Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction
2.2. Sequencing and Genome Assembly
2.3. Annotation and Genome Mapping
2.4. Comparative Genomics and Phylogenetic Analysis
2.5. Protein Modelling and Molecular Docking
3. Results
3.1. Sequencing
3.2. Annotation, Genome Mapping and Sequence Analysis
3.3. Comparative Genomics and Phylogenetic Analysis
3.4. Receptor Binding Interaction Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Name | Family/Subfamily/ Genus | Accession Number | Reference |
---|---|---|---|
Salmonella phage SE2 | Jerseyvirus | JQ007353.1 | [37] |
Salmonella phage ST4 | JX233783.1 | ||
Salmonella phage vB SenS-Ent2 | HG934469.1 | [37] | |
Salmonella phage vB SenS-Ent1 | HE775250.1 | [37] | |
Salmonella phage vB SenS-Ent3 | HG934470.1 | [37] | |
Salmonella phage SETP3 | EF177456.2 | [37] | |
Salmonella phage vB SenS AG11 | JX297445.1 | [37] | |
Salmonella phage SETP13 | KF562864.1 | [37] | |
Salmonella phage SETP7 | KF562865.1 | [37] | |
Salmonella phage FSL SP-101 | KC139511.1 | [37] | |
Salmonella phage LSPA1 | KM272358.1 | [38] | |
Salmonella phage Jersey | KF148055.1 | ||
Salmonella phage SS3e | AY730274.2 | [37] | |
Salmonella phage wksl3 | JX202565.1 | [39] | |
Salmonella phage fSE1C | KT962832.1 | [40] | |
Salmonella phage fSE4C | KT881477.1 | [40] | |
Salmonella phage f18SE | KR270151.1 | [41] | |
Salmonella phage f2SE | KU951146.1 | Santander Lab | |
Salmonella phage f3SE | KU951147.1 | Santander Lab | |
Escherichia phage K1G | Kagunavirus | GU196277.1 | [42] |
Escherichia phage K1H | GU196278.1 | [42] | |
Escherichia phage K1ind1 | GU196279.1 | [42] | |
Escherichia phage K1ind2 | GU196280.1 | [42] | |
Escherichia phage K1ind3 | GU196281.1 | [42] | |
Shigella phage EP23 | Dhillonvirus | JN984867.1 | [43] |
Salmonella phage STsAS | Seoulvirus | MH221128.1 | |
Salmonella phage FSL SP-031 | Guernseyvirinae | KC139518.1 | [37] |
Salmonella phage E1 | Macdonaldcampvirus | AM491472.1 | [44] |
Salmonella phage S130 | Demerecviridae | MH370377.1 | [45] |
Salmonella phage VSe12 | NC048794.1 | ||
Bacteriophage T5 | AY543070 | [46] | |
Escherichia phage T5_ev219 | LR597655.1 | ||
Escherichia virus VEc33 | NC_048818 | ||
Escherichia phage vB_EcoS_HdH2 | NC_048748 | ||
Salmonella phage Th1 | NC_048795 | ||
Salmonella phage SP01 | NC_047859 | ||
Salmonella phage SE11 | NC_048786 | ||
Salmonella phage vB_Sen_l1 | MT233524 | ||
Salmonella phage vB_SalS_SA001 | MN445182 | ||
Enterobacteria phage P22 | Lederbergvirus | NC_002371.2 | [47] |
Enterobacteria phage lambda | Lambdavirus | J02459.1 | [48] |
Enterobacteria phage M13 | Inoviridae | NC_003287.2 | [49] |
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Vasquez, I.; Retamales, J.; Parra, B.; Machimbirike, V.; Robeson, J.; Santander, J. Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor. Viruses 2023, 15, 379. https://doi.org/10.3390/v15020379
Vasquez I, Retamales J, Parra B, Machimbirike V, Robeson J, Santander J. Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor. Viruses. 2023; 15(2):379. https://doi.org/10.3390/v15020379
Chicago/Turabian StyleVasquez, Ignacio, Julio Retamales, Barbara Parra, Vimbai Machimbirike, James Robeson, and Javier Santander. 2023. "Comparative Genomics of a Polyvalent Escherichia-Salmonella Phage fp01 and In Silico Analysis of Its Receptor Binding Protein and Conserved Enterobacteriaceae Phage Receptor" Viruses 15, no. 2: 379. https://doi.org/10.3390/v15020379