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

MarQuardt

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.

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

compared work

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.

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.

• GeneMark didn’t call this gene at bp41199 because it has a TTG start cite.

Gene 61

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

Finding Functions:

Finding Functions:

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.

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.

Gene Phamily

# Of Members

Gene Phamily

# Of Members

40 2110 12 53 1801 14041 7248 76 54 271 9142 6719 2134 55 1921 10943 7457 68 56 272 1244 27 140 57 1448 4745 4173 30 58 1924 14046 265 19 59 6167 14847 266 16 60 273 1248 1920 140 61 6719 213449 267 15 62 6715 14050 2113 19 63 1932 16251 6429 185 64 6719 213452 270 85 65 276 67

MarQuardt’s Genes:

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.

Interesting Phamilies: Gene 43 in MarQuardt is from Phamily

7457. 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.

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.