SEA-PHAGES | Called an orpham but isn't?

Link to this post \| posted 05 Apr, 2022 21:14
uOttawaPHAGE	We are annotating the singleton Arzan. Gene 58 (in the phamerator draft; 36,809 to 37,624) is listed as being in pham 100827, but matches to pham 101472 members on Blastp with very low e-values. This looks like a mistake. Can we use the pham 101472 starterator report?

Link to this post \| posted 06 Apr, 2022 16:29
debbie	All information is informative. I guess it depends on how you use it! It might be helpful to do a protein alignment. debbie

Link to this post \| posted 06 Apr, 2022 16:36
uOttawaPHAGE	I think the alignment is nearly identical, which is why we think it is an error. Do errors like this happen?

Link to this post \| posted 06 Apr, 2022 16:50
DanRussell	Hi Adam, Actually, they're not nearly nearly identical; there's only 32% amino acid identity between Arzan 58 and the next best match in the DB! (Which is Heisenberger 58 as of me writing this.) That's quite a lot of differences, and while it's probably reasonable to consider these homologs, they're still different enough that: 1. Phamerator's algorithm put them in different phams and 2. trying to make start calls on Arzan 58 based on Heisenberger 58 is not advisable. The AA sequences are 32% identical, but the nucleotide sequences show almost no similarity at all, so using a starterator report isn't a good idea in this situation, since SD sites and potential start codons have had lots of evolutionary time to change. This one you'll have to call on its own! –Dan

Link to this post | posted 06 Apr, 2022 16:50

DanRussell

Hi Adam,

Actually, they're not nearly nearly identical; there's only 32% amino acid identity between Arzan 58 and the next best match in the DB! (Which is Heisenberger 58 as of me writing this.)

That's quite a lot of differences, and while it's probably reasonable to consider these homologs, they're still different enough that:

1. Phamerator's algorithm put them in different phams and
2. trying to make start calls on Arzan 58 based on Heisenberger 58 is not advisable.

The AA sequences are 32% identical, but the nucleotide sequences show almost no similarity at all, so using a starterator report isn't a good idea in this situation, since SD sites and potential start codons have had lots of evolutionary time to change.

This one you'll have to call on its own!
–Dan

Link to this post \| posted 06 Apr, 2022 18:28
uOttawaPHAGE	Thanks Dan, sort of embarrassing….When I said nearly identical I was basing that not on looking at the aa comparison but on the e values in blastp, and that they are almost the same length. Obviously low e values don't mean identity and I should have looked at this with the students. thanks for your help on this. Still learning…A

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Called an orpham but isn't?