Rationale:

The purpose of today’s lab was to go over and correct the previous annotations of Elesar genes 30 and 31, and practice using additional methods of protein sequence analysis.

Tools:

• DNA Master
• HHPred
• NCBI BLAST and BLASTp

Procedure:

• Began the lab with information regarding HHPred use and protein domains.
• Once complete, was given feedback regarding previous annotations of Elesar genes 30 and 31
• Updated gene annotations of genes 3o and 31 by adding SIF BLAST and SIF HHPred information regarding protein function.

Results:

• Updated Annotation Notes for Gene 30:
  • SSC:22118, 22477 CP:yes SCS:Both BLAST-Start: Nandita gp29, NCBI,  q1:s1, 78%, 9E-62 Gap:overlap 1bp LO: yes RBS: Kibler7, Karlin Medium, 2.408, -3.770, yes F:NKF SIF-BLAST:NKF, no putative conserved domains have been detected SIF-HHPred: NKF, no matches with a probability above 90% SIF-Syn
  • 
• Updated Annotation Notes for Gene 31:
  • SSC:22487, 23215 CP:yes SCS:Both ST: BLAST-Start:Ryan, gp30, NCBI, q1:s1, 83%, 2e-139   Gap:9 LO:yes RBS: Kibler7, Karlin Medium, 2.117, -4.325, yes F:NKF SIF-BLAST:NKF, no putative conserved domains have been detected  SIF-HHPred:NKF, no matches with a probability above 90% SIF-Syn
  • BLASTp Protein Domain results yielded no conserved domains
  • HHPred result yielded a viral coat protein hit, but the probability was too low to call.
  • 

Conclusions:

No known function could be determined from the information given from the BLASTp and HHPred results. The few hits that were given had incredibly low probabilities and did not contribute to function determination. Could be a possibility that there is very few data on this given gene, or that it actually does not have a function.

Next Steps:

The next steps are to check with annotated phage genomes in the same cluster and determine if they have a similar gene that codes for the same protein to help determine protein function. Also further annotation practice is required as Starterator and synteny have yet to be used in the annotation notes.