SEA-PHAGES | Hypothetical Proteins in the Product Field

Link to this post \| posted 14 Dec, 2020 22:08
Juan.MartinezV	Our group are about to finish the annotation of two phages (Parliament and Illumine) and we are checking for all the details prior the submit but I have a question regarding two points: 1) I use other phage annotations (Tubs or OkCentral2016) to check that I have not missed anything but in the complete notes (.dnam5) these phages are already assigned with the gene protein number (gp12, 48 and so on). All I've have seen in the annotation guide is that we should rename the product field with hypotetical proteins when we don't know the fuction (throughthe renumbing method) but then, this label of gpXY is done by us or is it assigned when is already on GenBank? 2) Kind of the same question regarding the hypotetical proteins. I am generating the minimal file and what I suposed to have is CDS 379 - 1161 /gene="1" /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" but I am having CDS 379 - 1161 /gene="1" /function: terminase (as example) /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" If I am not wrong, I just need to have a hypotetical protein in product when the fuction is unknow and a function for that gene (when we know it) but not both right? I appreciatethe time to answer Thanks! JM

Link to this post | posted 14 Dec, 2020 22:08

Our group are about to finish the annotation of two phages (Parliament and Illumine) and we are checking for all the details prior the submit but I have a question regarding two points:

1) I use other phage annotations (Tubs or OkCentral2016) to check that I have not missed anything but in the complete notes (.dnam5) these phages are already assigned with the gene protein number (gp12, 48 and so on). All I've have seen in the annotation guide is that we should rename the product field with hypotetical proteins when we don't know the fuction (throughthe renumbing method) but then, this label of gpXY is done by us or is it assigned when is already on GenBank?

2) Kind of the same question regarding the hypotetical proteins. I am generating the minimal file and what I suposed to have is

CDS 379 - 1161
/gene="1"
/product="Hypothetical Protein"
/locus tag="SEA_MYPHAGE_1"

but I am having

CDS 379 - 1161
/gene="1"
/function: terminase (as example)
/product="Hypothetical Protein"
/locus tag="SEA_MYPHAGE_1"

If I am not wrong, I just need to have a hypotetical protein in product when the fuction is unknow and a function for that gene (when we know it) but not both right?

I appreciatethe time to answer
Thanks!

Link to this post \| posted 15 Dec, 2020 13:17
debbie	Juan, GpXX is incorrect. You should use the buttons of DNA Master to overwrite gpXX with Hypothetical Protein. The function field is empty. The Bioinformatic guide should be followed. CDS 379 - 1161 /gene="1" /product="Hypothetical Protein" /locus tag="SEA_MYPHAGE_1" Good luck! debbie

Link to this post \| posted 21 May, 2022 13:28
Tamarah_Adair	I was checking my Review to Improve on Casserole and there are changes to gpXX for each hypothetical protein. Is this an update?

Link to this post \| posted 22 May, 2022 01:50
debbie	Nope. Thanks for checking. We can correct this. debbie

Link to this post \| posted 22 May, 2022 22:03
debbie	Tammy, The corrected file has been uploaded to phagesDB and sent to GenBank. Thanks, debbie

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Hypothetical Proteins in the Product Field