH 3 pH 11 Fig. 2. Deletion of...”
- Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
Li, Journal of proteome research 2007 - “...MA3865 NIH-PA Author Manuscript MA3916 MA3972 MA4026 MA4103 MA4391 MA4392 MA4399 MA4413 MA4542 MA4566 MA4567 MA4568 MA4569 MA4570 MA4572 MA4671 Page 22 Proteome...”
MSMTP_RS14235, WP_048180700 uroporphyrinogen decarboxylase family protein from Methanosarcina sp. MTP4
28% identity, 17% coverage
- Several ways one goal-methanogenesis from unconventional substrates
Kurth, Applied microbiology and biotechnology 2020 - “...METHO_RS03770 METHO_RS05605 WP_015324657 WP_015323796 WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid...”
- “...WP_015324192 WP_015324567 Methanosarcina MTP4 Methyl sulfides MtsD MtsF MtsH MtpCAP MSMTP_RS14200 MSMTP_RS14235 MSMTP_RS00505 MSMTP_RS03110-20 WP_048180685 WP_048180700 WP_048177073 WP_052718253 WP_048177774 WP_082090704 Methanosarcina semesiae Methyl sulfides ? ? ? Methermicoccus shengliensis ZC-1 Methoxylated aromatic compounds MtvB O-demethylase BP07_RS03255 WP_042685518 MtvB O-demethylase BP07_RS03250 WP_042685515 Corrinoid protein BP07_RS03260 WP_042685521 MtrH-like...”
MTQC_EUBLI / P0DX07 Quaternary-amine-specific corrinoid protein; Corrinoid protein MtqC from Eubacterium limosum (see 2 papers)
35% identity, 11% coverage
- function: Involved in the degradation of the quaternary amines L- proline betaine and L-carnitine (PubMed:31341018, PubMed:32571881). Component of a corrinoid-dependent methyltransferase system that transfers a methyl group from L-proline betaine or L-carnitine to tetrahydrofolate (THF), forming methyl-THF, a key intermediate in the Wood-Ljungdahl acetogenesis pathway (PubMed:31341018, PubMed:32571881). Acts as a methyl group carrier between MtpB or MtcB, and MtqA (PubMed:31341018, PubMed:32571881). A methyl group from L-proline betaine or L-carnitine is first transferred to the corrinoid prosthetic group of MtqC by MtpB or MtcB, respectively, and then transferred from MtqC to THF by MtqA (PubMed:31341018, PubMed:32571881).
subunit: The proline betaine:THF methyl transfer system is composed of two methyltransferases, MtpB and MtqA, and the corrinoid protein MtqC (PubMed:31341018). The L-carnitine:THF methyl transfer system is composed of two methyltransferases, MtcB and MtqA, and the corrinoid protein MtqC (PubMed:32571881).
MM_1687 dimethylamine corrinoid protein MtbC from Methanosarcina mazei Go1
31% identity, 15% coverage
- Compiling a versatile toolbox for inducible gene expression in <i>Methanosarcina mazei</i>
Hüttermann, microLife 2024 - “...shuttle vector Nde I restiction site This study pRS1797 Cloning vector + synthesized 5-UTR of MM_1687 This study pRS1807 pRS1665 + p mcrB This study pRS1809 Expression vector pET21a(+) + glnK 1 _his 6 This study pRS1826 pRS1595 + p mcrB + glnK 1 _his 6...”
- “...pRS1893 Cloning vector + synthesized 5-UTR of MM_1687 This study pRS1913 pRS1665 + 5-UTR of MM_1687 + glnK 1 _his 6 This study pRS1931 TOPO + synthesized p mcrB + RNAT No. 1 + glnK 1 _his 6 This study pRS1935 TOPO + synthesized p mcrB...”
MA1617 methanol-5-hydroxybenzimidazolylcobamide co-methyltransferase, isozyme 3 from Methanosarcina acetivorans C2A
32% identity, 15% coverage
- Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Buan, Microbiology spectrum 2024 - “...mtaCB2 methanol corrinoid methyltransferases and nearby genes (MA4389, MA4391, MA4393, MA4394), mtaCB3 methanol corrinoid methyltransferases (MA1617, MA1616), methylsulfide corrinoid protein mtaC MA4164, iron-sulfur flavoprotein MA1773, and coenzyme B biosynthesis gene 2-isopropyl malate synthase MA4615. In addition to hdrD MA0688, transcripts with decreased abundance when averaged across...”
