PaperBLAST
PaperBLAST Hits for sp|Q9HZ63|UBIG_PSEAE Ubiquinone biosynthesis O-methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=ubiG PE=3 SV=1 (232 a.a., MSNVDHAEIA...)
Show query sequence
>sp|Q9HZ63|UBIG_PSEAE Ubiquinone biosynthesis O-methyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=ubiG PE=3 SV=1
MSNVDHAEIAKFEALAHRWWDRESEFKPLHDINPLRVNWIDERAGLAGKKVLDIGCGGGI
LSEAMAQRGASVTGIDMGEAPLAVARLHQLESGVAVDYRQITAEQMAEEMPGQFDVVTCL
EMLEHVPDPASVIRACHRLVKPGGQVFLSTINRNPKAYLFAVIGAEYILQLLPRGTHDFR
KFIRPSELGAWSREAGLEVKDIIGLTYNPLTKHYKLANDVDVNYMVQTKREA
Running BLASTp...
Found 250 similar proteins in the literature:
PA3171 3-demethylubiquinone-9 3-methyltransferase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
PA14_23220 3-demethylubiquinone-9 3-methyltransferase from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage
- The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature
Wurtzel, PLoS pathogens 2012 - “...the highest concentrations (30 pM) tested. No binding of LasR to the promoter region of PA14_23220 was detected. To determine whether the newly identified LasR-dependent binding sites indeed respond to LasR in vivo , we have cloned the same fragments used in the EMSAs into a...”
- “...this, no LasR-dependent regulation was observed for the fusions transcribed from the promoters of PA14_03490, PA14_23220, PA14_18800, and PA14_33890. This lack of expression is consistent with the transcriptome data (RPKM values of 30 or less for these genes) suggesting they are not expressed under these conditions....”
ELZ14_08475 bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG from Pseudomonas brassicacearum
90% identity, 100% coverage
PP_1765 3-demethylubiquinone-9 3-methyltransferase from Pseudomonas putida KT2440
87% identity, 100% coverage
Alvin_0579 ubiquinone biosynthesis O-methyltransferase from Allochromatium vinosum DSM 180
66% identity, 96% coverage
- Complete genome sequence of Allochromatium vinosum DSM 180(T)
Weissgerber, Standards in genomic sciences 2011 - “...in H. halophila the A. vinosum genome reveals three distinct rnf gene clusters (Alvin_0562 to Alvin_0579, Alvin_1169 to Alvin_1179 and Alvin_2673 to Alvin_2681). The Rnf complex was shown to play a role in nitrogen fixation as overproduction of the rnf operon increased nitrogenase activity in Rhodobacter...”
Spro_3270 ubiquinone biosynthesis O-methyltransferase from Serratia proteamaculans 568
67% identity, 95% coverage
C3T302 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222); 3-demethylubiquinol 3-O-methyltransferase (EC 2.1.1.64) from Escherichia coli (see paper)
64% identity, 95% coverage
SF2312 3-demethylubiquinone-9 3-methyltransferase and 2-octaprenyl-6-hydroxy phenol methylase from Shigella flexneri 2a str. 301
64% identity, 95% coverage
- Structure-guided microbial targeting of antistaphylococcal prodrugs
Miller, eLife 2021 - “...and Lipinski, PMID: 28623818). However, small molecule substrate-mimetic phosphonates (e.g., fosmidomycin, PubChem CID 572; and SF2312, PubChem CID 52913330) have excellent engagement of their protein targets in vitro but poor drug-like properties (logP < -2); in such cases, lipophilic ester prodrugging may improve both bioavailability, cellular...”
PufX / b2232 bifunctional 3-demethylubiquinone-8 3-O-methyltransferase and 2-octaprenyl-6-hydroxyphenol methylase (EC 2.1.1.64; EC 2.1.1.222) from Escherichia coli K-12 substr. MG1655 (see 22 papers)
ubiG / P17993 bifunctional 3-demethylubiquinone-8 3-O-methyltransferase and 2-octaprenyl-6-hydroxyphenol methylase (EC 2.1.1.64; EC 2.1.1.222) from Escherichia coli (strain K12) (see 20 papers)
UBIG_ECOLI / P17993 Ubiquinone biosynthesis O-methyltransferase; 2-octaprenyl-6-hydroxyphenol methylase; 3-demethylubiquinone-8 3-O-methyltransferase; EC 2.1.1.222; EC 2.1.1.64 from Escherichia coli (strain K12) (see 2 papers)
P17993 polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114); 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222) from Escherichia coli (see paper)
NP_416735 bifunctional 3-demethylubiquinone-8 3-O-methyltransferase and 2-octaprenyl-6-hydroxyphenol methylase from Escherichia coli str. K-12 substr. MG1655
b2232 3-demethylubiquinone-9 3-methyltransferase from Escherichia coli str. K-12 substr. MG1655
64% identity, 95% coverage
- function: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway.
catalytic activity: a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + S-adenosyl-L-homocysteine + H(+) (RHEA:44380)
catalytic activity: a 3-(all-trans-polyprenyl)benzene-1,2-diol + S-adenosyl-L- methionine = a 2-methoxy-6-(all-trans-polyprenyl)phenol + S-adenosyl- L-homocysteine + H(+) (RHEA:31411)
subunit: Homodimer (Probable). Component of the Ubi complex metabolon, which regroups five ubiquinone biosynthesis proteins (UbiE, UbiF, UbiG, UbiH and UbiI) and two accessory factors (UbiK and the lipid-binding protein UbiJ) (PubMed:30686758). - Structural assembly of the bacterial essential interactome
Gómez, eLife 2024 - “...the Ubi metabolon. Uniprot codes used for AF2: ubiA: P0AGK1, ubiE: P0A887, ubiF: P75728, ubiG: P17993, ubiH: P25534, ubiI: P25535, ubiJ: P0ADP7, ubiK: Q46868. Through our analysis, we have identified high-confidence binary complexes involved in consecutive enzymatic steps, supporting the existence of the Ubi metabolon complex....”
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...control, cell division, chromosome partitioning Cytoplasm 119 P0A6T3 GAL1 Carbohydrate transport and metabolism Cytoplasm 120 P17993 UBIG Coenzyme transport and metabolism Cytoplasm 121 P0ABF1 PCNB Translation, ribosomal structure and biogenesis Cytoplasm 122 P0A988 DPO3B Replication, recombination and repair Cytoplasm 123 P0A993 F16PA Carbohydrate transport and metabolism...”
- Crystallization and preliminary crystallographic studies of UbiG, an O-methyltransferase from Escherichia coli.
Xing, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - GeneRIF: Crystals of UbiG grown by the hanging-drop vapour-diffusion method diffracted to 2.00 A resolution and belonged to space group C121, with unit-cell parameters a = 119.8, b = 58.6, c = 40.2 A, beta = 105.3 degrees
- Expression plasmids for use in Candida glabrata
Zordan, G3 (Bethesda, Md.) 2013 - “...] pGRB2.1 b2452 This work KF040386 45331 pCU-LYS21-GFP LYS21pr-GFP [Ap R , URA3 ] pGRB2.3 b2232 This work KF040387 45332 pCN-LYS21 LYS21pr empty vector [Ap R , NAT R ] pBM16.1 b2458 This work KF040388 45334 pCN-LYS21-GFP LYS21pr-GFP [Ap R , NAT R ] pBM16 b2239...”
- Experimental and computational assessment of conditionally essential genes in Escherichia coli
Joyce, Journal of bacteriology 2006 - “...pdxH (b1638) pdxJ (b2564) ubiG (b2232) ubiH (b2907) Regulatory proteins...................................................... cysB (b1275) fruR (b0080) [leuL...”
- “...Unaccounted-for metabolic enzymes Gene(s) (Blattner no.) ubiG (b2232); ubiH (b2907) pdxA (b0052); pdxB (b2320); pdxH (b1638); pdxJ (b2564) iscC (b2530) carA...”
c2774 3-demethylubiquinone-9 3-methyltransferase from Escherichia coli CFT073
63% identity, 95% coverage
ETAE_2337 3-demethylubiquinone-9 3-methyltransferase from Edwardsiella tarda EIB202
65% identity, 98% coverage
VP1933 3-demethylubiquinone-9 3-methyltransferase from Vibrio parahaemolyticus RIMD 2210633
62% identity, 97% coverage
- Bacteriostatic effects of benzyl isothiocyanate on Vibrio parahaemolyticus: Transcriptomic analysis and morphological verification
Liu, BMC biotechnology 2021 - “...transferring one-carbon groups, there are multiple methyltransferase-related genes such as VPA0046, ubiE, VP0594, VP0954, yebU, VP1933, VP2477, and gidB , which regulate methylated-DNAprotein -cysteine S-methyltransferase, ubiquinone/menaquinone biosynthesis methyltransferase, RNA methyltransferase, 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF, 3-demethylubiquinone-9 3-methyltransferase, 16S rRNA methyltransferase and 16S rRNA methyltransferase GidB (see Additional...”
BCAL2959 3-demethylubiquinone-9 3-methyltransferase from Burkholderia cenocepacia J2315
61% identity, 100% coverage
- The Burkholderia cenocepacia OmpA-like protein BCAL2958: identification, characterization, and detection of anti-BCAL2958 antibodies in serum from B. cepacia complex-infected Cystic Fibrosis patients
Sousa, AMB Express 2016 - “...frames BCAL2957 (GyrA, DNA gyrase subunit A), BCAL2958 (OmpA, outer membrane protein A family protein), BCAL2959 (UbiG, 3-demethylubiquinone-9 3-demethyltransferase), BCAL2960 (Gph, putative 2-phosphoglycolate phosphatase), and BCALr2960 (SsrA, transfer-messenger RNA) are represented in scale; b Alignment of amino acid sequences of the OmpA-like proteins BCAL2958 from B....”
SO_2413 3-demethylubiquinone-9 3-methyltransferase from Shewanella oneidensis MR-1
60% identity, 97% coverage
Q9JWE6 Ubiquinone biosynthesis O-methyltransferase from Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491)
57% identity, 95% coverage
- Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates.
Seo, Biodegradation 2013 - “...partitioning protein (ParB) 41/4 Q9JW77 Sensors/regulators 3-Isopropylmalate dehydratase 33/4 Q8UBY9 Primary metabolism 3-Demethylubiquinone-9 3-methyltransferase 31/4 Q9JWE6 Primary metabolism Tryptophan synthase alpha chain 15/3 Q6AF66 Primary metabolism 5-Methyltetrahydropteroyltriglutamate-homocysteine methyltransferase 23/4 Q82LG4 Primary metabolism 2-Isopropylmalate synthase 39/5 Q8FU05 Primary metabolism Dihydrodipicolinate reductase 26/4 Q9JX48 Primary metabolism Threonine-phosphate decarboxylase...”
NMB2030 3-demethylubiquinone-9 3-methyltransferase from Neisseria meningitidis MC58
57% identity, 94% coverage
Smlt3314 putative 3-demethylubiquinone-9 3-methyltransferase from Stenotrophomonas maltophilia K279a
55% identity, 97% coverage
Q5F562 Ubiquinone biosynthesis O-methyltransferase from Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)
NGO2074 UbiG from Neisseria gonorrhoeae FA 1090
55% identity, 94% coverage
ubiG / Q4UVL4 bifunctional 3-demethylubiquinol 3-O-methyltransferase/polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114; EC 2.1.1.64) from Xanthomonas campestris pv. campestris (strain 8004) (see paper)
55% identity, 94% coverage
4kdrA / P17993 Crystal structure of ubig/sah complex
58% identity, 99% coverage
- Ligand: s-adenosyl-l-homocysteine (4kdrA)
PVU19_RS01000 bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG from Roseovarius tolerans
45% identity, 92% coverage
- Chemical quantification of N-acyl alanine methyl ester (NAME) production and impact on temporal gene expression patterns in Roseovarius tolerans EL-164
Leinberger, BMC microbiology 2024 - “...to primary metabolism and encode components of ribosomal subunits (PVU19_RS06060, PVU19_RS07965, PVU19_RS08950, PVU19_RS18125), ubiquinone biosynthesis (PVU19_RS01000, PVU19_RS01250), diverse transporters (e.g., PVU19_RS02070, PVU19_RS02405, PVU19_RS02835, PVU19_RS03345, PVU19_RS05975, PVU19_RS06130) and the general regulator sigma factor 70 (PVU19_RS11495) (Supplement F3 ). As expected, these primary metabolic genes were upregulated in...”
ubiG / Q3IYM5 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.64; EC 2.1.1.222) from Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (see paper)
Q3IYM5 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222) from Cereibacter sphaeroides (see paper)
RSP_1175 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4 benzoquinol methylase from Rhodobacter sphaeroides 2.4.1
44% identity, 94% coverage
- CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1
Luo, Microbial cell factories 2020 - “...), ubiD ( RSP_0467 ), ubiE ( RSP_1338 ), ubiF ( RSP_1492 ), ubiG ( RSP_1175 ), ubiH ( RSP_1869 ), and ubiX ( RSP_0468 ) genes all participated in CoQ10 biosynthesis (Fig. 5 a) [ 33 ]. Hence, we designed appropriate targets for the above...”
- Convergence of the transcriptional responses to heat shock and singlet oxygen stresses
Dufour, PLoS genetics 2012 - “...carriers Glutathione and analogs RSP_3272 Heme, porphyrin, and cobalamin RSP_1197, RSP_1692, RSP_2831 Menaquinone and ubiquinone RSP_1175, RSP_1338, RSP_1492, RSP_1869 Other RSP_0750, RSP_0898, RSP_2314 Transport and binding proteins Amino acids, peptides and amines RSP_1542, RSP_3274 Carbohydrates, organic alcohols, and acids RSP_0149, RSP_0150 Cations and iron carrying compounds...”
Q2YLN5 Ubiquinone biosynthesis O-methyltransferase from Brucella abortus (strain 2308)
BAB1_1875 SAM (and some other nucleotide) binding motif:Generic methyltransferase from Brucella melitensis biovar Abortus 2308
44% identity, 93% coverage
- Immunoproteomic identification of immunodominant antigens independent of the time of infection in Brucella abortus 2308-challenged cattle
Lee, Veterinary research 2015 - “...5.88 29 ribosome J: Translation, ribosomal structure and biogenesis 204 ubiG 3340925 3-demethylubiquinone-9 3-methyltransferase YP_415219.1 Q2YLN5 248 BAB1_1875 410 27653 27486 5.79 31 cytoplasm E: Amino acid transport and metabolism 207 dapB 3341712 dihydrodipicolinate reductase YP_223731.1 Q576R4 268 BruAb2_0991 536 28792 27605 5.92 45 cytoplasm E:...”
- Immunoproteomic identification of immunodominant antigens independent of the time of infection in Brucella abortus 2308-challenged cattle
Lee, Veterinary research 2015 - “...ribosome J: Translation, ribosomal structure and biogenesis 204 ubiG 3340925 3-demethylubiquinone-9 3-methyltransferase YP_415219.1 Q2YLN5 248 BAB1_1875 410 27653 27486 5.79 31 cytoplasm E: Amino acid transport and metabolism 207 dapB 3341712 dihydrodipicolinate reductase YP_223731.1 Q576R4 268 BruAb2_0991 536 28792 27605 5.92 45 cytoplasm E: Amino acid...”
- Brucella abortus choloylglycine hydrolase affects cell envelope composition and host cell internalization
Marchesini, PloS one 2011 - “...5.50 48.7 41.8 3.8 BAB1_1616 U 69 3-demethylubiquinone-9 3-methyltransferase gi|17986472 5.54 5.79 29.2 27.5 4.7 BAB1_1875 C 70 Cell division inhibitor MinD gi|17989271 5.49 5.42 27.7 27.1 8.6 BAB2_0883 C 80 LSU ribosomal protein L25P gi|17986764 5.54 5.92 24.8 25.1 5.2 BAB1_1551 C 84 Co-chaperonin GroES...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...Practically all the components involved in oxidative phosphorylation were either reduced early after infection (BAB1_1901, BAB1_1875, BAB1_1558, BAB1_1807 and BAB1_1808) or remained unaltered (BAB1_0824, BAB1_0828, BAB1_0414). While components of the NADH dehydrogenase complex-I and proteins of the cytochrome bc complex-III remained low through all the intracellular...”
- “...and 44 hours after infection. In addition, the riboflavin synthase (BAB2_0545) and the demethylubiquinone methyltransferase (BAB1_1875) required for the synthesis of cofactors for flavoproteins and ubiquinone, respectively, follow the same kinetics as the complex II proteins. None of the proteins of complex IV which mediate the...”
BMEI0188 HEXAPRENYLDIHYDROXYBENZOATE METHYLTRANSFERASE PRECURSOR from Brucella melitensis 16M
44% identity, 93% coverage
FTN_0321 3-demethylubiquinone 3-methyltransferase/ 2-octaprenyl-6-hydroxyphenol methylase from Francisella tularensis subsp. novicida U112
43% identity, 99% coverage
Rru_A0742 Ubiquinone biosynthesis O-methyltransferase from Rhodospirillum rubrum ATCC 11170
42% identity, 91% coverage
WD0350 3-demethylubiquinone-9 3-methyltransferase/sugar-phosphate isomerase family protein from Wolbachia endosymbiont of Drosophila melanogaster
41% identity, 56% coverage
RP622 3-DEMETHYLUBIQUINONE-9 3-METHYLTRANSFERASE (ubiG) from Rickettsia prowazekii str. Madrid E
37% identity, 92% coverage
O49354 polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114); 3-demethylubiquinol 3-O-methyltransferase (EC 2.1.1.64) from Arabidopsis thaliana (see paper)
AT2G30920 ATCOQ3 (ARABDIOPSIS THALIANA COENZYME Q 3); hexaprenyldihydroxybenzoate methyltransferase/ polyprenyldihydroxybenzoate methyltransferase from Arabidopsis thaliana
42% identity, 71% coverage
- Identification of internal reference genes for gene expression normalization between the two sexes in dioecious white Campion
Zemp, PloS one 2014 - “...TAGACGAATCTGCGCTCGTCCTCTT 187 59.5 1.89 Q8RY89 GARX01000000 (contig_2735.1) SL_COQ3 F: ACGGTCTACGCTTTGCCATCACTTC R: AACACCTGTCACCGTAGCTCCCA 142 59.6 1.86 O49354 GARX01000000 (contig_3547.1) SL_BL52 F: TGGTTTTGTCCCCACCGAAACGAA R: TATCCCCATCTGGTTGAGCGGTTCT 124 59.2 1.84 O22232 GARX01000000 (contig_38083.1) SL_RPM1 F: AGAGTGTATGTCTGCCAACTGCCCT R: CGGGGAAAGCGAGAATTTGGAGGTT 183 59.6 1.88 Q39214 GARX01000000 (contig_38634.1) SL_PDXK F: TCATCAATGGCGCAACCTCCGATT R: ACCGGGTCAACATCAAAACCAAGCA 152...”
- Antioxidants of Non-Enzymatic Nature: Their Function in Higher Plant Cells and the Ways of Boosting Their Biosynthesis
Rudenko, Antioxidants (Basel, Switzerland) 2023 - “...Coq6 Flavin-dependent monooxygenases Aromatic hydroxylation of C-H in different positions in UQ biosynthesis At1g24340 CoqF At2g30920 Coq3 S-adenosyl-l-methionine (SAM)-dependent methyl transferases At5g57300 Coq5 At2g03690 Coq4 Presumably a scaffold protein, which is responsible for organization of UQ biosynthetic complex [ 22 ] At5g17230 PSY, phytoene synthase Condensation...”
- How plants synthesize coenzyme Q
Xu, Plant communications 2022 - “...Coq2 AT4G23660 4-hydroxybenzoate polyprenyl diphosphate transferase C 3 prenylation ( Okada etal., 2004 ) Coq3 AT2G30920 SAM-dependent methyltransferase O methylations ( Avelange-Macherel and Joyard, 1998 ) Coq5 AT5G57300 SAM-dependent methyltransferase C 2 methylation ( Toda etal., 2014 ) Coq6 AT3G24200 flavin-dependent monooxygenase C 5 hydroxylation (...”
- A unique flavoenzyme operates in ubiquinone biosynthesis in photosynthesis-related eukaryotes
Xu, Science advances 2021 - “...from ATTED-II ( http://atted.jp/ ) using Arabidopsis CoQ biosynthetic genes Coq1 (At2g34630), Coq2 (At4g23660), Coq3 (At2g30920), Coq4 (At2g03690), Coq5 (At5g57300), Coq6 (At3g24200), Coq8 (At4g01660), Coq9 (At1g19140), Coq10 (At4g17650), Coq11A (At5g10730), and Coq11B (At5g15910) as queries. The network was drawn on the basis of rank of correlation....”
- Epigenetic regulation of spurious transcription initiation in Arabidopsis
Le, Nature communications 2020 - “...which include SQN (AT2G15790) , a gene critical for vegetative shoot maturation 57 , COQ3 (AT2G30920) , a gene encoding a mitochondria-localized methyltransferase important for ubiquinone biosynthesis and embryo development 58 , 59 , and a gene of unknown function ( AT2G16050 ) (Fig. 6 b,...”
- Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana
Carrie, Journal of experimental botany 2015 - “...Pentatricopeptide repeat (PPR) superfamily protein Y YLTSTGVNCSFEISR 77 AT1G72330 Alanine aminotransferase 2 F SSTSEMSASDSTSSLPVTLDSINPKVLKCEYAVR 78 AT2G30920 Coenzyme Q 3 F STSDTDASAASFSSSHPKIQTLEGKASNKSR 79 AT3G17465 Ribosomal protein L3 F SSDTGLMDGGGSDIIGAQTR 80 AT3G56030 Pentatricopeptide repeat (PPR) superfamily protein F STVNPNPTASPGR 81 AT4G11120 Translation elongation factor Ts F SSEAPPAVSDQMSLIKQLR 82...”
- Functional conservation of coenzyme Q biosynthetic genes among yeasts, plants, and humans
Hayashi, PloS one 2014 - “...At PPT1 ( At4g23660 ) PHB-polyprenyldiphosphate transferase COQ3 coq3 Hs COQ3 (AF193016) At COQ3 ( At2g30920 ) O-Methyltransferase COQ4 coq4 Hs COQ4 (BQ685658) At COQ4 ( At2g03690 ) Unknown COQ5 coq5 Hs COQ5 (BC004916) At COQ5 ( At5g57300 ) C-Methyltransferase COQ6 coq6 Hs COQ6 (BQ668512) At...”
- Molecular foundations of reproductive lethality in Arabidopsis thaliana
Muralla, PloS one 2011 - “...Inner Mitochondrial Membrane Import Protein At1g71440 PFI C 11.1 Tubulin Folding Cofactor E; Microtubule Dynamics At2g30920 EMB3002 NC 9 Methyltransferase; Ubiquinone Biosynthesis At2g32590 EMB2795 C 6.2 Condensin Complex Subunit; Sister Chromatid Segregation At2g34780 EMB1611 C 13 Uncertain At2g38280 FAC1 C 10.1 AMP Deaminase; Purine Biosynthesis At2g38670...”
RC0965 3-demethylubiquinone-9 3-methyltransferase from Rickettsia conorii str. Malish 7
33% identity, 80% coverage
GOX_RS01330 bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG from Gluconobacter oxydans 621H
GOX0038 3-Demethylubiquinone-9 3-methyltransferase from Gluconobacter oxydans 621H
40% identity, 89% coverage
- Novel plasmid-free Gluconobacter oxydans strains for production of the natural sweetener 5-ketofructose
Battling, Microbial cell factories 2020 - “...of G. japonicus under the control of the P264 promoter integrated between GOX0038 and GOX0039 (GOX_RS01330 and GOX_RS01335) This work IK003.1 sdh :: fdhSCL IK003.1 with the fdhSCL genes of G. japonicus under control of the P264 promoter replacing the genes GOX2095-6 (GOX_RS11750) encoding an inactive...”
- “...of the fdhSCL genes under the control of the P264 promoter between GOX0038 and GOX0039 (GOX_RS01330 and GOX_RS01335) This work pAJ63a sdh :: fdhSCL Km R , FU S , derivative of pAJ63a for integration of the fdhSCL genes under the control of the P264 promoter...”
- Novel plasmid-free Gluconobacter oxydans strains for production of the natural sweetener 5-ketofructose
Battling, Microbial cell factories 2020 - “...were selected: igr1 between GOX0013 and GOX0014, igr2 between GOX0028 and GOX0029, and igr3 between GOX0038 and GOX0039. The exact integration sites were positioned directly downstream of the terminator of the upstream gene, as predicted with the online tool ARNold [ 34 ]. The fdhSCL integration...”
- “...the fdhSCL genes of G. japonicus under the control of the P264 promoter integrated between GOX0038 and GOX0039 (GOX_RS01330 and GOX_RS01335) This work IK003.1 sdh :: fdhSCL IK003.1 with the fdhSCL genes of G. japonicus under control of the P264 promoter replacing the genes GOX2095-6 (GOX_RS11750)...”
COQ3 / Q9NZJ6 hexaprenyldihydroxybenzoate methyltransferase (EC 2.1.1.222; EC 2.1.1.64; EC 2.1.1.114) from Homo sapiens (see 3 papers)
COQ3_HUMAN / Q9NZJ6 Ubiquinone biosynthesis O-methyltransferase, mitochondrial; 3-demethylubiquinol 3-O-methyltransferase; Polyprenyldihydroxybenzoate methyltransferase; EC 2.1.1.64; EC 2.1.1.114 from Homo sapiens (Human) (see paper)
Q9NZJ6 polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114); 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222); 3-demethylubiquinol 3-O-methyltransferase (EC 2.1.1.64) from Homo sapiens (see paper)
35% identity, 60% coverage
- function: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway.
catalytic activity: a 3,4-dihydroxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl- L-methionine = a 4-hydroxy-3-methoxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl-L-homocysteine + H(+) (RHEA:44452)
catalytic activity: a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + S-adenosyl-L-homocysteine + H(+) (RHEA:44380)
subunit: Component of a multi-subunit COQ enzyme complex, composed of at least COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9. - Insight into the Molecular Signature of Skeletal Muscle Characterizing Lifelong Football Players
Orrù, International journal of environmental research and public health 2022 - “...nonsense transcripts 1 UPF1 2.58 Q9Y490 Talin-1 TLN1 2.58 Q8NEZ4 Histone-lysine N-methyltransferase 2C KMT2C 2.58 Q9NZJ6 Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial COQ3 2.38 O94874 E3 UFM1-protein ligase 1 UFL1 2.38 Q5T440 Putative transferase CAF17, mitochondrial IBA57 2.38 Q15642 Cdc42-interacting protein 4 TRIP10 2.38 Q16795 NADH dehydrogenase (ubiquinone) 1...”
- Predicting and Understanding the Pathology of Single Nucleotide Variants in Human COQ Genes
Wang, Antioxidants (Basel, Switzerland) 2022 - “...remaining variants were assessed using their AlphaFold models. AlphaFold models used in this study include Q9NZJ6 (COQ3), Q9Y3A0 (COQ4), Q5HYK3 (COQ5), Q9Y2Z9 (COQ6), Q99807 (COQ7), and O75208 (COQ9). Structures were visualized using PyMOL (PyMOL Molecular Graphics System, Version 2.4.2, Schrdinger, LLC, New York, NY, USA). 3....”
- Proteomic and Molecular Assessment of the Common Saudi Variant in ACADVL Gene Through Mesenchymal Stem Cells.
Alfares, Frontiers in cell and developmental biology 2019 - “...O, mitochondrial 1.5 0.028 Down P10809 60 kDa heat shock protein, mitochondrial 1.6 0.024 Up Q9NZJ6 Ubiquinone biosynthesis Omethyltransferase, mitochondrial 1.5 0.03 Up P68104 Elongation factor 1-alpha 1 2.8 0.03 Down P11142 Heat shock cognate 71 kDa protein 1.8 0.05 Up P13639 Elongation factor 2 1.8...”
XP_006715563 ubiquinone biosynthesis O-methyltransferase, mitochondrial isoform X1 from Homo sapiens
35% identity, 54% coverage
COQ3 / Q63159 3-demethylubiquinone-9 3-O-methyltransferase (EC 2.1.1.64; EC 2.1.1.114) from Rattus norvegicus (see 2 papers)
Q63159 polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114); 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222); 3-demethylubiquinol 3-O-methyltransferase (EC 2.1.1.64) from Rattus norvegicus (see 4 papers)
35% identity, 66% coverage
NP_766275 ubiquinone biosynthesis O-methyltransferase, mitochondrial isoform 1 from Mus musculus
Q8BMS4 Ubiquinone biosynthesis O-methyltransferase, mitochondrial from Mus musculus
35% identity, 62% coverage
- Calorie restriction modifies ubiquinone and COQ transcript levels in mouse tissues.
Parrado-Fernández, Free radical biology & medicine 2011 - GeneRIF: Calorie restriction modifies ubiquinone and COQ transcript levels in mouse tissues
- Tandem mass tag-based quantitative proteomic analysis of effects of multiple sevoflurane exposures on the cerebral cortex of neonatal and adult mice.
Feng, Frontiers in neurology 2022 - Functional, proteomic and bioinformatic analyses of Nrf2- and Keap1- null skeletal muscle
Gao, The Journal of physiology 2020 - “...membrane calcium-transporting ATPase 1 0.0084 1.76 Gclc P97494 Glutamate--cysteine ligase catalytic subunit 0.0085 2.14 Coq3 Q8BMS4 Ubiquinone biosynthesis 0.0097 1.74 Uba1 Q02053 Ubiquitin-like modifier-activating enzyme 1 0.01 1.29 Tuba4a P68368 Tubulin alpha-4A chain 0.01 1.57 Taldo1 Q93092 Transaldolase 0.01 4.04 Gstm2 P15626 Glutathione S-transferase Mu 2...”
- Cardiac metabolic pathways affected in the mouse model of barth syndrome
Huang, PloS one 2015 - “...Heat shock protein beta-1 Hspb1 P14602 100 1.91 Cellular stress response 40 Hexaprenyldihydroxybenzoate methyltransferase Coq3 Q8BMS4 97 1.83 Ubiquinone biosynthesis 71 Cyclophilin D Ppif Q99KR7 100 1.65 Apoptosis, PTP-regulation 61 Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 Oxct1 Q9D0K2 100 1.79 Metabolism of ketone bodies 79 Ubiquinone biosynthesis protein...”
