BASIL2022GV3HDT: Difference between revisions

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===='''Pfam'''====
===='''Pfam'''====
We used the FASTA sequence from 3HDT to do a comparative search in Pfam to find similar protein families our protein may belong. Pfam predicted that our protein is part of the cytidylate kinase which was also shown in the BLASTp results.  
We used the FASTA sequence from 3HDT to do a comparative search in Pfam<ref>2</ref> to find similar protein families our protein may belong. Pfam predicted that our protein is part of the cytidylate kinase which was also shown in the BLASTp results.  


[[Image:Pfam search resultsJRAF2022.png |800px| center | thumb | Pfam query aligned with a cytidylate kinase-like family.]]
[[Image:Pfam search resultsJRAF2022.png |800px| center | thumb | Pfam query aligned with a cytidylate kinase-like family.]]
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1. National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2022 April 23].
1. National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2022 April 23].


2. Holm L (2020) Using Dali for protein structure comparison. Methods Mol. Biol. 2112, 29-42.
2. Pfam: The protein families database in 2021: J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, R.D. Finn, A. Bateman
Nucleic Acids Research (2020) doi: 10.1093/nar/gkaa913


3. Pfam: The protein families database in 2021: J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G.A. Salazar, E.L.L. Sonnhammer, S.C.E. Tosatto, L. Paladin, S. Raj, L.J. Richardson, R.D. Finn, A. Bateman
3. Holm L (2020) Using Dali for protein structure comparison. Methods Mol. Biol. 2112, 29-42.
Nucleic Acids Research (2020) doi: 10.1093/nar/gkaa913


4. The PyMOL Molecular Graphics System, Version 1.7.4.5 Edu Schrödinger, LLC.
4. The PyMOL Molecular Graphics System, Version 1.7.4.5 Edu Schrödinger, LLC.


5. Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.
5. Small-Molecule Library Screening by Docking with PyRx. Dallakyan S, Olson AJ. Methods Mol Biol. 2015;1263:243-50.
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