- A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer
Holmes, mBio 2019 - “...10 6 MA1616 Methanol:5-hydroxybenzimidazolylcobamide methyltransferase, isozyme 3 mtaB3 9.66 5.24 10 8 4.89 10 6 MA1617 Corrinoid-containing methyl-accepting protein, isozyme 3 mtaC3 8.49 2.52 10 7 1.00 10 5 a Cells were grown with methanol provided as an electron donor and AQDS provided as an electron...”
- Genetic basis for metabolism of methylated sulfur compounds in Methanosarcina species
Fu, Journal of bacteriology 2015 - “...vs DMS MeOH vs MeSH MA4164 MA4165 MA4166 MA4167 MA1617 MA1616 MA0849 MA3860 MA3861 MA3862 MA3863 MA3864 MA3865 MA3300 MA0859 MA4384 MA4558 MA3302 MA3130 MA0685...”
- Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol
Li, Journal of proteome research 2007 - “...MA1122 MA1189 MA1469 MA1477 MA1479 MA1487 MA1616 MA1617 MA1682 MA1763 Proteome Annotationa polyphosphate kinase small heat shock protein molybdenum cofactor...”
Desti_5437 MtaA/CmuA family methyltransferase from Desulfomonile tiedjei DSM 6799
33% identity, 16% coverage
MM_1438 methyltransferase cognate corrinoid protein from Methanosarcina mazei Go1
29% identity, 16% coverage
Q8DZ17 Homocysteine S-methyltransferase MmuM, putative from Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)
25% identity, 26% coverage
Q8PXZ3 Methanol corrinoid protein from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
MM1073 Methanol corrinoid protein from Methanosarcina mazei Goe1
32% identity, 17% coverage
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...58 Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096 Thermosome, gamma subunit 5 137 Q8PXW0 MM1106...”
- Mining proteomic data to expose protein modifications in Methanosarcina mazei strain Gö1
Leon, Frontiers in microbiology 2015 - “...Q8PXZ6 MM1070 MtaA1 methylcobalamin:CoM methyltransferase 7 374 Q8PXZ5 MM1071 4Fe:4S ferredoxin, hypothetical 2 121 Q8PXZ3 MM1073 MtaC2 methyl corrinoid protein 6 230 Q8PXZ2 MM1074 MtaB2 9 250 Q8PXZ1 MM1075 Putative regulatory protein 2 92 1 Y Q8PXX0 MM1096 Thermosome, gamma subunit 5 137 Q8PXW0 MM1106 Putative...”
- “...(Hovey et al., 2005 ; Krtzer et al., 2009 ), while the operon's other genes, MM1073 and MM1074, are among the most highly regulated genes known in the Archaea (Bose et al., 2006 ). It will be interesting to monitor modifications of MM1075 as culture conditions...”
- Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15
Cao, Applied and environmental microbiology 2014 - “...(MM1647), mtaB2 (MM1074), mtaB3 (MM0175), mtaC1 (MM1648), mtaC2 (MM1073), mtaC3 (MM0174), pta (MM0496), and ackA (MM0495). Cao et al. and mtaC1B1), acetate...”
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...standard deviation of three biologically independent experiments. MM0174, mta C 1 encoding methanol corrinoid protein; MM1073, mta C 2 encoding methanol corrinoid protein; MM1070, mta A 1 encoding methylcobalamin-coenzyme M methyltransferase; MM1438, mtm C 1 encoding monomethylamine corrinoid protein; MM1687, mtb C 1 encoding dimethylamine corrinoid...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...domain) MM0174 MM0175 MM0312 MM0408 MM0479 MM0924 MM1071 MM1073 MM1074 MM1075 MM1112 MM1271 MM1272 MM1273 MM1274 MM1275 MM1647 MM1648 MM1761 MM1762 MM1977...”