- CypD(-/-) hearts have altered levels of proteins involved in Krebs cycle, branch chain amino acid degradation and pyruvate metabolism
Menazza, Journal of molecular and cellular cardiology 2013 - “...0.008 28 (Q9R112) Sulfide:quinone oxidoreductase, mitochondrial SQRD_MOUSE 13.33 6 1.056 0.061 1.328 0.070 0.027 26 (Q8BMS4) Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial COQ3_MOUSE 15.41 7 0.988 0.019 1.187 0.027 0.001 20 (P42125) 3,2-trans-enoyl-CoA isomerase, mitochondrial D3D2_MOUSE 42.56 69 0.979 0.030 1.166 0.033 0.006 19 (Q9D1I6) 39S ribosomal protein L14,...”
Q54XD0 Ubiquinone biosynthesis O-methyltransferase, mitochondrial from Dictyostelium discoideum
DDB_G0279037 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase from Dictyostelium discoideum AX4
35% identity, 70% coverage
COQ3_SCHPO / O74421 Ubiquinone biosynthesis O-methyltransferase, mitochondrial; 3-demethylubiquinol 3-O-methyltransferase; Polyprenyldihydroxybenzoate methyltransferase; EC 2.1.1.64; EC 2.1.1.114 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
41% identity, 78% coverage
- function: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway.
catalytic activity: a 3,4-dihydroxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl- L-methionine = a 4-hydroxy-3-methoxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl-L-homocysteine + H(+) (RHEA:44452)
catalytic activity: a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + S-adenosyl-L-homocysteine + H(+) (RHEA:44380)
subunit: Component of a multi-subunit COQ enzyme complex, composed of at least coq3, coq4, coq5, coq6, coq7 and coq9.
disruption phenotype: Leads to respiration deficiency. - Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity
McDonald, PLoS genetics 2016 - “...Function SAINT score Abp1 P49777 ARS-binding protein, CENP-B homologue, less abundant in G2 0.83 Coq3 O74421 Mitochondrial hexaprenyldihydroxybenzoate methyltransferase 0.86 Dna2 Q9URU2 ATP-dependent helicase-nuclease, processes Okazaki fragments 0.95 Fbh1 Q9USU3 F-box DNA helicase, modulates homologous recombination 0.97 Irc3 Q1MTR1 Putative mitochondrial ATP-dependent helicase 1.00 Mcm2 P40377...”
coq3 / GI|3218395 hexaprenyldihydroxybenzoate methyltransferase Coq3; EC 2.1.1.114 from Schizosaccharomyces pombe (see 2 papers)
SPCC162.05 hexaprenyldihydroxybenzoate methyltransferase from Schizosaccharomyces pombe
41% identity, 79% coverage
Q5VMJ1 Dihydroxypolyprenylbenzoate methyltransferase from Oryza sativa subsp. japonica
39% identity, 84% coverage
NP_001041045 Ubiquinone biosynthesis O-methyltransferase, mitochondrial from Caenorhabditis elegans
32% identity, 83% coverage
CPAR2_602300 uncharacterized protein from Candida parapsilosis
31% identity, 64% coverage
COQ3 / P27680 hexaprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114; EC 2.1.1.64) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 2 papers)
COQ3_YEAST / P27680 Ubiquinone biosynthesis O-methyltransferase, mitochondrial; 3,4-dihydroxy-5-hexaprenylbenzoate methyltransferase; DHHB methyltransferase; DHHB-MT; DHHB-MTase; 3-demethylubiquinol 3-O-methyltransferase; 3-demethylubiquinone-6 3-O-methyltransferase; Hexaprenyldihydroxybenzoate methyltransferase; Polyprenyldihydroxybenzoate methyltransferase; EC 2.1.1.64; EC 2.1.1.114 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 7 papers)
P27680 polyprenyldihydroxybenzoate methyltransferase (EC 2.1.1.114); 2-polyprenyl-6-hydroxyphenol methylase (EC 2.1.1.222); 3-demethylubiquinol 3-O-methyltransferase (EC 2.1.1.64) from Saccharomyces cerevisiae (see 3 papers)
NP_014545, YOL096C Coq3p from Saccharomyces cerevisiae
NP_014545 hexaprenyldihydroxybenzoate methyltransferase from Saccharomyces cerevisiae S288C
29% identity, 67% coverage
- function: O-methyltransferase that catalyzes the 2 O-methylation steps in the ubiquinone biosynthetic pathway. Catalyzes the methylation of 3,4-dihydroxy-5-hexaprenylbenzoate (DHHB) to 3-methoxy-4-hydroxy-5- hexaprenylbenzoate (HMHB) and the methylation of 2-hexaprenyl-3-methyl- 5-hydroxy-6-methoxy-1,4-benzoquinol (3-demethylubiquinol-6) to ubiquinol-6.
catalytic activity: a 3,4-dihydroxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl- L-methionine = a 4-hydroxy-3-methoxy-5-(all-trans-polyprenyl)benzoate + S-adenosyl-L-homocysteine + H(+) (RHEA:44452)
catalytic activity: a 3-demethylubiquinol + S-adenosyl-L-methionine = a ubiquinol + S-adenosyl-L-homocysteine + H(+) (RHEA:44380)
subunit: Component of a multi-subunit COQ enzyme complex, composed of at least COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9 (PubMed:15792955, PubMed:24406904). Interacts directly with COQ4 (PubMed:15792955). - Predicting and Understanding the Pathology of Single Nucleotide Variants in Human COQ Genes
Wang, Antioxidants (Basel, Switzerland) 2022 - “...and Methods and include Homo sapiens (NCBI accession number NP_059117.3) and homologs in Saccharomyces cerevisiae (NP_014545), Drosophila melanogaster (NP_610092.2), Danio rerio (NP_001002620.1), Mus musculus (NP_766275.1), Rickettsia prowazekii (WP_004596275.1), Schizosaccharomyces pombe (NP_588239.2), Escherichia coli (NP_416735.1), and Pseudomonas aeruginosa (WP_003122245.1). See KEY for descriptions of the figure annotations....”
- Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae
Stenger, Microbial cell (Graz, Austria) 2020 - “...OCT1 YKL134C COQ10 YOL008W HEM14 YER014W OXA1 YER154W COQ2 YNR041C HTD2 YHR067W PPA2 YMR267W COQ3 YOL096C IBA57 YJR122W PPT2 YPL148C COQ4 YDR204W ISA1 YLL027W SOM1 YEL059C-A COQ5 YML110C ISA2 YPR067W SSQ1 YLR369W COQ6 YGR255C KGD2 YDR148C SUV3 YPL029W COQ9 YLR201C LIP2 YLR239C YTA12 YMR089C DSS1 YMR287C...”
- Invertebrate models for coenzyme q10 deficiency
Fernández-Ayala, Molecular syndromology 2014 - “...COQ1 (YBR003W) coq-1 (C24A11.9) COQ2 (YNR041C) COQ3 (YOL096C) COQ4 (YDR204W) COQ5 (YML110C) COQ6 (YGR255C) COQ7/CAT5 (YOR125C) COQ8 (YGL119W) COQ9 (YLR201C)...”
- Inaccurately assembled cytochrome c oxidase can lead to oxidative stress-induced growth arrest
Bode, Antioxidants & redox signaling 2013 - “...YER058W PET117 Reduced Reduced Strong None Minor None YOL096C COQ3 Poor Reduced None Minor None Minor Reduced Strong Strong Strong Strong Mitochondrial protein...”
- Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome
Wlodarski, PloS one 2011 - “...mRNA YBR236C (ABD1) , YGL192W (IME4) telomerase/sn/snoRNA YPL157W (TGS1) Small molecule YER175C (TMT1), YML110C (COQ5), YOL096C (COQ3) Lipid YML008C (ERG6) Unknown YCL055W (KAR4) , YGR001C (AML1) , YHR209W (CRG1) , YMR209C , YMR228W (MTF1) , YNL092W , YBR225W , YKL162C , YLR137W SPOUT RNA tRNA YDL112W...”
- Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
Cheng, BMC bioinformatics 2008 - “...YIL111W, YIL125W, YJL131C, YJL171C, YKL087C, YLL041C, YLR168C, YLR395C, YML120C, YMR145C, YMR167W, YNL037C, YNL073W, YOL038W, YOL059W, YOL096C, YOR065W, YOR317W, YOR356W, YOR386W, YPL005W, YPL029W, YPL103C respiratory chain complex III (sensu Eukaryota) 4.23E-04 2.84E-02 YEL024W, YHR001W, YOR065W endosome 9.02E-05 6.04E-03 YAL030W, YDL113C, YJL053W, YLR119W, YLR408C, YNR006W, YOR036W 9 bud...”
- Overlapping functions of the yeast oxysterol-binding protein homologues
Beh, Genetics 2001 - “...YML008C YMR202W YLR056W YMR015C YGL012W YBR003w YNR041C YOL096C YGR255c YOR125C YPL172C YOR274W YDL090C YKL019w YJR117w YMR274C YDR410C YPL069C YGL155W YPR176C...”
- Coq3p relevant residues for protein activity and stability.
Paulela, FEMS yeast research 2021 (PubMed)- GeneRIF: Coq3p relevant residues for protein activity and stability.
- Ubiquinone biosynthesis in Saccharomyces cerevisiae: the molecular organization of O-methylase Coq3p depends on Abc1p/Coq8p.
Tauche, FEMS yeast research 2008 (PubMed)- GeneRIF: putative candidate for phosphorylation by Coq8p.
- Coq3 and Coq4 define a polypeptide complex in yeast mitochondria for the biosynthesis of coenzyme Q.
Marbois, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: study identifies Coq3 peptide and Coq4 peptide as defining members of a Q-biosynthetic Coq polypeptide complex
DMR_39330 putative 3-demethylubiquinone-9 3-methyltransferase from Desulfovibrio magneticus RS-1
33% identity, 81% coverage
ETH_00031320 3-demethylubiquinone-9 3-methyltransferase, putative from Eimeria tenella
30% identity, 54% coverage
- Isoprenoid metabolism in apicomplexan parasites
Imlay, Current clinical microbiology reports 2014 - “...cgd4_1510 Ubiquinone synthesis Coq2 2.5.1.39 PF3D7_0607500 TGGT1_259130 * BBM_III09587 TP03_0802 * Coq3 2.1.1.64 PF3D7_0724300 TGGT1_266850 ETH_00031320 BBM_III02105 TP02_0197 cgd2_2830 tRNA MiaA 2.5.1.75 PF3D7_1207600 TGGT1_312520 ETH_00042745 BBM_II01495 TP01_0445 Cgd6_2540 N- glycosylation GPT 2.7.8.15 PF3D7_0321200 TGGT1_244520 ETH_00020690 BBM_II00105 TP01_0118 e cgd5_2240 OST, Stt3p subunit 2.4.99.18 PF3D7_1116600 TGGT1_231430 ETH_00007235...”
TP02_0197 3-demethylubiquinone-9 3-O-methyltransferase from Theileria parva strain Muguga
26% identity, 71% coverage
- Isoprenoid metabolism in apicomplexan parasites
Imlay, Current clinical microbiology reports 2014 - “...synthesis Coq2 2.5.1.39 PF3D7_0607500 TGGT1_259130 * BBM_III09587 TP03_0802 * Coq3 2.1.1.64 PF3D7_0724300 TGGT1_266850 ETH_00031320 BBM_III02105 TP02_0197 cgd2_2830 tRNA MiaA 2.5.1.75 PF3D7_1207600 TGGT1_312520 ETH_00042745 BBM_II01495 TP01_0445 Cgd6_2540 N- glycosylation GPT 2.7.8.15 PF3D7_0321200 TGGT1_244520 ETH_00020690 BBM_II00105 TP01_0118 e cgd5_2240 OST, Stt3p subunit 2.4.99.18 PF3D7_1116600 TGGT1_231430 ETH_00007235 Homolog found...”
RHA1_ro05098 3-demethylubiquinone-9 3-O-methyltransferase from Rhodococcus sp. RHA1
Q0S6F7 3-demethylubiquinone-9 3-O-methyltransferase from Rhodococcus jostii (strain RHA1)
33% identity, 71% coverage
- Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency
Suyal, Scientific reports 2019 - “...debranching enzyme, Q0SHV3), PanB, ProA, AroE1, Rha1_ro01447 (Glycogen phosphorylase, Q0SGS1), RpiA, PurM (Phosphoribosylformylglycinamidine cyclo-ligase, Q0S760), Rha1_ro05098 (3-demethylubiquinone-9 3-O-methyltransferase, Q0S6F7), Rha1_ro06238, AroA, GltX2, MiaA, AroK, AcnA2 (Aconitate hydratase, Q0S0G5) and HemZ were under NB. CowN as a protein biomarker In order to identify the protein biomarker(s) associated...”
- Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency
Suyal, Scientific reports 2019 - “...PanB, ProA, AroE1, Rha1_ro01447 (Glycogen phosphorylase, Q0SGS1), RpiA, PurM (Phosphoribosylformylglycinamidine cyclo-ligase, Q0S760), Rha1_ro05098 (3-demethylubiquinone-9 3-O-methyltransferase, Q0S6F7), Rha1_ro06238, AroA, GltX2, MiaA, AroK, AcnA2 (Aconitate hydratase, Q0S0G5) and HemZ were under NB. CowN as a protein biomarker In order to identify the protein biomarker(s) associated with the nitrogen...”
PF3D7_0724300 ubiquinone biosynthesis O-methyltransferase, putative from Plasmodium falciparum 3D7
26% identity, 56% coverage
- Exploring Ubiquinone Biosynthesis Inhibition as a Strategy for Improving Atovaquone Efficacy in Malaria
Verdaguer, Antimicrobial agents and chemotherapy 2021 (secret) - Signaling transcript profile of the asexual intraerythrocytic development cycle of Plasmodium falciparum induced by melatonin and cAMP
Lima, Genes & cancer 2016 - “...translation 5.5 PF3D7_0316800 PFC0735w MAL3P6.30 40S ribosomal protein S15A, putative Ribosome, translation 0.1 Trophozoite (cAMP) PF3D7_0724300 MAL7P1.130 3-demethylubiquinone-9 3-methyltransferase, putative UPS 3.4 PF3D7_1338100 MAL13P1.190 26S proteasome regulatory subunit RPN3, putative (RPN3) UPS 3.3 PF3D7_0313100 MAL3P4.5, PFC0550w ubiquitin-protein ligase, putative (HRD3) UPS 0.4 PF3D7_1116000 PF11_0168, RON4 rhoptry...”
- A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases
Berenstein, PLoS neglected tropical diseases 2016 - “...targets in P . falciparum . This is the case of a putative 3-demethylubiquinone-9 3-methyltransferase (PF3D7_0724300), a putative 3-oxo-5-alpha-steroid 4-dehydrogenase (PF3D7_1135900), and a putative polyprenol reductase (DFG-like protein, PF3D7_1455900) [ 106 ]. An exception is perhaps the putative glycerol-3-phosphate acyltransferase (LPAAT, PF3D7_1444300), an ortholog of which...”
- Isoprenoid metabolism in apicomplexan parasites
Imlay, Current clinical microbiology reports 2014 - “...BBM_I01680 TP03_0421 cgd4_1510 Ubiquinone synthesis Coq2 2.5.1.39 PF3D7_0607500 TGGT1_259130 * BBM_III09587 TP03_0802 * Coq3 2.1.1.64 PF3D7_0724300 TGGT1_266850 ETH_00031320 BBM_III02105 TP02_0197 cgd2_2830 tRNA MiaA 2.5.1.75 PF3D7_1207600 TGGT1_312520 ETH_00042745 BBM_II01495 TP01_0445 Cgd6_2540 N- glycosylation GPT 2.7.8.15 PF3D7_0321200 TGGT1_244520 ETH_00020690 BBM_II00105 TP01_0118 e cgd5_2240 OST, Stt3p subunit 2.4.99.18 PF3D7_1116600...”
BBM_III02105 Ubiquinone biosynthesis O-methyltransferase from Babesia microti strain RI
27% identity, 64% coverage
- Isoprenoid metabolism in apicomplexan parasites
Imlay, Current clinical microbiology reports 2014 - “...Ubiquinone synthesis Coq2 2.5.1.39 PF3D7_0607500 TGGT1_259130 * BBM_III09587 TP03_0802 * Coq3 2.1.1.64 PF3D7_0724300 TGGT1_266850 ETH_00031320 BBM_III02105 TP02_0197 cgd2_2830 tRNA MiaA 2.5.1.75 PF3D7_1207600 TGGT1_312520 ETH_00042745 BBM_II01495 TP01_0445 Cgd6_2540 N- glycosylation GPT 2.7.8.15 PF3D7_0321200 TGGT1_244520 ETH_00020690 BBM_II00105 TP01_0118 e cgd5_2240 OST, Stt3p subunit 2.4.99.18 PF3D7_1116600 TGGT1_231430 ETH_00007235 Homolog...”
PBANKA_0621800 ubiquinone biosynthesis O-methyltransferase, putative from Plasmodium berghei ANKA
22% identity, 62% coverage
cgd2_2830 Coenzyme Q3, methyltransferase from Cryptosporidium parvum Iowa II
24% identity, 57% coverage
- Isoprenoid metabolism in apicomplexan parasites
Imlay, Current clinical microbiology reports 2014 - “...Coq2 2.5.1.39 PF3D7_0607500 TGGT1_259130 * BBM_III09587 TP03_0802 * Coq3 2.1.1.64 PF3D7_0724300 TGGT1_266850 ETH_00031320 BBM_III02105 TP02_0197 cgd2_2830 tRNA MiaA 2.5.1.75 PF3D7_1207600 TGGT1_312520 ETH_00042745 BBM_II01495 TP01_0445 Cgd6_2540 N- glycosylation GPT 2.7.8.15 PF3D7_0321200 TGGT1_244520 ETH_00020690 BBM_II00105 TP01_0118 e cgd5_2240 OST, Stt3p subunit 2.4.99.18 PF3D7_1116600 TGGT1_231430 ETH_00007235 Homolog found only...”
SCO0995 methyltransferase from Streptomyces coelicolor A3(2)
40% identity, 41% coverage
- Genome Analysis of a Variant of Streptomyces coelicolor M145 with High Lipid Content and Poor Ability to Synthetize Antibiotics
Dulermo, Microorganisms 2023 - “...includes the genes sco0985 (5 methyltetrahydropteroyltriglutamate/homocysteineS-methyltransferase involved in methionine biosynthesis), sco0988 (acetyltransferase), sco0992 (cysteine synthase), sco0995 (methyltransferase), sco0999 (superoxide dismutase) and sco0996-97-98 encoding an iron uptake system. The deletion of the sco0996-97-98 operon might reduce iron supply and, interestingly, some reports in the literature mention that...”
- The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2)
Pisciotta, Scientific reports 2018 - “...SCO0835 0.7845 MII SCO0826 0.8163 MII SCO7452 0.8841 MII SCO5257 1.3063 MII SCO0392 2.0070 MII SCO0995 2.4922 MII Ratios of log 2 of gene expression between MII24 h/MI are reported. A negative ratio indicates that the gene is more transcribed in MI, a positive one that...”
- Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization
Lewis, BMC genomics 2010 - “...the present study include SCO0985 ( metE , encoding methionine synthase) and the methyltransferase genes SCO0995 (absent in both S. lividans 66 and TK24) and SCO3452 (absent in TK24). It may be significant that both absent methyltransferase genes possess sequence similarity to SAM-dependent methyltransferases. Whilst we...”
- New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures
Hesketh, BMC genomics 2007 - “...down Predicted transmembrane domain SCO0994 integral membrane protein 0.0317 N/A down Predicted 9 transmembrane domains SCO0995 probable methyltransferase 9.76E-04 N/A down Predicted 2 transmembrane domains SCO1089 unknown N/A 0* up None SCO1815 probable 3-oxacyl-(acyl-carrier-protein) reductase N/A 0.084* down Predicted 2 transmembrane domains SCO1845 possible low-affinity phosphate...”
- “...transcribed late in the wild-type, and transcription of SCO0991 (protein kinase), SCO0994 (function unknown) and SCO0995 (methyl transferase) was reduced in the bldA mutant. SCO0992, the TTA-containing gene encoding a putative cysteine synthase, and SCO0993 were not identified as being significantly affected by bldA mutation, presumably...”
D2S319 Methyltransferase type 11 from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
34% identity, 42% coverage
sll0487 hypothetical protein from Synechocystis sp. PCC 6803
36% identity, 24% coverage
- cKMT1 is a New Lysine Methyltransferase That Methylates the Ferredoxin-NADP(+) Oxidoreductase and Regulates Energy Transfer in Cyanobacteria
Cao, Molecular & cellular proteomics : MCP 2023 - “...the purified slr0095, sll0171, sll0829, slr1115, sll1237, sll1300, sll0487, sll1909, slr1610, L11, PrmA, and sll1526 proteins from Escherichia coli . B L...”
- “...length cKMT1 (sll1526 ), sll0171 , sll0829 , sll1909 , sll0487 , sll1300 , sll1237 , slr1610 , slr1115 , slr0095 , slr1643 , and sll1743 (L11) were amplified...”
- Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803
Lin, Genomics, proteomics & bioinformatics 2020 - “...PCC 6803 ID Description (prediction) Length (aa) MW (kDa) Domain E value Accession From To Sll0487 SAM-dependent methyltransferase 402 45.85 58 155 8.56E25 pfam13649 Sll1237 N(5)-glutamine methyltransferase 299 33.82 6 299 1.68E131 TIGR00536 Sll0171 Probable aminomethyltransferase 372 41.02 7 367 0 TIGR00528 Sll0829 Probable methyltransferase 212...”
- Biogenesis of phycobiliproteins. III. CpcM is the asparagine methyltransferase for phycobiliprotein beta-subunits in cyanobacteria
Miller, The Journal of biological chemistry 2008 (PubMed)- “...here the biochemical characterization of the product of sll0487, which we have named cpcM, from the cyanobacterium Synechocystis sp. PCC 6803. Recombinant...”
- “...The primers used to amplify cpcM (sll0487) from Synechocystis sp. PCC 6803 were sll04875.2 (5-TTCGGATCCATGTTGTCCAACTCCGAC-3) and sll0487.3.2...”
- CpcM posttranslationally methylates asparagine-71/72 of phycobiliprotein beta subunits in Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803
Shen, Journal of bacteriology 2008 - “...1.3-kb DNA fragment carrying the open reading frame sll0487 was amplified by PCR using primers sll04875.2 (5 TTCGGATCCATGTTGTCCAACTCCGAC 3) and sll0487.3.2 (5...”
- “...analysis, we identified highly conserved open reading frames, sll0487 in Synechocystis sp. strain PCC 6803 and SYNPCC7002_A2010 in Synechococcus sp. strain PCC...”
STY4649 Putative methyltransferase from Salmonella enterica subsp. enterica serovar Typhi str. CT18
32% identity, 38% coverage
SYNPCC7002_A2010 hypothetical protein from Synechococcus sp. PCC 7002
36% identity, 24% coverage
RL1651 putative 3-demethylubiquinone-9 3-methyltransferase from Rhizobium leguminosarum bv. viciae 3841
30% identity, 66% coverage
8zc8B / Q9X5Q9 The structure of mitm and mitomycin a with sah in mitomycin
29% identity, 74% coverage
- Ligands: s-adenosyl-l-homocysteine; [(1as,8s,8ar,8bs)-6,8a-dimethoxy-5-methyl-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazireno[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate (8zc8B)
rif14 / G0FUS0 27-O-demethyl-rifamycin SV methyltransferase subunit (EC 2.1.1.315) from Amycolatopsis mediterranei (strain S699) (see paper)
DMRMT_AMYMS / G0FUS0 27-O-demethylrifamycin SV methyltransferase; DMRSV methyltransferase; EC 2.1.1.315 from Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei) (see paper)
31% identity, 68% coverage
- function: Catalyzes the methylation of 27-O-demethylrifamycin SV (DMRSV) to rifamycin SV.
catalytic activity: 27-O-demethylrifamycin SV + S-adenosyl-L-methionine = rifamycin SV + S-adenosyl-L-homocysteine + H(+) (RHEA:44740)
subunit: Exists probably as a trimer.
disruption phenotype: Mutant loses its ability to produce rifamycin B, but accumulates 27-O-demethylrifamycin SV (DMRSV) as the major new metabolite, together with a small quantity of 27-O-demethyl-25-O- desacetylrifamycin SV (DMDARSV).
staMB / Q83WF7 3'-O-demethyl-staurosporine methyltransferase (EC 2.1.1.139) from Streptomyces sp. TP-A0274 (see 2 papers)
29% identity, 67% coverage
sll0829 methyltransferase from Synechocystis sp. PCC 6803
38% identity, 49% coverage
- cKMT1 is a New Lysine Methyltransferase That Methylates the Ferredoxin-NADP(+) Oxidoreductase and Regulates Energy Transfer in Cyanobacteria
Cao, Molecular & cellular proteomics : MCP 2023 - “...Blue stained gel of the purified slr0095, sll0171, sll0829, slr1115, sll1237, sll1300, sll0487, sll1909, slr1610, L11, PrmA, and sll1526 proteins from...”
- “...from E. coli DH5a. Full length cKMT1 (sll1526 ), sll0171 , sll0829 , sll1909 , sll0487 , sll1300 , sll1237 , slr1610 , slr1115 , slr0095 , slr1643 , and...”
- Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803
Lin, Genomics, proteomics & bioinformatics 2020 - “...299 33.82 6 299 1.68E131 TIGR00536 Sll0171 Probable aminomethyltransferase 372 41.02 7 367 0 TIGR00528 Sll0829 Probable methyltransferase 212 37.07 49 139 9.24E29 pfam13649 Sll1300 Guanine-N(7)-methyltransferase 211 24.42 21 211 3.97E94 TIGR00091 Sll1407 Probable methyltransferase 265 30.75 45 139 1.61E31 pfam08241 Sll1909 Ribosomal protein L11 methyltransferase...”
XP_005645141 methyltransferase type 11 from Coccomyxa subellipsoidea C-169
29% identity, 37% coverage
- Molecular Origins of Functional Diversity in Benzylisoquinoline Alkaloid Methyltransferases
Morris, Frontiers in plant science 2019 - “...thaliana phosphoethanolamine NMT (AtPEANMT; NP_188427); Spinacea oleracea phosphoethanolamine NMT (SoPEANMT; Q9M571). Coccomyxa subellipsoidea NMT (CsubNMT; XP_005645141); Chlamydomonas reinhardtii NMT (CreiNMT; XP_001695187). Intriguingly, BLAST searches of publicly available nucleotide sequence databases (NCBI NR, OneKP) reveal that transcripts encoding BIA NMT-like proteins (4070% amino acid identity; Supplementary Data...”
LIC12378 3-demethylubiquinone-9 3-O-methyltransferase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
29% identity, 38% coverage
PA4790 hypothetical protein from Pseudomonas aeruginosa PAO1
32% identity, 44% coverage
B5Y5J4 Methyltransferase type 11 domain-containing protein from Phaeodactylum tricornutum (strain CCAP 1055/1)
28% identity, 45% coverage
PEAM3_ARATH / Q9C6B9 Phosphoethanolamine N-methyltransferase 3; EC 2.1.1.103 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
Q9C6B9 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Arabidopsis thaliana (see paper)
28% identity, 31% coverage
- function: Involved in phosphocholine biosynthesis (PubMed:29777000). Catalyzes the N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PC) (PubMed:29777000). In association with NMT1, regulates PC homeostasis, phase transition at the shoot apex, coordinated organ development, and fertility (PubMed:29777000). In associtation with NMT1, involved in phosphatidylcholine biosynthesis and vascular development (PubMed:30218542).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
disruption phenotype: No visible phenotype under normal growth conditions (PubMed:29777000). The double mutant nmt1 and nmt3 exhibit severe compromised aerial growth and reproduction, extensive sterility, drastically reduced phosphocholine concentrations, and altered lipid profiles (PubMed:29777000, PubMed:30218542). The triple mutant nmt1, nmt2 and nmt3 is seedling lethal (PubMed:30518673). - CysQuant: Simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry
Huang, Redox biology 2023 - “...GRANULE-BOUND STARCH SYNTHASE 1 (Q9MAQ0); IPS1, INOSITOL 3-PHOSPHATE SYNTHASE 1 (P42801); NMT3, PHOSPHOETHANOLAMINE N-METHYLTRANSFERASE 3 (Q9C6B9); RD20, RESPONSIVE TO DESICCATION 20 (O22788); SQE3, SQUALENE OXIDASE 3 (Q8VYH2); VTC2, VITAMIN C DEFECTIVE 2 (Q8RWE8). Fig. 5 Furthermore, the redox enzymes ADENOSINE PHOSPHOSULFATE REDUCTASE 3 (APR3) and VITAMIN...”
NP_974139 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein from Arabidopsis thaliana
AT1G73600 methyltransferase/ phosphoethanolamine N-methyltransferase from Arabidopsis thaliana
28% identity, 30% coverage
- A pair of phospho-base methyltransferases important for phosphatidylcholine biosynthesis in Arabidopsis.
Liu, The Plant journal : for cell and molecular biology 2018 (PubMed)- GeneRIF: It is suggested that PMT1 and PMT3 are the primary enzymes for phosphocholine biosynthesis and are involved in phosphatidylcholine biosynthesis and vascular development in Arabidopsis seedlings. [PMT3]
- A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism
Correa, Plant physiology 2025 (no snippet) - A Methyltransferase Trio Essential for Phosphatidylcholine Biosynthesis and Growth
Liu, Plant physiology 2019 (PubMed)- “...At3g18000), PMT2 (or PMEAMT; At1g48600), and PMT3 (or NMT3, At1g73600), are shown to catalyze all of the three methylation steps in vitro (Lee and Jez, 2017)....”
- “...mutants of the second and third isoforms (At1g48600 and At1g73600) do not cause any swelling phenotype, which suggests that XPL may not be a suitable name for...”
- Loss of Phosphoethanolamine N-Methyltransferases Abolishes Phosphatidylcholine Synthesis and Is Lethal
Chen, Plant physiology 2019 (PubMed)- “...TAIR, At3g18000), NMT3 (Arabidopsis thaliana, TAIR, At1g73600), SoPEAMT (Spinacia oleracea, NCBI, Q9M571), TaPEAMT1 (Triticum aestivum, NCBI, AAL40895),...”
