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Potential minor tail proteins in cluster GK
| Link to this post | posted today, 17:24 | |
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I’m working on three cluster GK phages, all three have a podoviridae morphology and the genomes are less than 18,000 base pairs. The genome arrangements is a bit different from anything I’ve annotated before, for example, the terminase is in between two endolysins (genes 1 and 12 in phage Smelly) and two transmembrane proteins (genes 14 and 15 in Smelly). Immediately upstream of the transmembrane protein encoding genes, there’s two genes that I’m debating whether to call minor tail proteins based on HHPRED hits ( (I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral). The top hit for gene 17 (348 bp) is the L-shaped tail fiber protein p132 of phage T5, with a 99.83% probability and an e-value 1.1 e-18 (https://toolkit.tuebingen.mpg.de/jobs/5744600). The top hit for gene 18 (1131 bp) is a Collagen-like protein 1 from Acanthamoeba polyphaga mimivirus with a 96.73% probability (https://toolkit.tuebingen.mpg.de/jobs/2916481). Based on size gene 17 wouldn’t qualify to be called a minor tail protein. Any input is greatly appreciated. Thank you, Arturo |
| Link to this post | posted today, 17:36 | |
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Aurturo, Please use PineapplePizza as your prototype as to what to call each tail type in your pododvirus. I used P68 and phi29 as the prototypes to call that one. For genes 17 and 18 of Smelly (phamerator_draft), you can call both as minor tail proteins. Once you do that, If you have any questions, continue on the forum post. Thanks, debbie |