- “...the genes are as follows: mtaA1, MM1070; mtaC2, MM1073; mtaB2, MM1074; mtaR ( putative regulatory gene), MM1075; mtaB1, MM1647; mtaC1, 1648; mtaC3, MM0174;...”
mtbC / O93657 dimethylamine corrinoid protein from Methanosarcina barkeri (see paper)
MTBC_METBA / O93657 Dimethylamine corrinoid protein from Methanosarcina barkeri (see 2 papers)
mtbC / GB|AAD14629.1 dimethylamine corrinoid protein from Methanosarcina barkeri (see 2 papers)
33% identity, 15% coverage
- function: Acts as a methyl group carrier between MtbB1 and MtbA. Binds 1 corrinoid cofactor per protein, is subsequently demethylated by MtbA.
subunit: Copurifies with MtbA.
D9S248 Methyltransferase cognate corrinoid protein from Thermosediminibacter oceani (strain ATCC BAA-1034 / DSM 16646 / JW/IW-1228P)
31% identity, 16% coverage
- Kelch-like homologue 9 mutation is associated with an early onset autosomal dominant distal myopathy.
Cirak, Brain : a journal of neurology 2010 - “...D2S148, D2S300, D2S385, D2S324, D2S2310, D2S1391, D2S152, D2S389 and D2S315; Locus 9p12-p13 (Nonaka myopathy): D9S43, D9S248, D9S165 and D9S50; and locus 14q11 (Laing myopathy): D14S72, D14S283, D14S50, MYH7, D14S64, D14S54 and D14S49. Polymerase chain reactions (PCRs) were performed with fluorescent end-labelled microsatellite markers and semi-automated genotyping...”
MM1438 Monomethylamine corrinoid protein from Methanosarcina mazei Goe1
30% identity, 16% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mta C 2 encoding methanol corrinoid protein; MM1070, mta A 1 encoding methylcobalamin-coenzyme M methyltransferase; MM1438, mtm C 1 encoding monomethylamine corrinoid protein; MM1687, mtb C 1 encoding dimethylamine corrinoid protein; MM1690, mtt C 1 encoding dimethylamine corrinoid protein; MM2047, mtt C 2 encoding trimethylamine corrinoid...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...mtmB2, MM3335; mtmP, MM1434/MM1435; mtmB1, MM1436/MM1437; mtmC1, MM1438; mtbA, MM1439. Black horizontal arrows show the orientation and length of genes; boxes...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...MM2050 to pRS256 ..............................orfs MM2961 to vector (QIAGEN) MM1438 cloned in MM3336 cloned in MM1690 cloned in MM2049 cloned in MM1694 cloned...”
- “...MM1215 rev.rt Mm nifH for.rt Mm nifH rev.rt MM1438 for.rt MM1438 rev.rt MM3334 for.rt MM3334 rev.rt MM2052 for.rt MM2052 rev.rt MM1688 for.rt MM1688 rev.rt...”
NP_001012498 betaine--homocysteine S-methyltransferase 1 from Danio rerio
30% identity, 22% coverage
MA0145 monomethylamine corrinoid protein from Methanosarcina acetivorans C2A
29% identity, 16% coverage
Q8PUA7 Methylated-thiol--corrinoid protein MtsB from Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
35% identity, 13% coverage
- Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments
Tsola, Microbiome 2024 - “...Search Tool, these genomes were screened for the presence of the Mts proteins (Q48924, Q8PUA8, Q8PUA7, AAM04298.1, WP_048180685.1, AAM07726, WP_048180700.1, AAM07897.1, WP_048177073.1) downloaded from the Uniprot and NCBI databases [ 49 , 50 ]. Phylogenetic analysis The PhyloFunDB pipeline was used for the construction of the...”
