GOMASHI ANNOTATION GENES 1-13 DOMINIQUE KAITLYNN DYLAN SAMANTHA

Gene Functions Here is a peek ahead at our gene functions that we uncovered. They are structure related. We were surprised to see that many genes do not have a known function, as this is the beginning of the genome sequence.

Gp 1-3 Glimmer call at 44 : GeneMark call at 2 Agreed with Glimmer call – Matched 1:1 with Halo Gene 2 – second longest Possible overlap if chosen longest Gene 3 – 4th longest with best Sd Score Between genes 3 and 4 there is NO gap and NO overlap (Portal and Protease)

Gene 1 Pham #3205 Related to all G’s only Terminase small subunit

Gene 2 Pham #6356 Related to many different clusters Terminase large Gp2 was supposedly very closely related to many different phages in clusters K, O, F, I1, and singleton Muddy. However, I was not able to find any genes that were closely related to gp2 in these clusters. They did not have the same Pham numbers whatsoever.

Pham circle of gp 2

Gene 3 Pham #2409 Related to F2 cluster phages. Portal This was my most interesting gene because I found out that it was a similar portal protein to gp4 of both Yoshi and Avani in the F2 phage cluster. Gp3 was also supposedly similar to Ogopogo draft from the F1 cluster, however, this was not the case.

Gene product 4 Shares same promoter as gene 3 Longest gene in our group with 2790 base pairs Blast matches 1:1 Includes all coding potential Function: Protease Many different clusters have this gene Gene 4 shares the same promoter as gene 3 due to no gap nor overlap between the two genes (top picture). The Blast matched 1:1 with Halo and Liefie. No change was needed to be made. Function matched with other cluster G phages to be the Protease on the phamerator map. Matches on HHPred where low percent, but matched with various structural proteins. As shown on bottom picture, the phamily circle shows the similarities of clusters about that specific gene. Clusters F1, K1, K2, K3, K4, K5, T, DS6A, and Sparky-Draft all share this same gene. Samantha

Gene products 5 & 7 Gp 5 - found to have no known function No match on HHPred nor Phamerator map Found in many different clusters Gp 7 – best SD Score of 672; 46 bp gap Matched Capsid gene on Pham map only Gene found in all Cluster G, as well in F1 & F2 Gp 5 did not match up with any function on phamerator. Gp 5 is found in many different clusters including: K1, K2, K3, K4, K5, T, DS6A, whereas gp 7 is only found in G, F1, F2. Neither showed any similarities in HHPred. Samantha

Gene product 6 Not highest SD Score Includes all coding potential Function Scaffold Only cluster G carries this gene (red) Shine Delgarno Score of 504 was not highest. Did not go with the highest score because it wouldn’t include all coding potential. Function found on Phamerator map to be Scaffold. The nucleotide conservation on Phamerator showed gene 6 to be found only in cluster G phage. Top left picture shows the phamily circle (12 in phamily, all cluster G). Samantha

Gene 8 No Known Function Pham 1393, 12 members Unique to Cluster G Phages.

Gene 9 No Known Function Pham 538, 17 members Found in all G, F1 and F2 Possible that gene was shared between 4 different F2 phages and 1- F1 phage. The F2 phages that share Pham 538 are Che9d, Avani, Jabbawokkie, and Yoshi. The shared F1 phage is Ogopogo. With the sharing being mainly in the F2 phages I believe that the gene was spread to an F2 phage and incorporated into a few then went on to an F1 phage.

Gene 10 HHPred’s Findings Bacillus Phage SPP1. 92.5% probability of a match. No known function.

Extra Research gp 10 Common name Bacteriophage SPP1. Expression system E. Coli. The key to why it matched. Gene product 16. Head-Tail joining protein. Make-up of the gene is similar to another phage family.

Gene 10 Head-Tail Binding Protein Pham3166, 32 members In all G and K1-K5 Gene is more closely related to cluster K1, although found in many others. Pham 3166 is shared with 11- K1, 3- K2, 2- K4, and 2- K5 phages.

Genes 11 & 12 Glimmer call gp 12 at 9155bp. Doesn’t contain all coding potential. Would override gp11 if it contained all potential.

Gene 11 No Known Function Pham 3167, 32 members Found in all Cluster G and all K1-K5 Possibly came from Cheetoro or Pixie, but may have branched from G to them Genes 11-13 are very closely related to genes from Cluster K, it is unknown whether K gave these genes to G or the other way around.

Gene 12 No Known Function Pham 1329, 32 members In all Cluster G and K1-K5 Shared more than gp11

Gene 13 Major Tail Subunit Pham 3203, 33 members In all G, K1-K5 and singleton Muddy Very closely shared between G and all subclusters of K Muddy is only a 62.6% match Muddy most likely gained its gene from a Cluster G or K phage.

Summary of gp 1-13 Agreed with Glimmer calls, no changes made Mosaicism of different phamilies 10 of the 13 genes are blue, only 3 are red Each gene of a different phamily Structural Region of Gomashi All glimmer calls on these four genes were not changed. Each gene is of different phamilies, showing a form of mosaicism. The nucleotide conservation view on Phamerator showed that ten genes were blue, meaning that all cluster G has them and that other cluster may have them too. Red means that they are found ONLY in cluster G, but not in all cluster G. The functions known are that of the structural region of Gomashi.