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Annotation Adventures with MarQuardt (an A3 phage)

Join Bobbi, Alexis, Erich (Kevin), and Mikayla in their gene annotation mission, diving into genes 40-65 in MarQuardt phage. Discover their process, challenges, and insights using DNA Master, and how they tackled discrepancies. Explore their encounters with gene 61 and 65, exhibiting modifications for better results and discussing findings through Phamerator. Dive into the unique Phamilies MarQuardt genes belong to, uncovering intriguing functions and comparisons in sub-cluster A3 and beyond.

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Annotation Adventures with MarQuardt (an A3 phage)

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  1. MarQuardt Annotation Adventures with MarQuardt(an A3 phage) By: Bobbi Kelling, Alexis Barna, Erich Butterbrodt (Kevin Butters), Mikayla Mack

  2. Overview: • We were assigned to annotate genes 40-65 • All of our genes were reverse. Going right to left. • Very little discrepancies between what we decided and what Glimmer and GeneMark had called.

  3. Process: individual annotation • Alexis and Erich: gp40-53 • Bobbi and Mikayla: gp53-65 • Used DNA Master • Each individually annotated genes, then compared work

  4. Gene observations: gp40-53 • Most Blast matches were Q1:S1 with JCH117 in our assigned section. • Few genes needed changes in the ORF. • Had trouble determining the gaps and overlaps at first because of the reverse reading frame of the genes.

  5. Problem genes: gp53-65 • Gene 61 • Changed the start gene from bp39629 to bp39623 to minimize overlap and acquire a higher SD score. • Gene 65 • Changed the start gene from bp41172 to bp41199 in order to include all the coding potential of the gene. • GeneMarkdidn’t call this gene at bp41199 because it has a TTG start cite.

  6. Gene 61

  7. Table Revisions: • Merged files from each individual into a single file in DNA Master • Each individual checked a separate component • Mikayla: SD scores and ORFs • Alexis: Gaps and Overlaps • Erich: BLAST matches • Bobbi: merged files and updates final draft • As a group found the functions of each gene

  8. Finding Functions:

  9. Finding Functions:

  10. Phamerator • We used Phamerator to compare MarQuardt’s genes with other phages in the sub-cluster A3, other cluster A phages and phages from all other clusters. • With Phamerator we were also able to see which Phamilies MarQuardt’s genes belong to.

  11. Overview: • MarQuardt shares phams with all A sub-clusters, and clusters B, C, D, E, F, I, J, K, L, M, N, O, P, S. • 18 Phamilies (27, 265, 266, 267, 270, 271, 272, 273, 1448, 1801, 1920, 1921, 1924, 2110, 2113, 2715, 4173, 7248) are unique to cluster A phages • 5 Phamilies (266, 267, 272, 273, and 2110) are unique to sub-cluster A3 phages.

  12. MarQuardt’s Genes:

  13. Interesting Phamilies: • Gene 42 in MarQuardt belongs to Phamily 6719. The function of this gene is a protein that binds extracellular solutes. • Almost all other phage clusters belong to this Phamily. (all A sub-clusters, B, C, D, E, F, J, K, L, M, N, O, P, and S) • The only clusters that do not have a gene in this Phamily are G, Q, and R, meaning that those phages have found another protein to carry out this function.

  14. Interesting Phamilies: • Gene 43 in MarQuardt is from Phamily7457. The function of this gene is not known by Phamerator or HHpred. • All sub-cluster A phages are members of this Phamily along with cluster J phages.

  15. Summary: • All in all, we had few problems with our genes. • Our genes were reverse which caused some confusion with finding gaps/ overlap. • We only disagreed with GeneMark twice. • We are still working to assign functions to all our genes. • In Phamerator we compared MarQuardt’s genes and the Phamilies they belong to with that of other sub-cluster A3 phages and phages from other clusters.

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