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Identification of Conserved Domain Combinations in S.cerevisiae Proteins

Suk Hoon Jung, Hee-Young Hur, Desok Kim, Dong-Soo Han
2007 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering  
The method is useful to estimate the meaningfulness of a given domain combination in terms of conservation.  ...  Using the method, we extracted domain patterns in S.cerevisiae proteins and investigated GO term annotations of the domains.  ...  CONSERVED DOMAIN COMBINATION IDENTIFICATION A.  ... 
doi:10.1109/bibe.2007.4375539 dblp:conf/bibe/JungHKH07 fatcat:nso4c5skrvbdrpocfmlmdvtl5e

Computational discovery and annotation of conserved small open reading frames in fungal genomes

Shuhaila Mat-Sharani, Mohd Firdaus-Raih
2019 BMC Bioinformatics  
In this study, we specifically targeted the identification of ORFs encoding for 80 amino acid residues or less from 31 fungal genomes.  ...  A total of 1986 conserved sORFs were predicted and characterized.  ...  identified in this study are in the Additional file 2 provided.  ... 
doi:10.1186/s12859-018-2550-2 pmid:30717662 pmcid:PMC7394265 fatcat:hc5v63eu5vg2dcgw6wxwsgydtu

Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to theSaccharomyces cerevisiaeRAD2 gene

Antony M. Carr, Katherine S. Sheldrick, S. Sheldrick, Johanne M. Murray, Rowyda Al-Harithy, Felicity Z. Watts, Alan R. Lehmann
1993 Nucleic Acids Research  
The first and third domains are also found In a related yet distinct pair of homologous S.pombe/S.cerevisiae DNA repair genes (rad2/YKL510), which have only a very short region between these two conserved  ...  These findings define new functional domains involved In excision-repair, as well as identifying a conserved family of genes related to RAD2.  ...  The identification of conserved genes in the two highly diverged yeasts strongly suggests that these genes will be conserved throughout the eukaryotic kingdom.  ... 
doi:10.1093/nar/21.6.1345 pmid:8464724 pmcid:PMC309318 fatcat:4ql7qsubdvbt3hqhv6ws3czgmq

Unusual features of fibrillarin cDNA and gene structure in Euglena gracilis: evolutionary conservation of core proteins and structural predictions for methylation-guide box C/D snoRNPs throughout the domain Eucarya

A. G. Russell
2005 Nucleic Acids Research  
This increase in complexity raises questions about the evolutionary emergence of the eukaryote-specific proteins and structural conservation in these RNPs throughout the eukaryotic domain.  ...  The predicted fibrillarin protein sequence itself is unusual in that it contains a glycine-lysine (GK)-rich domain at its N-terminus rather than the glycine-arginine-rich (GAR) domain found in most other  ...  An alignment of the most highly conserved portion of the two proteins, corresponding to S.cerevisiae Nop56p residues 312-380 and containing part of the predicted RNA-binding domain (47) , is shown in  ... 
doi:10.1093/nar/gki574 pmid:15894796 pmcid:PMC1126904 fatcat:n4t6dunmuvhfncd5x27admzudm

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

A. Flaus
2006 Nucleic Acids Research  
Baumann for coordinates of eIF4A with ADP, Dr Kathleen Sandman and Prof. John Reeve for providing a Conflict of interest statement. None declared.  ...  However, many domain profiles in resources used for domain analysis have unidentified function or are unreliable in the context of Snf2 proteins.  ...  For some subfamilies there is good correlation with the presence of particular accessory domain combinations (Supplementary Table S9 ).  ... 
doi:10.1093/nar/gkl295 pmid:16738128 pmcid:PMC1474054 fatcat:sqvuudzrsraxznpyqvdrq3dkvi

Identification and characterization of transcription factor IIIA from Schizosaccharomyces pombe

D. B. Schulman
2002 Nucleic Acids Research  
is well conserved.  ...  We now describe the identification and characterization of TFIIIA from Schizosaccharomyces pombe.  ...  We would also like to thank Greg Hannon for providing an S.pombe cDNA library prepared in vector pGAD-GH.  ... 
doi:10.1093/nar/gkf385 pmid:12087160 pmcid:PMC117040 fatcat:jizlw2jmwbaw3csmszsi574kri

Yarrowia lipolytica vesicle-mediated protein transport pathways

Dominique Swennen, Jean-Marie Beckerich
2007 BMC Evolutionary Biology  
are closer to animal ones, whereas they are only 13% in the case of S.cerevisiae.  ...  Quantification of the percentages of proteins with the greatest homology between S.cerevisiae, Y.lipolytica and animal homologues involved in vesicular transport shows that 40% of Y.lipolytica proteins  ...  Galan from Institut Jacques Monod-CNRS (France) for helpful discussions about membrane protein recycling. We thank C.R. Tinsley for the copyediting of the manuscript.  ... 
doi:10.1186/1471-2148-7-219 pmid:17997821 pmcid:PMC2241642 fatcat:kmchiu6rwvb7xac7uyo65asmu4

Cloning and characterization of the Schizosaccharomyces pombe tRNA:pseudouridine synthase Pus1p

K. Hellmuth
2000 Nucleic Acids Research  
The sequence and functional conservation of the Pus1p proteins in fungi and mammalian species and their notable absence from prokaryotes suggest that this family of pseudouridine synthases is required  ...  The corresponding protein, spPus1p, shows sequence similarity to S.cerevisiae and murine Pus1p as well as other known members of the pseudouridine synthase family.  ...  However, in the Pus1-like proteins the two conserved domains are connected via a species-specific linker sequence of variable length.  ... 
doi:10.1093/nar/28.23.4604 pmid:11095668 pmcid:PMC115158 fatcat:rlcedx2gtrdcpf34uym7ygmihy

