Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Functional Annotations for Bacillus Phage Phrodo
Document related concepts
no text concepts found
Transcript
Bacillus Phage Annotation Phage Lab II, Spring 2015 Complete annotation of other phages, explore those genomes Claudi (Demetrius) Nemo (Sathya & Molly) Didn’t annotate yet Jugalone (Herleen) Zuko(Sailasya) DIGNKC (Ryan) + Genomic Comparison of VCU’s 2014-2015 Bacillus Phages Characteristic Phrodo Jugalone Zuko DIGNKC Claudi Troll Troll Megatron Hakuna MG-B1 94 96 91 92 33 % Identity 98 99 88 87 74 % GC 37.8 37.8 38.6 38.7 30.3 164443 164227 163345 161552 26504 288 293 296 296 48 0 0 3 3 0 Best Blast Match % Query Cover Genome Length, bp # predicted ORFs # predicted tRNAs Phage # Predicted ORFs # tRNAs # ORFS with Functional Annotation/ % of total # of novel genes Zuko 296 3 37 2 Vinny 274 7 60 1 SageFayge 302 0 70 0 Phrodo 288 0 62 2 NotTheCreek 297 0 48 0 NIgalana 302 0 43 1 Jugalone 293 0 56 0 296 3 47 - 48 0 48 16 DIGNKC Claudi a DNA Binding protein Thioredoxin Ribonucleotide diphosphate reductase beta subunit Flavodoxin Ribonucleotide diphosphate reductase alpha subunit Holiday junction resolvase RecA Metalloprotease Methyltransferase RNA Helicase Ligase RNA Ligase HNH Homing Endonuclease DNA Binding Protein Metal Dependent Hydrolase Functional annotation for 62 proteins, (62/288)*100 = a little over 21% Transposase DNA Polymerase 1 Exopolyphosphatase Holin HNH Homing Endonuclease Sigma Factor RecA ssDNA Binding Protein DNA Polymerase II HNH Endonuclease HNH Homing Endonuclease Ftsk/ SpoIIIE Protein ParM dUTP nucleotidylhydrolase DNA Helicase 2 HTH binding domain protein DNA Binding Protein Terminase Baseplate protein J Baseplate assembly Endolysin protein PhoH Minor tail protein Thymidylate synthase Dephospho – CoA kinase Dihydrofolate reductase Tail fiber protein Tail lysin 1 Tape measure, tail lysin Tail assembly chaperone Tail assembly chaperone Tail spike Tail Assembly Chaperone DNA Primase Tail Sheath Portal Prohead Protease Major Capsid Protein Functional Annotations for Bacillus Phage Phrodo What are the differences in Jugalone and Phrodo? Jugalone vs. Phrodo • 17 protein phams in Phrodo that aren’t in Jugalone • 3 are homing endonucleases • 20 protein phams in Jugalone that aren’t in Phrodo • DNA Primase • dUTP nucleotidylhydrolase • 229 genes: same gene length in Phrodo and Jugalone. • 39 genes in Phrodo and Jugalone have the same function and exact gene length. How as Phrodo 106 inserted, and what does it do? Novel Gene • Gene 106 encodes for an HNH Endonuclease III protein. • Located between gene 105 which codes for DNA Helicase II and gene 107 which codes for an HTH Binding Domain Protein • Gene 106 was inserted into Phrodo through an illegitimate recombination process (no overlap in purple shading.) Can you determine how gene 114 was inserted into Jugalone? • Matches Hmu1 HNH endonuclease • Non bastille HNH endonuclease • Non intron space on either side of gene 114, or non coding space • Intron-mediated recombination Are Jugalone 218 and 221 are transcribed? Phrodo 214, 217 and 219 ? • Yes, transcribed in reverse direction • 214: SD 504 217: SD 273 • 219: SD 567 Is there a missing gene in between Jugalone gp 138 and 139? • There is 261 bp gap between both genes. • A gene with starting codon 97791 and stop codon 97920 was found • Coding potential of the gene is too low, so it should not be added Coding Potential Phrodo SD: 567 Jugalone SD: 609
