Meredith Kim

February 7, 2017

Rationale of today’s work: Starting initial work on Lore. Today we aim to complete the annotations for gene 23 and 24.

Tools used and/or Methods: NCBI, PhagesDB, HHPred, Phamerator, Starterator, Glimmer, GeneMark

Results:

GENE 23:  Start: 14113bp Stop: 14781bp FWD GAP: 4bp Overlap

According to GeneMark, all typical and atypical potential is covered.

NCBI blast: Identified HTH superfam, supports helix-turn-helix DNA binding function, q:1 s:1

Phages DB blast: does not give any known function for the gene

HHPred: supports helix-turn-helix DNA binding function

Final Annotation for Lore Gene 23:

Start: 14113bp Stop: 14781bp FWD GAP: 4bp Overlap SD Final Value: SD Score: -3.246 (Best score) Z-Value: 2.847 CP: The gene is covered SCS: Agrees with Glimmer, Disagrees with GeneMark Genemark called a reverse gene, but there was more potential in the forward gene that was not called NCBI BLAST: Helix-turn-helix DNA binding domain protein [Arthrobacter phage Decurro] q:1 s:1 E-Value: 2e-156 CDD: pfam13730, Helix-turn-helix domain E-Value: 1.09e-06 PhagesDB BLAST: StewieGriff_Draft_23, function unknown, q:1 s:1 E-Value: 1e-134 HHPred: Transcriptional Regulator E-Value: 5.9E-08 LO: Yes ST: Agrees with Starterator F: helix-turn-helix DNA binding domain FS: NCBI, HHPred, Phamerator Notes:

GENE 24: Start: 14768bp Stop: 14983bp FWD GAP: 14bp

According to GeneMark, all typical and atypical coding potential is covered.

NCBI blast: StewieGriff_Draft_24, no known function, q:1 s:1

Phages DB blast: does not provide known function, no CDD

HHPred: does not provide known function, best hit had too high of an e value

Final Annotation for Lore Gene 24:

Start: 14768bp Stop: 14983bp FWD GAP: 14bp Overlap SD Final Value: SD Score: -2.171 (Best score) Z-Value: 3.342 CP: The gene is covered SCS: Disagrees with Glimmer, Agrees with GeneMark Glimmer’s call does not cover all the typical coding potential, and the final score for GeneMark’s call was higher NCBI BLAST: hypothetical protein SEA_DECURRO_24 [Arthrobacter phage Decurro], q:1 s:12 E-Value: 1e-28 CDD: No good hit PhagesDB BLAST: StewieGriff_Draft_24, function unknown, q:1, s:1 E-Value: 1e-30 HHPred: No good hit LO: Yes ST: Agrees with Starterator F: NKF FS: NCBI, Phages DB, HHPred Notes:

Conclusions and Next Steps: Not very many chances were made to this gene, and there were no known functions. Next step would be to complete genes 25-26 and then go back and annotate gene 22.