- “...accession numbers: NMT1 (At3g18000), NMT3 (At1g73600), NMT2 (At1g48600), NMT2.1 (NM_103756.3), NMT2.2 (NM_202264.2), APT1 (At1g27450), PDF2/PP2AA3 (At1g13320),...”
- OXS2 is Required for Salt Tolerance Mainly through Associating with Salt Inducible Genes, CA1 and Araport11, in Arabidopsis
Jing, Scientific reports 2019 - “...AT2G34430 0.9983498 DEG14 AT2G29290 0.9854896 DEG21 AT2G34170 0.9825152 DEG8 AT5G38930 0.9305307 DEG27 AT1G62500 0.8855457 DEG26 AT1G73600 0.8696551 DEG17 AT1G10657 0.8609541 CTTCTTTTC (174182) DEG9 AT2G41900 CTCCCTCTC (375383) CTCCTTCTC (476483) Numbers in the parenthesis represent the position of the motif from 2 Kb before the coding region. Figure...”
- A pair of phospho-base methyltransferases important for phosphatidylcholine biosynthesis in Arabidopsis
Liu, The Plant journal : for cell and molecular biology 2018 (PubMed) (secret) - NMT1 and NMT3 N-Methyltransferase Activity Is Critical to Lipid Homeostasis, Morphogenesis, and Reproduction
Chen, Plant physiology 2018 (PubMed)- “...NMT1 (locus At3g18000), NMT2 (locus At1g48600), and NMT3 (locus At1g73600; Bolognese and McGraw, 2000; BeGora et al., 2010; Lee and Jez, 2017). NMT1 is the best...”
- “...numbers: NMT1 (At3g18000), NMT2/PMEAMT (At1g48600), NMT3 (At1g73600), APT1 (At1g27450), PDF2/PP2AA3 (At1g13320), and GAPDH (AT1G13440). Supplemental Data The...”
- Pi starvation-dependent regulation of ethanolamine metabolism by phosphoethanolamine phosphatase PECP1 in Arabidopsis roots
Tannert, Journal of experimental botany 2018 - “...three gene loci are known which are associated with the methylation pathway (At3g18000, At1g48600, and At1g73600), but only two of them have been enzymatically characterized: At3g18000 catalyses all three methylation steps (PEAMT1; Bolognese and McGraw, 2000 ) and At1g48600 uses monomethylated PEA as substrate (PMEAMT; BeGora...”
- Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation
Lee, The Journal of biological chemistry 2017 - “...cress), AtPMT1 (At3g18000; xipotl1), AtPMT2 (At1g48600), and AtPMT3 (At1g73600). AtPMT1 is the best studied isoform in this model plant and, like the spinach...”
- “...of AtPMT1 (At3g18000), AtPMT2 (At1g48600), and AtPMT3 (At1g73600) were amplified by PCR from A. thaliana seedling cDNA with isoform-specific oligonucleotides...”
- More
BH2331 hypothetical protein from Bacillus halodurans C-125
36% identity, 45% coverage
T_RS23145 class I SAM-dependent methyltransferase from Salmonella enterica subsp. enterica serovar Typhi str. Ty2
31% identity, 21% coverage
STY4856 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
t4550 conserved hypothetical protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
31% identity, 21% coverage
- Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNA(leuX)
Bishop, Journal of bacteriology 2005 - “...and 56, and all Salmonella isolates tested positive for STY4856 (Fig. 2). P4 family phages as drivers of diversity in S. enterica. A P4-related prophage, termed...”
- “...the full Salmonella serovar Typhi CT18 yjhP-like gene STY4856. In E. coli K-12, the sgc operon, which codes for a potential phosphoenolpyruvate sugar...”
- Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7
Pickard, Journal of bacteriology 2003 - “...S061 of SXT element from Vibrio cholerae) 75 (288 aa to STY4856) 39 (472 aa to Orf193 of plasmid Rts1) 29 (451 aa to XAC2196), 28 (449 aa to Reut2852) 35 (265...”
- Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
Nickerson, EBioMedicine 2018 - “...0.0466588 Hypothetical protein T_RS09750 t1914 2.67E+00 0.0006626 Methyltransferase T_RS23210 t4563 2.66886 0.0212746 Membrane protein T_RS23145 t4550 2.6688 0.0477512 SAM-dependent methyltransferase T_RS08510 t1671 2.64519 0.0003457 Nitrate reductase molybdenum cofactor assembly chaperone T_RS06895 t1352 2.6331 0.0101017 Tail fiber protein T_RS14890 t2935 2.6154 0.0110453 Transcriptional regulator T_RS04790 t0937 2.59229...”
MA3459 conserved hypothetical protein from Methanosarcina acetivorans C2A
29% identity, 39% coverage
- 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 other groups (i.e., PylB, the hypothetical protein MA3459, and the putative histidine kinase MA3962). For these proteins, several amino acids residues are...”
- “...through, with the potential of a regulatory function. Although MA3459 and MA3962 are clearly expressed in cells, we do not have experimental evidence that their...”
LT85_RS25195 class I SAM-dependent methyltransferase from Collimonas arenae
31% identity, 41% coverage
Sare_1271 Methyltransferase type 11 from Salinispora arenicola CNS205
30% identity, 67% coverage
Eab7_0774 class I SAM-dependent methyltransferase from Exiguobacterium antarcticum B7
30% identity, 34% coverage
- Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance
da, PloS one 2018 - “...protein 23 Eab7_0741 IPR004394 Ribosomal silencing factor RsfS 24 Eab7_0770 IPR029063 Phosphotransferase system, EIIC 25 Eab7_0774 IPR029063 S-adenosylmethionine-dependent methyltransferases (AdoMet_Mtases) 26 Eab7_0783 IPR025945 SGNH hydrolase-like domain, acetyltransferase AlgX 27 Eab7_0789 IPR002810 NfeD-like C-terminal, partner-binding 28 Eab7_0806 IPR006901 tRNA (adenine-N1-)-methyltransferase 29 Eab7_0807 IPR002678 GTP cyclohydrolase 1 type...”
- “...of cobalamin has not yet been completely understood [ 108 , 109 ]. The proteins Eab7_0774 and Eab7_0707 were both predicted to be S-adenosylmethionine-dependent methyltransferases, known as AdoMet_Mtases (EC 2.1.1). The Eab7_0806 protein was identified as a tRNA (adenine-N1-)-methyltransferase (EC 2.1.1.217). Methyltransferases are a class of...”
PP0578 methyltransferase, putative from Pseudomonas putida KT2440
29% identity, 44% coverage
MMSR116_RS23260 ArsR/SmtB family transcription factor from Methylobacterium mesophilicum SR1.6/6
32% identity, 44% coverage
TM0938 conserved hypothetical protein from Thermotoga maritima MSB8
31% identity, 44% coverage
mll4091 fatty acid synthase, cyclopropane-fatty-acyl-phospholipid synthase from Mesorhizobium loti MAFF303099
Q98ET6 Fatty acid synthase cyclopropane-fatty-acyl-phospholipid synthase from Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
31% identity, 41% coverage
ARSM_AQUA1 / U2ZU49 Arsenite methyltransferase; EC 2.1.1.137 from Aquipseudomonas alcaligenes (strain ATCC 14909 / DSM 50342 / CCUG 1425 / JCM 20561 / NBRC 14159 / NCIMB 9945 / NCTC 10367 / 1577) (Pseudomonas alcaligenes) (see paper)
U2ZU49 arsenite methyltransferase (EC 2.1.1.137) from Pseudomonas alcaligenes (see paper)
WP_021703038 arsenite methyltransferase from Pseudomonas aeruginosa
37% identity, 31% coverage
- function: Catalyzes the transfer of a methyl group from AdoMet to arsenite, producing methylated arsenicals. Involved in the conversion of As(III) to dimethylarsenate as the main product in the medium and also produces dimethylarsine and trimethylarsine gases. Reduces the arsenic toxicity in the cell and may contribute to the global arsenic cycling.
catalytic activity: arsenic triglutathione + [thioredoxin]-dithiol + S-adenosyl-L- methionine + 2 H2O = methylarsonous acid + [thioredoxin]-disulfide + 3 glutathione + S-adenosyl-L-homocysteine + H(+) (RHEA:69460)
catalytic activity: arsenic triglutathione + 2 [thioredoxin]-dithiol + 2 S- adenosyl-L-methionine + H2O = dimethylarsinous acid + 2 [thioredoxin]-disulfide + 3 glutathione + 2 S-adenosyl-L-homocysteine + 2 H(+) (RHEA:69464)
catalytic activity: arsenic triglutathione + 3 [thioredoxin]-dithiol + 3 S- adenosyl-L-methionine = trimethylarsine + 3 [thioredoxin]-disulfide + 3 glutathione + 3 S-adenosyl-L-homocysteine + 3 H(+) (RHEA:69432)
disruption phenotype: Deletion mutant cannot methylate arsenic and becomes more sensitive to As(III). - Arsenite Methyltransferase Diversity and Optimization of Methylation Efficiency
Chen, Environmental science & technology 2023 - “...322 AAs, 3 (ABC) 42% As(III) DMAs(V) Yin et al., 2011 Pseudomonas alcaligenes NBRC14159, PaArsM (WP_021703038) Prokarya bacteria 346 AAs, 3 (ABC) 33% As(III) DMAs(V) Zhang et al., 2015 Chlamydomonas reinhardtii , CrArsM (AFS88933) Eukarya plantae 379 AAs, 3 (ABC) 37% As(III) DMAs(V) Pedersen et al.,...”
- Arsenic methylation and volatilization by arsenite S-adenosylmethionine methyltransferase in Pseudomonas alcaligenes NBRC14159
Zhang, Applied and environmental microbiology 2015 (secret)
ILID_HYPJQ / P9WEU0 S-adenosyl-L-methionine-dependent Diels-Alderase iliD; C-methyltransferase iliD; Ilicicolin H biosynthesis cluster protein D; Pericyclase iliD; EC 2.1.-.- from Hypocrea jecorina (strain QM6a) (Trichoderma reesei) (see paper)
31% identity, 36% coverage
- function: S-adenosyl-l-methionine-dependent Diels-Alderase; part of the gene cluster that mediates the biosynthesis of ilicicolin H, a 4- hydroxy-2-pyridonealkaloid that has potent and broad antifungal activities by inhibiting the mitochondrial respiration chain (PubMed:34947016). IliD catalyzes the Diels-Alder reaction that converts the acyclic 2-pyridone intermediate to 8-epi-ilicicolin H (PubMed:34947016). The biosynthesis of ilicicolin H starts with formation of the tetramic acid by the hybrid PKS-NRPS synthetase iliA with the partnering trans-enoyl reductase iliB since iliA lacks a designated enoylreductase (ER) domain. The cytochrome P450 monooxygenase iliC then catalyzes the ring expansion of the tetramate to the acyclic 2-pyridone. The pericyclase iliD further converts the acyclic 2-pyridone into 8-epi-ilicicolin H. 8-epi-ilicicolin H might then spontaneously convert to ilicicolin H since ilicicolin H is produced in the absence of the epimerase iliE, in contrast to what was observed for the Talaromyces variabilis ilicolin H biosynthetic pathway (Probable) (PubMed:34947016).
catalytic activity: 3-[(2E,4E,8S,10E,12Z)-4,8-dimethyltetradeca-2,4,10,12- tetraenoyl]-4-hydroxy-5-(4-hydroxyphenyl)-1,2-dihydropyridin-2-one = ilicicolin H (RHEA:64568)
cofactor: S-adenosyl-L-methionine
WP_108075233 ArsR/SmtB family transcription factor from Vitiosangium sp. GDMCC 1.1324
31% identity, 40% coverage
- 2-Hydroxysorangiadenosine: Structure and Biosynthesis of a Myxobacterial Sesquiterpene-Nucleoside
Okoth, Molecules (Basel, Switzerland) 2020 - “...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 O -acetylhomoserine sulfhydrylase WP_108075236 100/97.26 sora19...”
PFLU0633 putative methyltransferase from Pseudomonas fluorescens SBW25
31% identity, 44% coverage
- The birth of a bacterial tRNA gene by large-scale, tandem duplication events
Ayan, eLife 2020 - “...CmoA, CmoB, and CmoM against the SBW25 proteome give significant hits to Pflu1067, Pflu1066, and Pflu0633, respectively (BLASTp e-values<1e-50; Altschul et al., 1990 ). CmoA/B/M-mediated expansion of tRNA-Ser(UGA) translational capacity to include codon UCG is expected to rescue a serCGA deletion mutant. Such a rescue event...”
An12g02650 uncharacterized protein from Aspergillus niger
29% identity, 57% coverage
ADG881_908 SAM-dependent methyltransferase from Alcanivorax sp. DG881
32% identity, 37% coverage
- Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges
Pimentel-Elardo, Marine drugs 2012 - “...ORF24 52396-54060 Hypothetical protein ZP_05710821, (ZP_05710821), Desulfurivibrio alkaliphilus AHT2 49/68 554 ORF25 54272-58006 Cyclopropane-fatty-acyl-phospholipid synthase ADG881_908, (ZP_05041385), Alcanivorax sp. DG881 51/66 1244 ORF26 59373-60101 Nucleoside 2-deoxyribosyltransferase P9211_14861, (YP_001551371), Prochlorococcus marinus str. MIT 9211 63/76 242 3. Experimental Section 3.1. Sponge Collection Marine sponges were collected by...”
SahR / VIMSS10188691 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Azospirillum sp. B510
30% identity, 48% coverage
Rfer_1612 UbiE/COQ5 methyltransferase from Rhodoferax ferrireducens DSM 15236
34% identity, 30% coverage
PEAM2_WHEAT / C8YTM5 Phosphoethanolamine N-methyltransferase; TaPEAMT2; EC 2.1.1.103 from Triticum aestivum (Wheat) (see paper)
30% identity, 26% coverage
- function: Involved in phosphocholine biosynthesis (PubMed:19762471). Catalyzes the N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PC) (PubMed:19762471).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
CD1759 hypothetical protein from Clostridium difficile 630
CD630_17590, CDIF630_01955 class I SAM-dependent methyltransferase from Clostridioides difficile 630
30% identity, 42% coverage
- The current riboswitch landscape in <i>Clostridioides difficile</i>
Badilla, Microbiology (Reading, England) 2024 - “...system (PTS), lactose/cellobiose family (ComFC-like protein encoded by CD0133 upstream of the raiA motif) speF CD1759 Methyltransferase domain protein Table 2. T-box riboswitches identified in C. difficile Functional class regulated by the T-box riboswitch CDS downstream the T-box riboswitch Associated function Aminoacyl-tRNA synthetase CD0014 Serine-tRNA ligase...”
- Clostridioides difficile Modifies its Aromatic Compound Metabolism in Response to Amidochelocardin-Induced Membrane Stress
Brauer, mSphere 2022 - “...adj. P value threshold0.05). Also additional proteins encoded nearby to each putative phenazine biosynthesis-like protein, CD630_17590 and CD630_30340, respectively, were higher abundant upon CDCHD stress ( Fig.2A , Table S2 in the supplemental material). Second, ClnA from the ClnAB antimicrobial peptide efflux system, previously described as...”
- An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium
Fuchs, Proceedings of the National Academy of Sciences of the United States of America 2021 - “...). Interestingly, we detected a speF riboswitch previously only documented in gram-negative alphaproteobacteria associated with CDIF630_01955, encoding a methyltransferase domain protein. As before, the associated termination site suggests that the riboswitch is functional, which is further supported by a 220-nt Northern blot signal ( SI Appendix...”
GFSG_STRHA / E0D208 Methyltransferase GfsG; EC 2.1.1.- from Streptomyces halstedii (see 3 papers)
31% identity, 48% coverage
- function: Methylase required for synthesis of the 16-membered macrolide antibiotics FD-891 and FD-892 (PubMed:20589823, PubMed:26630077). In vitro uses S-adenosyl-L-methionine to methylate a number of biosynthetic intermediates in the synthesis of FD-891 (PubMed:26630077).
disruption phenotype: Bacteria make 25-O-demethyl-FD-891. Double gfsF- gfsG deletions make a diastereomeric mxiture of 25-oxo-FD-892.
F2DR04 phosphoethanolamine N-methyltransferase from Hordeum vulgare subsp. vulgare
30% identity, 26% coverage
WP_030734046 SAM-dependent methyltransferase from Streptomyces sp. NRRL F-2890
35% identity, 36% coverage
SCO3091 cyclopropane-fatty-acyl-phospholipid synthase from Streptomyces coelicolor A3(2)
31% identity, 25% coverage
- Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes
Kim, Molecular microbiology 2012 - “...in the sigR-rsrA mutant but with delayed response. A similar phenomenon was also observed for SCO3091 ( cfa ) encoding a putative cyclopropane-fatty acyl phospholipid synthase ( Fig. 1A ). The delayed induction kinetics in sigR-rsrA mutant suggests that these SigR-dependent promoters may also be recognized...”
- “...Transfer messenger RNA (tmRNA) (S1) 7 SCO3083 * Possible integral membrane protein (S1, A) 12 SCO3091 * cfa Cyclopropane-fatty-acyl-phospholipid synthase, SAM-dependent methylase (A), S1 13 SCO3162 * Possible esterase, -lactamase superfamily (S1, A) 14 SCO3187 * Hypothetical protein (S1) 7 SCO3206 * Probable transmembrane efflux protein...”
6uakA / A0A3D0LE54 Lahsb - c-terminal methyltransferase involved in ripp biosynthesis (see paper)
31% identity, 42% coverage
- Ligand: s-adenosyl-l-homocysteine (6uakA)
BMF77_01250 class I SAM-dependent methyltransferase from Dolichospermum sp. UHCC 0315A
27% identity, 39% coverage
FOIG_12358 sterol 24-C-methyltransferase from Fusarium odoratissimum NRRL 54006
X0JEW4 Sterol 24-C-methyltransferase from Fusarium odoratissimum NRRL 54006
34% identity, 25% coverage
- RNA Sequencing Reveals that Endoplasmic Reticulum Stress and Disruption of Membrane Integrity Underlie Dimethyl Trisulfide Toxicity against Fusarium oxysporum f. sp. cubense Tropical Race 4
Zuo, Frontiers in microbiology 2017 - “...Moreover, the expression of genes encoding enzymes involved in ergosterol biosynthesis, such as ERG 6 (FOIG_12358, FOIG_07540), ERG 2 (FOIG_02847), ERG 3 (FOIG_8856), and ERG 5 (FOIG_13497), was clearly reduced following DT exposure. FIGURE 6 Expression profiles of steroid biosynthesis-related genes. In the heatmap, (AC) represent...”
- “...qRT-PCR assay ( Figure 7 ). These included DEGs involved in steroid biosynthesis (FOIG_07540, FOIG_08157, FOIG_12358, and FOIG_15550), and related to the ER (FOIG_05398, FOIG_08856, FOIG_14848, and FOIG_16063). The changes observed in trends were similar between RNA-seq and qRT-PCR assays, although several genes presented different expression...”
- Multi-site fungicides suppress banana Panama disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4
Cannon, PLoS pathogens 2022 - “...1e-162 Erg11_2 23.74 X0LR56 Lanosterol demethylase Erg11p, S . cerevisiae 1e-169 Pathway alteration Erg6_1 462.52 X0JEW4 Sterol 24-C-methyltransferase, S . cerevisiae 2e-127 Sim1 131.24 X0JVY8 3-hydroxysteroid-(8)(7)isomerase, human h 5e-47 Erg13 12.74 X0K3N0 hydroxymethylglutaryl-CoA synth., S . cerevisiae 0.0 Erg25_1 13.73 X0J3L6 C-4 methylsterol oxidase, S ....”
FOXG_08765 sterol 24-C-methyltransferase from Fusarium oxysporum f. sp. lycopersici 4287
34% identity, 25% coverage
- Iturin A Strongly Inhibits the Growth and T-2 Toxin Synthesis of Fusarium oxysporum: A Morphological, Cellular, and Transcriptomics Study
Hua, Foods (Basel, Switzerland) 2023 - “...encoding ergosterol were up-regulated following 25 and 50 g/mL iturin A treatment, including sterol 25-C-methyltransferase (FOXG_08765), sterol 15-demethylase (FOXG_11555), sterol carrier protein 2 (FOXG_12787), delta25(25(1))-sterol reductase (FOXG_05355), and C-5 sterol desaturase (FOXG_10530) was also up-regulated. Sterol 15-demethylase, as one of the cytochrome P-550 (cytochrome P550) protein...”
PVX_096130 3-demethylubiquinone-9 3-methyltransferase, putative from Plasmodium vivax
33% identity, 19% coverage
- Heterogeneous Network Model to Identify Potential Associations Between Plasmodium vivax and Human Proteins
Suratanee, International journal of molecular sciences 2020 - “..., SDHA , SDHB , SDHC , and SDHD ) and five malaria proteins ( PVX_096130 , PVX_123265 , PVX_003675 , PVX_113540 , and PVX_003575 ). This enzyme complex can be found in many bacterial cells and in the inner mitochondrial membrane of eukaryotes. It is...”
- “..., SDHA , SDHB , SDHC , and SDHD ) and five malaria proteins ( PVX_096130 , PVX_123265 , PVX_003675 , PVX_113540 , and PVX_003575 ). ( b ) Cluster c1073 consists of 16 associations of sixteen human proteins and only one malaria protein ( PVX_098735...”
5wp4A / Q9FR44 Arabidopsis thaliana phosphoethanolamine n-methyltransferase 1 (atpmt1, xioptl) in complex with sah and phosphocholine (see paper)
30% identity, 23% coverage
- Ligands: s-adenosyl-l-homocysteine; phosphocholine (5wp4A)
PEAM1_ARATH / Q9FR44 Phosphoethanolamine N-methyltransferase 1; AtNMT1; PEAMT1; Protein DEFECTIVE PRIMARY ROOT 2; Protein XIPOTL 1; EC 2.1.1.103 from Arabidopsis thaliana (Mouse-ear cress) (see 10 papers)
Q9FR44 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Arabidopsis thaliana (see 4 papers)
AT3G18000 XPL1 (XIPOTL 1); methyltransferase/ phosphoethanolamine N-methyltransferase from Arabidopsis thaliana
NP_188427 S-adenosyl-L-methionine-dependent methyltransferases superfamily protein from Arabidopsis thaliana
30% identity, 22% coverage
- function: Involved in phosphocholine biosynthesis (PubMed:11115895, PubMed:15295103, PubMed:30218542). Catalyzes the N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PC) (PubMed:11115895). Required for root system development and epidermal cell integrity through its role in choline and phospholipid metabolism (PubMed:15295103). In association with NMT3, regulates PC homeostasis, phase transition at the shoot apex, coordinated organ development, and fertility (PubMed:29777000). In association with NMT3, involved in phosphatidylcholine biosynthesis and vascular development (PubMed:30218542). In association with NMT2, involved in the production of phosphatidylcholine in roots, essential for root development (PubMed:30518673). In association with NMT2 produce phosphocholine mainly for leaf growth maintenance (PubMed:35560207). Contributes to the regulation of overall root zonation dynamics through reactive oxygen species (ROS) and auxin-regulated cell differentiation (PubMed:31246280). Participates in root development of primary root elongation under salt stress conditions by balancing reactive oxygen species (ROS) production and distribution through abscisic acid (ABA) signaling (PubMed:35789105).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
disruption phenotype: Altered root development due to defect in primary root elongation and root epidermal cell development (PubMed:15295103, PubMed:31246280). Temperature-sensitive male sterility and salt hypersensitivity phenotypes (PubMed:12215503). The double mutant nmt1 and nmt3 exhibit severe compromised aerial growth and reproduction, extensive sterility, drastically reduced phosphocholine concentrations, and altered lipid profiles (PubMed:29777000, PubMed:30218542, PubMed:30381317). The triple mutant nmt1, nmt2 and nmt3 is seedling lethal (PubMed:30518673). - A data-integrative modeling approach accurately characterizes the effects of mutations on Arabidopsis lipid metabolism
Correa, Plant physiology 2025 (no snippet) - Advances in plant male sterility for hybrid seed production: an overview of conditional nuclear male sterile lines and biotechnology-based male sterile systems
Vasupalli, Frontiers in plant science 2025 (no snippet) - Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia
Tamura, Life (Basel, Switzerland) 2022 - “...AT1G28570 AT4G23400 PIP1;5 AT4G18570 AT1G16880 ACR11 AT3G55760 AT4G19170 CCD4 AT5G42510 DIR1 AT1G62180 APR2 AT1G20020 LFNR2 AT3G18000 NMT1 AT5G11420 AT5G05980 FPGS1...”
- Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana
Krzyszton, Scientific reports 2022 - “...example, AT3G03710 , AT3G27906 and AT5G54390 ) or containing an upstream ORF (for example, AT1G36730, AT3G18000 ) 46 as they were identified among the genes producing more sRNAs in upf3 or upf1 mutants but only from their coding strand (Supplementary Dataset 1 ). Another criterion for...”
- Cloning and Functional Identification of Phosphoethanolamine Methyltransferase in Soybean (Glycine max)
Ji, Frontiers in plant science 2021 - “...identified, using BLASTN at the Phytozome v12.1 website 2 based on Arabidopsis thaliana PEAMT1 ( At3g18000 ). The results were filtered with a score value 100 and an E -value 1e-10. The filtered genes were further analyzed for the potential domains, using SMART 3 ( Letunic...”
- Non-specific phospholipases C, NPC2 and NPC6, are required for root growth in Arabidopsis
Ngo, The Plant journal : for cell and molecular biology 2019 (PubMed) (secret) - A Methyltransferase Trio Essential for Phosphatidylcholine Biosynthesis and Growth
Liu, Plant physiology 2019 (PubMed)- “...Arabidopsis. The three PMTs, PMT1 (or NMT1, PEAMT1, XPL1; At3g18000), PMT2 (or PMEAMT; At1g48600), and PMT3 (or NMT3, At1g73600), are shown to catalyze all of...”
- “...abbreviation. XPL The abbreviation "XPL" was given to At3g18000 because a forward-genetic screen found that mutation in this gene causes swelling in epidermal...”
- Loss of Phosphoethanolamine N-Methyltransferases Abolishes Phosphatidylcholine Synthesis and Is Lethal
Chen, Plant physiology 2019 (PubMed)- “...NCBI, NM_202264.2), NMT1 (Arabidopsis thaliana, TAIR, At3g18000), NMT3 (Arabidopsis thaliana, TAIR, At1g73600), SoPEAMT (Spinacia oleracea, NCBI, Q9M571),...”
- “...databases under accession numbers: NMT1 (At3g18000), NMT3 (At1g73600), NMT2 (At1g48600), NMT2.1 (NM_103756.3), NMT2.2 (NM_202264.2), APT1 (At1g27450),...”
- More
- Molecular Origins of Functional Diversity in Benzylisoquinoline Alkaloid Methyltransferases
Morris, Frontiers in plant science 2019 - “...putrescine NMT (DaPNMT; CAE47481); Nicotiana sylvestris putrescine NMT (NsPNMT; BAA74544); Arabidopsis thaliana phosphoethanolamine NMT (AtPEANMT; NP_188427); Spinacea oleracea phosphoethanolamine NMT (SoPEANMT; Q9M571). Coccomyxa subellipsoidea NMT (CsubNMT; XP_005645141); Chlamydomonas reinhardtii NMT (CreiNMT; XP_001695187). Intriguingly, BLAST searches of publicly available nucleotide sequence databases (NCBI NR, OneKP) reveal that...”
- Phosphoethanolamine N-methyltransferase 1 contributes to maintenance of root apical meristem by affecting ROS and auxin-regulated cell differentiation in Arabidopsis.
Zou, The New phytologist 2019 (PubMed)- GeneRIF: Loss-of-function of DPR2/PEAMT1 resulted in root apical meristem consumption by affecting root stem cell niche, division zone, elongation and differentiation zone.[PEAMT1]
- NMT1 and NMT3 N-Methyltransferase Activity Is Critical to Lipid Homeostasis, Morphogenesis, and Reproduction.
Chen, Plant physiology 2018 - GeneRIF: At3g18000 (NMT3) catalyzes the triple methylation of phosphoethanolamine to phosphocholine.NMT3 role in reproduction and seed development.
- Conformational changes in the di-domain structure of Arabidopsis phosphoethanolamine methyltransferase leads to active-site formation.
Lee, The Journal of biological chemistry 2017 - GeneRIF: Crystal structure shows the di-domain architecture.
- Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30.
Alatorre-Cobos, Journal of experimental botany 2012 (PubMed)- GeneRIF: Data suggests that phosphocholine (PCho) is the true mediator of upstream open reading frame 30-driven translational repression. Because XIPOTL1 is preferentially expressed in Arabidopsis root tips, higher PCho levels are found in roots than shoots.
- Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways
Déchamps, Journal of lipid research 2010 - “...of A. thaliana (AtPMT, spliced variant 1, NP_188427, NCBI-REFSEQ), of C. elegans (CePMT1: NP_871998, CePMT2: NP_504248) and P. falciparum (MAL13P1.214,...”
CYPM_STRSQ / E5KIC0 Cypemycin N-terminal methyltransferase; EC 2.1.1.301 from Streptomyces sp. (see 2 papers)
31% identity, 47% coverage
- function: Involved in the biosynthesis of the lanaridin cypemycin. The enzyme can methylate a variety of oligopeptides, cyclic peptides and the epsilon-amino group of lysine.
catalytic activity: N-terminal L-alanyl-[cypemycin] + 2 S-adenosyl-L-methionine = N-terminal N,N-dimethyl-L-alanyl-[cypemycin] + 2 S-adenosyl-L- homocysteine + 3 H(+) (RHEA:14393)
slr1071 unknown protein from Synechocystis sp. PCC 6803
31% identity, 47% coverage
- Ethylene causes transcriptomic changes in Synechocystis during phototaxis
Lacey, Plant direct 2018 - “...slr5054 , slr5055 , slr5056 ) and methyltransferases ( sll1693 , slr1068 , slr1069 , slr1071 , slr1436 , slr1610 ). Using the Kyoto Encyclopedia of Genes and Genomes website (KEGG; http://www.genome.jp/kegg/ ), we evaluated whether or not these 62 genes encode for proteins involved in...”
- “...1.1110 7 Chromosome sll5057 Glycosyltransferase 2.17 5.8810 3 pSYM slr0362 Hydrolase 2.17 2.1110 6 Chromosome slr1071 Methyltransferase 2.13 8.3010 10 Chromosome slr1215 Hypothetical protein 2.13 2.8310 7 Chromosome slr1076 Glycosyltransferase 2.12 2.2310 16 Chromosome sll0808 ISY508a Putative transposase 2.10 2.9910 3 Chromosome slr1456 pilA4, gspG Type...”
