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Group 4

こんにちは私は Gomashi よ Hello I’m Gomashi !. 您好，我 Gomashi. “Little Sesame Seed”. Group 4. By: Lucas Zellmer Ciara Buechner Emily Falch Lauren Schlitz. Annotation for Gomashi. These are pictures of the plaques that Gomashi produces. I’m a cluster G phage!.

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Group 4

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  1. こんにちは私はGomashiよ Hello I’m Gomashi! 您好，我Gomashi “Little Sesame Seed” Group 4 By: Lucas Zellmer Ciara Buechner Emily Falch Lauren Schlitz

  2. Annotation for Gomashi These are pictures of the plaques that Gomashi produces. I’m a cluster G phage!

  3. DNA Master • This program helped us to annotate the genes we were assigned. • It helped us to become more familiar with genes, and to figure out the best starting sequences. • It provided the amino acid sequence so we could find the functions of each gene with the HHpred program.

  4. DNA MASTER THIS

  5. HHpred • This handy online resource helped us determine the functions of each gene.

  6. A-plaque-able • Original start at 26866 called by Glimmer and 26854 called by GeneMark • Start changed to 26791 • Includes coding potential • Strongest Shine Delgarno Score (399) • Longest Open Reading Frame (321) GENE 30

  7. DN-Ayy Gene 33, a repressor, is 486 base pairs long. It is one of 2 reverse genes on Gomashi. I had to change the start from 29490 to 29400 to improve the BLAST match ratio. It includes all coding potential and the longest possible open reading frame. Gene 33

  8. Phagetastic • Original start of 30214 • Found I could change the start to 30151which had a 1 base pair over lap • It did not agree with either Glimmer or Genemark • The blast matched both Halo, Liefie, and Angel with a 1:1 ratio for each. • It was interesting because I had to reblast it. Gene 36 **Gene 39 did not have any blast matches.

  9. Gene-asmic • Originally: • 33,011- 34,399 • 465 SD Score • 1389 ORF Length • 17 bp gap Gene 43 • Changed to: • 32,990-34,399 • 336 SD Score • 1410 ORF Length • 4 bp overlap!

  10. Phamilies • There are 17 different phams between genes 28 and 44. • 12/17 of them belong only to cluster G phages. • 5/17 of them belong to all G phages, and a few other clusters.

  11. Gomashi and Related Phages • Gomashi shares phams with the following clusters; A1-5, A7, A8, A10, B1, B3, B4, B5, C1, D, F1, F2, G, H1, I1, I2, J, K1, K2, K3, K4, K5, L1, L2, L3, M, N, O, P, Q, R, T. • There are a lot of phage that have phams in common with Gomashi.

  12. Pham Bubbles • The function that highlights corresponding phams was a useful tool to compare and contrast locations of similar genes.

  13. Genes 28-44 • Our section was limited to cluster G phams only. • We did not have any non- cluster G phams inserted. • It is not missing a cluster G pham that corresponds to that area.

  14. Location and Cluster G Phages • Here are some locations of Cluster G phages.

  15. Site of Soil Collection: Ames Suites

  16. Phamerator and Color Coding

  17. Reflections • The most interesting part of this experience was finding out that our phage could be useful in real life. • The most challenging part for us was acclimating to using the new programs, but once we got the hang of it, they were valuable to figuring out important information.

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