In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals
This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from Nationa...
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ftmyresearchjour:oai:ojs.pkp.sfu.ca:article/14453 2023-05-15T17:03:37+02:00 In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals Sahoo, P.R. Mishra, S.R. Mohapatra, S. Sahu, Santoswini Sahoo, G. Behera, P.C. 2019-01-07 application/pdf http://myresearchjournals.com/index.php/IJAR/article/view/14453 https://doi.org/10.18805/ijar.B-3712 eng eng Agricultural Research Communication Centre http://myresearchjournals.com/index.php/IJAR/article/view/14453/13635 Copyright (c) 2019 Indian Journal Of Animal Research Indian Journal of Animal Research; Vol 0, No of (2019) 0976-0555 0367-6722 ExPASy”s ProtParam GAPDH Insilco platform Molecular evolutionary genetics analysis phylogenetic analysis. info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Peer-reviewed Article 2019 ftmyresearchjour https://doi.org/10.18805/ijar.B-3712 2019-02-08T23:13:19Z This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species. Article in Journal/Newspaper Killer Whale Killer whale MRJ - MyResearchJournals (MRI Publications Lucknow, Uttar Pradesh, India) Indian Journal of Animal Research of |
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MRJ - MyResearchJournals (MRI Publications Lucknow, Uttar Pradesh, India) |
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ftmyresearchjour |
language |
English |
topic |
ExPASy”s ProtParam GAPDH Insilco platform Molecular evolutionary genetics analysis phylogenetic analysis. |
spellingShingle |
ExPASy”s ProtParam GAPDH Insilco platform Molecular evolutionary genetics analysis phylogenetic analysis. Sahoo, P.R. Mishra, S.R. Mohapatra, S. Sahu, Santoswini Sahoo, G. Behera, P.C. In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
topic_facet |
ExPASy”s ProtParam GAPDH Insilco platform Molecular evolutionary genetics analysis phylogenetic analysis. |
description |
This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species. |
format |
Article in Journal/Newspaper |
author |
Sahoo, P.R. Mishra, S.R. Mohapatra, S. Sahu, Santoswini Sahoo, G. Behera, P.C. |
author_facet |
Sahoo, P.R. Mishra, S.R. Mohapatra, S. Sahu, Santoswini Sahoo, G. Behera, P.C. |
author_sort |
Sahoo, P.R. |
title |
In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
title_short |
In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
title_full |
In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
title_fullStr |
In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
title_full_unstemmed |
In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals |
title_sort |
in silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (gapdh) in domestic animals |
publisher |
Agricultural Research Communication Centre |
publishDate |
2019 |
url |
http://myresearchjournals.com/index.php/IJAR/article/view/14453 https://doi.org/10.18805/ijar.B-3712 |
genre |
Killer Whale Killer whale |
genre_facet |
Killer Whale Killer whale |
op_source |
Indian Journal of Animal Research; Vol 0, No of (2019) 0976-0555 0367-6722 |
op_relation |
http://myresearchjournals.com/index.php/IJAR/article/view/14453/13635 |
op_rights |
Copyright (c) 2019 Indian Journal Of Animal Research |
op_doi |
https://doi.org/10.18805/ijar.B-3712 |
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Indian Journal of Animal Research |
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