MM_3334 methyltransferase cognate corrinoid protein from Methanosarcina mazei Go1
MM3334 Monomethylamine corrinoid protein from Methanosarcina mazei Goe1
29% identity, 16% coverage
- The CARF Protein MM_0565 Affects Transcription of the Casposon-Encoded cas1-solo Gene in Methanosarcina mazei Gö1
Ulbricht, Biomolecules 2020 - “...Trimethylamine corrionid protein 1.78 0.0005 MM_2084 CO dehydrogenase/acetyl-CoA synthase, gamma subunit 1.83 7.47 10 12 MM_3334 Monomethylamine corrinoid protein MtmC2 1.83 3.26 10 10 MM_3335 Monomethylamine:corrinoid methyltransferase MtmB2 2.08 1.44 10 11 MM_0465 Cobalamin biosynthesis protein CbiM 1.95 5.94 10 15 MM_0337 Tryptophan synthase, beta chain...”
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...mtb C 2 encoding dimethylamine corrinoid protein; MM2961, mtb C 3 encoding dimethylamine corrinoid protein; MM3334, monomethylamine corrinoid protein; MM2440, hypothetical protein; MM2441, : transcriptional regulator, ArsR family; MM2442, hypothetical protein; MM2446, conserved protein. On the basis of these findings, we hypothesize that MM2441 is most...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...mtbC3, MM2961; mtbB3, MM2962/MM2963; mtbP, MM2964; mtmC2, MM3334; mtmB2, MM3335; mtmP, MM1434/MM1435; mtmB1, MM1436/MM1437; mtmC1, MM1438; mtbA, MM1439. Black...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...MM1436 to pRS250 ..............................orfs MM3334 to pRS251 ..............................orfs MM1687 to pRS252 ..............................orfs...”
- “...for.rt Mm nifH rev.rt MM1438 for.rt MM1438 rev.rt MM3334 for.rt MM3334 rev.rt MM2052 for.rt MM2052 rev.rt MM1688 for.rt MM1688 rev.rt MM2049 for.rt MM2049...”
BHMT2 / Q9H2M3 S-methylmethionine--homocysteine S-methyltransferase (EC 2.1.1.10) from Homo sapiens (see 4 papers)
BHMT2_HUMAN / Q9H2M3 S-methylmethionine--homocysteine S-methyltransferase BHMT2; SMM-hcy methyltransferase; Betaine--homocysteine S-methyltransferase 2; EC 2.1.1.10 from Homo sapiens (Human) (see 2 papers)
NP_060084 S-methylmethionine--homocysteine S-methyltransferase BHMT2 isoform 1 from Homo sapiens
27% identity, 28% coverage
- function: Involved in the regulation of homocysteine metabolism. Converts homocysteine to methionine using S-methylmethionine (SMM) as a methyl donor.
catalytic activity: S-methyl-L-methionine + L-homocysteine = 2 L-methionine + H(+) (RHEA:26337)
cofactor: Zn(2+) (Binds 1 zinc ion per subunit.)
subunit: Homotetramer (By similarity). May interact with PRNP. - Identification of hepatic protein-protein interaction targets for betaine homocysteine S-methyltransferase
Garrido, PloS one 2018 - “...HBV/LAMTOR5 O43504 YTH d (cDNA liver library) human [ 57 ] S-methylmethionine homocysteine S-methyltransferase BHMT2 Q9H2M3 Affinity purification and MS a human [ 34 , 35 ] E3 ubiquitin-protein ligase ZNRF1 Q8ND25 Affinity purification and MS a human [ 34 ] Melanoregulain (MREG) Q8N565 Affinity purification...”
- [Quantitative and comparative proteomics analysis in clear cell renal cell carcinoma and adjacent noncancerous tissues by 2-D DIGE].
Chen, Nan fang yi ke da xue xue bao = Journal of Southern Medical University 2017 - Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring.
Luo, Reproductive sciences (Thousand Oaks, Calif.) 2023 (PubMed)- GeneRIF: Association of Maternal Betaine-Homocysteine Methyltransferase (BHMT) and BHMT2 Genes Polymorphisms with Congenital Heart Disease in Offspring.
- Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft.
Wang, Oral diseases 2018 (PubMed)- GeneRIF: Our study suggested markers in BHMT/BHMT2 and DMGDH might affect the risk of NSCL/P through pairwise interaction.
- A Three-Way Interaction among Maternal and Fetal Variants Contributing to Congenital Heart Defects.
