SEA-PHAGES | Scaffolding protein

Link to this post \| posted 19 Jan, 2023 16:37
hnance@ccga.edu	Hi, This function is on the Official List and the example to check is D29_16. This gene has no functional domains and the HHPred match is to 6BOXG (a scaffolding protein), probability 97.98%. In the phage we're annotating, Mopey, gene 14 has BLAST hits to scaffolding protein and the same HHPred hit to 6BOXG, probability 96.2%. In phage most similar to Mopey in cluster D1, this gene is most often called NKF. HHPred results for both Mopey_14 and D29_16 seem similar in their alignment to 6BOXG, and it seems the only compelling reason to not call Mopey_14 a scaffold protein is because most other D1 phage call this gene NKF. I guess I'm really considering the Bioinformatics meeting last Friday (1/13) and trying to not just call a function a certain way because that's what everyone else did. Is there a compelling reason to not call Mopey_14 a scaffolding protein? Thanks!!!

Link to this post | posted 19 Jan, 2023 16:37

Hi, This function is on the Official List and the example to check is D29_16. This gene has no functional domains and the HHPred match is to 6BOXG (a scaffolding protein), probability 97.98%. In the phage we're annotating, Mopey, gene 14 has BLAST hits to scaffolding protein and the same HHPred hit to 6BOXG, probability 96.2%. In phage most similar to Mopey in cluster D1, this gene is most often called NKF. HHPred results for both Mopey_14 and D29_16 seem similar in their alignment to 6BOXG, and it seems the only compelling reason to not call Mopey_14 a scaffold protein is because most other D1 phage call this gene NKF. I guess I'm really considering the Bioinformatics meeting last Friday (1/13) and trying to not just call a function a certain way because that's what everyone else did. Is there a compelling reason to not call Mopey_14 a scaffolding protein? Thanks!!!

Link to this post \| posted 20 Jan, 2023 03:24
debbie	Hi Holly, hmmm. I think that Mopey_14 (stop codon 10436), can be called the scaffolding protein because of the InterPro hit at HHPred (Q38580). It is a 99.5% probability (evalue is e-12) and has protein homology to the scaffolding protein of SPP1 (evidence is from UniProt database. Granted that the example used by the approved function list is D29, but your protein doesn't have to hit the example (and it doesn't, does it?)

Link to this post | posted 20 Jan, 2023 03:24

debbie

Hi Holly,
hmmm. I think that Mopey_14 (stop codon 10436), can be called the scaffolding protein because of the InterPro hit at HHPred (Q38580). It is a 99.5% probability (evalue is e-12) and has protein homology to the scaffolding protein of SPP1 (evidence is from UniProt database.
Granted that the example used by the approved function list is D29, but your protein doesn't have to hit the example (and it doesn't, does it?)

Link to this post \| posted 20 Jan, 2023 11:52
hnance@ccga.edu	Hi Debbie, Thanks for your prompt reply! Mopey_14 doesn't hit D29_16 in HHPred or BLAST, but it hits the same protein that D29_16 hits if you run D29_16 in HHPred (both Mopey_14 and D29_16 hit 6BOXG, which is a scaffolding protein). After asking my question yesterday, I had convinced myself that it was a silly question because Mopey_14 and D29_16 are not in the same phamilies. But it sounds like despite that, the structural homology warrants both being scaffolding proteins. So far, Mopey has several genes for which the function call is tricky as there is not consensus in the cluster. The timing of your meeting last Friday was great! Thanks again so much for your help - Holly

Link to this post | posted 20 Jan, 2023 11:52

hnance@ccga.edu

Hi Debbie,

Thanks for your prompt reply! Mopey_14 doesn't hit D29_16 in HHPred or BLAST, but it hits the same protein that D29_16 hits if you run D29_16 in HHPred (both Mopey_14 and D29_16 hit 6BOXG, which is a scaffolding protein).

After asking my question yesterday, I had convinced myself that it was a silly question because Mopey_14 and D29_16 are not in the same phamilies. But it sounds like despite that, the structural homology warrants both being scaffolding proteins.

So far, Mopey has several genes for which the function call is tricky as there is not consensus in the cluster. The timing of your meeting last Friday was great!

Thanks again so much for your help - Holly

Link to this post \| posted 20 Jan, 2023 15:37
debbie	Holly, Exactly! You've got it! debbie

Recent Activity

Scaffolding protein