Family Search for PF10354 (DUF2431)

PF10354.9 hits 8 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

BMT5_SCHPO / O94480 25S rRNA (uridine-N(3))-methyltransferase; EC 2.1.1.- from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
Aligns to 61:226 / 282 (58.9%), covers 100.0% of PF10354, 187.7 bits

• function: S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(3) position of a uridine in 25S rRNA.
  catalytic activity: S-adenosyl-L-methionine + uridine in 25S rRNA = H(+) + N(3)- methyluridine in 25S rRNA + S-adenosyl-L-homocysteine (RHEA:54588)

BMT5_YEAST / P40493 25S rRNA (uridine(2634)-N(3))-methyltransferase; Base methyltransferase of 25S RNA 5; EC 2.1.1.313 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
P40493 25S rRNA (uracil2634-N3)-methyltransferase (EC 2.1.1.313) from Saccharomyces cerevisiae (see paper)
BMT5 / P40493 25S rRNA (uracil²⁶³⁴-N³)-methyltransferase (EC 2.1.1.313) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see paper)
YIL096C Putative protein of unknown function; associates with precursors of the 60S ribosomal subunit (RefSeq) from Saccharomyces cerevisiae
NP_012170 25S rRNA (uracil2634-N3)-methyltransferase from Saccharomyces cerevisiae S288C
Aligns to 75:292 / 336 (64.9%), covers 99.4% of PF10354, 177.2 bits

• function: S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(3) position of uridine 2634 (m3U2634) in 25S rRNA.
  catalytic activity: S-adenosyl-L-methionine + uridine(2634) in 25S rRNA = H(+) + N(3)-methyluridine(2634) in 25S rRNA + S-adenosyl-L-homocysteine (RHEA:43188)
• Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae
  Sharma, Nucleic acids research 2014
  • “...other known base methylations have been recently identified. Here we report the identification of BMT5 (YIL096C) and BMT6 (YLR063W) , two previously uncharacterized genes, to be responsible for m 3 U2634 and m 3 U2843 methylation of the 25S rRNA, respectively. These genes were identified by...”
  • “...residues, m 3 U (N3 methyl uridine) and m 5 U (C5 methyl uridine). Bmt5 (Yil096c) and Bmt6 (Ylr063w), two previously uncharacterized proteins, turned out to be the base methyltransferases responsible for m 3 U2634 and m 3 U2843 base methylation, respectively. The genes were identified...”
• Probabilistic approach to predicting substrate specificity of methyltransferases
  Szczepińska, PLoS computational biology 2014
  • “...tested protein methylation for selected Rossmann-like fold MTases with unknown substrate specificity: YNL092W, YDR316W (OMS1), YIL096C and YKL155C (RSM22). An in vitro MTase activity assay suggests that YNL092W is a protein MTase. For this MTase we detected on tritium screen a methylated product corresponding to the...”
  • “...second yeast protein, after MGT1, capable of automethylation. For the remaining Rossmann-like MTases: YDR316W (OMS1), YIL096C and YKL155C (RSM22), predicted to methylate RNA, we did not observe any protein methylation ( Fig. S2 ), supporting their predicted substrate specificity. Our prediction that YHR209W (CRG1) methylates substrates...”
• Dissecting the cis and trans elements that regulate adjacent-gene coregulation in Saccharomyces cerevisiae
  Arnone, Eukaryotic cell 2014
  • “...YDR101C YDR365C YER049W YGL099W YGR103W YGR145W YGR283C YHL039W YHR196W YIL096C YIL127C RBG1 TOD6 ENP1 RSA4 SYO1 ARX1 ESF1 TPA1 LSG1 NOP7 ENP2 EFM1 UTP9 RRT14...”
• Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions
  Kuppuswamy, Algorithms for molecular biology : AMB 2014
  • “...YNL132W, YMR031C, YFR032C-A, YNL162W, YML017W, YEL054C GO:0001510 18/20 YDR161W, YHR052W, YGR162W, YIL091C, YDR101C, YDL063C, YLR009W, YIL096C, YJR032W, YCR016W, YLR287C , YKL078W, YGR071C, YOL077C, YPL226W, YOR361C, YGR173W, YPL193W GO:0018193 17/20 YOR182C, YHR021C, YJL189W, YLR287C-A, YNL313C, YLR185W, YNL162W, YDL075W, YJL136C, YMR282C, YHR141C, YOL098C, YGR034W, YLR406C, YGR162W, YFR032C-A, YIL069C...”
• Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome
  Wlodarski, PloS one 2011
  • “...MTases, their enzymatic activity has not been confirmed. We also identified one completely novel MTase (YIL096C) among the hypothetical proteins with unknown function. 10.1371/journal.pone.0023168.t001 Table 1 The S. cerevisiae methyltransferome. Fold Substrate MTase Rossmann-like Protein YBR034C (HMT1), YBR133C (HSL7), YDR140W (MTQ2) , YDR435C (PPM1), YDR440W (DOT1),...”
  • “..., YPL266W (DIM1) tRNA/rRNA YDR083W (RRP8) , YNL022C (RCM1) , YNL061W (NOP2) , YBR141C , YIL096C , YLR063W 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...”
• Simultaneous clustering of multiple gene expression and physical interaction datasets
  Narayanan, PLoS computational biology 2010
  • “...EBP2, all of which were implicated in ribosome biogenesis. Cluster #22 had 9 uncharacterized ORFs, YIL096C, YOR021C, YIL091C, YBR269C, YCR087C-A, YDL199C, YKL171W, YMR148W, and YOR006C. Two of them (YIL096C and YOR021C) have predicted roles in ribosome biogenesis based on function predictions collected from the literature by...”
• Rational extension of the ribosome biogenesis pathway using network-guided genetics
  Li, PLoS biology 2009
  • “...showed 40S biogenesis defects at 30C but no defects at 20C. Several nonessential genes, including YIL096C , YCR016W , YJL122W , YNL022C , BUD20 , and NOP13 , form a tight cluster with known ribosome biogenesis genes in the gene network, and their encoded proteins co-sedimented...”
• Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data
  Bryan, BMC genomics 2008 (no snippet)
• More
• Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae.
  Sharma, Nucleic acids research 2014
  • GeneRIF: Identification of BMT5 (YIL096C)as being responsible for m3U2634 methylation of the 25S rRNA.