7wzgB / E5KIC0 Cypemycin n-terminal methyltransferase cypm
30% identity, 48% coverage
- Ligand: s-adenosyl-l-homocysteine (7wzgB)
RTCIAT899_RS18960 SAM-dependent methyltransferase from Rhizobium tropici CIAT 899
35% identity, 30% coverage
- Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899
Guerrero-Castro, Frontiers in microbiology 2018 - “...cfa3 RTCIAT899_RS24775 0.7897075 0.08312349 Class I SAM-dependent methyltransferase cfa4 RTCIAT899_RS18940 0.67863217 0.54558424 SAM-dependent methyltransferase cfa5 RTCIAT899_RS18960 0.18275374 0.45288988 SAM-dependent methyltransferase Exo RTCIAT899_RS06570 1.33771965 0.11074631 EPS transporter family Yuan et al., 2008 exoX RTCIAT899_RS29115 0.10549587 0.69617043 EPS production repressor protein ExoX Hellweg et al., 2009 Exo RTCIAT899_RS29675...”
U5HK48 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Haemonchus contortus (see paper)
34% identity, 24% coverage
SahR / VIMSS2676094 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Oceanicaulis alexandrii HTCC2633
28% identity, 61% coverage
4krhA / U5HK48 Semet haemonchus contortus phosphoethanolamine n-methyltransferase 2 in complex with s-adenosyl-l-methionine (see paper)
34% identity, 24% coverage
- Ligand: s-adenosylmethionine (4krhA)
Y2350_MYCS2 / A0QUV5 Probable S-adenosylmethionine-dependent methyltransferase MSMEG_2350/MSMEI_2290; EC 2.1.1.- from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium smegmatis) (see paper)
MSMEG_2350 hypothetical protein from Mycobacterium smegmatis str. MC2 155
29% identity, 63% coverage
- function: Probable S-adenosylmethionine-dependent methyltransferase required for the 6-O-methylation of the polysaccharide backbone of 6-O- methylglucosyl lipopolysaccharides (MGLP).
disruption phenotype: Inactivation of this gene results in a dramatic reduction in the amounts of 6-O-methylglucosyl lipopolysaccharides (MGLP) synthesized and in the accumulation of precursors of these molecules. Cells lacking this gene do not grow at high temperature (42 degrees Celsius) in Sauton's medium, although their growth is comparable to that of wild-type at 30 and 37 degrees Celsius in this medium. - Targeting drug tolerance in mycobacteria: a perspective from mycobacterial biofilms
Islam, Expert review of anti-infective therapy 2012 - “...MSMEG_2268 Thioredoxin-like protein MSMEG_2269 Conserved hypothetical protein MSMEG_2293 Conserved hypothetical protein MSMEG_2311 Predicted protein, putative MSMEG_2350 Conserved hypothetical protein Rv3030 MSMEG_2380 Sugar transporter family protein Rv2994 MSMEG_2601 Protocatechuate 3,4-dioxygenase subunit MSMEG_2735 Diaminopimelateepimerase Rv2726c MSMEG_2740 LexA repressor Rv2720 MSMEG_2743 Conserved hypothetical protein TIGR00244 Rv2718c MSMEG_2774 GGDEF domain...”
- Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria
Kaur, PloS one 2009 - “...and our own observations on a Rv3032 knock-out mutant of M. tuberculosis H37Rv and a MSMEG_2350 knock-out mutant of M. smegmatis mc 2 155, both of which were found to be significantly impaired in MGLP biosynthesis but not in that of fatty acids and mycolates [9]...”
RPA0924 possible cyclopropane-fatty-acyl-phospholipid synthase from Rhodopseudomonas palustris CGA009
Q6NBA4 Cyclopropane-fatty-acyl-phospholipid synthase from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
32% identity, 33% coverage
- A bacterial biosynthetic pathway for methylated furan fatty acids
Lemke, The Journal of biological chemistry 2020 - “...+ ufaD ; F , RPA2570 ; G , RPA2570 + ufaO ; H , RPA0924 ; I , RPA0924 + FufM . Bacterial synthesis of a dimethyl-FuFA The above analysis of R. palustris phospholipid FAMEs showed that this bacterium contained a product with a molecular...”
- “...R. palustris genome contains two genes annotated as SAM-dependent fatty acidmodifying enzymes ( RPA3082 and RPA0924 ) with 38 and 26% amino acid identity, respectively, to the known R. sphaeroides fatty acyl methylase UfaM ( 26 ). To test the role of these putative fatty acidmodifying...”
- Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle
McKinlay, The Journal of biological chemistry 2014 - “...three potential cyclopropane-fatty-acyl-phospholipid synthase genes (RPA0924, 2569, 3082) that showed significantly higher transcript levels (supplemental Table...”
- Lipid droplets in Arabidopsis thaliana leaves contain myosin-binding proteins and enzymes associated with furan-containing fatty acid biosynthesis.
Omata, Frontiers in plant science 2024 - “...be found in UniProt (The UniProt, 2017) under the following accession numbers: UfaO (Q3IYV8), FufM (Q6NBA4), UfaM (Q3J4I7), and UfaD (Q3IYV7). Results Proteomic analysis of LDs isolated from hise1 mutant leaves To perform leaf LD proteomics, we isolated LDs from leaves of the A. thaliana hise1-2...”
MA0303 conserved hypothetical protein from Methanosarcina acetivorans C2A
29% identity, 57% coverage
SCO2317 methyltransferase from Streptomyces coelicolor A3(2)
31% identity, 62% coverage
ERG6B_GIBZE / A0A0E0SMA3 Sterol 24-C-methyltransferase ERG6B; SCMT; SMT; Delta(24)-sterol C-methyltransferase ERG6B; Ergosterol biosynthesis protein 6B; EC 2.1.1.- from Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (Wheat head blight fungus) (Fusarium graminearum) (see 3 papers)
33% identity, 26% coverage
- function: Sterol 24-C-methyltransferase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (By similarity). ERG6A and ERG6B methylate lanosterol at C-24 to produce eburicol (By similarity). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase ERG9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, squalene is converted into lanosterol by the consecutive action of the squalene epoxidase ERG1 and the lanosterol synthase ERG7. Then, the delta(24)-sterol C-methyltransferase ERG6 methylates lanosterol at C-24 to produce eburicol. Eburicol is the substrate of the sterol 14-alpha demethylase encoded by CYP51A, CYP51B and CYP51C, to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol. CYP51B encodes the enzyme primarily responsible for sterol 14-alpha- demethylation, and plays an essential role in ascospore formation. CYP51A encodes an additional sterol 14-alpha-demethylase, induced on ergosterol depletion and responsible for the intrinsic variation in azole sensitivity. The third CYP51 isoform, CYP51C, does not encode a sterol 14-alpha-demethylase, but is required for full virulence on host wheat ears. The C-14 reductase ERG24 then reduces the C14=C15 double bond which leads to 4,4-dimethylfecosterol. A sequence of further demethylations at C-4, involving the C-4 demethylation complex containing the C-4 methylsterol oxidases ERG25, the sterol-4-alpha- carboxylate 3-dehydrogenase ERG26 and the 3-keto-steroid reductase ERG27, leads to the production of fecosterol via 4-methylfecosterol. ERG28 has a role as a scaffold to help anchor ERG25, ERG26 and ERG27 to the endoplasmic reticulum. The C-8 sterol isomerase ERG2 then catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5- desaturases ERG3A and ERG3BB then catalyze the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The C-22 sterol desaturases ERG5A and ERG5B further convert 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)- tetraen-3beta-ol is substrate of the C-24(28) sterol reductase ERG4 to produce ergosterol (Probable).
catalytic activity: lanosterol + S-adenosyl-L-methionine = eburicol + S-adenosyl- L-homocysteine + H(+) (RHEA:52652)
SahR / VIMSS1093566 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Hahella chejuensis KCTC 2396
30% identity, 35% coverage
NP_001034928 arsenite methyltransferase from Danio rerio
32% identity, 29% coverage
- Arsenite Methyltransferase Diversity and Optimization of Methylation Efficiency
Chen, Environmental science & technology 2023 - “...plantae 405 AAs, 3 (ABC) 42% As(III) MAs(V) Pedersen et al., 2020 Danio rerio zAS3MT (NP_001034928) Eukarya animalia 377 AAs, 3 (ABC) 40% As(III) MAs(V) Pedersen et al., 2020 Homo sapiens hAS3MT (NP_065733.2) Eukarya animalia 375 AAs, 3 (ABC) 33% As(III) MAs(V) Pedersen et al., 2020...”
- Insights into S-adenosyl-l-methionine (SAM)-dependent methyltransferase related diseases and genetic polymorphisms
Li, Mutation research. Reviews in mutation research 2021 - “...sapiens As(III) S -adenosylmethionine methyltransferase (AAI19639) was aligned with eukaryotic orthologues from Danio rerio (zAS3MT, NP_001034928), Rattus norvegicus (rAS3MT, NP_543166) and Cyanidioschyzon merolae (CmArsM, FJ476310). Black shading indicates conserved residues, grey shading indicates conservative replacements, * denotes conserved cysteine residues, # denotes polymorphic residues. Fig. 4....”
- Arsenic Methyltransferase and Methylation of Inorganic Arsenic.
Roy, Biomolecules 2020 - “...GenBank. The accession numbers of the sequences are: ghost shark (XP_007882715.1), Florida lancelet (XP_002609029.1), zebrafish (NP_001034928.1), Mexican tetra (XP_007253206.1), ocean coelacanth (XP_006007443.1), western clawed frog (NP_001135714.1), chicken (XP_421735.3), green sea turtle (XP_007057932.1), house mouse (NP_065602.2), West Indian manatee (XP_004370149.1), human (Q9HBK9), rhesus monkey (XP_001113391.2), and Angola...”
PEAM1_WHEAT / Q8VYX1 Phosphoethanolamine N-methyltransferase 1; TaPEAMT1; Phosphoethanolamine N-methyltransferase; WPEAMT; EC 2.1.1.103 from Triticum aestivum (Wheat) (see 2 papers)
Q8VYX1 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Triticum aestivum (see paper)
31% identity, 23% coverage
- function: Involved in phosphocholine biosynthesis (PubMed:12011366, PubMed:19762471). Catalyzes the N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PC) (PubMed:12011366, PubMed:19762471).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325) - Identification of Two Novel Wheat Drought Tolerance-Related Proteins by Comparative Proteomic Analysis Combined with Virus-Induced Gene Silencing
Wang, International journal of molecular sciences 2018 - “...M8BCR3, M8BTH4, and T1N5G8), and 3 common responsive proteins in both varieties (W5H6J0, V9QGR5, and Q8VYX1) for analysis of their RNA levels. TaActin and TaGAPDH were used as reference genes to normalize the expression level of target genes, respectively. Results showed that the expression levels of...”
FPSE_08317 hypothetical protein from Fusarium pseudograminearum CS3096
33% identity, 26% coverage
- Transcriptomic Profiling of Fusarium pseudograminearum in Response to Carbendazim, Pyraclostrobin, Tebuconazole, and Phenamacril
Zhang, Journal of fungi (Basel, Switzerland) 2023 - “...group, the over-expression of three encoding steroid biosynthesis-related genes including FPSE_00109 (sterol 14-alpha-demethylase, CYP51 ), FPSE_08317 (sterol 24-C-methyltransferase, SMT1 ), and FPSE_01847 (sterol 22-desaturase, ERG5 ) were found. These results primarily revealed the functional similarities and dissimilarities between the four fungicides. 3.4. The Common Genes Affected...”
- “...sulfur metabolism were significantly enriched in C3. In particular, FPSE_00109 (sterol 14-alpha-demethylase, CYP51 ) and FPSE_08317 (sterol 24-C-methyltransferase, SMT1 ) were up-regulated significantly, by more than 200-fold. The genes in C5 were mainly involved in Butanoate metabolism. Of these, FPSE_01151 (3-ketoacid coenzyme A transferase, OXCT )...”
PEAMT_SPIOL / Q9M571 Phosphoethanolamine N-methyltransferase; EC 2.1.1.103 from Spinacia oleracea (Spinach) (see paper)
Q9M571 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Spinacia oleracea (see 2 papers)
28% identity, 27% coverage
- function: Catalyzes N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PubMed:10799484). Mediates a key step in the biosynthesis of choline, a precursor of the osmoprotectant glycine betaine (PubMed:10799484). Has no ethanolamine- or phosphatidylethanolamine-N-methyltransferase activity (PubMed:10799484).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
subunit: Monomer. - Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.
Foong, Scientific reports 2020 - “...stage capsule vs. leaf Early stage capsule vs. flower CL2491.Contig8_All 0.808** 6.905 (Up) 6.190 (Up) Q9M571 Phosphoethanolamine N -methyltransferase CL2491.Contig17_All 0.818** 6.217 (Up) 4.090 (Up) Q9M571 Phosphoethanolamine N -methyltransferase CL2491.Contig3_All 0.886** 5.720 (Up) 4.992 (Up) Q9M571 Phosphoethanolamine N -methyltransferase Correlation analysis was performed using Spearman correlation...”
- Molecular Origins of Functional Diversity in Benzylisoquinoline Alkaloid Methyltransferases.
Morris, Frontiers in plant science 2019 - “...putrescine NMT (NsPNMT; BAA74544); Arabidopsis thaliana phosphoethanolamine NMT (AtPEANMT; NP_188427); Spinacea oleracea phosphoethanolamine NMT (SoPEANMT; Q9M571). Coccomyxa subellipsoidea NMT (CsubNMT; XP_005645141); Chlamydomonas reinhardtii NMT (CreiNMT; XP_001695187). Intriguingly, BLAST searches of publicly available nucleotide sequence databases (NCBI NR, OneKP) reveal that transcripts encoding BIA NMT-like proteins (4070%...”
XP_008675146 phosphoethanolamine N-methyltransferase 1-like isoform X2 from Zea mays
30% identity, 22% coverage
FGSG_05740 sterol 24-C-methyltransferase from Fusarium graminearum PH-1
33% identity, 26% coverage
- FgFAD12 Regulates Vegetative Growth, Pathogenicity and Linoleic Acid Biosynthesis in Fusarium graminearum
Zhang, Journal of fungi (Basel, Switzerland) 2024 - “...addition, RNA-seq analysis displayed that the expression levels of eight genes (FGSG_06215, FGSG_04994, FGSG_02502, FGSG_02783, FGSG_05740, FGSG_01000, FGSG_04092 and FGSG_09830) related to ergosterol biosynthesis were prominently increased in the mutant strains compared with wild type. Ergosterol extraction assay revealed that the ergosterol content in the Fgfad12...”
- Functional Analysis of Genes Specifically Expressed during Aerial Hyphae Collapse as a Potential Signal for Perithecium Formation Induction in Fusarium graminearum
Choi, The plant pathology journal 2024 - “...FGSG_03638 Choline dehydrogenase 0.5 101.4 FGSG_03708 Hypothetical protein 1.1 646.5 FGSG_05589 Hypothetical protein 470.9 2.4 FGSG_05740 FgERG6B 623.7 8.0 FGSG_07741 Hypothetical protein 12.3 2,574.2 FGSG_08076 Butenolide gene cluster member 4,274.6 19.3 FGSG_08087 Hypothetical protein 0.0 207.1 FGSG_08210 Fusaristatin A gene cluster member 0.0 261.2 FGSG_08354 Hypothetical...”
- Voriconazole Treatment Induces a Conserved Sterol/Pleiotropic Drug Resistance Regulatory Network, including an Alternative Ergosterol Biosynthesis Pathway, in the Clinically Important FSSC Species, Fusarium keratoplasticum
James, Journal of fungi (Basel, Switzerland) 2022 - “...[ 36 ] caused the downregulation of cyp51A (FGSG_04092; 19-fold), erg5A (FGSG_03686; 29-fold) and erg6A (FGSG_05740; 46-fold) which are clearly the orthologs of Fk-cyp51A (81% protein identity), Fk-erg5A (80%) and Fk-erg6A (86%), respectively ( Supplementary Figure S1a,b ). Unfortunately, FGSG_03686 and FGSG_05740 were named Fg-erg5B and...”
- The Transcription Factor FgAtrR Regulates Asexual and Sexual Development, Virulence, and DON Production and Contributes to Intrinsic Resistance to Azole Fungicides in Fusarium graminearum
Zhao, Biology 2022 - “...CYP51A genes. Moreover, RNA-seq data showed that six genes involved in sterol biosynthesis; i.e., FGSG_11714, FGSG_05740, FGSG_03686 ( FgERG5B ), FGSG_04092 ( FgCYP51A ), FGSG_13888, and FGSG_06215, were all significantly reduced in the FgAtrR mutant. In addition, the expression of FGSG_02814, a homolog of SREBP1, was...”
- “...involved in the phenotype mentioned above. Protein Name Gene Locus Log2(Mutant/Wild-Type) Reference Sterol-biosynthesis-related genes FgERG6B FGSG_05740 5.52 [ 71 ] FgERG5B FGSG_03686 4.87 [ 71 ] FgCYP51A FGSG_04092 4.25 [ 72 , 73 ] Aurofusarin biosynthesis gene cluster GIP3/AurO FGSG_02321 5.00 [ 69 , 74 ]...”
- Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole
Zhao, BMC genomics 2022 - “...3-dehydrogenase (decarboxylating) [EC:1.1.1.170] 2 0 FGRAMPH1_ 01T26961 A0A1C3YLL7 ERG27; 3-keto steroid reductase [EC:1.1.1.270] 1 0 FGSG_05740 A0A0E0SMA3 SMT1A, ERG6A; sterol 24-C-methyltransferase [EC:2.1.1.41] 1 0 FGSG_02783 I1RGC4 SMT1B, ERG6B; sterol 24-C-methyltransferase [EC:2.1.1.41] 1 1 down FGSG_07315 I1RT23 ERG2; C-8 sterol isomerase [EC:5.-.-.-] 2 0 a Number of...”
- Functional Characterization of Calcineurin-Responsive Transcription Factors Fg01341 and Fg01350 in Fusarium graminearum
Zhang, Frontiers in microbiology 2020 - “...3.72 C2H2-type zinc finger FGSG_01350 Fg01350 ND 6.73 C2H2-type zinc finger Response to tebuconazole treatment FGSG_05740 Erg6 1.80 1.94 Sterol 24-C-methyltransferase FGSG_02783 Erg6 1.08 3.55 Sterol 24-C-methyltransferase FGSG_04092 Cyp51 2.74 8.18 Cytochrome P450 51 FGSG_01000 Erg11 1.17 4.43 Cytochrome P450 51 FGSG_09266 Erg13 1.45 5.11 Hydroxymethylglutaryl-CoA...”
- A phosphorylated transcription factor regulates sterol biosynthesis in Fusarium graminearum
Liu, Nature communications 2019 - “...addition, we conducted ChIP-qPCR assays with three selected genes, FgCTK1 ( FGSG_13888 ), FgERG6A ( FGSG_05740 ), and FgERG6B ( FGSG_02783 ), to verify ChIP-Seq data (Supplementary Fig. 8c ). Consistently, qRT-PCR assays showed that the expression levels of these genes were significantly down-regulated in FgSR...”
- Involvement of FgERG4 in ergosterol biosynthesis, vegetative differentiation and virulence in Fusarium graminearum
Liu, Molecular plant pathology 2013 (secret)
staMA / Q83WG2 3'-O-demethyl-4'-N-demethyl-staurosporine methyltransferase from Streptomyces sp. TP-A0274 (see paper)
28% identity, 50% coverage
PEAM1_MAIZE / A0A1D6NER6 Phosphoethanolamine N-methyltransferase 1; ZmPEAMT1; EC 2.1.1.103 from Zea mays (Maize) (see paper)
30% identity, 22% coverage
- function: Involved in phosphocholine biosynthesis (By similarity). Catalyzes the N-methylation of phosphoethanolamine, phosphomonomethylethanolamine and phosphodimethylethanolamine, the three methylation steps required to convert phosphoethanolamine to phosphocholine (PC) (By similarity). May be involved in root development (Probable).
catalytic activity: phosphoethanolamine + S-adenosyl-L-methionine = N- methylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:20365)
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
4ineA / Q22993 Crystal structure of n-methyl transferase (pmt-2) from caenorhabditis elegant complexed with s-adenosyl homocysteine and phosphoethanolamine
33% identity, 24% coverage
- Ligands: s-adenosyl-l-homocysteine; phosphoric acid mono-(2-amino-ethyl) ester (4ineA)
LHK_01324 Cfa from Laribacter hongkongensis HLHK9
29% identity, 43% coverage
- General metabolism of Laribacter hongkongensis: a genome-wide analysis
Curreem, Cell & bioscience 2011 - “...- - + - In addition, the presence of two homologues of cyclopropane fatty-acyl-phospholipid synthases (LHK_01324 and LHK_03103) (CFA synthase) suggested the possibility for L. hongkongensis to synthesize cyclopropane fatty acid. Cyclopropane fatty acids are found in the bacterial membrane and are believed to be involved...”
SA2383 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SA0767 hypothetical protein within Tn554 from Staphylococcus aureus subsp. aureus N315
SA1950 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAR1734 transposon Tn554 hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
SERP2512 hypothetical protein from Staphylococcus epidermidis RP62A
33% identity, 53% coverage
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...hypothetical protein sa_c5492s4755_a_at * 2.1 2.5 30 SA2373 hypothetical protein sa_c9334s8169_a_at * 5.1 2.5 2.5 SA2383 hypothetical protein sa_c5606s4859_a_at * 2.8 2.5 30 SA2402 hypothetical protein sa_c6038s5239_a_at * 3.6 2.5 2.5 SA2528 hypothetical protein sa_c6102s5291_a_at 5.1 2.5 2.5 SA2548 hypothetical protein sa_c6151s5333_a_at * 3.5 2.5 ND...”
- “...hypothetical protein sa_c5492s4755_a_at * 3.9 2.5 ND SA2373 hypothetical protein sa_c9334s8169_a_at * 5.1 2.5 2.5 SA2383 hypothetical protein sa_c5606s4859_a_at * 2.1 2.5 ND SA2402 hypothetical protein sa_c5620s4877_a_at 3.2 2.5 2.5 SA2407 putative lipoprotein sa_c5624s4878_a_at 5.7 2.5 2.5 SA2408 putative lipoprotein sa_c5727s4967_a_at 6.0 2.5 ND SA2438 hypothetical...”
- Direct targets of CodY in Staphylococcus aureus
Majerczyk, Journal of bacteriology 2010 - “...SA07607, saeRS Regulatory protein, putative Regulators SA2585 SA0767 SA0765 Virulence factors SA2026 SA2022 SA0136 SA0138 SA0139 SA0141 SA0142 SA0148 SA0149...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...SA0721 hypothetical protein sa_c8928s7841_a_at * 4.5 2.5 2.5 SA0755 hypothetical protein sa_c8934s7849_a_at 7.5 2.5 2.5 SA0767 hypothetical protein sa_c8196s7173_a_at 12.2 2.5 stable SA0768 hypothetical protein sa_c8228s7205_a_at * 3.6 2.5 30 SA0777 hypothetical protein sa_c8262s7237_a_at * 2.1 2.5 30 SA0790 membrane domain protein sa_c8296s7275_a_at * 5.9 2.5...”
- Sulfide Homeostasis and Nitroxyl Intersect via Formation of Reactive Sulfur Species in Staphylococcus aureus
Peng, mSphere 2017 - “...5.0 Putative thiosulfate (TS) importer + NWMN_2049 SA1949 czrA 15.9 Zinc-specific repressor (ArsR family) NWMN_2050 SA1950 czrB 14.0 Zinc cation diffusion facilitator (CDF) transporter NWMN_2075 SA1976 11.8 Hypothetical NWMN_2186 SA2080 ydbM 9.3 Putative CiaA; acyl (butyryl)-CoA dehydrogenase + NWMN_2199 SA2093 2.1 e 4.2 Secretory antigen precursor...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...ABC transporter sa_c3655s3137_a_at 3.3 5 ND SA1916 amino acid ABC transporter, sa_c3759s3231_a_at 3.3 2.5 2.5 SA1950 putative cobyric acid synthase sa_c3810s3279_a_at 2.9 2.5 ND SA1963 high affinity proline permease sa_c4189s3541_a_at 4.9 2.5 2.5 SA2038 O-sialoglycoprotein endopeptidase sa_c4197s3549_at 7.3 2.5 2.5 SA2039 putative ribosomal-protein-alanine acetyltransferase sa_c9831s8573_a_at 4.2...”
- An approach to identifying drug resistance associated mutations in bacterial strains
Wozniak, BMC genomics 2012 - “...0.47 0.44 17.19 2.98e-05 conserved hypothetical protein SAR0054(tnpA1) 0.75 0.39 72.00 8.12e-05 transposase for transposon SAR1734 0.75 0.39 72.00 8.12e-05 methylase SAR1736(spc2) 0.75 0.39 72.00 8.12e-05 spectinomycin 9-o-adenylyltransferase SaurJH9_1711(radC) 0.72 0.38 62.00 8.83e-05 predicted protein SAUSA300_pUSA030006 0.20 0.35 4.75 1.65e-04 replication and maintenance protein SAR1737(tnpC2) 0.72...”
- Novel staphylococcal cassette chromosome mec type, tentatively designated type VIII, harboring class A mec and type 4 ccr gene complexes in a Canadian epidemic strain of methicillin-resistant Staphylococcus aureus
Zhang, Antimicrobial agents and chemotherapy 2009 - “...(RP62A) SERP2515 (RP62A) SERP2514 (RP62A) SERP2513 (RP62A) SERP2512 (RP62A) SERP2511 (RP62A) SERP2510 (RP62A) SERP2509 (RP62A) SERP2508 (RP62A) SERP2507 (RP62A)...”
SA0047 hypothetical protein in transposon Tn554 from Staphylococcus aureus subsp. aureus N315
33% identity, 53% coverage
SCO1731 hypothetical protein from Streptomyces coelicolor A3(2)
34% identity, 42% coverage
- The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145
Pisciotta, Scientific reports 2023 - “...Indeed, by decreasing the cytosine methylation level using a hypomethylation agent or by deleting the SCO1731 gene coding for a methyltransferase, a series of striking effects were noted, such as delay in spore germination, mycelium differentiation, and sporulation, alongside the delayed undecylprodigiosin production and impairment of...”
- “...2012 36 1 206 231 10.1111/j.1574-6976.2011.00317.x 22092088 30. Pisciotta A Manteca A Alduina R The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2) Sci. Rep. 2018 8 13686 10.1038/s41598-018-32027-8 30209340 31. Puglia AM Vohradsky J Thompson CJ Developmental control of the heat-shock...”
- Improved Production of ε-Poly-L-Lysine in Streptomyces albulus Using Genome Shuffling and Its High-Yield Mechanism Analysis
Liu, Frontiers in microbiology 2022 - “...role in peptide chain extension in protein synthesis. Pisciotta et al. (2018) also found that SCO1731 methyltransferase can regulate the production of actinomycin and morphological differentiation in Streptomyces coeruleus A3(2). Whether it plays the same role in SG-86 needs to be further verified. SNP Mutation Analysis...”
- “...proteins . eLS. doi: 10.1002/9780470015902.a0003743.pub2 Pisciotta A. Manteca A. Alduina R. ( 2018 ). The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2) . Sci. Rep. 8 : 13686 . doi: 10.1038/s41598-018-32027-8 , PMID: 30209340 Ren X. Xu Y. Zeng X. Chen...”
- The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2)
Pisciotta, Scientific reports 2018 - “...Sci Rep Scientific Reports 2045-2322 Nature Publishing Group UK London 6135851 32027 10.1038/s41598-018-32027-8 Article The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2) Pisciotta Annalisa 1 Manteca Angel 2 http://orcid.org/0000-0003-1054-6915 Alduina Rosa valeria.alduina@unipa.it 1 1 0000 0004 1762 5517 grid.10776.37 Department of...”
- “...searched for putative DNA methyltransferase genes in the genome and constructed a mutant of the SCO1731 gene. The analysis of the SCO1731 ::Tn5062 mutant strain demonstrated that inactivation of SCO1731 leads to a strong decrease of cytosine methylation and almost to the same phenotype obtained after...”
LOC106440921 cycloartenol-C-24-methyltransferase from Brassica napus
35% identity, 29% coverage
- Melatonin-Induced Transcriptome Variation of Rapeseed Seedlings under Salt Stress
Tan, International journal of molecular sciences 2019 - “...which would positively increase the product. Expression of the sterol methyl-transferase ( SMT ) gene (LOC106440921), encoding an S-adenosylmethionine-dependent C-24 SMT that catalyzes a single methyl addition during cycloartenol formation, was downregulated, which may affect the products of the following steps. However, this enzyme of the...”
PMT2_CAEEL / Q22993 Phosphoethanolamine N-methyltransferase 2; PMT-2; S-adenosyl-L-methionine:phosphomethylethanolamine N-methyltransferase; EC 2.1.1.103 from Caenorhabditis elegans (see paper)
NP_504248 Phosphoethanolamine N-methyltransferase 2 from Caenorhabditis elegans
33% identity, 23% coverage
- function: Catalyzes the last two methylation reactions in the synthesis of phosphocholine, by converting phospho-monomethylethanolamine (N- methylethanolamine phosphate) into phospho-dimethylethanolamine (N,N- dimethylethanolamine phosphate) and the latter into phosphocholine. Phosphocholine is a precursor for phosphatidylcholine, a major component in membranes and a precursor itself in the production of glycoconjugates secreted by parasitic nematodes to avoid host immune responses.
catalytic activity: N-methylethanolamine phosphate + S-adenosyl-L-methionine = N,N-dimethylethanolamine phosphate + S-adenosyl-L-homocysteine + H(+) (RHEA:25321)
catalytic activity: N,N-dimethylethanolamine phosphate + S-adenosyl-L-methionine = phosphocholine + S-adenosyl-L-homocysteine + H(+) (RHEA:25325)
disruption phenotype: Essential in multiple developmental steps, its disruption causes developmentally impaired worms. - Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways
Déchamps, Journal of lipid research 2010 - “...NCBI-REFSEQ), of C. elegans (CePMT1: NP_871998, CePMT2: NP_504248) and P. falciparum (MAL13P1.214, PlasmoDB) have been previously characterized (11, 18-20) but...”
