Link to this post | posted 13 May, 2021 19:33

tsosieRL

Good Afternoon, We identified JalFarm20_51 as a gene in PECAAN. The original start was 34172 - Glimmer start and the GeneMark start 34331. It is an orpham. The stop is 34047 and is a reverse gene. We concluded it was a gene based on coding potential. In addition to coding potential both Glimmer and GeneMark did call the gene. The phagedb blast with the original start (34172), shows partial alignment with DNA primase/polymerase. If we use this start JalFArm20 will be 41 AA long but all the other best matches are 239 AA long. NCBI blast with the same start did not find a putative conserved domain. When we do a blastp with start 34331 (Longest ORF), the phage SiSi_42 had the best alignment. And JalFarm20 was 51 AA long and SiSi_42 was 58 AA long. The HHPred had better coverage with the 34331 start. We are requesting assistance to determine which start to use.

Link to this post | posted 06 May, 2021 19:50
tsosieRL	Thank you Debbie, We agree with your response because we did not see a clear function for this gene. Ranalda and SKC team

Link to this post | posted 04 May, 2021 20:48
tsosieRL	Attached is the dnam5 file for your reference. Thanks again. 30Kb

Link to this post | posted 04 May, 2021 20:47
tsosieRL	Hi, Thank you for your help. Upstream: NKF downstream: holin Gap between 36 and 37 is -211. (see attached) 494Kb

Link to this post | posted 04 May, 2021 19:55

tsosieRL

We're working on an F1 cluster phage, JalFarm20. And we would like a second opinion if this region is in fact a gene. Conclusion: Is the ORF a gene? NO? Rationale for the decision: 1. GeneMark did not call this as a gene 2. Coding potential is mostly atypical 3. Starterator was not informative; only draft genomes in Pham #6182 4. In DNAMaster: Forward genes 35 and 37; this gene, 36, is a reverse gene that overlaps: 29,822-29,586 (reverse) 5. No synteny evident We've added an attachment with screenshots. Thank you for your help. 869Kb