Three classes of mammalian transcription activation domain stimulate transcription in Schizosaccharomyces pombe

J. E. Remacle
1997 EMBO Journal  
Additional support upstream of the neo gene in pTG4726 (E.Jacobs, Transgène, Strasbourg) was obtained within a framework of a collaboration agreement between to generate pPIARG3GAL4/ADHNEO.  ...  This vector contains the ARG3 the Faculty of Medicine of the University of Leuven and Innogenetics SA. gene for stable integration at the ARG3 locus.  ...  cells, may enable the identification of the target of these domains, which in in vitro assay, whereas crude TFIID preparations support Protein extracts were prepared from yeast harvested 8 h after shifting  ... 
doi:10.1093/emboj/16.18.5722 pmid:9312030 pmcid:PMC1170203 fatcat:ev3d6eaj5zab7et4zdfhy3ynei

Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway

H. van Bakel, M. Huynen, C. Wijmenga
2004 Bioinformatics  
For this purpose, we developed a Web tool (SHOPS) to display the operon context for a given set of proteins. In total, a set of 43 putative operons was identified.  ...  However, the degree to which these genes share their functional context as members of the same pathway in the prokaryotic domain is less clear.  ...  ACKNOWLEDGEMENTS We would like to thank Gabriel Moreno-Hagelsieb for kindly providing us with operon predictions for all prokaryotes in the dataset.  ... 
doi:10.1093/bioinformatics/bth298 pmid:15145814 fatcat:blip2pez6zhodohhsjrsjtwbzm

U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementaritiesm to 28S rRNA

Liang-Hu Qu, Yves Henry, Monique Nicoloso, Bernard Michot, Marie-Claude Azum, Marie-Hélène Renalier, Michele Caizergues-Ferrer, Jean-Pierre Bachellerie
1995 Nucleic Acids Research  
Following computer searches of sequence banks, we have positively identified a novel intronic snoRNA, U24, encoded in the ribosomal protein L7a gene in humans and chicken.  ...  Identification of the yeast Saccharomyces cerevisiae U24 gene directly confirms the outstanding conservation of the complementarity to 28S rRNA during evolution, suggesting a key role of U24 pairing to  ...  Hurt for the yeast S.cerevisiae strains expressing protein A-tagged NOPI and protein A-tagged NSP1.  ... 
doi:10.1093/nar/23.14.2669 pmid:7651828 pmcid:PMC307091 fatcat:mxsegngy4fabpbucozrzqjau7i

Inferring protein-protein interactions through high-throughput interaction data from diverse organisms

Y. Liu, N. Liu, H. Zhao
2005 Bioinformatics  
The estimated domain-domain interaction probabilities are then used to predict protein-protein interactions in S.cerevisiae.  ...  The fact that protein domains are likely evolutionarily conserved allows us to pool information from data across multiple organisms for the inference of domain-domain and protein-protein interaction probabilities  ...  ACKNOWLEDGEMENTS This research was supported in part by National Science Foundation grant DMS-0241160 and Y.L. was supported by the NIH Institutional Training Grants for Informatics Research.  ... 
doi:10.1093/bioinformatics/bti492 pmid:15905281 fatcat:i4r5d7w5ajgh3knem53tki5piq

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

K. L. Posey
2004 Nucleic Acids Research  
A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10.  ...  Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A +5 , and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this  ...  ACKNOWLEDGEMENTS We thank Dr Hongye Li for performing the western analysis of the purified VDE proteins. We thank Dr Carmen Moure and Dr Florante Quiocho for valuable discussions.  ... 
doi:10.1093/nar/gkh734 pmid:15280510 pmcid:PMC506816 fatcat:endxacqlevdirfbmbensranl4a

Characterization of the rhp7+ and rhp16+ genes in Schizosaccharomyces pombe

M. Lombaerts, P. H. Peltola, R. Visse, H. den Dulk, J. A. Brandsma, J. Brouwer
1999 Nucleic Acids Research  
Schizosaccharomyces pombe rhp7 or rhp16 deficient cells are, in contrast to S.cerevisiae rad7 and rad16 mutants, not sensitive to UV irradiation.  ...  In S.pombe an alternative repair mechanism, UV damage repair (UVDR), is capable of efficiently removing photolesions from DNA.  ...  McNabb (Massachusetts Institute of Technology, Cambridge, MA) and Dr. P.  ... 
doi:10.1093/nar/27.17.3410 pmid:10446227 pmcid:PMC148581 fatcat:q72wruxnn5ha5ehrwjzfahrsa4

gar2 is a nucleolar protein fromSchizosaccharomyces pomberequired for 18S rRNA and 40S ribosomal subunit accumulation

Marie-Pierre Gulli, Jean-Philippe Girard, Dan Zabetakis, Bruno Lapeyre, Teri Melese, Michele Caizergues-Ferrer
1995 Nucleic Acids Research  
In addition, like these proteins, gar2 has a nucleolar localisatlon.  ...  Here we report the identification and characterization of a S.pombe gene coding for a novel nucleolar protein, designated gar2.  ...  Ferrer for critical reading of the manuscript and other members of our group for fruitful discussions. We are grateful to J. Feliu and M.  ... 
doi:10.1093/nar/23.11.1912 pmid:7596817 pmcid:PMC306962 fatcat:wqwljiq6draopopbtvwqbhpdoy
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