scholarly journals PENGELOMPOKKAN SEPULUH VARIETAS TEMBAKAU (Nicotiana tabacum) BERDASARKAN KERAGAMAN RUNUTAN BASA PARSIAL GEN PMT(PUTRESCINE N-METHYLTRANSFERASE) Clustering of ten tobacco (Nicotiana tabacum) varieties based on the partial PMT (putrescine N-methyltranfera

2017 ◽  
Vol 23 (1) ◽  
pp. 36
Author(s):  
Sesanti Basuki ◽  
Sudarsono Sudarsono
Keyword(s):  
Nicotiana Tabacum ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Gene Sequence ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Multiple Sequence Alignment Analysis ◽  
Nicotine Level ◽  
Alignment Analysis ◽  
The Relationship

<p align="center">Abstrak</p><p>Gen <em>PMT</em> adalah gen penyandi enzim putresina N-metiltransferase (PMT) yang berperan dalam lintasan biosintesis nikotin pada tanaman tembakau (<em>Nicotiana tabacum</em>). Sepuluh varietas tembakau yang memiliki perbedaan tingkat kadar nikotin diuji untuk mempelajari: (1) keragaman runutan basa parsial gen <em>PMT</em> dari masing-masing varietas, dan (2) kekerabatan antara sepuluh varietas tembakau yang diuji berdasarkan keragaman runutan basa parsial gen <em>PMT</em>. Keragaman runutan basa dianalisis dengan mensejajarkan data runutan basa dari sepuluh varietas tembakau yang diuji dengan runutan basa dari <em>Ntpmt_Sindoro1</em> (JQ438825) yang telah tersimpan dalam <em>database</em><em> </em><em>genbank NCBI</em>. Hasil pensejajaran digunakan untuk menghitung matriks jarak, yang selanjutnya digunakan untuk menganalisis hubungan kekerabatan diantara sepuluh varietas tembakau. Hasil analisis memperlihatkan adanya variasi ukuran dan jumlah runutan basaparsial gen <em>PMT</em> asal sepuluh varietas tembakau yang dianalisis. Hasil analisis juga memperlihatkan bahwa runutan basa parsial gen <em>PMT</em> tersebut berasal/diturunkan dari sumber (<em>ancestor</em>) yang sama dan  terkait dengan biosintesis nikotin pada tembakau. Runutan basaparsial gen <em>PMT</em> dari sepuluh varietas yang dianalisis memisahkan antara kelompok tembakau introduksi (kadar nikotin rendah-sedang) dengan kelompok tembakau lokal (kadar nikotin sedang-tinggi). Dua kelompok memisah berdasarkan level kadar nikotin, danperbedaan/perubahan susunan basa pada situs-situs tertentu dari runutan basaparsial gen <em>PMT</em>  yang dianalisis. Informasi tentang mutasi yang terjadi pada situs-situs runutan basa dari parsial gen <em>PMT</em><em> </em>dapat digunakan untuk mempelajari keterkaitan antara perubahan basa pada fragmen gen <em>PMT</em> dengan kandungan nikotin total tembakau yang terjadi selama proses evolusi.</p><p>Kata kunci: Analisis pengelompokkan, gen <em>PMT,</em>Nikotin, <em>Nicotiana tabacum</em></p><p align="center"><strong> </strong></p><p align="center">Abstract</p><p><strong> </strong><em>PMT</em> gene is the gene encoded putrescine N-methiltransferase which is related to nicotine biosinthesis in tobacco (<em>Nicotiana  tabacum</em>). Ten tobacco varieties with different nicotine level were used inthis study. The aims of this study were: (1) to analyze thepartial <em>PMT</em> gene sequence diversity among ten tobacco varieties, and (2) to evaluate the closed-relationship amongten tobacco varieties based on their partial<em>PMT</em> gene sequences diversity.Sequence diversity was analyzed by multiple sequence alignment between the partial<em>PMT</em> gene sequence of the ten tobacco varietiesand <em>Ntpmt_Sindoro1 </em>sequence deposited in the NCBI gene-bank database.The phylogenetic relationship amongthe sequences was inferred by genetic distancebetween pairs of sequences using the pairwise and multiple sequence alignment analysis. Analysis of the sequences showed that all varieties analyzed had varied in size and number of the <em>PMT</em> gene fragments yielded. The analysis also revealed that thepartial<em>PMT</em> gene sequencesarecoming from the same ancestor which related to nicotine biosynthesis in tobacco. Phylogenetic analysis separated the partial<em>PMT</em> gene sequences into two different branches significantly (bootstrap value = 100), and clustered together based on tobacco types with different nicotine level in whichcould be due to some baseschanged on the specific sites of the<em>PMT</em> gene sequences.  This information could be used to study the relationship between some bases changed on the specific sites of the<em>PMT</em> gene sequences and the nicotine content variation yielded by the ten tobacco varieties that is happened during evolution time.</p><p>Key words: Clustering analysis, <em>PMT</em> gene, nicotine, <em>Nicotiana tabacum</em></p>

