Meredith Kim

April 4, 2017

Rationale of today’s work: Delegate jobs to each group member and begin researching promoter sequences for the phages containing genes in pham 7442. This pham has 16 members, all of which are in the AO cluster.

Tools used and/or Methods: PhagesDB glossary, Phamerator, DNA Master, NCBI, ExPASy

Results:

Barret lemon Gene #7:

Previous gene (#6) is a reverse gene… Gap: 128bp

Blast NCBI for Gene #6 is hypothetical protein BARRETLEMON_6 e-value: 1e-48, q:1 s:1, no CDD

NCBI Blast for Gene #7: scaffolding protein [Arthrobacter phage BarretLemon], e-value: 0.0, q:1 s:1, Mu-Like_Pro superfamily

Boss Lady Gene #7:

Previous gene (#6) is a reverse gene… Gap: 134bp

Blast NCBI for Gene #6: hypothetical protein MARTHA_6 [Arthrobacter phage Martha], e-value 1e-47, q:1 S:1

NCBI Blast for Gene #7: scaffolding protein [Arthrobacter phage Sonny], e-value: 0.0, q:1 s:1, Mu-Like_Pro superfamily

Beans Gene #6:

Previous gene (#5) is a forward gene… Gap: 156bp

NCBI Blast for gene #5: hypothetical protein SEA_BRENT_5 [Arthrobacter phage Brent], e-value: 1e-53, q:1 s:1, no CDD

NCBI Blast for Gene #6: scaffolding protein [Arthrobacter phage Jawnski], e-value:0.0, q:1 s:1, Mu-Like_Pro superfamily

Brent Gene #6:

Previous gene (#5) is a forward gene… Gap: 157bp

NCBI Blast for Gene #5: hypothetical protein SEA_BRENT_5 [Arthrobacter phage Brent], e-vlaue: 7e-60, q:1 s:1, no CDD

NCBI Blast for gene #6: scaffolding protein [Arthrobacter phage Brent], e-value: 0.0, q:1 s:1, Mu-Like_Pro superfamily

Conclusion: All the genes in the pham are scaffolding proteins. However, there was not a very clear correlation in promoter sequences. We may need to try promoter prediction on the entire genome instead of just on the gap sequence. That way, we can get the most accurate prediction.

Next Steps: We should look at promoter sequences that are not within the actual genes themselves. After all, promoter sequences are typically found before the gene. We need to insert a new “gene” in the gap in DNA master in order to run Promoter Prediction and further investigate.