Li, Annals of human genetics 2016 - GeneRIF: A three-way interaction among maternal and fetal variants in BHMT2, GSTP1 and GPX3 contribute to congenital heart defects
- Obstructive heart defects associated with candidate genes, maternal obesity, and folic acid supplementation.
Tang, American journal of medical genetics. Part A 2015 - GeneRIF: Multiple SNPs in BHMT and BHMT2 were identified to be associated with the occurrence of infant obstructive heart defects and interaction effects with maternal use of folic acid supplements.
- Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.
Ganu, PloS one 2015 - GeneRIF: The faster evolutionary rate of BHMT2 overall suggests that selective constraints were reduced relative to BHMT.
- New evidence for the role of cystathionine beta-synthase in non-syndromic cleft lip with or without cleft palate.
Martinelli, European journal of oral sciences 2011 (PubMed)- GeneRIF: No significant level of association was found with cleft lip with or without cleft palate and BHMT2 variants.
- Associations of folate and choline metabolism gene polymorphisms with orofacial clefts.
Mostowska, Journal of medical genetics 2010 (PubMed)- GeneRIF: Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
- Early-onset ischaemic stroke: analysis of 58 polymorphisms in 17 genes involved in methionine metabolism.
Giusti, Thrombosis and haemostasis 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- More
A7RIN6 Hcy-binding domain-containing protein from Nematostella vectensis
28% identity, 25% coverage
SMU_952 homocysteine S-methyltransferase from Streptococcus mutans UA159
25% identity, 25% coverage
- Mechanistic insights into the inhibitory effect of theaflavins on virulence factors production in Streptococcus mutans
Kong, AMB Express 2021 - “...(e.g., hisA , hisF , and hisG ), and cysteine and methionine (e.g., cysD , SMU_952 , and metC ) (Fig. 9 ). Notably, the expression of genes coding for 3-isopropylmalate dehydratase ( leuD ), 3-isopropylmalate dehydrogenase ( leuB ), and acetolactate synthase ( ilvH )...”
D7024_14070 B12-binding domain-containing protein from Desulfofundulus salinus
27% identity, 15% coverage
gbs1377 unknown from Streptococcus agalactiae NEM316
24% identity, 24% coverage
Toce_1533 MtaA/CmuA family methyltransferase from Thermosediminibacter oceani DSM 16646
31% identity, 16% coverage
1y80A / Q2RJ67 Structure of a corrinoid (factor iiim)-binding protein from moorella thermoacetica
44% identity, 8% coverage
- Ligand: co-5-methoxybenzimidazolylcobamide (1y80A)
Q32LQ4 Betaine--homocysteine S-methyltransferase 1 from Danio rerio
30% identity, 22% coverage
Q68FT5 S-methylmethionine--homocysteine S-methyltransferase BHMT2 from Rattus norvegicus
29% identity, 23% coverage
- Identification of hepatic protein-protein interaction targets for betaine homocysteine S-methyltransferase
Garrido, PloS one 2018 - “...9 b Q5RK26 Polr3a protein b Q7TPK7 Ac2-048 b Q80WM6 2',5'-oligoisoadenylate synthetase-dependent ribonuclease L b Q68FT5 a BHMT2 S-methylmethionine homocysteine S-methyltransferase b a In bold, proteins selected for validation by immunoprecipitation. b Proteins found in only one experiment, but that are related to BHMT protein function...”
- “...isoform b Rtn3 1 P00481 ornithine transcarbamylase Otc 2 P00884 Aldolase b protein Aldob 1 Q68FT5 hypothetical protein LOC365972/S-methylmethionine homocysteine methyltransferase 2 Bhmt2 3 P02793 ferritin light chain subunit Ftl1 1 Twenty additional proteins were selected from AP-MS data, together with MAT 1, MAT 2, HPD...”
- Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry.
Callet, PloS one 2018 - “...related to amino acid metabolism. Swiss Prot Description Genotype effect Diet effect R23h AB1h A22h Q68FT5 Betainehomocysteine S-methyltransferase 2 (BHMT2) R23h >AB1h, R23h >A22h up up ns Q32LQ4 Betainehomocysteine S-methyltransferase 1 (BHMT1) R23h >AB1h, R23h >A22h up up ns Q58DW2 Cystathionine gamma-lyase (CTH) R23h >A22h up...”