scholarly journals SHOOT: phylogenetic gene search and ortholog inference

2021 ◽  
Author(s):  
David Emms ◽  
Steven Kelly
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Phylogenetic Trees ◽  
Query Sequence ◽  
Gene Tree ◽  
Biological Research ◽  
Gene Sequences ◽  
Multiple Sequence ◽  
Gene Search

Determining the evolutionary relationships between gene sequences is fundamental to comparative biological research. However, conducting such analyses requires a high degree of technical proficiency in several computational tools including gene family construction, multiple sequence alignment, and phylogenetic inference. Here we present SHOOT, an easy to use phylogenetic search engine for fast and accurate phylogenetic analysis of biological sequences. SHOOT searches a user-provided query sequence against a database of phylogenetic trees of gene sequences (gene trees) and returns a gene tree with the given query sequence correctly grafted within it. We show that SHOOT can perform this search and placement with comparable speed to a conventional BLAST search. We demonstrate that SHOOT phylogenetic placements are as accurate as conventional multiple sequence alignment and maximum likelihood tree inference approaches. We further show that SHOOT can be used to identify orthologs with equivalent accuracy to conventional orthology inference methods. In summary, SHOOT is an accurate and fast tool for complete phylogenetic analysis of novel query sequences. An easy to use webserver is available online at www.shoot.bio.

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

2020 ◽  
Vol 17 (1) ◽  
pp. 59-77
Author(s):  
Anand Kumar Nelapati ◽  
JagadeeshBabu PonnanEttiyappan
Keyword(s):  
Uric Acid ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Multiple Sequence ◽  
Physiochemical Properties ◽  
Pharmaceutical Industries

Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

2019 ◽  
Vol 15 (4) ◽  
pp. 353-362
Author(s):  
Sambhaji B. Thakar ◽  
Maruti J. Dhanavade ◽  
Kailas D. Sonawane
Keyword(s):  
Phylogenetic Analysis ◽  
Medicinal Plants ◽  
Homology Modeling ◽  
Sequence Alignment ◽  
Vigna Unguiculata ◽  
Multiple Sequence Alignment ◽  
Legume Species ◽  
Mangrove Species ◽  
Multiple Sequence ◽  
Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

A Hierarchical Classification for the Selection of the Most Suitable Multiple Sequence Alignment Methodology

2015 ◽  
Vol 10 (2) ◽  
pp. 199-207
Author(s):  
Francisco Ortuño ◽  
Hector Pomares ◽  
Olga Valenzuela ◽  
Carolina Torres ◽  
Ignacio Rojas
Keyword(s):  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Hierarchical Classification ◽  
Multiple Sequence ◽  
Selection Of

Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach

2020 ◽  
Vol 14 (3) ◽  
pp. 235-246
Author(s):  
Sara Abdollahi ◽  
Mohammad H. Morowvat ◽  
Amir Savardashtaki ◽  
Cambyz Irajie ◽  
Sohrab Najafipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
In Silico ◽  
Bacterial Species ◽  
Arginine Deiminase ◽  
Antitumor Effects ◽  
Multiple Sequence ◽  
In Silico Studies

Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.

Sign in / Sign up

Export Citation Format

Share Document