- Defining the role of phosphomethylethanolamine N-methyltransferase from Caenorhabditis elegans in phosphocholine biosynthesis by biochemical and kinetic analysis.
Palavalli, Biochemistry 2006 (PubMed)- GeneRIF: Cloning and biochemical characterization of pmt-2 from C. elegans; PMT-2 is essential for worm viability.
B7FTQ8 Magnesium-protoporphyrin IX methyltransferase from Phaeodactylum tricornutum (strain CCAP 1055/1)
27% identity, 63% coverage
WP_172554314 class I SAM-dependent methyltransferase from Bacillus thuringiensis serovar andalousiensis
26% identity, 38% coverage
PPA1943 ubiquinone/menaquinone biosynthesis methyltransferase from Propionibacterium acnes KPA171202
30% identity, 67% coverage
OJ1119_B04.1 / Q6ZIX2 24-methylenesterol C-methyltransferase (EC 2.1.1.143) from Oryza sativa subsp. japonica (see 2 papers)
37% identity, 29% coverage
VC1114 biotin synthesis protein BioC from Vibrio cholerae O1 biovar eltor str. N16961
38% identity, 34% coverage
A7XZC6 phosphoethanolamine N-methyltransferase from Zea mays
GRMZM2G170400, LOC100383478 uncharacterized protein LOC100383478 from Zea mays
30% identity, 22% coverage
- Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection
Yue, BMC plant biology 2018 - “...over 1.5-fold by RBSDV infection compared with the control. Five proteins, including a phosphoethanolamine N-methyltransferase (A7XZC6), a manganese transport protein-like protein (A0A096QZB3), a probable 5-adenylylsulfate reductase 1 (A0A096RBY4), a putative glucose-6-phosphate/phosphate-translocator (A0A0B4J2Y0), and O-methyltransferase ZRP4 (K7UX80), were down-regulated over 1.5-fold by RBSDV infection compared with the...”
- “...were significantly down-regulated by RBSDV infection. In the glycerophospholipid metabolism pathway, two proteins (B4FKD4 and A7XZC6) were significantly reduced by RBSDV infection. In the Glyoxylate and dicarboxylate metabolism pathway, two proteins (B7ZYT6 and K7U1Y7) were significantly reduced by RBSDV infection. In the biosynthesis of amino acids...”
- Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection
Yue, BMC plant biology 2018 - “...synthethase 53.78 0.793914246 0.017550865 Glycerophospholipid metabolism B4FKD4 LOC100283662 Acyl-protein thioesterase 2 26.847 0.777615216 0.036845308 A7XZC6 LOC100383478 Phosphoethanolamine N-methyltransferase 56.774 0.640561507 0.019112186 Glyoxylate and dicarboxylate metabolism B7ZYT6 LOC100279574 Ribulose bisphosphate carboxylase small chain 17.859 0.803660566 0.00348751 K7U1Y7 Zm.133422 Glyoxylate/hydroxypyuvate reductase HPR3 35.576 0.78506559 0.035887012 Biosynthesis of amino...”
- Comparative transcriptome analysis reveals that tricarboxylic acid cycle-related genes are associated with maize CMS-C fertility restoration
Liu, BMC plant biology 2018 - “...these genes have various functions in pollen development (Fig. 4b ). Importantly, four of them, GRMZM2G170400 (phosphoethanolamine N-methyltransferase 3), GRMZM2G060886 (S-adenosyl-L-methionine-dependent methyltransferase), GRMZM2G122296 (phosphoethanolamine N-methyltransferase 1-like), and GRMZM2G113506 (galacturonosyltransferase), are associated with all of the GO terms related to pollen development, implying their crucial effect on...”
ZMO1033 Cyclopropane-fatty-acyl-phospholipid synthase from Zymomonas mobilis subsp. mobilis ZM4
32% identity, 26% coverage
A0A2U7MCR4 cycloartenol 24-C-methyltransferase (EC 2.1.1.142) from Tripterygium wilfordii (see paper)
35% identity, 29% coverage
CC2141 transcriptional regulator, ArsR family from Caulobacter crescentus CB15
28% identity, 48% coverage
Q9KX74 Methyltransferase type 12 from Staphylococcus aureus
33% identity, 53% coverage
- Clonal Complexes Distribution of Staphylococcus aureus Isolates from Clinical Samples from the Caribbean Islands
Monecke, Antibiotics (Basel, Switzerland) 2023 - “...erm (A) 30,128 to 30,187 30,127 to 30,186 rev. compl. 53,277 to 53,336 forward - Q9KX74 putative methyltransferase 30,579 to 31,241 30,578 to 31,240 forward 52,223 to 52,885 rev. compl. - Q4W1I0 putative DNA binding regulator 31,789 to 32,661 31,788 to 32,660 forward 50,803 to 51,675...”
F8WRI3 Gamma-tocopherol methyltransferase from Glycine max
32% identity, 34% coverage
SahR / VIMSS2776407 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Reinekea sp. MED297
25% identity, 48% coverage
NP_001240883 gamma-tocopherol methyltransferase from Glycine max
32% identity, 34% coverage
A9762_13065 class I SAM-dependent methyltransferase from Pandoraea sp. ISTKB
29% identity, 45% coverage
RD2015_RS05005 magnesium protoporphyrin IX methyltransferase from Roseateles depolymerans
30% identity, 61% coverage
Smlt2368 putative cyclopropane-fatty-acyl-phospholipid synthase from Stenotrophomonas maltophilia K279a
26% identity, 65% coverage
PSCT_04351 methyltransferase domain-containing protein from Pseudomonas sp. SCT
33% identity, 31% coverage
LOC114365517 juvenile hormone acid O-methyltransferase from Ostrinia furnacalis
26% identity, 44% coverage
B6T8R8 phosphoethanolamine N-methyltransferase from Zea mays
31% identity, 22% coverage
MSMEG_0098 methyltransferase from Mycobacterium smegmatis str. MC2 155
35% identity, 42% coverage
vte1 / P74388 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase (EC 2.1.1.295) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 2 papers)
BQMT_SYNY3 / P74388 2-methyl-6-phytyl-1,4-hydroquinone methyltransferase; 2-methyl-6-phytylbenzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase; MPBQ/MSBQ methyltransferase; EC 2.1.1.295 from Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) (see paper)
sll0418 sterol-C-methyltransferase from Synechocystis sp. PCC 6803
37% identity, 33% coverage
- function: Involved in a key methylation step in both tocopherol (vitamin E) and plastoquinone synthesis. Catalyzes the conversion of 2- methyl-6-phytyl-1,4-hydroquinol (MPBQ) to 2,3-dimethyl-6-phytyl-1,4- hydroquinol (DMPQ, a substrate for tocopherol cyclase), and 2-methyl-6- solanyl-1,4-benzoquinol (MSBQ) to plastoquinol.
catalytic activity: 2-methyl-6-phytyl-1,4-benzene-1,4-diol + S-adenosyl-L- methionine = 2,3-dimethyl-6-phytylbenzene-1,4-diol + S-adenosyl-L- homocysteine + H(+) (RHEA:37979)
catalytic activity: 2-methyl-6-(all-trans-nonaprenyl)benzene-1,4-diol + S- adenosyl-L-methionine = plastoquinol-9 + S-adenosyl-L-homocysteine + H(+) (RHEA:37999)
catalytic activity: 6-geranylgeranyl-2-methylbenzene-1,4-diol + S-adenosyl-L- methionine = 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol + S- adenosyl-L-homocysteine + H(+) (RHEA:38007) - A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism
Elling, 2024 - Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium
Liberton, Molecular & cellular proteomics : MCP 2016 - “...oxide reductase (NorB), and two proteins (DesD and Sll0418) from fatty acid metabolism were identified as integral TM proteins, whereas just one protein,...”
- Chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium Synechocystis sp. PCC6803
Pfaff, The Journal of biological chemistry 2014 - “...methylation reactions give likely rise to PQ. Sll0418 (5) and some unknown methyltransferases may be involved in the methylation of 2-solanesyl-1,4-benzoquinol...”
- Replacement of alpha-tocopherol by beta-tocopherol enhances resistance to photooxidative stress in a xanthophyll-deficient strain of Chlamydomonas reinhardtii
Sirikhachornkit, Eukaryotic cell 2009 - “...strain PCC 6803, a mutant of MPBQ methyltransferase (sll0418) showed no effect on the plastoquinone level (4), but both the tocopherol content and composition...”
- “...by agarose gel electrophoresis. A marker for the sll0418 gene product homolog was scored by PCR using a forward primer, 5-GAGCCAACGCGATGGGTGCTAGATG-3, and a...”
- Alpha-tocopherol is essential for acquired chill-light tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803
Yang, Journal of bacteriology 2008 - “...(ii) catalyzed by MPBQ methyltransferase encoded by sll0418, MPBQ is transformed into 2,3-dimethyl-6-phytylbenzoquinone (DMPBQ) after methylation (1, 4, 34),...”
- Influences on tocopherol biosynthesis in the cyanobacterium Synechocystis sp. PCC 6803
Backasch, Journal of plant physiology 2005 (PubMed)- “...is diminutive. The methyltransferase encoded by the gene sll0418 is not essential either for tocopherol or plastoquinone synthesis. 0 false false Antioxidant...”
- “...Tocopherol and carbon dioxide The role of methyltransferase SLL0418 Acknowledgement References ALFONSO 2000 505 515 M ANDERSON 1991 2761 2767 S ARANGO 1998 531...”
- Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes
Cheng, The Plant cell 2003 (PubMed)- “...equivalent of the previously characterized MPBQ/MSBQ MT (Sll0418) from Synechocystis sp PCC6803, although the two proteins are highly divergent in primary...”
- “...been identified previously as open reading frame (ORF) sll0418 (Shintani et al., 2002). Sll0418 orthologs were identified using tBLASTn (Basic Local Alignment...”
- The role of 2-methyl-6-phytylbenzoquinone methyltransferase in determining tocopherol composition in Synechocystis sp. PCC6803
Shintani, FEBS letters 2002 (PubMed)- “...AbstractA putative 2-methyl-6-phytylbenzoquinone (MPBQ) methyltransferase gene, SLL0418, was identified from the Synechocystis PCC6803 genome based on its...”
- “...biochemical evidence confirmed open reading frame (ORF) SLL0418 encodes a MPBQ methyltransferase. An SLL0418 partial knockout mutant accumulated -tocopherol...”
Geob_0241 class I SAM-dependent methyltransferase from Geotalea daltonii FRC-32
Geob_0241 Methyltransferase type 11 from Geobacter sp. FRC-32
34% identity, 38% coverage
YP_001177854 Methyltransferase type 11 from Enterobacter sp. 638
34% identity, 43% coverage
- Plant-bacteria association and symbiosis: are there common genomic traits in alphaproteobacteria?
Pini, Genes 2011 - “...2898 Unknown YP_002236173 2908 Electron transfer flavoprotein, alpha subunit YP_001796224 2912 Methyltransferase YP_935409 YP_001176000 YP_002237443 YP_001177854 YP_002239590 2927 Aminoacid aldolase or racemase YP_002007445 2981 Mg 2+ and Co 2+ transporters YP_002006900 YP_001176870 YP_002238775 YP_002238859 3082 Ferredoxin-like protein YP_001796222 3137 Unknown YP_002236905 3. Experimental Section 3.1. Phylogenetic...”
RPA3082 cyclopropane-fatty-acyl-phospholipid synthase from Rhodopseudomonas palustris CGA009
35% identity, 26% coverage
C9MT2_GIBZE / I1RNL0 Sphingolipid C9-methyltransferase 2; C-9-MT2; EC 2.1.1.317 from Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (Wheat head blight fungus) (Fusarium graminearum) (see paper)
33% identity, 25% coverage
- function: Catalyzes methylation of the sphingoid base component of glucosylceramides (GluCers) at the C9-position. Sphingolipid C9- methylation requires 4,8-desaturated ceramides as substrates. Glucosylceramides play important roles in growth, differentiation and pathogenicity. The methyl group at the C9-position distinguishes fungal glucosylceramides from those of plants and animals and may thus play a role in host-pathogen interactions enabling the host to recognize the fungal attack and initiate specific defense responses. However, C-9 methylation of GlcCers is not essential for the sensitivity of F.graminearum to plant defensins MsDef1 and RsAFP2.
catalytic activity: a (4E,8E)-4-sphinga-4,8-dienine ceramide + S-adenosyl-L- methionine = a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide + S- adenosyl-L-homocysteine + H(+) (RHEA:46804)
disruption phenotype: Produces 65 to 75% nonmethylated and 25 to 35% methylated GlcCers. Exhibits severe growth defects and produces abnormal conidia. Also exhibits drastically reduced disease symptoms in wheat and much-delayed disease symptoms in Arabidopsis thaliana. A double-knockout with its paralog MT1 is not viable.
BnaA.VTE4.a1 / ACD03285.1 gamma-tocopherol methyltransferase from Brassica napus (see paper)
32% identity, 31% coverage
Alvin_2638 magnesium protoporphyrin O-methyltransferase from Allochromatium vinosum DSM 180
28% identity, 66% 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 - “...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 ( circles ) (Weissgerber et al. 2014 ) and...”
- “...because methyl transfer to magnesium protoporphyrin IX yielding Mg protoporphyrin IX 13-methylester (catalyzed by BchM, Alvin_2638) is the first step specific for bacteriochlorophyll synthesis (Sganga et al. 1992 ). AdoMet is transformed into S -adenosylhomocysteine (AdoHomoCys) in the course of this reaction. AdoHomoCys non-competitively inhibits methyl...”
HMPREF3211_00337 class I SAM-dependent methyltransferase from Staphylococcus aureus
32% identity, 58% coverage
- Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Tsuchiya, The Biochemical journal 2018 - “...36.29 INDC*IVEAAR 113.37 glpK Glycerol kinase 55.625 ATLESLC*YQTR 158.91 glpK Glycerol kinase 55.625 QTQSIC*SELKQQGYEQTFR 125.84 HMPREF3211_00337 Methyltransferase domain protein 21.763 ALDIGC*GSGLLVEK 55.031 tarJ Ribulose-5-phosphate reductase 1 38.451 IPEGLTFDHAFEC*VGGR 60.968 MW2550 MW2550 protein 29.096 LLIMC*GK 113.41 gpmI 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase 56.423 AIEAVDEC*LGEVVDK 144.75 SAR1875 Putative membrane protein...”
Rru_A2553 Methylase involved in ubiquinone/menaquinone biosynthesis-like from Rhodospirillum rubrum ATCC 11170
33% identity, 44% coverage
- Investigation of candidate genes involved in the rhodoquinone biosynthetic pathway in Rhodospirillum rubrum
Campbell, PloS one 2019 - “...-57.8 179MD methyltransferase Rru_A1274 24.3 -67.6 176BB Radical SAM family protein Rru_A2871 15.2 -18.3 Peptidase/amidohydrolase Rru_A2553 13.5 -5.1 Ubiquinone/menaquinone biosynthesis methyltransferase Rru_A2106 7.7 -68.4 16QF5 Hypothetical protein Rru_A3606 7.1 -31.8 16RW4 Hypothetical protein Rru_A1729 6.9 -35.2 16YKK Hypothetical protein Rru_A3004 4.5 -73.4 16Q21 Class I and...”
- “...with transferase activities, or perhaps proteins with no known function. We chose to delete the Rru_A2553 gene since it was annotated in the NCBI genome database as a ubiquinone/menaquinone methyltransferase. We predicted that if Q levels were reduced in this mutant, a similar effect would be...”
SMTA_EMENI / A0A1U8QYZ5 Sphingolipid C9-methyltransferase A; EC 2.1.1.317 from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
37% identity, 20% coverage
- function: Catalyzes methylation of the sphingoid base component of glucosylceramides (GluCers) at the C9-position (PubMed:27479571). Sphingolipid C9-methylation requires 4,8-desaturated ceramides as substrates (By similarity). Glucosylceramides play important roles in growth, differentiation and pathogenicity (PubMed:27479571). The methyl group at the C9-position distinguishes fungal glucosylceramides from those of plants and animals and may thus play a role in host-pathogen interactions enabling the host to recognize the fungal attack and initiate specific defense responses (By similarity).
catalytic activity: a (4E,8E)-4-sphinga-4,8-dienine ceramide + S-adenosyl-L- methionine = a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide + S- adenosyl-L-homocysteine + H(+) (RHEA:46804)
disruption phenotype: Leads to increased resistance to cell-wall- damaging agents, such as calcofluor white (CFW) and Congo red (CR) (PubMed:27479571). Accumulates unmethylated glucosylceramides (PubMed:27479571).
SahR / VIMSS7056499 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Teredinibacter turnerae T7901
24% identity, 46% coverage
CHLM / A8JGJ6 Mg-protoporphyrin IX methyltransferase (EC 2.1.1.11) from Chlamydomonas reinhardtii (see paper)
XP_001702380 uncharacterized protein from Chlamydomonas reinhardtii
33% identity, 28% coverage
- CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii
Shin, Scientific reports 2016 - “...gene (GenBank accession: XM_001702328) encodes chloroplast SRP43 (XP_001703704) and Mg-protoporphyrin IX S-adenosyl methionine O-methyl transferase (XP_001702380), respectively. For the latter two genes, we co-transformed cells with a hygromycin-resistance vector and used antibiotic selection to improve the delivery efficiency in Chlamydomonas . The sgRNAs were designed by...”
bll6500 bll6500 from Bradyrhizobium japonicum USDA 110
31% identity, 45% coverage
- Identification of Genes Regulated by the Antitermination Factor NasT during Denitrification in Bradyrhizobium diazoefficiens
Sánchez, Microbes and environments 2019 - “...two putative systems for LIV transport (blr2922-2926 and bll3383-3386); genes putatively involved in LIV synthesis: bll6500, bll6502 (threonine dehydratase ilvA ), and mvrA (ferredoxin NADP + reductase that may provide low-potential electrons for amino acid synthesis); and rocD encoding ornithine aminotransferase for arginine catabolism ( 7...”
- “...) +5.04 bll3377 Oxidoreductase; putative aerobic carbon monoxide dehydrogenase medium subunit ( coxM ) +4.74 bll6500 Putative SAM (S-adenosyl-L-methionine)-dependent methyltransferase +2.26 bll6502 Putative threonine dehydratase ( ilvA ) +2.03 blr3831 mvrA ; ferredoxin NADP + reductase +4.24 bll2855 rocD ; ornithine aminotransferase +2.18 bll3993 Conserved hypothetical...”
Q725Q5 Conserved domain protein from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)
DVU3369 conserved domain protein from Desulfovibrio vulgaris Hildenborough
35% identity, 43% coverage
- Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.
Waller, Journal of proteome research 2008 - “...1 38154 P02750 4 0.09 DJ-1 protein 19878 Q99497 2 0.08 Hypothetical protein LOC79441 69606 Q725Q5 7 0.08 Complement component 1, r subcomponent 80147 Q53HT9 8 0.08 Hypothetical protein LOC160518 140512 Q6NUJ0 14 0.08 PREDICTED: similar to Prostate, ovary, testis alpha-N- acetylglucosaminidase 121366 P54802 12 0.08...”
- Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome
Chhabra, Applied and environmental microbiology 2011 - “...patB [4]), and a protein with predicted methyltransferase activity (DVU3369, similar to metW [19]). We verified all gene deletion mutations by PCR as well as...”
- “...biosynthesis pathway knockouts (DVU1585, DVU3371, DVU0890, DVU0171, and DVU3369) did not result in methionine auxotrophy. A surprising result of this study was...”
SahR / VIMSS3528495 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Geobacter uraniumreducens Rf4
29% identity, 49% coverage
MAV_0854 methyltransferase-UbiE family protein from Mycobacterium avium 104
34% identity, 37% coverage
MAB_1977 Putative methyltransferase from Mycobacterium abscessus ATCC 19977
34% identity, 43% coverage
DR0026 methyltransferase, putative from Deinococcus radiodurans R1
33% identity, 39% coverage
SahR / VIMSS83942 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Mesorhizobium loti MAFF303099
30% identity, 46% coverage
Dshi_3538 magnesium protoporphyrin O-methyltransferase from Dinoroseobacter shibae DFL 12
29% identity, 71% coverage
P67055 Demethylmenaquinone methyltransferase from Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
lmo1931 similar to 2-heptaprenyl-1,4-naphthoquinone methyltransferase from Listeria monocytogenes EGD-e
LMRG_01078 2-heptaprenyl-1,4-naphthoquinone methyltransferase from Listeria monocytogenes 10403S
35% identity, 47% coverage
- Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
Melian, Frontiers in microbiology 2021 - “...Q8Y5Q4 Ferrichrome-binding protein lmo1959 Q8Y5U6 Heavy metal-transporting ATPase lmo1853 Q8Y647 Vitamin metabolism Demethylmenaquinone methyltransferase lmo1931/ubiE P67055 Dihydropteroate synthase lmo0224/sul Q8YAC2 1,4-dihydroxy-2-naphthoate octaprenyltransferase mo1677/menA Q8Y6K7 Precorrin-3 methylase lmo1197/cbiF Q8Y7S4 Uncharacterized Hypothetical protein lmo2209 Q8Y567 Hypothetical protein lmo2486 Q8Y4F8 Hypothetical protein lmo1466 Q8Y746 Hypothetical protein lmo2843 Q8Y3J2 Hypothetical...”
- Listeria monocytogenes {sigma}B has a small core regulon and a conserved role in virulence but makes differential contributions to stress tolerance across a diverse collection of strains
Oliver, Applied and environmental microbiology 2010 - “...lmo1713 lmo1749 lmo1790 lmo1806 lmo1883 lmo1929 lmo1930 lmo1931 lmo1932 lmo1933 lmo2031 lmo2033 lmo2159 lmo2160 lmo2161 lmo2162 lmo2169 lmo2196 lmo2230 lmo2231...”
- Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall, and stress response
Severino, Applied and environmental microbiology 2007 - “...lmo1372 lmo1439 lmo1688 lmo1830 lmo2573 lmo0014 lmo2389 lmo2390 lmo1931 lmo1227 lmo1639 lmo1929 GO term identification no. 6084 SEVERINO ET AL. APPL. ENVIRON....”
- Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB
Liu, Frontiers in microbiology 2017 - “...LMRG_00908, LMRG_00907 A , H , B No RpoD ( A ) 10 LMRG_01076, LMRG_01077 LMRG_01078, LMRG_01079, LMRG_01080 A , B LMRG_01078, LMRG_01079, LMRG_01080 11 LMRG_01140 A , B No Alpha-acetotactate decarboxylase 12 LMRG_01284 B , A Frag 86921 to 86928 DE fragments identified in 5'UTR...”
slr1618 unknown protein from Synechocystis sp. PCC 6803
30% identity, 40% coverage
PSPPH_4654 smtA protein from Pseudomonas syringae pv. phaseolicola 1448A
29% identity, 44% coverage
GTOMC_ARATH / Q9ZSK1 Tocopherol O-methyltransferase, chloroplastic; Gamma-tocopherol methyltransferase; Vitamin E pathway gene 4 protein; AtVTE4; EC 2.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
Q9ZSK1 tocopherol C-methyltransferase (EC 2.1.1.95) from Arabidopsis thaliana (see 2 papers)
NP_176677 gamma-tocopherol methyltransferase from Arabidopsis thaliana
AT1G64970 G-TMT (GAMMA-TOCOPHEROL METHYLTRANSFERASE); tocopherol O-methyltransferase from Arabidopsis thaliana
31% identity, 31% coverage
- function: Involved in the synthesis of tocopherol (vitamin E). Methylates gamma- and delta-tocopherol to form beta- and alpha- tocopherol, respectively.
catalytic activity: gamma-tocopherol + S-adenosyl-L-methionine = (+)-alpha- tocopherol + S-adenosyl-L-homocysteine + H(+) (RHEA:24012)
catalytic activity: delta-tocotrienol + S-adenosyl-L-methionine = beta-tocotrienol + S-adenosyl-L-homocysteine + H(+) (RHEA:38091)
catalytic activity: gamma-tocotrienol + S-adenosyl-L-methionine = alpha- tocotrienol + S-adenosyl-L-homocysteine + H(+) (RHEA:38095)
catalytic activity: delta-tocopherol + S-adenosyl-L-methionine = beta-tocopherol + S-adenosyl-L-homocysteine + H(+) (RHEA:37991)
disruption phenotype: Slight reduction of fresh weight in mature plants. Leaves with high levels of gamma-tocopherol and absence of alpha-tocopherol. - Expression of γ-tocopherol methyltransferase in chloroplasts results in massive proliferation of the inner envelope membrane and decreases susceptibility to salt and metal-induced oxidative stresses by reducing reactive oxygen species.
Jin, Plant biotechnology journal 2014 - GeneRIF: The role of gamma-TMT in regulating abiotic stress within chloroplasts, was investigated.
- Accumulation of γ- rather than α-tocopherol alters ethylene signaling gene expression in the vte4 mutant of Arabidopsis thaliana.
Cela, Plant & cell physiology 2011 - GeneRIF: Jasmonic acid and ethylene signaling pathways are down-regulated in mature leaves of salt-stressed vte4 plants.
- Inactivation of genes, encoding tocopherol biosynthetic pathway enzymes, results in oxidative stress in outdoor grown Arabidopsis thaliana.
Semchuk, Plant physiology and biochemistry : PPB 2009 (PubMed)- GeneRIF: Results show that both vte1 and vte4 mutant plant lines had higher concentration of protein carbonyl groups and oxidized glutathione compared to the wild type, indicating the development of oxidative stress.
- Unusual vitamin E profile in the oil of a wild African oil palm tree (Elaeis guineensis Jacq.) enhances oxidative stability of provitamin A
Gutbrod, Frontiers in plant science 2024 - “...the putative substrate binding site Analysis of the domain structures of the Arabidopsis AtVTE4 protein (Q9ZSK1) at EMBL ( http://pfam.xfam.org/ ) revealed the presence of a conserved -tocopherol methyltransferase region (accession PLN02244) which includes the S-adenosyl-methionine (SAM)-dependent methyltransferase domain (pfam08241) at positions 131-229. For three-dimensional modeling...”
- Comparative transcriptome analysis provides novel insights into molecular response of salt-tolerant and sensitive polyembryonic mango genotypes to salinity stress at seedling stage
Perveen, Frontiers in plant science 2023 - “...sativum Cluster-5747.11416 0.756717 24.22475 -4.93559 Q42564 L-ascorbate peroxidase 3 A. thaliana Cluster-5747.8136 0.618353 20.95974 -5.01794 Q9ZSK1 Tocopherol O-methyltransferase, chloroplastic A. thaliana Cluster-5747.6755 1.102863 35.82512 -4.95662 Q9M7I9 Stress enhanced protein 1, chloroplastic A. thaliana Cluster-5747.14351 1.20265 29.15839 -4.56708 Q6PL11 SKP1-like protein 1 O. sativa subsp. japonica Cluster-5747.21026...”
- Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)
Behringer, PloS one 2015 - “...- Patatin-like protein 3 - B6TPQ5 Z . mays -8.02 VTE4 - Tocopherol O-methyltransferase - Q9ZSK1 A . thaliana -8.72 INR1 - Inducible nitrate reductase [NADH] 1 - P54233 Glycine max -9.01 - PUP3 Putative uncharacterized protein 3 - F6HZZ7 Vitis vinifera -10.32 Gene names according...”
- Unusual vitamin E profile in the oil of a wild African oil palm tree (Elaeis guineensis Jacq.) enhances oxidative stability of provitamin A
Gutbrod, Frontiers in plant science 2024 - “...and flanking intron sequences of the locus LOC105033221 which shows sequence similarity to Arabidopsis AtVTE4 (At1g64970) were amplified by PCR using the oligonucleotides Bn3839, Bn3840, Bn3841, Bn3842, Bn3843, Bn3844, Bn3845 and Bn3846 ( Supplementary Table2 ), and the PCR products were sequenced by Sanger sequencing. The...”
- “...of AtVTE4 was analyzed using pfam (pfam.xfam.org) ( Mistry etal., 2021 ). The AtVTE4 sequence (At1g64970) was used for homology-modeling of the three-dimensional structure at Swiss-Model ( https://swissmodel.expasy.org/ ) ( Waterhouse etal., 2018 ). 2.4 Expression of EgVTE4 in E. coli and tocochromanol supplementation For expression...”
- SEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E
Hornbergs, Plant physiology 2023 - “...At2g28160; FRO2, At1g01580; IRT1, At4g19690; bHLH039, At3g56980; VTE1, AT4G32770; VTE2, AT2G18950; VTE3, AT3G63410; and VTE4, AT1G64970. Supplemental data The following materials are available in the online version of this article. Supplemental Figure S1 . Localization of fluorescence protein-tagged PATL2 and IRT1 proteins suggest that PATL2 and...”
- Antioxidants of Non-Enzymatic Nature: Their Function in Higher Plant Cells and the Ways of Boosting Their Biosynthesis
Rudenko, Antioxidants (Basel, Switzerland) 2023 - “...tocopherol cyclase Plastochromanol-8 synthesis from PQH 2 ; -tocopherol biosynthesis from -tocopherol [ 37 ] At1g64970 VTE4, G-TMT, -tocopherol methyltransferase Conversion of - and -tocopherols (and tocotrienols) to - and -tocopherols [ 37 ] antioxidants-12-02014-t002_Table 2 Table 2 Engineering plants through CRISPR/Cas9 editing of the genes...”
- Chloroplast-localized PITP7 is essential for plant growth and photosynthetic function in Arabidopsis
Kim, Physiologia plantarum 2022 - “...PITP7 (At5g63060), PSY (At5g17230), SPS1 (At1g78510), SPS2 (At1g17050), VTE1 (At4g32770), VTE2 (At2g18950), VTE3 (At3g63410), VTE4 (At1g64970), ZDS (At3g04870), DVR (At5g18660), HCAR (At1g04620), HEMA1 (At1g58290), HEMA2 (At1g09940), NOL (At5g04900), NYC1 (At4g13250), PorA (At5g54190), and PorB (At4g27440). Supporting information Figure S1. Molecular phylogenetic analysis of Sec14like proteins in...”