- Functional proteomic analysis of corticosteroid pharmacodynamics in rat liver: Relationship to hepatic stress, signaling, energy regulation, and drug metabolism.
Ayyar, Journal of proteomics 2017 - “...L-aspartate to iminoaspartate UP P50431 Shmt1 Serine hydroxymethyltransferase, cytosolic Interconversion of serine and glycine DOWN Q68FT5 Bhmt2 S-methylmethionine-homocysteine S-methyltransferase Regulation of homocysteine metabolism UP P21643 Tdo2 Tryptophan 2,3-dioxygenase Amino acid (tryptophan) metabolism UP P04694 Tat Tyrosine aminotransferase (TAT) Conversion of tyrosine to 4-hydroxyphenylpyruvate (liver-specific) UP P29266...”
NP_001014278 S-methylmethionine--homocysteine S-methyltransferase BHMT2 from Rattus norvegicus
29% identity, 23% coverage
4jgiB / Q8RPG0 1.5 angstrom crystal structure of a novel cobalamin-binding protein from desulfitobacterium hafniense dcb-2 (see paper)
31% identity, 12% coverage
- Ligand: co-methylcobalamin (4jgiB)
MM0174 Methanol corrinoid protein from Methanosarcina mazei Goe1
29% identity, 15% coverage
- Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15
Cao, Applied and environmental microbiology 2014 - “...(MM1074), mtaB3 (MM0175), mtaC1 (MM1648), mtaC2 (MM1073), mtaC3 (MM0174), pta (MM0496), and ackA (MM0495). Cao et al. and mtaC1B1), acetate kinase (ackA), and...”
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...(vs. wt) are given by mean values and standard deviation of three biologically independent experiments. MM0174, mta C 1 encoding methanol corrinoid protein; MM1073, mta C 2 encoding methanol corrinoid protein; MM1070, mta A 1 encoding methylcobalamin-coenzyme M methyltransferase; MM1438, mtm C 1 encoding monomethylamine corrinoid...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...MtmB2 Monomethylamine:corrinoid methyltransferase MtmB2 (C-terminal domain) MM0174 MM0175 MM0312 MM0408 MM0479 MM0924 MM1071 MM1073 MM1074 MM1075 MM1112 MM1271...”
- “...gene), MM1075; mtaB1, MM1647; mtaC1, 1648; mtaC3, MM0174; mtaB3, MM0175; mtaA2, MM0176; mtbC1, MM1687; mttB1, MM1688/MM1689; mttC1, MM1690; mttP1, MM1691/...”
YagD / b0261 CP4-6 prophage; homocysteine S-methyltransferase (EC 2.1.1.10) from Escherichia coli K-12 substr. MG1655 (see 8 papers)
mmuM / Q47690 CP4-6 prophage; homocysteine S-methyltransferase (EC 2.1.1.10) from Escherichia coli (strain K12) (see 5 papers)
MMUM_ECOLI / Q47690 Homocysteine S-methyltransferase; S-methylmethionine:homocysteine methyltransferase; EC 2.1.1.10 from Escherichia coli (strain K12) (see 2 papers)
Q47690 homocysteine S-methyltransferase (EC 2.1.1.10); selenocysteine Se-methyltransferase (EC 2.1.1.280) from Escherichia coli (see 3 papers)
b0261 homocysteine methyltransferase from Escherichia coli str. K-12 substr. MG1655
NP_414795 homocysteine S-methyltransferase from Escherichia coli str. K-12 substr. MG1655
27% identity, 24% coverage
- function: Catalyzes methyl transfer from S-methylmethionine or S- adenosylmethionine (less efficient) to homocysteine, selenohomocysteine and less efficiently selenocysteine.
catalytic activity: S-methyl-L-methionine + L-homocysteine = 2 L-methionine + H(+) (RHEA:26337)
cofactor: Zn(2+)
subunit: Monomer. - Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
Ge, Journal of biosciences 2011 - “...log 2 BBP scores ID START END SCORE Name bnum 0 274480 276449 1.7 mmuM b0261 1 430474 431171 1.7 tsx b0411 2 1150750 1151231 1.7 acpP b1094 3 1715057 1715202 1.7 tyrS b1637 4 1797488 1798185 1.7 rpIT b1716 5 2175874 2177627 1.7 yegT b2098...”
- Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
Gyaneshwar, Journal of bacteriology 2005 - “...hierarchical clusters but not in the k-means cluster were b0261 (mmuM), b1919 (dcyD), b2012 (yeeD), b2423 (cysW), and b2764 (cysJ). The latter genes were in...”
- Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli.
Li, The Biochemical journal 2016 (PubMed)- GeneRIF: The structures of mmuM reveal a metal/substrate-binding pocket distinct from those in related enzymes.
- Cell division, one-carbon metabolism and methionine synthesis in a metK-deficient Escherichia coli mutant, and a role for MmuM.
El-Hajj, Microbiology (Reading, England) 2013 (PubMed)- GeneRIF: The metK deficient Escherichia coli mutant uses externally provided S-adenosylmethionine as methyl donor to produce most but not all of its methionine, by methylation of homocysteine catalysed by MmuM.
T303_04075 homocysteine S-methyltransferase from Streptococcus thermophilus ASCC 1275
26% identity, 25% coverage
M5595_18435 B12-binding domain-containing protein from Eubacterium limosum
33% identity, 13% coverage
MM1687 dimethylamine corrinoid protein from Methanosarcina mazei Goe1
34% identity, 12% coverage
- An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Jäger, Nucleic acids research 2012 - “...B 2 C 2 , MM2049-47), dimethylamine-dependent methyltransferases ( mtb C 1 B 1 , MM1687, 1693-94; mtb C 2 B 2 , MM2052-50) and monomethylamine-dependent methyltransferases ( mtm C 1 B 1 , MM1438-36) ( Figure 6 and Supplementary Figure S6 ), explaining the reduced...”
- “...mta A 1 encoding methylcobalamin-coenzyme M methyltransferase; MM1438, mtm C 1 encoding monomethylamine corrinoid protein; MM1687, mtb C 1 encoding dimethylamine corrinoid protein; MM1690, mtt C 1 encoding dimethylamine corrinoid protein; MM2047, mtt C 2 encoding trimethylamine corrinoid protein; MM2052, mtb C 2 encoding dimethylamine corrinoid...”
- Transcriptional profiling of methyltransferase genes during growth of Methanosarcina mazei on trimethylamine
Krätzer, Journal of bacteriology 2009 - “...in methanol-grown cells (Table 1). These genes (MM1687 to MM1694) encode TMA- and DMA-dependent methyltransferases involved in degradation of the corresponding...”
- “...the transcript levels of mttC1 (MM1690) and mtbC1 (MM1687) were essentially the same under all growth conditions tested, indicating that the genes are...”
- Effects of nitrogen and carbon sources on transcription of soluble methyltransferases in Methanosarcina mazei strain Go1
Veit, Journal of bacteriology 2005 - “...MM3334 to pRS251 ..............................orfs MM1687 to pRS252 ..............................orfs MM2047 to pRS254 ..............................orfs...”
- “...a mtbB1 and mttB1C1 form a transcriptional unit (MM1687 to MM1694). Only mttB1C1 was analyzed to determine the transcriptional regulation of the complete...”
Awo_c10730 carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit from Acetobacterium woodii DSM 1030
27% identity, 22% coverage
- A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii
Moon, Environmental microbiology reports 2023 - “...CFeS protein, SSU AcsD 16,808 36,479 1.11 Awo_c10720 CFeS protein, LSU AcsC 28,276 63,571 1.16 Awo_c10730 Methyltransferase 2 14,878 20,910 0.49 Awo_c10740 CODH, catalytic subunit AcsA 34,576 40,024 0.2 Awo_c10750 CODH Ni 2+ insertion accessory protein CooC2 13,543 10,313 0.39 Awo_c10760 ACS, catalytic subunit AcsB 36,085...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory