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Annotation Adventures with MarQuardt (an A3 phage)

MarQuardt. Annotation Adventures with MarQuardt (an A3 phage). By: Bobbi Kelling, Alexis Barna, Erich Butterbrodt (Kevin Butters), Mikayla Mack. Overview:. We were assigned to annotate genes 40-65 All of our genes were reverse. Going right to left.

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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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