- COMPILE: a GWAS computational pipeline for gene discovery in complex genomes
Hill, BMC plant biology 2022 - “...8 107 6.29E28 5 205,827,506 2.28E12*** 105 Zm00001d017746 VTE4 Os02g0701600 Tocopherol O -methyltransferase 543 0.0 At1g64970 -tocopherol methyltransferase 420 2.31E147 7 14,373,377 1.61E06** 785 Zm00001d019057 Unknown Os07g0189700 Similar to JHL07K02.7 protein 180 1.31E56 At3g23760 Glycosyl group transferase 129 2.87E37 8 132,442,986 1.54E06** 3544 Zm00001d010894 None Os01g0229300...”
- ROS-Scavengers, Osmoprotectants and Violaxanthin De-Epoxidation in Salt-Stressed Arabidopsis thaliana with Different Tocopherol Composition
Surówka, International journal of molecular sciences 2021 - “...in the Col background with an insertion in the first intron of the open-reading frame (At1g64970) of the gene encoding -tocopherol methyltransferase; devoid of -tocopherol methyltransferase (- TMT , catalyses the conversion -TCs to -TC) gene, accumulating - instead of -TC (3), and transgenic - TMT...”
- cROStalk for Life: Uncovering ROS Signaling in Plants and Animal Systems, from Gametogenesis to Early Embryonic Development
Lodde, Genes 2021 - “.../ vitamin E deficient 1 (VTE1) 0.00 175.02 0.00 At3g63410 S-adenosyl-L-methionine-dependent methyltransferase 0.00 414.27 0.00 At1g64970 Gamma-tocopherol methyltransferase 0.00 0.00 0.00 At2g18950 Homogentisate phytyltransferase 1 0.00 0.00 0.00 At3g11945 Homogentisate prenyltransferase 0.00 180.24 5.89 At1g06570 Phytoene desaturation 1 8.55 50.43 5.26...”
- Vitamin E Is Superior to Vitamin C in Delaying Seedling Senescence and Improving Resistance in Arabidopsis Deficient in Macro-Elements
Zhang, International journal of molecular sciences 2020 - “...Primer Sequences The Reverse Primer Sequences VTC1 At2g39770 GGCAACCCCGTGACTACATAAC CCAATCAAACATCCTTCCCCAA VTC2 At4g26850 GGTCGTCACTTGAAGAAGAGGC GGGAAGAACTGAACTTGGGCAT VTE4 At1g64970 AGCAGCACCCTCTTCTCTCACA CCCAAATCTCTTCCCACAAACC GGR At4g38460 ATGGTGGAGCAGAGAAGGGAAT AGGTGGTAGCGAAGATGAATGG ACS2 At1g01480 GTGTCTCCTGGCTCTTCCTTCC GCCGTCAAAAACAACCCTAATG ACO1 At2g19590 TCCTGAGCTTATGAGAGGGCTG AATGGTATTGTTCTTGGATGGC EIN3 At3g20770 ACAACAATAACAGTAGCGGCAACA AGCGATAGAGACAGAGAGACCCAG ERF1 At3g23240 GCAGTCCACGCAACAAACCTA CTTGAACTCTCTCCGCCGAAA PDF1.2 At5g44420 CTTGTTCTCTTTGCTGCTTTCG CATGATCCATGTTTGGCTCCTT COL1 At5g15850 AATGGCTTCTCGATTGGGGAT TGGAGGGTAAGGTGGTTGGTC...”
- More
BAB1_0476 SAM (and some other nucleotide) binding motif:Generic methyltransferase:Cyclopropane-fatty-acyl-phospholipid synthase from Brucella melitensis biovar Abortus 2308
WP_002963607 SAM-dependent methyltransferase from Brucella abortus 2308
31% identity, 36% coverage
- Identification and functional analysis of the cyclopropane fatty acid synthase of Brucella abortus
Palacios-Chaves, Microbiology (Reading, England) 2012 (PubMed)- “...abortus virulence by creating a mutant in ORF BAB1_0476, the putative CFA synthase gene. The mutant did not incorporate [14C]methyl groups into lipids, lacked...”
- “...and synthesized the unsaturated precursors, proving that BAB1_0476 actually encodes a CFA synthase. BAB1_0476 promoter-luxAB fusion studies showed that CFA...”
- Transcriptome analysis of the Brucella abortus BvrR/BvrS two-component regulatory system
Viadas, PloS one 2010 - “...sugar phosphate isomerase/epimerase 2.1 BAB1_0320 fadD , acyl-CoA synthetase 2.1 BAB1_1397 aspB , aminotransferase 2.0 BAB1_0476 cfa , methyltransferase 1.9 BAB1_1366 fhuD , ABC transporter 1.8 BAB1_0666 dapA , dihydrodipicolinate synthase 1.8 BAB2_0712 lpdA , dihydrolipoamide dehydrogenase 1.7 BAB1_0260 flgJ , flagellar protein 1.6 BAB2_0863 glutaminase...”
- “...BAB1_2043; fabF , oxoacyl-acyl-carrier-protein synthase, BAB1_0872; fadD , fatty-acyl-CoA synthase, BAB1_0320; cfa , cyclopropane-fatty-acyl-phospholipid synthase, BAB1_0476; BAB1_1357). These data confirm that BvrR/BvrS regulates bacterial envelope changes that could modify surface properties relevant for Brucella virulence [6] . Regulation of carbon and nitrogen metabolism One of the...”
- Identification and functional analysis of the cyclopropane fatty acid synthase of Brucella abortus.
Palacios-Chaves, Microbiology (Reading, England) 2012 (PubMed)- GeneRIF: B. abortus cfa synthase occurs during the exponential phase of growth and increases in acid or hyperosmotic media but it is not involved in virulence.
Mb0862 CONSERVED HYPOTHETICAL PROTEIN from Mycobacterium bovis AF2122/97
BCG_0891 hypothetical protein from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv0839 hypothetical protein from Mycobacterium tuberculosis H37Rv
34% identity, 37% coverage
- Circulating Mycobacterium bovis peptides and host response proteins as biomarkers for unambiguous detection of subclinical infection
Lamont, Journal of clinical microbiology 2014 - “...months p.i. Predicted function Subcellular location MB2515c MB0862 MB1482c MB2883c MB1929 MB1886c MB1192 MB2441c MB2275 MB2122c MB1672c MB1554c (pks5) MB1895c...”
- Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...dolichyl-phosphate-mannoseprotein mannosyltransferase domain 0.707 0.005819792 xerC BCG_2915c Rv2894c Probable integrase/recombinase xerC 0.7054 0.009092191 MtrA regulon BCG_0891 BCG_0891 Rv0839 Conserved hypothetical protein with class I SAM-dependent methyltransferase domain 0.7016 0.001141476 BCG_1349c BCG_1349c Rv1290c Conserved hypothetical protein 0.7016 0.005788882 celA1 BCG_0093 Rv0062 Possible cellulase celA1 (ENDOGLUCANASE) 0.7013 0.011925226...”
- Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...domain 0.707 0.005819792 xerC BCG_2915c Rv2894c Probable integrase/recombinase xerC 0.7054 0.009092191 MtrA regulon BCG_0891 BCG_0891 Rv0839 Conserved hypothetical protein with class I SAM-dependent methyltransferase domain 0.7016 0.001141476 BCG_1349c BCG_1349c Rv1290c Conserved hypothetical protein 0.7016 0.005788882 celA1 BCG_0093 Rv0062 Possible cellulase celA1 (ENDOGLUCANASE) 0.7013 0.011925226 BCG_1518c BCG_1518c...”
- Immunopeptidomics reveals determinants of Mycobacterium tuberculosis antigen presentation on MHC class I
Leddy, eLife 2023 - “...data but failed SureQuant validation. Source protein Peptide sequence Rv0383c AAPGRPVAPG pyrD GDRLALISV Rv2303c KHPNVYLEL Rv0839 YTHGYHES kgd AERAAAAAP Rv1375 EAAQSRITA GabD1 AKVGASAAY PE1 AAGNLRAAI HlfX IPYDRGDLV Rv2807 AKWILEGIK Rv3818 IAPELVRT Rv1065 YTRIHGDEEL Rv0293c DELIAGLAY Rv3779 VAIAVGPALT PPE55 TVAPINLNP Rv2263 QEIEEGIL Rv0333 GEDPGIAR Of the 16...”
- HigB1 Toxin in Mycobacterium tuberculosis Is Upregulated During Stress and Required to Establish Infection in Guinea Pigs
Sharma, Frontiers in microbiology 2021 - “...PPE51 Rv2625c Rv2625c 2.64 Up Conserved protein Rv0651 rplJ 2.47 Up 50S ribosomal protein L10 Rv0839 Rv0839 2.46 Up Hypothetical protein Rv0054 ssb 2.44 Up Single-strand DNA-binding protein Rv2959c Rv2959c 2.42 Up Methyltransferase Rv0652 rplL 2.35 Up 50S ribosomal protein L7/L12 Rv0346c ansP2 2.31 Up L...”
- The oxidation-sensing regulator (MosR) is a new redox-dependent transcription factor in Mycobacterium tuberculosis
Brugarolas, The Journal of biological chemistry 2012 - “...which showed 2-5-fold change (fadA2, rpsS, rplP, rpsQ, rv0839, rv1884c, rv2558, rv3614c, and rv3615c). None of these genes contain the consensus sequence in...”
8rdlA / A0A068QT41 Xenorhabdin methyltransferase xrdm with sah (see paper)
27% identity, 46% coverage
- Ligand: s-adenosyl-l-homocysteine (8rdlA)
FOXG_15629 sterol 24-C-methyltransferase from Fusarium oxysporum f. sp. lycopersici 4287
27% identity, 32% coverage
- Comparative Transcriptome Analysis Unravels the Response Mechanisms of Fusarium oxysporum f.sp. cubense to a Biocontrol Agent, Pseudomonas aeruginosa Gxun-2
Li, International journal of molecular sciences 2022 - “...the steroid biosynthesis pathway, of which 13 genes (FOXG_11545, FOXG_02348, FOXG_08223, FOXG_03780, FOXG_06186, FOXG_03780, FOXG_06186, FOXG_15629, FOXG_01590, FOXG_10530, FOXG_09168, FOXG_04166, and FOXG_05355) were significantly upregulated in the ergosterol pathway. FOC TR4 increases the efficiency of ergosterol synthesis by up-regulating the genes mentioned above. 2.4.4. Autophagy-Related DEGs...”
Cj1183c putative cyclopropane-fatty-acyl-phospholipid synthase from Campylobacter jejuni subsp. jejuni NCTC 11168
34% identity, 27% coverage
- The CJIE1 prophage of Campylobacter jejuni affects protein expression in growth media with and without bile salts
Clark, BMC microbiology 2014 - “...Flippase Cj1130c gi|218562744 0.270.38 0.670.42 Cytochrome c553 Cj1153 gi|157415419 0.770.25 0.530.38 Cyclopropane fatty acid biosynthesis Cj1183c gi|57238055 1.070.67 0.730.32 NLPA family lipoprotein, putative Cj1200 gi|218562812 0.470.83 1.200.56 Hemerythrin family non-heme iron protein Cj1224 gi|121612625 0.730.25 0.070.21 Quinone-reactive Ni/Fe-hydrogenase, small subunit Cj1267c gi|157415531 0.630.46 0.570.21 Endoribonuclease L-PSP,...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj1046c, cj1048c, cj1067, cj1080c, cj1081c, cj1088c, cj1096c, cj1104, cj1114c, cj1133, cj1149c, cj1150c, cj1151c, cj1152c, cj1177c, cj1183c, cj1196c, cj1198, cj1202, cj1213c, cj1238, cj1243, cj1248, cj1364c, cj1398, cj1400c, cj1401c, cj1402c, cj1404, cj1407c, cj1424c, cj1428c, cj1476c, cj1498c, cj1515c, cj1529c, cj1530, cj1605c, cj1634c, cj1641, cj1645, cj1672c, cj1685c FBA & transposon...”
- Campylobacter jejuni gene expression in the chick cecum: evidence for adaptation to a low-oxygen environment
Woodall, Infection and immunity 2005 - “...1015 0.21 0.224 9.32 109 1.01 109 Cj0297c Cj1183c Cj0095 Cj0094 Cj1228c Cj1360c 50S ribosomal protein, rpmA 50S ribosomal protein, rplU Serine protease, htrA...”
Bd1029 methyltransferase from Bdellovibrio bacteriovorus HD100
32% identity, 38% coverage
MXAN_3779 non-ribosomal peptide synthetase/polyketide synthase from Myxococcus xanthus DK 1622
27% identity, 1% coverage
- Combining culture optimization and synthetic biology to improve production and detection of secondary metabolites in <i>Myxococcus xanthus</i>: application to myxoprincomide
Sourice, Microbiology spectrum 2024 - “...the corresponding SM. ( B ) Scheme of the construction to express myxoprincomide BGC ( mxan_3779 ) with the synthetic strong promoter BBA_J23104 and the RBS BBa_B0034 inserted into the locus by a single step of homologous recombination. ( C ) The production of myxoprincomide c-506...”
- “...followed by the RBS B0034 ( 28 ), was inserted at the locus to overexpress mxan_3779 , giving the resulting BOOST_MXP strain ( Fig. 6B ). Overall, the combination of a synthetic strong promoter, the BOOST chassis, and the 2PRIM protocol led to an increased production...”
- Structural and Biosynthetic Analysis of the Fabrubactins, Unusual Siderophores from Agrobacterium fabrum Strain C58
Vinnik, ACS chemical biology 2021 - “...structure of myxoprincomide from Myxococcus xanthus DK1622 suggested to us the FMO domain associated with MXAN_3779 is likely to catalyze a Favorskii-like rearrangement 31 . FbnE is a homolog of the MXAN_3779 FMO domain (43% identical), yet it is not homologous to either EncM or AmbI,...”
- Whole transcriptome analysis and gene deletion to understand the chloramphenicol resistance mechanism and develop a screening method for homologous recombination in Myxococcus xanthus
Yang, Microbial cell factories 2019 - “...The gene expression level of Myxochromide (MXAN_4077 to MXAN_4079), myxochelin (MXAN_3647 to MXAN_3640) and myxoprincomide (MXAN_3779) gene clusters were not changed in Cm5_36h vs NDK. The transcription levels of TA clusters Dkxanthene, Myxalamid, Myxochromide, myxochelin, and myxoprincomide were not changed in Cm_8h vs NDK. MXAN_3462, located...”
- An Orphan MbtH-Like Protein Interacts with Multiple Nonribosomal Peptide Synthetases in Myxococcus xanthus DK1622
Esquilín-Lebrón, Journal of bacteriology 2018 - “...A domains or the associated modules from 193 MXAN_3779 and MXAN_3634-3636 to evaluate them for interactions with MXAN_3118. 194 195 MXAN_3118 196 megasynthase....”
- “...stipitatus DSM 14675. B) 545 Schematic of the MXAN_3779 and MXAN_3634-6 NRPS/PKS hybrid megasynthases 546 from M. xanthus DK1622. Domain abbreviations: AL,...”
- Identification of Functions Affecting Predator-Prey Interactions between Myxococcus xanthus and Bacillus subtilis
Müller, Journal of bacteriology 2016 - “...LOF transposon mutant had an insertion in locus MXAN_3779 encoding a mixed NRPS/PKS biosynthetic module, previously identified for its production of the...”
t1943 SmtA protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
33% identity, 39% coverage
- Staphylococcus aureus Isolated From Retail Meat and Meat Products in China: Incidence, Antibiotic Resistance and Genetic Diversity
Wu, Frontiers in microbiology 2018 - “...t127 (1) ST4470 * (1) t127 (1) CC7 (174) ST7 (151) t091 (92), t796 (26), t1943 (3), t085 (3), t2616 (4), t289 (3)t10370 (3), t7568 (4), t10332 (1), t3932 (2), t605 (2), t3437 (2), t1689 (1), t304 (1), t3092 (1), t8927 (1), t1685 (1), t127 (1)...”
BMEI1484 CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE from Brucella melitensis 16M
31% identity, 35% coverage
SahR / VIMSS1780926 SahR regulator of Methionine metabolism, effector S-adenosylhomocysteine (repressor) from Mesorhizobium sp. BNC1
36% identity, 30% coverage
A0A125SQH6 phosphoethanolamine N-methyltransferase (EC 2.1.1.103) from Chlamydomonas asymmetrica (see paper)
33% identity, 18% coverage
P65347 Uncharacterized methyltransferase Mb0092 from Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
MT0098 methyltransferase, putative from Mycobacterium tuberculosis CDC1551
Rv0089 POSSIBLE METHYLTRANSFERASE/METHYLASE from Mycobacterium tuberculosis H37Rv
34% identity, 48% coverage
- Characterization and overproduction of cell-associated cholesterol oxidase ChoD from Streptomyces lavendulae YAKB-15
Yamada, Scientific reports 2019 - “...dehydrogenase Scad, Megasphaera elsdenii 33/27 Q06319 6 ORF C 226 Methyltransferase BQ2027_MB0092, Mycobacterium bovis 49/40 P65347 Enzyme kinetics of recombinant ChoD In order to characterize ChoD, we ordered a synthetic gene codon optimized for expression in E . coli and cloned it in a modified pBAD...”
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...Rv2655c Rv2646 Rv2885c Intermediary metabolism and respiration MT0098 MT0207 MT0337 MT0511 Rv0089 Rv0197 Rv0322 Rv0492c Information pathways Gene lpqK mce2E...”
- Transcriptomic responses to antibiotic exposure in <i>Mycobacterium tuberculosis</i>
Poonawala, Antimicrobial agents and chemotherapy 2024 (secret) - Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice
Meade, G3 (Bethesda, Md.) 2023 - “...97.465 3.71 83.879 128.058 3.89E02 hp050 Rv0878c PPE13 7 97.685 4.10 89.870 127.500 2.49E02 hp051 Rv0089 Rv0089 7 116.709 4.08 98.124 127.989 3.64E02 hp052 Rv1912c fadB5 7 134.484 4.49 51.060 134.831 1.14E02 hp053 Rv3868 eccA1 7 134.598 3.80 17.136 144.445 4.40E02 hp054 Rv2637 dedA 7 140.297...”
- Biochemical characterisation of pimelate biosynthetic genes of Mycobacterium tuberculosis
Gugu, 2019 - Transition State Analogue Inhibitors of 5'-Deoxyadenosine/5'-Methylthioadenosine Nucleosidase from Mycobacterium tuberculosis
Namanja-Magliano, Biochemistry 2017 - “..., a nearby open reading frame, the sequence of amino acids 32146 (of 197) of Rv0089 is 41% identical with that of the E. coli BioC protein, a SAM-dependent malonyl-acyl carrier protein methyltransferase, an early step in biotin synthesis. 40 In E. coli , the BioC...”
- Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress
Lin, Infection and immunity 2016 - “...metabolism and respiration MT0098 MT0207 MT0337 MT0511 Rv0089 Rv0197 Rv0322 Rv0492c Information pathways Gene lpqK mce2E (lprL) lpqP pstS1 (phoS1) mscL...”
- Mycobacterium tuberculosis Transcriptome Profiling in Mice with Genetically Different Susceptibility to Tuberculosis
Skvortsov, Acta naturae 2013 - “...frdB, cmk, plcD, lipJ, cobK, cobS, cysK1, cysE, gdh, gabT, miaA, ilvC, guaB2, cyp142, hsaD, Rv0089, Rv0331, aspC, hemA, Rv0567, atsA, gltA2, Rv0943c, Rv1096, Rv1106c, narH, thrB, hisB, ilvG, rocD1, plcB, phoH1, ggtB, lepA, Rv2499c, dapF, purU, kstD, folP1 IMaR intermediary metabolism and respiration end, fusA1,...”
- Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis
Shi, Journal of the American Chemical Society 2011 - “...coli co-opts the fatty acid synthase type II pathway along with BioC ( Mtb ortholog: Rv0089) and BioH ( Mtb ortholog: Rv2715) for synthesis of pimeloyl-ACP, which is proposed as the physiologically relevant substrate for BioF. 7 Amiclenomycin (ACM) isolated from Streptomyces lavendulae subsp. amiclenomycini and...”
- Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis
Tsolaki, Journal of clinical microbiology 2005 - “...Gene(s) deleted Rv0071, Rv0072, Rv0073, Rv0074 hycE, Rv0088, Rv0089, Rv0090 fadD4, nadR, Rv0213c fabD2, Rv0650 end, Rv0669c kdpA, kdpB, kdpC, trcS Rv1190,...”
SCO0190 methyltransferase from Streptomyces coelicolor A3(2)
34% identity, 40% coverage
SMTB_EMENI / A0A1U8QNM5 Sphingolipid C9-methyltransferase B; EC 2.1.1.317 from Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (Aspergillus nidulans) (see paper)
27% identity, 33% coverage
- function: Catalyzes methylation of the sphingoid base component of glucosylceramides (GluCers) at the C9-position (PubMed:27479571). Sphingolipid C9-methylation requires 4,8-desaturated ceramides as substrates (By similarity). Glucosylceramides play important roles in growth, differentiation and pathogenicity (PubMed:27479571). The methyl group at the C9-position distinguishes fungal glucosylceramides from those of plants and animals and may thus play a role in host-pathogen interactions enabling the host to recognize the fungal attack and initiate specific defense responses (By similarity).
catalytic activity: a (4E,8E)-4-sphinga-4,8-dienine ceramide + S-adenosyl-L- methionine = a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide + S- adenosyl-L-homocysteine + H(+) (RHEA:46804)
disruption phenotype: Leads to increased resistance to cell-wall- damaging agents, such as calcofluor white (CFW) and Congo red (CR) (PubMed:27479571). Accumulates unmethylated glucosylceramides (PubMed:27479571).
An02g04530 uncharacterized protein from Aspergillus niger
30% identity, 25% coverage
SMT1 / Q9LM02 sterol methyltransferase (EC 2.1.1.41) from Arabidopsis thaliana (see 4 papers)
SMT1_ARATH / Q9LM02 Cycloartenol-C-24-methyltransferase; 24-sterol C-methyltransferase 1; Sterol C-methyltransferase 1; Protein CEPHALOPOD; Protein STEROL METHYLTRANSFERASE 1; EC 2.1.1.41 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_196875 sterol methyltransferase 1 from Arabidopsis thaliana
AT5G13710 SMT1 (STEROL METHYLTRANSFERASE 1); sterol 24-C-methyltransferase from Arabidopsis thaliana
33% identity, 30% coverage
- function: Catalyzes the methyl transfer from S-adenosyl-methionine to the C-24 of cycloartenol to form 24-methylene cycloartenol.
catalytic activity: cycloartenol + S-adenosyl-L-methionine = 24- methylenecycloartanol + S-adenosyl-L-homocysteine + H(+) (RHEA:59012) - Microsome-associated proteome modifications of Arabidopsis seedlings grown on board the International Space Station reveal the possible effect on plants of space stresses other than microgravity
Mazars, Plant signaling & behavior 2014 - “...pyruvate dehydrogenase E2 component P33207 AT1G24360 1.964 3-oxoacyl-[acyl-carrier-protein] reductase Q56WD9 AT2G33150 1.961 3-ketoacyl-CoA thiolase 2 Q9LM02 AT5G13710 1.939 cycloartenol-c-24-methyltransferase Q9LTV6 AT3G12800 1.914 peroxisomal 2,4-dienoyl-CoA reductase Q9LSQ0 AT3G16910 1.874 acyl-activating enzyme 7 C0Z3A0 1.793 AT3G06850 Q9ZPI5 AT3G06860 1.688 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase Q8LAZ1 1.681 very-long-chain fatty acid condensing...”
- The sterol methyltransferases SMT1, SMT2, and SMT3 influence Arabidopsis development through nonbrassinosteroid products.
Carland, Plant physiology 2010 - GeneRIF: Mutants deficient in both SMT1 and SMT2 are embryo lethal.
- Plasticity of the Arabidopsis leaf lipidome and proteome in response to pathogen infection and heat stress
Scholz, Plant physiology 2025 (no snippet) - Two structurally different oomycete lipophilic microbe-associated molecular patterns induce distinctive plant immune responses
Monjil, Plant physiology 2024 - “...AT4G33430 EFR Gramene: AT5G20480 EFR Araport: AT5G20480 FLS2 Gramene: AT5G46330 FLS2 Araport: AT5G46330 smt1 Gramene: AT5G13710 smt1 Araport: AT5G13710 CERK1 Gramene: AT3G21630 CERK1 Araport: AT3G21630 ALA CHEBI: CHEBI:17549 oligosaccharides CHEBI: CHEBI:50699 PTI Gramene: pattern-triggered immunity PTI Araport: pattern-triggered immunity References Adarme-Vega TC , Lim DK ,...”
- Characterization of Subcellular Dynamics of Sterol Methyltransferases Clarifies Defective Cell Division in smt2 smt3, a C-24 Ethyl Sterol-Deficient Mutant of Arabidopsis
Ohta, Biomolecules 2024 - “...pBI101 and pBI121 to express the fusion proteins with mCherry. Arabidopsis sterol biosynthetic enzymes SMT1 (AT5G13710), SMT2 (AT1G20330), SMT3 (AT1G76090), and CYP710A1 (AT2G34500) with a short-linker AAAAGGS at their C-terminus were fused to the coding sequences for the fluorescent marker proteins (GFP, mGFP, or mCherry). The...”
- “...respectively. Briefly, for the plasmid construction of proSMT1::SMT1-GFP , a coding sequence region for SMT1 (AT5G13710) together with the short-linker sequence was amplified by RT-PCR using the primer set SMT1_Fw and SMT1-linker_Rv. As an endogenous promoter region for SMT1 , a 1629-bp fragment upstream of the...”
- Targeted modulation of pennycress lipid droplet proteins impacts droplet morphology and seed oil content
Guzha, The Plant journal : for cell and molecular biology 2024 - “...oil content including HYDROSTEROID DEHYDROGENASE ( HSD1 AT5G50600), ALPHA/BETA HYDROLASEs (AT5G11650 and AT2G47630), STEROL METHYLTRANSFERASE (AT5G13710), RABA3 homolog (AT1G01200), LDAP3 (AT3G05500), ACYLCOABINDING PROTEIN 6 ( ACBP6 AT1G31812), RNA BINDING PROTEIN (AT5G06210), LDAP2 (AT2G47780), MONOACYLGLYCEROL LIPASE (AT2G39400), SEIPIN1 (AT5G16460), LYSOPHOSPHATIDYLETHANOLAMINE ACYLTRANSFERASE1 ( LPEAT1 AT1G80950), OLEOSIN (AT4G25140) and...”
- Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana
Soto-Cardinault, Genes 2023 - “...Chr2 Vacuolar protein sorting 11 1 AT3G13300 VCS Chr3 VARICOSE. Transducin/WD40 repeat-like superfamily protein 26 AT5G13710 SMT1 Chr5 Sterol methyltransferase 1 2 AT4G12110 SMO1-1 Chr4 Sterol-4alpha-methyl oxidase 1-1 2 AT1G47290 3BETAHSD/D1 Chr1 3beta-hydroxysteroid-dehydrogenase/decarboxylase isoform 1 3 AT2G47760 ALG3 Chr2 Asparagine-linked glycosylation 3 3 AT1G71990 FUT13 Chr1...”
- Elucidation of sterol biosynthesis pathway and its co-regulation with fatty acid biosynthesis in the oleaginous marine protist Schizochytrium sp
Bi, Frontiers in bioengineering and biotechnology 2023 - “...- - - hsa: 51478 18 7.00E-05 KN805382.1_orf01293 24-Methylenesterol C-methyltransferase 2.1.1.41 SMT YML008C 36 5.00E-55 AT5G13710 39 9.00E-61 - - - KN805382.1_orf01293 24-Methylenesterol C-methyltransferase 2.1.1.41 SMT YML008C 36 5.00E-55 AT1G20330 34 1.00E-48 - - - KN805382.1_orf01293 24-Methylenesterol C-methyltransferase 2.1.1.41 SMT YML008C 36 5.00E-55 AT1G76090 33 1.00E-46...”
- Salt stress alters membrane lipid content and lipid biosynthesis pathways in the plasma membrane and tonoplast
Guo, Plant physiology 2022 - “...PM iceplant_tr_24046 Phospholipase D alpha 1 AT3G15730 0.69 7.7E-03 Decreased PL signaling Cytosol iceplant_tr_19120 Cycloartenol-C-24-methyltransferase AT5G13710 1.15 1.9E-03 Increased Sterol synthesis Golgi iceplant_tr_128900 Cytochrome P450 51G1 AT1G11680 2.42 2.5E-02 Increased Sterol synthesis ER iceplant_tr_102394 Ankyrin repeat domain-containing protein 2B AT2G17390 0.71 3.7E-02 Decreased Lipid binding Nucleus...”
- Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism
Arias, Plant biotechnology journal 2022 - “...6 phosphate/phosphate translocator 2 Glyma.15G276300 1.6 1.8 1.4 1.6 1.6 1.1 1.2 1.2 405 0.95 AT5G13710 Sterol methyltransferase 1 Glyma.06G214800 1.3 1.1 1.7 1.6 1.8 1.7 3.0 3.0 1890 0.95 AT2G26640 KetoacylCoA synthase 11 Glyma.13G152500 1.0 1.3 1.5 1.1 1.3 1.5 1.2 1.6 1.5 1971 0.95...”
- More
XP_421735 arsenite methyltransferase isoform X2 from Gallus gallus
30% identity, 29% coverage
SO_4199 ubiquinone/menaquinone biosynthesis methlytransferase UbiE from Shewanella oneidensis MR-1
24% identity, 69% coverage
NP_001238391 S-adenosyl-L-methionine:delta24-sterol-C- methyltransferase from Glycine max
33% identity, 28% coverage
- Identification and Mode of Action of a Plant Natural Product Targeting Human Fungal Pathogens
Dorsaz, Antimicrobial agents and chemotherapy 2017 - “...AOW28252 ; P. carinii , KTW25893 ; G. zeae , ESU10532 ; G. max , NP_001238391 ; A. thaliana , NP_173458 ; and T. brucei , AAZ40214 . A multiple-sequence alignment was performed using the MUSCLE program in Geneious software (version 9.1.4; default parameters). TABLE 3...”
- Sterol methyltransferase a target for anti-amoeba therapy: towards transition state analog and suicide substrate drug design
Kidane, Journal of lipid research 2017 - “...(XP_002617229), Monosiga brevicollis (XP_001748534), Chlamydomonas reinhardtii (XP_001690775), Trypanosoma brucei (XP_822930), Yarrowia lipolytica (XP_505173), Glycine max-1 (NP_001238391), Zea mays- 1 (ACG33830), Z. mays -2 (NP_001149131), Trypanosoma cruzi (EKG01467), Candida albicans (EEQ44277), Paracoccidioides brasiliensis (EEH21414), G. max-2 (ACS93764), Arabidopsis thaliana -1 (AAM53553), A. thaliana- 2 (AAM91592) and S.cerevisiae...”
VC0083 ubiquinone/menaquinone biosynthesis methlytransferase UbiE from Vibrio cholerae O1 biovar eltor str. N16961
Q9KVQ6 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
25% identity, 67% coverage
- Transient Glycolytic Complexation of Arsenate Enhances Resistance in the Enteropathogen Vibrio cholerae
Bueno, mBio 2022 - “...FrdA, VC2656 fumarate reductase; IspH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; AceF, VC2413 pyruvate dehydrogenase, E2 component; UbiE, VC0083 ubiquinone/menaquinone biosynthesis methyltransferase. (E) Representative dot plots from V. cholerae WT and var mutant cells stained with DiOC2 following growth in the presence of 1mM As V for 5h. The...”
- Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
Krin, BMC genomics 2018 - “...: Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides ; 2.8 New SOS regulon genes VC0083 ubiE Ubiquinone/menaquinone biosynthesis methyltransferase UbiE e : enzyme 1.5.3.11 : Menaquinone (MK), ubiquinone (Q) ; 4.5 : Menaquinone and ubiquinone ; 9.0 VC0084 ubiJ Ubiquinone biosynthesis protein UbiJ e :...”
- Proteomic analysis of Vibrio cholerae in human stool
LaRocque, Infection and immunity 2008 - “...human serum TIGR locusa SWISS-PROT accession no. VC0027 VC0083 Q9KVW1 Q9KVQ6 VC0093 Q9KVP8 VC0306 VC0809 VC1354 VC1456 Q9KV51 Q9KTS9 Q9KSA5 P01556 VC1457 P01555...”
- Proteomic analysis of Vibrio cholerae in human stool
LaRocque, Infection and immunity 2008 - “...TIGR locusa SWISS-PROT accession no. VC0027 VC0083 Q9KVW1 Q9KVQ6 VC0093 Q9KVP8 VC0306 VC0809 VC1354 VC1456 Q9KV51 Q9KTS9 Q9KSA5 P01556 VC1457 P01555 VC1604...”
1wznA / O59000 Crystal structure of the sam-dependent methyltransferase from pyrococcus horikoshii ot3
31% identity, 44% coverage
- Ligand: s-adenosyl-l-homocysteine (1wznA)
PH1305 hypothetical protein from Pyrococcus horikoshii OT3
32% identity, 40% coverage
- Crystallization and preliminary crystallographic studies of UbiG, an O-methyltransferase from Escherichia coli
Xing, Acta crystallographica. Section F, Structural biology and crystallization communications 2011 - “...by the molecular-replacement method using the structure of PH1305 (a putative uncharacterized protein from Pyrococcus horikoshii OT3) as a search model (PDB...”
- Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3
Usui, Genome biology 2005 - “...Triosephosphate isomerase Ortholog to eubacteria and archaea proteins PH0385 MorR-like ATPase PH0008 PH0596* Pyrrolidone-carboxylate peptidase PH1305 PH0634* 6-pyruvoyl-tetrahydropterin synthase PH1503 PH0762* Probable thymidylate synthase PH1950 PH0776 Methanol dehalogenase regulatory protein PH0519 PH0986 Lactam utilization protein PH1474 PH1153* Putative acetylornithine deacetylase PH1918 PH1408 Putative uridylate kinase PH1692*...”
- Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi
Ishikawa, Nucleic acids research 2005 - “...the first round of trials, five of the ORFs identified by bioinformatics, namely, PAB0105, PH0583, PH1305, PH0904 and PH1033 (see Table 1 ), were tested because they are associated with genome rearrangement ( 7 ) and, in some cases, bear some similarity to restriction endonuclease genes....”
MXAN_1970 transcriptional regulator, ArsR family from Myxococcus xanthus DK 1622
28% identity, 40% coverage
- Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Robinson, BMC genomics 2014 - “...might be activated by MrpC. Four of these are predicted to code for transcription factors (MXAN_1970, 2902, 5041, 5899) and the fifth codes for C-signal ( csgA , MXAN_1294). Therefore, MrpC is implicated to up-regulate 18 promoters that are located immediately upstream of genes known or...”
- “...an EBP but a null mutant showed no developmental defect [ 100 ]. Characterization of MXAN_1970 and 5899 has not been reported. MrpC is implicated as a direct activator or repressor of genes involved in signal production, spore formation, protein fate, and motility during development Three...”
VP0095 ubiquinone/menaquinone biosynthesis methlytransferase UbiE from Vibrio parahaemolyticus RIMD 2210633
25% identity, 67% coverage
ERG6A_GIBZE / I1RGC4 Sterol 24-C-methyltransferase ERG6A; SCMT; SMT; Delta(24)-sterol C-methyltransferase ERG6A; Ergosterol biosynthesis protein 6A; EC 2.1.1.- from Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1) (Wheat head blight fungus) (Fusarium graminearum) (see 3 papers)
FGSG_02783 sterol 24-C-methyltransferase from Fusarium graminearum PH-1
27% identity, 32% coverage
- function: Sterol 24-C-methyltransferase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (By similarity). ERG6A and ERG6B methylate lanosterol at C-24 to produce eburicol (By similarity). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase ERG9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, squalene is converted into lanosterol by the consecutive action of the squalene epoxidase ERG1 and the lanosterol synthase ERG7. Then, the delta(24)-sterol C-methyltransferase ERG6 methylates lanosterol at C-24 to produce eburicol. Eburicol is the substrate of the sterol 14-alpha demethylase encoded by CYP51A, CYP51B and CYP51C, to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol. CYP51B encodes the enzyme primarily responsible for sterol 14-alpha- demethylation, and plays an essential role in ascospore formation. CYP51A encodes an additional sterol 14-alpha-demethylase, induced on ergosterol depletion and responsible for the intrinsic variation in azole sensitivity. The third CYP51 isoform, CYP51C, does not encode a sterol 14-alpha-demethylase, but is required for full virulence on host wheat ears. The C-14 reductase ERG24 then reduces the C14=C15 double bond which leads to 4,4-dimethylfecosterol. A sequence of further demethylations at C-4, involving the C-4 demethylation complex containing the C-4 methylsterol oxidases ERG25, the sterol-4-alpha- carboxylate 3-dehydrogenase ERG26 and the 3-keto-steroid reductase ERG27, leads to the production of fecosterol via 4-methylfecosterol. ERG28 has a role as a scaffold to help anchor ERG25, ERG26 and ERG27 to the endoplasmic reticulum. The C-8 sterol isomerase ERG2 then catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5- desaturases ERG3A and ERG3BB then catalyze the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The C-22 sterol desaturases ERG5A and ERG5B further convert 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)- tetraen-3beta-ol is substrate of the C-24(28) sterol reductase ERG4 to produce ergosterol (Probable).
catalytic activity: lanosterol + S-adenosyl-L-methionine = eburicol + S-adenosyl- L-homocysteine + H(+) (RHEA:52652) - Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole
Zhao, BMC genomics 2022 - “...steroid reductase [EC:1.1.1.270] 1 0 FGSG_05740 A0A0E0SMA3 SMT1A, ERG6A; sterol 24-C-methyltransferase [EC:2.1.1.41] 1 0 FGSG_02783 I1RGC4 SMT1B, ERG6B; sterol 24-C-methyltransferase [EC:2.1.1.41] 1 1 down FGSG_07315 I1RT23 ERG2; C-8 sterol isomerase [EC:5.-.-.-] 2 0 a Number of Khib sites which influenced by TEC In addition, we also...”
- FgFAD12 Regulates Vegetative Growth, Pathogenicity and Linoleic Acid Biosynthesis in Fusarium graminearum
Zhang, Journal of fungi (Basel, Switzerland) 2024 - “...In addition, RNA-seq analysis displayed that the expression levels of eight genes (FGSG_06215, FGSG_04994, FGSG_02502, FGSG_02783, FGSG_05740, FGSG_01000, FGSG_04092 and FGSG_09830) related to ergosterol biosynthesis were prominently increased in the mutant strains compared with wild type. Ergosterol extraction assay revealed that the ergosterol content in the...”
- Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole
Zhao, BMC genomics 2022 - “...control protein FGSG_02770 114 0.34 Down Fructose-bisphosphate aldolase FGSG_01099 132 0.32 Down GTP-binding nuclear protein FGSG_02783 60 0.31 Down Sterol 24-C-methyltransferase FGSG_02770 308 0.31 Down Fructose-bisphosphate aldolase To further understand the distribution of proteins with identified changes in Khib caused by TEC, we performed a subcellular...”
- “...suppression, approximately 3.24-fold, of the Khib level on the only identified Khib site in ERG6B (FGSG_02783) by TEC. In addition, two Khib sites on FgERG9 (FGSG_09381) were identified, and the Khib modification was enhanced at one site, K381, after TEC treatment. Six Khib sites from FgCYP51B...”
- Voriconazole Treatment Induces a Conserved Sterol/Pleiotropic Drug Resistance Regulatory Network, including an Alternative Ergosterol Biosynthesis Pathway, in the Clinically Important FSSC Species, Fusarium keratoplasticum
James, Journal of fungi (Basel, Switzerland) 2022 - “...the Fg-cyp51A and Fg-cyp51B orthologs, they are less well conserved than Fg-erg5B (FGSG_01959) and Fg-erg6B (FGSG_02783) and expressed at much lower levels than Fg-erg5B and Fg-erg6B under normal growth conditions and two of the most downregulated genes in the FgSR strain ( Figure 5 a and...”
- Functional Characterization of Calcineurin-Responsive Transcription Factors Fg01341 and Fg01350 in Fusarium graminearum
Zhang, Frontiers in microbiology 2020 - “...ND 6.73 C2H2-type zinc finger Response to tebuconazole treatment FGSG_05740 Erg6 1.80 1.94 Sterol 24-C-methyltransferase FGSG_02783 Erg6 1.08 3.55 Sterol 24-C-methyltransferase FGSG_04092 Cyp51 2.74 8.18 Cytochrome P450 51 FGSG_01000 Erg11 1.17 4.43 Cytochrome P450 51 FGSG_09266 Erg13 1.45 5.11 Hydroxymethylglutaryl-CoA synthase Reproductive process FGSG_08892 Mat1-1-1 ND...”
- A phosphorylated transcription factor regulates sterol biosynthesis in Fusarium graminearum
Liu, Nature communications 2019 - “...with three selected genes, FgCTK1 ( FGSG_13888 ), FgERG6A ( FGSG_05740 ), and FgERG6B ( FGSG_02783 ), to verify ChIP-Seq data (Supplementary Fig. 8c ). Consistently, qRT-PCR assays showed that the expression levels of these genes were significantly down-regulated in FgSR (Supplementary Fig. 8d ). Among...”
- Involvement of FgERG4 in ergosterol biosynthesis, vegetative differentiation and virulence in Fusarium graminearum
Liu, Molecular plant pathology 2013 (secret)
Q43445 cycloartenol 24-C-methyltransferase (EC 2.1.1.142) from Glycine max (see 3 papers)
33% identity, 26% coverage
spnL / Q9ALN3 rhamnosyl-spinosyn tetracyclic macrolactone synthase from Saccharopolyspora spinosa (see 4 papers)
28% identity, 59% coverage
BMULJ_05696 cyclopropane-fatty-acyl-phospholipid synthase from Burkholderia multivorans ATCC 17616
32% identity, 33% coverage
Q5CB51 tocopherol C-methyltransferase (EC 2.1.1.95) from Chlamydomonas reinhardtii (see paper)
28% identity, 36% coverage
SMAC_02133 uncharacterized protein from Sordaria macrospora
33% identity, 20% coverage
- Analysis of the Putative Nucleoporin POM33 in the Filamentous Fungus Sordaria macrospora
Groth, Journal of fungi (Basel, Switzerland) 2021 - “...putative interaction candidate of POM33. Besides, proteins involved in lipid metabolism, like a cyclopropane-fatty-acyl-phospholipid synthase (SMAC_02133), or the putative phosphatidyl inositol 4-phosphatase SAC1 (SMAC_01583) were determined. Moreover, a fatty acid desaturase (SMAC_03650), an acyl-CoA desaturase 1 (SMAC_01733) and a very-long-chain 3-oxoacyl-CoA reductase (SMAC_01146) which play roles...”
novO / Q9L9F3 8-demethylnovobiocic acid C8-methyltransferase (EC 2.1.1.284) from Streptomyces niveus (see paper)
NOVO_STRNV / Q9L9F3 8-demethylnovobiocic acid C(8)-methyltransferase; Novobiocin biosynthesis protein O; EC 2.1.1.284 from Streptomyces niveus (Streptomyces spheroides) (see paper)
5mgzA / Q9L9F3 Streptomyces spheroides novo (8-demethylnovbiocic acid methyltransferase) with sah (see paper)
31% identity, 45% coverage
- function: C-methyltransferase that methylates 8-demethylnovobiocic acid to produce novobiocic acid in the novobiocin biosynthesis pathway. Novobiocin is an aminocoumarin family antibiotic that targets bacterial DNA gyrases.
catalytic activity: 8-desmethylnovobiocic acid + S-adenosyl-L-methionine = novobiocic acid + S-adenosyl-L-homocysteine + H(+) (RHEA:36651) - Ligand: s-adenosyl-l-homocysteine (5mgzA)
rebM / Q8KI52 demethylrebeccamycin--D-glucose O-methyltransferase (EC 2.1.1.164) from Lentzea aerocolonigenes (see 2 papers)
33% identity, 38% coverage
WP_055793823 class I SAM-dependent methyltransferase from Williamsia sp. Leaf354
30% identity, 67% coverage
- Phytopathogenic Rhodococcus Have Diverse Plasmids With Few Conserved Virulence Functions
Savory, Frontiers in microbiology 2020 - “...similarity) to Mtr1 and Mtr2 in Leaf225 (WP_027503960.1 and WP_056447883.1) and Leaf354 (WP_055787211.1, WP_055786245.1, WP_055790396.1, WP_055793823, WP_082501997.1, and WP_156378120.1 of Leaf354). However, use of these eight sequences as queries in reciprocal searches against the D188 genome sequence yielded better hits to genes in the chromosome, not...”
REBMT_LENAE / Q8KZ94 Demethylrebeccamycin-D-glucose O-methyltransferase; Rebeccamycin O-methyltransferase; Rebeccamycin sugar 4'-O-methyltransferase RebM; EC 2.1.1.164 from Lentzea aerocolonigenes (Lechevalieria aerocolonigenes) (Saccharothrix aerocolonigenes) (see 2 papers)
Q8KZ94 demethylrebeccamycin-D-glucose O-methyltransferase (EC 2.1.1.164) from Lentzea aerocolonigenes (see 3 papers)
33% identity, 36% coverage
- function: Glycosyl O-methyltransferase that catalyzes the final step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid that inhibits topoisomerase 1. Has broad substrate specificity and functions as glycosyl O-methyltransferase on a number of rebeccamycin analogs.
catalytic activity: 4'-demethylrebeccamycin + S-adenosyl-L-methionine = rebeccamycin + S-adenosyl-L-homocysteine + H(+) (RHEA:27353)
subunit: Monomer.
BCIN_08g01540 hypothetical protein from Botrytis cinerea B05.10
30% identity, 26% coverage
ERG6_PNEC8 / Q96WX4 Sterol 24-C-methyltransferase; Delta(24)-sterol C-methyltransferase; S-adenosyl-L-methionine:sterol C-24 methyl transferase; SAM:SMT; EC 2.1.1.- from Pneumocystis carinii (strain B80) (Rat pneumocystis pneumonia agent) (Pneumocystis carinii f. sp. carinii) (see 2 papers)
Q96WX4 cycloartenol 24-C-methyltransferase (EC 2.1.1.142); sterol 24-C-methyltransferase (EC 2.1.1.41) from Pneumocystis carinii (see paper)
28% identity, 28% coverage
- function: Catalyzes the transfer of 2 methyl groups from 2 S-adenosyl- methionine molecules to the C-24 of lanosterol, producing first eburicol (24-methylenelanosterol) from lanosterol and then pneumocysterol (24Z-ethylidenelanosterol) from eburicol.
catalytic activity: lanosterol + S-adenosyl-L-methionine = eburicol + S-adenosyl- L-homocysteine + H(+) (RHEA:52652)
catalytic activity: eburicol + S-adenosyl-L-methionine = (24Z)- ethylidenelanosterol + S-adenosyl-L-homocysteine + H(+) (RHEA:55088)
PSPA7_6253 methyltransferase domain-containing protein from Pseudomonas aeruginosa PA7
34% identity, 38% coverage
3busA / Q8KZ94 Crystal structure of rebm (see paper)
33% identity, 41% coverage
- Ligand: s-adenosyl-l-homocysteine (3busA)
NCU07859 cyclopropane-fatty-acyl-phospholipid synthase from Neurospora crassa OR74A
33% identity, 20% coverage
- Genetic Characterization of the Acidic and Neutral Glycosphingolipid Biosynthetic Pathways in Neurospora crassa
Shoma, Microorganisms 2023 - “...gsl-6 mata (NCU06465), gsl-4 mata (NCU00008), gsl-11 mata (NCU02882), gsl-12 mata (NCU07761), and gsl-9 mata (NCU07859) deletion mutants are found as heterokaryotic isolates in the Neurospora knockout library. The library contains homokaryotic isolates (strains in which all the nuclei are deletion mutant nuclei) gsl-3 matA (NCU00302),...”
- Phenotype to genotype in Neurospora crassa: Association of the scumbo phenotype with mutations in the gene encoding ceramide C9-methyltransferase
Bredeweg, Current research in microbial sciences 2022 - “...as a ceramide C9 methyltransferase, previously annotated as similar to cyclopropane-fatty-acyl-phospholipidsynthase, encoded by the gene NCU07859. This enzyme performs a fungal-specific methyl modification of glycosyl-ceramides and has implications for membrane homeostasis and hyphal polarity in filamentous fungi. Graphical abstract Graphical abstract Image, graphical abstract . Keywords...”
- “...causal gene for the scumbo phenotype by sequencing allowed us to test the hypothesis that NCU07859 is scumbo by gene knockout. Testing and confirmation of historically collected mutants merges longstanding observations with gene function, and morphological structures and functional inter-dependencies. 2 Materials and Methods 2.1 Genomic...”
- Membrane Sphingolipids Regulate the Fitness and Antifungal Protein Susceptibility of Neurospora crassa
Huber, Frontiers in microbiology 2019 - “...a NCU02408, FGSC16221 FGSC N. crassa smt smt::hph r ; mus-51::bar + ; mat a NCU07859, FGSC13992 FGSC N. crassa gcs gcs::hph r ; mat A NCU01116, FGSC13794 FGSC P. chrysogenum paf OE paf ; nat1 r NCBI, Pc24g00380 Sonderegger et al., 2016 P. chrysogenum pafB...”
- “...4-desaturase ( Plesofsky et al., 2008 ), NCU02408 ( des-2 ) encoding the 8-sphingolipid desaturase, NCU07859 ( smt ) encoding the C9-methyltransferase ( Ramamoorthy et al., 2009 ) and NCU01116 ( gcs ) coding for the GlcCer synthase ( Plesofsky et al., 2008 ). The predicted...”
VV1_2142 SmtA protein from Vibrio vulnificus CMCP6
26% identity, 55% coverage
RTCIAT899_RS18940 SAM-dependent methyltransferase from Rhizobium tropici CIAT 899
27% identity, 33% coverage
- Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899
Guerrero-Castro, Frontiers in microbiology 2018 - “...0.03053786 0.92576353 Class I SAM-dependent methyltransferase cfa3 RTCIAT899_RS24775 0.7897075 0.08312349 Class I SAM-dependent methyltransferase cfa4 RTCIAT899_RS18940 0.67863217 0.54558424 SAM-dependent methyltransferase cfa5 RTCIAT899_RS18960 0.18275374 0.45288988 SAM-dependent methyltransferase Exo RTCIAT899_RS06570 1.33771965 0.11074631 EPS transporter family Yuan et al., 2008 exoX RTCIAT899_RS29115 0.10549587 0.69617043 EPS production repressor protein ExoX...”
CHLM / Q9SW18 magnesium protoporphyrin IX methyltransferase (EC 2.1.1.11) from Arabidopsis thaliana (see paper)
CHLM_ARATH / Q9SW18 Magnesium protoporphyrin IX methyltransferase, chloroplastic; EC 2.1.1.11 from Arabidopsis thaliana (Mouse-ear cress) (see 5 papers)
Q9SW18 magnesium protoporphyrin IX methyltransferase (EC 2.1.1.11) from Arabidopsis thaliana (see 2 papers)
AT4G25080 CHLM (magnesium-protoporphyrin IX methyltransferase); magnesium protoporphyrin IX methyltransferase from Arabidopsis thaliana
27% identity, 46% coverage
- function: Converts Mg-protoporphyrin IX to Mg-protoporphyrin IX methylester using S-adenosyl-L-methionine as a cofactor. Involved in chloroplast-to-nucleus signaling by acting as a negative effector of nuclear photosynthetic gene expression.
catalytic activity: Mg-protoporphyrin IX + S-adenosyl-L-methionine = Mg- protoporphyrin IX 13-monomethyl ester + S-adenosyl-L-homocysteine (RHEA:17809)
disruption phenotype: Lethal under normal growth conditions and stunted albino plants unable to produce seeds when grown in presence of sucrose. - Proteomic Analysis of Proteins Related to Defense Responses in Arabidopsis Plants Transformed with the rolB Oncogene
Vereshchagina, International journal of molecular sciences 2023 - “...stomata closure in drought conditions; involved in resistance to salt and drought 1.5 Photosynthesis 1 Q9SW18 Magnesium protoporphyrin IX methyltransferase, chloroplastic Chlorophyll biosynthesis 3.0 2 Q9LR75 Coproporphyrinogen-III oxidase 1, chloroplastic Chlorophyll biosynthesis 5.0 3 O22886 Uroporphyrinogen decarboxylase 2, chloroplastic Chlorophyll biosynthesis 2.8 4 P21218 Protochlorophyllide reductase...”
- Redox post-translational modifications and their interplay in plant abiotic stress tolerance
Martí-Guillén, Frontiers in plant science 2022 - “...2002 ) Spinach Lchb1 (P12333) Trp-132 oxidation Inactivation/Turnover ( Rinalducci etal., 2005 ) Arabidopsis CHLM (Q9SW18) Cys-111 oxidation Decreased activity ( Richter etal., 2016 ) CHLM (Q9SW18) Cys-115 oxidation Decreased activity ( Richter etal., 2016 ) Arabidopsis GAPDH (P25858) Cys-S-sulfhydration Increased activity ( Aroca etal., 2015...”
- Transcriptome analysis to identify candidate genes associated with the yellow-leaf phenotype of a Cymbidium mutant generated by γ-irradiation
Kim, PloS one 2020 - “...2.88577 7.76 10 13 TRINITY_DN59808_c0_g2 P27489 CAB13 Chlorophyll a-b binding protein 13 3.77677 0.006663 TRINITY_DN74933_c1_g1 Q9SW18 CHLM Magnesium protoporphyrin IX methyltransferase 1.00694 0.382536 TRINITY_DN83083_c8_g2 Q9M591 CRD1 Magnesium-protoporphyrin IX monomethylester cyclase 0.46194 0.787932 TRINITY_DN76234_c0_g1 Q5W6H5 CHLG Chlorophyll synthase 1.10377 0.092632 TRINITY_DN80530_c2_g1 Q41249 PORA Protochlorophyllide a reductase 4.57080...”
- Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach
Kumari, PeerJ 2024 - “...trichome initiation through gibberellin and cytokinin signaling. The homologous gene models in Arabidopsis , including AT4G25080, AT4G23940, AT5G08130 , and AT4G21440 genes, were identified as orthologs of VRADI07G29860, VRADI07G29450, VRADI07G17780 , and VRADI07G15650 , respectively ( Table S1 ). The digital gene expression analysis revealed that...”
- “...Figure 4 Digital gene expression patterns of identified candidate genes (depicted in Arabidopsis). (A) CHLM (AT4G25080) encodes magnesium protoporphyrin IX methyltransferase (orthologous to VRADIO7G29860); (B) FtsHi1 (AT4G23940) is involved in chloroplast biogenesis and division (orthologous to VRADIO7G29450); (C) BIM1 (AT5G08130) encodes bHLH transcription factors and is...”
- Anionic lipids facilitate membrane development and protochlorophyllide biosynthesis in etioplasts
Yoshihara, Plant physiology 2024 - “...ACT8 (AT1G49240), UBQ11 (AT4G05050), CHLH (AT5G13630), CHLD (AT1G08520), CHLI1 (AT4G18480), GUN4 (AT3G59400), HEMA1 (AT1G58290), CHLM (AT4G25080), CHL27 (AT3G56940), PORA (AT5G54190), and PORB (AT4G27440). Supplementary Material kiad604_Supplementary_Data Acknowledgments We thank Tatsuru Masuda (Graduate School of Arts and Sciences, The University of Tokyo) for providing antibody to LPORs....”
- “...AT4G18480 GUN4 Gramene: AT3G59400 GUN4 Araport: AT3G59400 HEMA1 Gramene: AT1G58290 HEMA1 Araport: AT1G58290 CHLM Gramene: AT4G25080 CHLM Araport: AT4G25080 CHL27 Gramene: AT3G56940 CHL27 Araport: AT3G56940 PORA Gramene: AT5G54190 PORA Araport: AT5G54190 PORB Gramene: AT4G27440 PORB Araport: AT4G27440 References Aoki M , Sato N , Meguro A...”
- Identification and Validation of qRT-PCR Reference Genes for Analyzing <i>Arabidopsis</i> Responses to High-Temperature Stress
Chen, Current issues in molecular biology 2024 - “...R: GACCGGTTTGCTTGTTACGA LHCB5 AT4G10340 F: CTGAGGTTGTTCTCCTCGGT R: AGAAGAGCTCCTTGCTCAGG PIP1C AT1G01620 F: ATTGGAATCGTCGCCAAGTG R: ATCGGAACCTTCGTCCTTGT CHLM AT4G25080 F: CTGCTGCTATGGTTGCTGAA R: CACGTCGAGACATACAACGG COL4 AT5G24930 F: CCGACGGTGAACGAGAATTG R: CCACTCCCACTTCCATCGAC SCA1 AT2G33800 F: AGAAGTTGTTGCTGCTGTTCA R: TGGTGAAGCAGGTCTAAGCA LHCA3 AT1G61520 F: TTGTGGTTTGCTTCATCGCA R: TCCTCCAGTACCTTCTGGGT PSBX AT2G06520 F: ACTTAACCAGACCCGTTCGT R: GGAGATACCGGTCAAAGCCT LHCB4.1 AT5G01530...”
- AtMYB72 aggravates photosynthetic inhibition and oxidative damage in Arabidopsis thaliana leaves caused by salt stress
Zhang, Plant signaling & behavior 2024 - “...degradation-related genes. In addition, NaCl stress down-regulated the expression of GSAM (AT3G48730), POR (AT1G03630), CHL (AT4G25080) and DVR (AT5G57850) genes in OE-10 plants. At the same time, the expression levels of a few chlorophyll synthesis-related genes GSAM (AT5G63570), ALAD (AT1G69740), CHLG (AT3G51820) and chlorophyll degradation-related genes...”
- “...of AtMYB72 gene significantly down-regulated chlorophyll synthesis genes such as GSAM (AT3G48730), POR (AT1G03630), CHL (AT4G25080), and DVR (AT5G18660) in A. thaliana leaves under salt stress, and the key enzyme genes of chlorophyll degradation PPH (AT5G13800), NYC1 (AT4G13250) and PAO (AT3G44880) were significantly up-regulated, thus further...”
- Integrative transcriptomics and proteomics profiling of <i>Arabidopsis thaliana</i> elucidates novel mechanisms underlying spaceflight adaptation
Olanrewaju, Frontiers in plant science 2023 - “...AT2G45290 Transketolase-2 0.23 0.045 -0.81 0.03 AT3G22960 Plastidial pyruvate kinase 1 0.29 0.013 -0.45 0.05 AT4G25080 Magnesium protoporphyrin IX methyltransferase 0.24 0.035 -0.78 0.03 AT4G38690 PLC-like phosphodiesterases 0.28 0.017 -0.41 0.02 AT5G01750 Protein LURP-one-related 15 0.44 0.044 -0.29 0.02 AT5G03300 Adenosine kinase 2 0.45 0.035 -0.44...”
- The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas
Bhattacharya, Frontiers in plant science 2023 - “...Solyc10g018300 TKL1 Transketolase 1 39 0.293 At3g60750 2 Solyc03g118240 CHLM Magnesium-protoporphyrin IX methyltransferase 40 0.280 At4g25080 nd Solyc02g083810 LFRN R PETH FerredoxinNADP reductase 41 0.275 At1g20020 3 Solyc02g084440 FBA3 M Fructose-bisphosphate aldolase 42 0.270 At4g38970 2 Solyc08g076220 PRK Phosphoribulokinase/uridine kinase 43 0.265 At1g32060 3 544163637 CLPP1...”
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
Zhang, Genome biology 2022 - “...KINASE 1 - CIPK1) and a novel isoform (AT4G25080.13) encoding an N-terminally truncated protein of AT4G25080 (MAGNESIUM-PROTOPORPHYRIN IX METHYLTRANSFERASE - CHLM) in AtRTD3 (Additional File 2 : Fig. S16 and S17, respectively). Cold- and blue light-induced differential TSS and poly(A) site usage Differential TSS and TES...”
- Investigating the Viral Suppressor HC-Pro Inhibiting Small RNA Methylation through Functional Comparison of HEN1 in Angiosperm and Bryophyte
Sanobar, Viruses 2021 - “...cacao (Thecc1EG026937); Cpa, Carica papaya (evm.model.supercontig_166.41), Vv, Vitis vinifera (GSVIVG01021670001) and Arabidopsis thaliana , CHLM (AT4G25080). The bootstrap values are shown above the branches at the nodes. Arrowheads indicate duplicated events. Figure 9 Multiple alignments of the MTase domain among different plant species. The arrowheads and...”
- More
LHK_03103 Cyclopropane-fatty-acyl-phospholipid synthase from Laribacter hongkongensis HLHK9
35% identity, 26% coverage
- General metabolism of Laribacter hongkongensis: a genome-wide analysis
Curreem, Cell & bioscience 2011 - “...+ - In addition, the presence of two homologues of cyclopropane fatty-acyl-phospholipid synthases (LHK_01324 and LHK_03103) (CFA synthase) suggested the possibility for L. hongkongensis to synthesize cyclopropane fatty acid. Cyclopropane fatty acids are found in the bacterial membrane and are believed to be involved in acid...”
MSMEG_6483 methyltransferase type 11 from Mycobacterium smegmatis str. MC2 155
34% identity, 45% coverage
NP_001328344 magnesium-protoporphyrin IX methyltransferase from Arabidopsis thaliana
27% identity, 44% coverage
ERG6_ASPFU / Q4W9V1 Sterol 24-C-methyltransferase erg6; Delta(24)-sterol C-methyltransferase erg6; 24-SMT; Ergosterol biosynthesis protein 6; S-adenosyl-L-methionine:sterol C-24 methyl transferase erg6; SAM:SMT; EC 2.1.1.- from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (Neosartorya fumigata) (see 2 papers)
AFUA_4G03630, Afu4g03630 sterol 24-c-methyltransferase, putative from Aspergillus fumigatus Af293
31% identity, 26% coverage
- function: Sterol 24-C-methyltransferase; part of the third module of ergosterol biosynthesis pathway that includes the late steps of the pathway (PubMed:18191972, PubMed:28224386). Methylates lanosterol at C- 24 to produce eburicol (PubMed:18191972, PubMed:28224386). The third module or late pathway involves the ergosterol synthesis itself through consecutive reactions that mainly occur in the endoplasmic reticulum (ER) membrane. Firstly, the squalene synthase erg9 catalyzes the condensation of 2 farnesyl pyrophosphate moieties to form squalene, which is the precursor of all steroids. Squalene synthase is crucial for balancing the incorporation of farnesyl diphosphate (FPP) into sterol and nonsterol isoprene synthesis. Secondly, squalene is converted into lanosterol by the consecutive action of the squalene epoxidase erg1 and the lanosterol synthase erg7. Then, the delta(24)- sterol C-methyltransferase erg6 methylates lanosterol at C-24 to produce eburicol. Eburicol is the substrate of the sterol 14-alpha demethylase encoded by cyp51A and cyp51B, to yield 4,4,24-trimethyl ergosta-8,14,24(28)-trienol. The C-14 reductase erg24 then reduces the C14=C15 double bond which leads to 4,4-dimethylfecosterol. A sequence of further demethylations at C-4, involving the C-4 demethylation complex containing the C-4 methylsterol oxidases erg25A or erg25B, the sterol-4-alpha-carboxylate 3-dehydrogenase erg26 and the 3-keto-steroid reductase erg27, leads to the production of fecosterol via 4- methylfecosterol. The C-8 sterol isomerase erg2 then catalyzes the reaction which results in unsaturation at C-7 in the B ring of sterols and thus converts fecosterol to episterol. The sterol-C5-desaturase erg3B then catalyzes the introduction of a C-5 double bond in the B ring to produce 5-dehydroepisterol. The 2 other sterol-C5-desaturases, erg3A and erg3C, seem to be less important in ergosterol biosynthesis. The C-22 sterol desaturase erg5 further converts 5-dehydroepisterol into ergosta-5,7,22,24(28)-tetraen-3beta-ol by forming the C-22(23) double bond in the sterol side chain. Finally, ergosta-5,7,22,24(28)- tetraen-3beta-ol is substrate of the C-24(28) sterol reductases erg4A and erg4B to produce ergosterol. Possible alternative sterol biosynthetic pathways might exist from fecosterol to ergosterol, depending on the activities of the erg3 isoforms (Probable) (PubMed:16110826, PubMed:18191972).
catalytic activity: lanosterol + S-adenosyl-L-methionine = eburicol + S-adenosyl- L-homocysteine + H(+) (RHEA:52652) - Toxic eburicol accumulation drives the antifungal activity of azoles against Aspergillus fumigatus
Elsaman, Nature communications 2024 - “...can be repressed. The genome of A. fumigatus harbors two genes that encode Erg6 homologs, AFUA_4G03630 and AFUA_4G09190, which we named erg6A and erg6B , respectively. Since we initially assumed that the two Erg6 homologs might be functionally redundant, we planned to generate a double mutant...”
- Genomic Epidemiology Identifies Azole Resistance Due to TR34/L98H in European Aspergillus fumigatus Causing COVID-19-Associated Pulmonary Aspergillosis
Simmons, Journal of fungi (Basel, Switzerland) 2023 - “...cyp51A Afu2g03700 hmg1 A640V/A9T [ 31 ] Afu4g06890 cyp51A Afu2g03700 hmg1 H237Y/N157S [ 31 ] Afu4g03630 erg6 Afu2g03700 hmg1 S269C/G54R [ 31 ] Afu4g06890 cyp51A Afu4g03630 erg6 W320G [ 83 ] Afu4g04820 erg25 W218 * Afu4g11240 aarA F481S Afu5g07960 C2H2 Y347 * Afu1g17440ABC drug transporter Y1149N...”
- “...(mg/L) POS MIC (mg/L) TR Gene of A. fumigatus Amino Acid Substitution Afu4g06890 Afu1g17440 AFu7g01960 Afu4g03630 C438* >16 4 2 TR 34 L98H E581A/Y1149N WT WT C441* 8 4 0.5 TR 34 L98H E581A/Y1149N WT WT C444 >32 2 1 TR 34 L98H E581A/Y1149N I149V/ P160S...”
- The Transcriptome Response to Azole Compounds in Aspergillus fumigatus Shows Differential Gene Expression across Pathways Essential for Azole Resistance and Cell Survival
Hokken, Journal of fungi (Basel, Switzerland) 2023 - “...in ergosterol biosynthesis, whereas itraconazole-resistant isolate V162(R)-ICZ showed only strong up-regulation for the erg6 gene (Afu4g03630). Our previous study on the immediate transcriptomic response of A. fumigatus to itraconazole also showed up-regulation of erg6 within 30 min of ICZ addition to the medium, which persisted until...”
- “...putative N/A 3,38 Afu4g09550 Putative uncharacterized protein N/A 3,36 Afu1g12420 Putative uncharacterized protein N/A 3,33 Afu4g03630 Sterol 24-c-methyltransferase; putative erg6 3,25 Afu3g10370 Putative uncharacterized protein N/A Down-regulated -2,60 Afu2g00570 GNAT family acetyltransferase; putative N/A -2,61 Afu2g17850 3-beta hydroxysteroid dehydrogenase/isomerase; putative N/A -2,71 Afu1g17270 FRE family ferric-chelate...”
- Genomic epidemiology of EuropeanAspergillus fumigatuscausing COVID-19-associated pulmonary aspergillosis in Europe
Simmons, 2023 - Genome-Wide Association Analysis for Triazole Resistance in Aspergillus fumigatus
Fan, Pathogens (Basel, Switzerland) 2021 - “...10 1 1.17 10 1 1.56 10 1 4.34 10 2 [ 33 ] erg6 (AFUA_4G03630) A350 NA 1 [ 34 ] cox10 (AFUA_4G08340) R243 NA 1 [ 35 ] AFUA_7G01960 L167 Stop Gained CHR 7531,582 1.00 1.00 1.00 4.66 10 1 [ 36 ] AFUA_2G10600...”
- Mutations in hmg1, Challenging the Paradigm of Clinical Triazole Resistance in Aspergillus fumigatus
Rybak, mBio 2019 - “...isolates were also observed in erg3B (Afu2g00320), erg3C (Afu8g01070), erg4B (Afu1g07140), erg5 (Afu1g03950), and erg6 (Afu4g03630). However, mutations occurred in these genes among only a small number of the clinical isolates (see TableS1 in the supplemental material). Intriguingly, 11 of the 21 triazole-resistant clinical isolates (52%)...”
- Aspergillus fumigatus High Osmolarity Glycerol Mitogen Activated Protein Kinases SakA and MpkC Physically Interact During Osmotic and Cell Wall Stresses
Manfiolli, Frontiers in microbiology 2019 - “...and Afu3g14420, Tables 1 4 ) and ergosterol (Afu3g10660, Afu6g14200, Afu5g02450, Afu7g03740, Afu4g06890, Afu4g07130, and Afu4g03630, Tables 1 3 ). The transcription factors DvrA (Afu3g09820, Table 1 ), the putative C. albicans Bcr1p ortholog, that regulates biofilm formation and expression of cell-surface genes, and NsdD (Afu3g13870,...”
- Phenotypic plasticity and the evolution of azole resistance in Aspergillus fumigatus; an expression profile of clinical isolates upon exposure to itraconazole
Hokken, BMC genomics 2019 - “...protein CbpA (Afu2g13060). Amongst the constant up-regulated genes were the putative sterol 14 demethylase Erg6 (Afu4g03630) and the fatty acid oxygenase PpoA (Afu4g10770). Fig. 4 Venn diagram showing the overlap between the differentially expressed genes on each time point. A core set of 186 genes was...”
- More
XP_016608596 uncharacterized protein from Spizellomyces punctatus DAOM BR117
30% identity, 31% coverage
- Arsenite Methyltransferase Diversity and Optimization of Methylation Efficiency
Chen, Environmental science & technology 2023 - “...379 AAs, 3 (ABC) 37% As(III) DMAs(V) Pedersen et al., 2020 Spizellomyces punctatus , SpArsM (XP_016608596) Eukarya fungi 346 AAs, 3 (ABC) 15% As(III) MAs(V) Pedersen et al., 2020 Ostreococcus tauri , OtArsM (XP_022840421) Eukarya plantae 405 AAs, 3 (ABC) 42% As(III) MAs(V) Pedersen et al.,...”
OFAG_00246 SAM-dependent methyltransferase from Oxalobacter paraformigenes
35% identity, 24% coverage
TMT3_CATRO / A0A8X8M4W6 Gamma-tocopherol methyltransferase, chloroplastic; pCrgammaTMT; Gamma-tocopherol-like methyltransferase 3; Picrinine-N-methytransferase TMT3; EC 2.1.1.- from Catharanthus roseus (Madagascar periwinkle) (Vinca rosea) (see paper)
30% identity, 27% coverage
- function: S-adenosyl-L-methionine-dependent N-methyltransferase involved in the biosynthesis of biologically active monoterpenoid indole alkaloids (MIAs) natural products including vindoline (By similarity). Inactive with picrinine as substrate (PubMed:35166361).
catalytic activity: picrinine + S-adenosyl-L-methionine = ervincine + S-adenosyl- L-homocysteine + H(+) (RHEA:76143)
subunit: Homodimer.
XP_004336540 sterol 24c-methyltransferase from Acanthamoeba castellanii str. Neff
25% identity, 57% coverage
- Steroidal antibiotics are antimetabolites of Acanthamoeba steroidogenesis with phylogenetic implications
Zhou, Journal of lipid research 2019 - “...lysate protein. Site-directed mutagenesis and Ac SMT purification The A. castellanii sterol C24-methyltransferase genes (24-SMT, XP_004336540 and 28-SMT, XP_004335307) were synthesized by Eurofin MWG Operon (Huntsville, AL) incorporating an Nde1 restriction site at the 5 end and a BAMHI restriction site at the 3 end of...”
- Sterol methyltransferase a target for anti-amoeba therapy: towards transition state analog and suicide substrate drug design
Kidane, Journal of lipid research 2017 - “...from S-adenosyl-L-methionine (SAM) at C24 and C28, respectively ( 27 ). The Acanthamoeba genes (24-SMT, XP_004336540 and 28-SMT, XP_004335307) were synthesized by Eurofin MWG (Huntsville, AL) incorporating an Nbe1 restriction site at the 5end and a BAMH1 restriction site at the 3 end of the open...”
- “...sequences used to evaluate the protein evolution across kingdoms were A. castellanii-1 (XP_004335307), A. castellanii-2 (XP_004336540), Leishmania mexicana (XP_003874589), Clavispora lusitaniae (XP_002617229), Monosiga brevicollis (XP_001748534), Chlamydomonas reinhardtii (XP_001690775), Trypanosoma brucei (XP_822930), Yarrowia lipolytica (XP_505173), Glycine max-1 (NP_001238391), Zea mays- 1 (ACG33830), Z. mays -2 (NP_001149131), Trypanosoma...”
HVO_0773 N-methyltransferase-like protein from Haloferax volcanii DS2
D4GTS8 S-adenosylmethionine-dependent methyltransferase from Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)
30% identity, 41% coverage
MMAR_1683 hypothetical protein from Mycobacterium marinum M
30% identity, 39% coverage
SPRG_05001 hypothetical protein from Saprolegnia parasitica CBS 223.65
32% identity, 20% coverage
- Comparative analysis of sterol acquisition in the oomycetes Saprolegnia parasitica and Phytophthora infestans
Dahlin, PloS one 2017 - “...at least 1.5 fold for the lanosterol synthase gene SPRG_11783, the 24 sterol methyltransferase gene SPRG_05001, and the 3 sterol keto reductase gene SPRG_16338 during growth in YM and Peptone media, compared to Machlis samples ( Fig 3 ). The 24 sterol reductase SPRG_04988 was upregulated...”
- “...Fig 3 ). The greatest increase in expression compared to Machlis medium was seen for SPRG_05001 (1.75 fold in Peptone medium and 2.2 fold in YM medium). 10.1371/journal.pone.0170873.g003 Fig 3 Gene expression analysis by qPCR of putative S . parasitica sterol related genes. Expression levels of...”
Glov_0357 transcriptional regulator, ArsR family from Geobacter lovleyi SZ
29% identity, 47% coverage
- Arsenic Detoxification by Geobacter Species
Dang, Applied and environmental microbiology 2017 - “...Geob_2213 Ga0098289_102202 Glov_1189 Glov_1665 Glov_0357 K419DRAFT_00674 K419DRAFT_00388 K419DRAFT_04127 Geob_3457 Geob_2249 Geob_0483 Geob_0528 Geob_2068...”
CSH63_31725 SAM-dependent methyltransferase from Micromonospora tulbaghiae
27% identity, 64% coverage
NGR_a02390 nodulation methyltransferase NodS from Sinorhizobium fredii NGR234
NGR_a02390 nodulation protein NodS; involved in N-methylation of Nodulation factor from Rhizobium sp. NGR234
31% identity, 52% coverage
CNC07040 hypothetical protein from Cryptococcus neoformans var. neoformans JEC21
34% identity, 21% coverage
XC_1689 hypothetical protein from Xanthomonas campestris pv. campestris str. 8004
32% identity, 53% coverage
- Xanthomonas campestris sensor kinase HpaS co-opts the orphan response regulator VemR to form a branched two-component system that regulates motility
Li, Molecular plant pathology 2020 - “...For example, XC_1660 , XC_1661 , XC_1664 , XC_1665 , XC_1667 , XC_1688 , and XC_1689 or genes that encode the proteins involved in EPS synthesis were downregulated in the hpaS mutant. XC_0738 , XC_0739 , XC_0740 , and XC_0744 thatencode proteins involved in the type...”
DET1420 methyltransferase, UbiE/COQ5 family from Dehalococcoides ethenogenes 195
28% identity, 48% coverage
SMb20238 HYPOTHETICAL PROTEIN from Sinorhizobium meliloti 1021
28% identity, 53% coverage
- Identification and characterization of a NaCl-responsive genetic locus involved in survival during desiccation in Sinorhizobium meliloti
Vriezen, Applied and environmental microbiology 2013 - “...smc04299 smc01445 ndiA1 loe3b 299-307 1-7 4-12 smb20238 loe2b/C1 17-26 smb20481 smb20482 smb20073 loe4b/asnO loe6b/ngg 979-987 1058-1066 273-281 HAD, haloacid...”
- FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti
Bobik, Journal of bacteriology 2006 - “...(9, 24, 48). Seven of these genes (SMa1447, SMb20238, SMb20481, SMb20482, SMb21441, SMc04299, and SMc03247) were not induced under microoxic conditions in our...”
A3AAG5 Methyltransferase type 11 domain-containing protein from Oryza sativa subsp. japonica
32% identity, 35% coverage
- Combining Proteomics and Metabolomics to Analyze the Effects of Spaceflight on Rice Progeny
Zeng, Frontiers in plant science 2022 - “...[H(+)-exporting diphosphatase), Q0JMV6 (Os01g0357100 protein), A2YC52 (Peroxidase), Q5U1N4 (Class III peroxidase 59), Q8GTK0 (Starch synthase), A3AAG5 (Methyltransf_11 domain-containing protein), B8AX06 (UbiA prenyltransferase family)] were related to changes in the content of 4-Hydroxycinnamic acid ( Figure 8A ). Interestingly, among these 11 proteins, there are proteins involved...”
6mroA / Q8TNZ0 Crystal structure of methyl transferase from methanosarcina acetivorans at 1.6 angstroms resolution, northeast structural genomics consortium (nesg) target mvr53.
26% identity, 60% coverage
- Ligands: s-adenosyl-l-homocysteine; calcium ion (6mroA)
PITG_15903 phosphoethanolamine N-methyltransferase from Phytophthora infestans T30-4
34% identity, 20% coverage
- MiR1918 enhances tomato sensitivity to Phytophthora infestans infection
Luan, Scientific reports 2016 - “...trafficking protein particle complex subunit ( pi-TG2 , PITG_14806) and phosphoethanolamine N-methyltransferase ( pi-TG3 , PITG_15903) ( Fig. 1a,c ). Quantitative real time RT-PCR ( q RT-PCR) was used to examine the expression of sly-miR1918 and pi-miR1918 as well as their target genes in tomato and...”
A0A2R2UK37 cycloartenol 24-C-methyltransferase (EC 2.1.1.142) from Paris polyphylla (see paper)
31% identity, 29% coverage
VP_RS05430 malonyl-ACP O-methyltransferase BioC from Vibrio parahaemolyticus RIMD 2210633
32% identity, 40% coverage
A0QRH1 demethylmenaquinone methyltransferase (EC 2.1.1.163) from Mycolicibacterium smegmatis (see paper)
28% identity, 67% coverage
Glov_0896 Methyltransferase type 11 from Geobacter lovleyi SZ
29% identity, 40% coverage
- Arsenic Detoxification by Geobacter Species
Dang, Applied and environmental microbiology 2017 - “...ArsM protein from Rhodopseudomonas palustris (33): the Glov_0896, Gura_2444, and Gmet_2791 gene products are 51%, 56%, and 55% similar, respectively. Similar...”
- “...Ga0098289_102212 Glov_1149 Ga0098289_10560 Glov_1148 Ga0098289_10559 Glov_0896 their overall genomes. Therefore, if these genes were acquired via...”
MSMEG_1049 methyltransferase, UbiE/COQ5 family protein from Mycobacterium smegmatis str. MC2 155
MSMEG_2329 methyltransferase, UbiE/COQ5 family protein from Mycobacterium smegmatis str. MC2 155
26% identity, 47% coverage
SPOA0294 class I SAM-dependent methyltransferase from Ruegeria pomeroyi DSS-3
34% identity, 44% coverage
- Transcriptional changes underlying elemental stoichiometry shifts in a marine heterotrophic bacterium
Chan, Frontiers in microbiology 2012 - “...( pstB ) 7.4 SPO1953 Phosphate regulon transcriptional regulatory protein ( phoB ) 10.7 26.1 SPOA0294 Phosphatidylethanolamine N -methyltransferase ( pmtA ) 3.6 1.2 S-LIMITED SPO1256 Polyphosphate kinase 2 ( ppk2 ) 5.0 4.0 SPO1409 RNA polymerase factor sigma-32 ( rpoH-2 ) 12.5 SPO2596 5-amino-levulinate synthase...”
- “...III 4.1 1.6 SPO3625 cspA Cold shock protein 2.6 4.2 SPO3868 Hypothetical protein 1.6 3.6 SPOA0294 pmtA Phosphatidylethanolamine N -methyltransferase 3.6 1.2 S-LIMITED (11 GENES) SPO0412 Hypothetical protein 13.2 SPO0636 EF hand domain-containing protein 3.9 SPO1256 ppk2 Polyphosphate kinase 2 5.0 4.0 SPO1330 hflC HflC protein...”
DR_2562 3-demethylubiquinone-9 3-methyltransferase, putative from Deinococcus radiodurans R1
A2G07_RS00780 class I SAM-dependent methyltransferase from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
29% identity, 51% coverage
RPPA04580 / C4R7Z3 sphingolipid C9-methyltransferase (EC 2.1.1.317) from Komagataella phaffii (strain GS115 / ATCC 20864) (see paper)
C9MT_KOMPG / C4R7Z3 Sphingolipid C9-methyltransferase; C-9-MT; EC 2.1.1.317 from Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) (Pichia pastoris) (see 2 papers)
31% identity, 21% coverage
- function: Catalyzes methylation of the sphingoid base component of glucosylceramides (GluCers) at the C9-position. Sphingolipid C9- methylation requires 4,8-desaturated ceramides as substrates. Glucosylceramides play important roles in growth, differentiation and pathogenicity. The methyl group at the C9-position distinguishes fungal glucosylceramides from those of plants and animals, and may thus play a role in host-pathogen interactions enabling the host to recognize the fungal attack and initiate specific defense responses.
catalytic activity: a (4E,8E)-4-sphinga-4,8-dienine ceramide + S-adenosyl-L- methionine = a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide + S- adenosyl-L-homocysteine + H(+) (RHEA:46804)
disruption phenotype: Produces only non-methylated glucosylceramides (PubMed:16339149). Shows no alteration of growth and no increase in the level of resistance to plant defensins MsDef1 and RsAFP2 (PubMed:19028992).
NNMT / A0A075D6M1 norajmaline N-methyltransferase from Rauvolfia serpentina (see paper)
31% identity, 51% coverage
C1GMW7 sphingolipid C(9)-methyltransferase from Paracoccidioides brasiliensis (strain Pb18)
34% identity, 15% coverage
- Extracellular vesicles from virulent P. brasiliensis induce TLR4 and dectin-1 expression in innate cells and promote enhanced Th1/Th17 response
Montanari, Virulence 2024 - “...C1FYE6 Glutaminase A UP(D) 3,433912 0,000121 Lipid metabolism C1GDH4 leukotriene-A4 hydrolase [EC:3.3.2.6] UP(D) 4,263176 0,000274 C1GMW7 Sphingolipid C9-methyltransferase A UP (8S) 3,572532 0,037729 C1G0P4 long-chain acyl-CoA synthetase [EC:6.2.1.3] UP (12S) 3,064416 0,032289 C1GBJ2 ATP citrate synthase UP(D) 2,453147 0,000166 Other metabolisms C1G421 acetyl-CoA C-acetyltransferase UP(D) 6,076812...”
XNC1_2300 non-ribosomal peptide synthetase from Xenorhabdus nematophila ATCC 19061
31% identity, 8% coverage
ABD52_RS02415 non-ribosomal peptide synthetase from Micromonospora sp. RV43
31% identity, 6% coverage
Q8VWX2 tocopherol C-methyltransferase (EC 2.1.1.95) from Perilla frutescens (see paper)
28% identity, 28% coverage
vte4 / Q55809 tocopherol methyltransferase (EC 2.1.1.95) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see paper)
slr0089 delta(24)-sterol C-methyltransferase from Synechocystis sp. PCC 6803
32% identity, 34% coverage
- Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium
Liberton, Molecular & cellular proteomics : MCP 2016 - “...signal peptides, including three proteins (Slr1744, Slr0089, and Slr1897) from cell envelope, fatty acid, and transport/binding processes, respectively,...”
- “...methyltrans- Molecular & Cellular Proteomics 15.6 ferase (Slr0089) from fatty acid metabolism, was identified as a PM protein. Compared with proteins...”
- Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis
Nogales, Proceedings of the National Academy of Sciences of the United States of America 2012 - “...lipid biosynthetic pathways. For instance, the genes slr0089 and slr1508 which are involved in the biosynthesis of tocopherols and digalactolipids,...”
- RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
Wang, Biotechnology for biofuels 2012 - “...anhydrase 1.55 1.60 slr0070 methionyl-tRNA formyltransferase 1.62 1.69 slr0086 similar to DnaK protein 1.50 2.50 slr0089 gamma-tocopherol methyltransferase 4.60 3.80 slr0091 aldehyde dehydrogenase 7.00 11.00 slr0242 bacterioferritin comigratory protein homolog 1.58 1.65 slr0328 low molecular weight phosphotyrosine protein phosphatase 2.75 2.00 slr0381 lactoylglutathione lyase 5.14 5.00...”
- Alpha-tocopherol is essential for acquired chill-light tolerance in the cyanobacterium Synechocystis sp. strain PCC 6803
Yang, Journal of bacteriology 2008 - “...unable to synthesize -tocopherol, such as slr1736, slr1737, slr0089, and slr0090 mutants, almost completely lost ACLT. When exposed to chill without light,...”
- “...difference from the wild type. When complemented, the slr0089 mutant regained its ACLT. Copper-regulated expression of slr0090 from PpetE controlled the level...”
A0A4D6L976 Magnesium-protoporphyrin O-methyltransferase from Vigna unguiculata
27% identity, 45% coverage
- Proteomic Insights of Cowpea Response to Combined Biotic and Abiotic Stresses
Ribeiro, Plants (Basel, Switzerland) 2023 - “...1.80 Decreased A0A4D6M6X8 Magnesium-protoporphyrin IX monomethyl ester (oxidative) cyclase 50.37 1.49 10 2 2.72 Decreased A0A4D6L976 Magnesium-protoporphyrin O-methyltransferase 252.45 5.47 10 4 2.26 Decreased A0A4D6N7U7 NADPH-protochlorophyllide oxidoreductase 281.88 1.81 10 5 2.45 Decreased A0A4D6KW86 Geranylgeranyl reductase 58.53 4.78 10 4 3.34 Decreased A0A4D6MNX0 Chlorophyll a-b binding...”
PA5457 hypothetical protein from Pseudomonas aeruginosa PAO1
32% identity, 36% coverage
- Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa
Hong, BMC microbiology 2017 - “...CPA, and show a reduced PAPI-1 transfer efficiency (Fig. 1 ). To the contrary, enzymes pa5457 and pa5458 are not essential for biosynthesis of a CPA structure [ 34 ], and mutants in these genes showed comparable transfer efficiency as the wild-type strain. Noticeably, the mutant...”
- Single-Nucleotide Polymorphisms Found in the migA and wbpX Glycosyltransferase Genes Account for the Intrinsic Lipopolysaccharide Defects Exhibited by Pseudomonas aeruginosa PA14
Hao, Journal of bacteriology 2015 - “...five-gene operon, pa5455 and pa5456 encode glycosyltransferases, pa5457 and pa5459 encode methyltransferases, and pa5458 codes for a putative acetyltransferase...”
- Five new genes are important for common polysaccharide antigen biosynthesis in Pseudomonas aeruginosa
Hao, mBio 2013 - “...pa5456 encode putative glycosyltransferases. The pa5458 gene encodes a protein with a conserved acetyltransferase domain. PA5457 and PA5459 contain conserved methyltransferase domains and show sequence similarity to E.coli O8 O-antigen terminator protein WbdD. As mentioned earlier, it is not known how the rhamnan is linked to...”
- “...Western blots obtained with MAb N1F10. The knockout mutants of the putative methyltransferase genes ( pa5457 and pa5459 ) exhibited different phenotypes. LPS from the pa5457 mutant was indistinguishable from LPS from the wild type by SDS-PAGE and silver staining analysis and by Western blotting (...”
- Screening for quorum-sensing inhibitors (QSI) by use of a novel genetic system, the QSI selector
Rasmussen, Journal of bacteriology 2005 - “...PA5171 PA5172 PA5173 PA5212 PA5235 PA5297 PA5352 PA5383 PA5457 PA5460 PA5468 PA5481 PA5482 PA5503 PA5506 PA5517 PA5541 PA5544 Gene 1810 RASMUSSEN ET AL. J....”
SCAB_31791 thaxtomin synthetase A from Streptomyces scabiei 87.22
SCAB_RS15085 thaxtomin non-ribosomal peptide synthetase TxtA from Streptomyces scabiei 87.22
29% identity, 9% coverage
- The leucine-responsive regulatory protein SCAB_Lrp modulates thaxtomin biosynthesis, pathogenicity, and morphological development in Streptomyces scabies
Liu, Molecular plant pathology 2023 - “...al., 2017a ). 4.8 EMSA The promoter regions of txtR ( SCAB_31801 ), txtA ( SCAB_31791 ), txtE ( SCAB_31831 ), amfC ( SCAB_49711 ), whiB ( SCAB_55081 ), ssgB ( SCAB_53351 ), and SACB_Lrp ( SCAB_77,931 ) were amplified from 87.22 genomic DNA by PCR...”
- The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors
Deflandre, Microbial genomics 2022 - “...cellobiose and cellotriose, respectively ( Fig. 2a ). The thaxtomin core biosynthetic genes, txtA ( scab_31791 ) and txtB ( scab_31781 ) are also known to be triggered by both cellobiose and cellotriose [ 25 ] and therefore can be regarded as additional positive controls for...”
- “...1.40.3 1.50.3 1.4 16 a Thaxtomins SCAB_RS15080 (SCAB_24681) 5.40.3 5.80.3 5.2 2.70.3 4.10.3 3.3 SCAB_RS15085 (SCAB_31791) 4.60.3 4.80.3 2.00.3 3.40.3 16b Unknown SCAB_RS15175 (SCAB_32031) 0.50.2 ns 0.6 ns 0.7 SCAB_RS15180 (SCAB_32041) ns ns ns 1.00.4 SCAB_RS15185 (SCAB_32051) ns 0.60.2 0.60.2 0.50.2 17 Spore pigment SCAB_RS20600 (SCAB_43301)...”
- The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors
Deflandre, Microbial genomics 2022 - “...1.5 1.40.3 1.50.3 1.4 16 a Thaxtomins SCAB_RS15080 (SCAB_24681) 5.40.3 5.80.3 5.2 2.70.3 4.10.3 3.3 SCAB_RS15085 (SCAB_31791) 4.60.3 4.80.3 2.00.3 3.40.3 16b Unknown SCAB_RS15175 (SCAB_32031) 0.50.2 ns 0.6 ns 0.7 SCAB_RS15180 (SCAB_32041) ns ns ns 1.00.4 SCAB_RS15185 (SCAB_32051) ns 0.60.2 0.60.2 0.50.2 17 Spore pigment SCAB_RS20600...”
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