AT1G55790 ATP binding / nucleotide binding / phenylalanine-tRNA ligase (RefSeq) from Arabidopsis thaliana
Aligns to 31:196 / 414 (40.1%), covers 100.0% of PF10354, 164.9 bits

• Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting
  Coker, Frontiers in plant science 2015
  • “...AT1G30730 AT4G01720 WRKY47 AT1G33960 AIG1 AT4G12490 AT1G34460 CYCB1;5, CYC3 AT4G09420 AT1G35710 AT4G12500 AT1G34670 MYB93 AT4G16563 AT1G55790 AT4G14400 ACD6 AT1G44130 AT4G18540 AT1G66280 BGLU22 AT4G16260 AT1G53830 PME2 AT4G21120 AAT1, CAT1 AT1G73805 AT4G20000 AT1G56550 RXGT1 AT4G23210 CRK13 AT1G74710 EDS16, ICS1, SID2 AT4G20110 VSR7, VSR3;1, BP80-3;1 AT1G58190 RLP9 AT4G38830 CRK26...”
• Functional analyses of cotton (Gossypium hirsutum L.) immature fiber (im) mutant infer that fiber cell wall development is associated with stress responses
  Kim, BMC genomics 2013
  • “...5.00 2.65 2.45 At3g24590 Signal peptidase 1 Biotic stress response (virus) GhiAffx.32033.1.A1_s_at 4.78 2.99 4.28 At1g55790 Unknown function (DUF2431) Metal ion transport GhiAffx.3843.1.A1_at 4.53 4.05 4.81 At3g11600 Response to karrikin Abiotic stress Ghi.8619.1.A1_at 4.38 2.68 2.43 At4g27220 NB-ARC disease resistance Biotic stress response Ghi.9264.2.A1_s_at 3.20 4.88...”

AT4G26485 methyltransferase small domain protein from Arabidopsis thaliana
Aligns to 18:185 / 209 (80.4%), covers 99.4% of PF10354, 156.2 bits

• The modulation of acetic acid pathway genes in Arabidopsis improves survival under drought stress
  Rasheed, Scientific reports 2018
  • “...2.58 AT4G12470 Azelaic acid induced 1 (AZI1) 0.14 0.64 2.57 AT3G24750 LAZY5 14.60 0.66 2.55 AT4G26485 Methyltransferase 1.22 0.76 2.55 AT5G43340 Phosphate Transporter 1;6 (PHT1;6) 1.68 1.01 2.50 AT3G24230 Pectate lyase 2.42 2.04 2.47 AT1G26680 B3 family TF 1.59 1.17 2.44 AT1G19230 Riboflavin synthase-like 2.46 1.78...”

NP_941077 ferredoxin-fold anticodon-binding domain-containing protein 1 homolog from Mus musculus
Aligns to 7:176 / 622 (27.3%), covers 99.4% of PF10354, 143.8 bits

• Tissue expression patterns identify mouse cilia genes.
  McClintock, Physiological genomics 2008 (PubMed)
  • GeneRIF: D630004A14Rik is most abundantly expressed in tissues rich in highly ciliated cells, such as olfactory sensory neurons, and is predicted to be important to cilia.

AT4G26480 KH domain-containing protein (RefSeq) from Arabidopsis thaliana
Aligns to 1:147 / 555 (26.5%), covers 86.9% of PF10354, 125.0 bits

• Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri
  Suryawanshi, BMC genomics 2016
  • “...0.95 0.67 0.00 0.00 258745_at At3g05920 HIPP43 Putative metallochaperone-like protein 0.93 0.45 0.00 0.06 253964_at At4g26480 NAS-like Protein with NAS domain and KH domain 0.93 0.37 0.01 0.14 247331_at At5g63530 FP3 Farnesylated protein 3, metal-binding 0.92 0.45 0.00 0.09 266091_at At2g37920 COPT4, EMB1513 Copper transporter 4,...”

AT1G55803 ferredoxin-fold anticodon-binding domain protein from Arabidopsis thaliana
Aligns to 29:127 / 127 (78.0%), covers 57.7% of PF10354, 99.1 bits

• Codon usage pattern and predicted gene expression in Arabidopsis thaliana
  Sahoo, Gene: X 2019
  • “...AT3G04840 AT2G24980 AT5G16250 AT4G34670 AT1G23720 AT5G04790 Dehydratase AT3G46440 AT5G06630 AT1G74458 AT3G51160 AT3G28550 AT3G28190 Aminoacyl-tRNA synthetase AT1G55803 AT3G54590 AT2G31090 Antibacterial response protein AT5G50840 AT1G21310 AT1G17090 ABC transporter AT5G60790 AT1G76930 AT3G14452 Ubiquitin/ubiquitin like UBQ11 Chaperone/heat shock protein AT1G27330 AT2G05310 UBQ13 AT4G02450 AT3G28193 UBQ4 AT5G12020 AT1G65720 UBQ5 HSC701 AT4G21500...”

AT1G55800 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 29:183 / 314 (49.4%), covers 73.2% of PF10354, 91.2 bits

• Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA
  Duc, PLoS genetics 2013
  • “...described as a chimeric RNA, results from read-through at the 3 end of At1g55805 into At1g55800 and is cleaved within a downstream intergenic space. A clear molecular phenotype associated with loss-of-function fpa mutants is the stable accumulation of RNAs that are cleaved and polyadenylated in intergenic...”
• RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription
  Sonmez, Proceedings of the National Academy of Sciences of the United States of America 2011
  • “...with the TAIR9 annotation) of the downstream gene At1g55800 (Fig. 2B). UA5 and UA10B correspond to polyadenylated read-through transcripts of At1g62820 and...”
  • “...in DNA methylation at two consecutive CG sites within At1g55800 in fcafpa, a twofold increase in CHH, and no change in CNG methylation (Fig. S5B). In the...”

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