cdc25 phosphorylated form

[nataled]

Hi, could I get an ID for a generic phophorylated form of cdc25 PMID: 15629716 I want to capture that rad24 binds to the phosphorylated form

(I should be able to identify the exact phospho sites eventually...but it will require multiple papers to be curated so I'll refine later)

Thanks

Val

Reported by: ValWood

[nataled]

• Description has changed:

Diff:

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 Hi, 
 could I get an ID for a generic phophorylated form of cdc25
 PMID: 15629716

• status: open --> closed
• assigned_to: Darren Natale
• Group: -->

Original comment by: nataled

[nataled]

Here is the term for the general form:

[Term] id: PR:000036912 name: M-phase inducer phosphatase phosphorylated form (Schizosaccharomyces pombe) def: "An M-phase inducer phosphatase phosphorylated form in Schizosaccharomyces pombe." [PRO:DAN, PomBase:VW, PMID:15629716] comment: Category=organism-modification. Requested by=PomBase. synonym: "Spom-cdc25/PhosRes+" EXACT PRO-short-label [PRO:DAN] intersection_of: PR:000027510 ! M-phase inducer phosphatase phosphorylated form intersection_of: only_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe relationship: has_part MOD:00696 ! phosphorylated residue

Let me know if/when you get additional information. If it occurs before our next release, I can modify this term if you desire or, whenever, I can mint a child term.

Original comment by: nataled

[nataled]

fab, thanks

Original comment by: ValWood

[nataled]

I am annotating a later paper and I found this ID had already been used, this was the 'child' that I needed http://research.bioinformatics.udel.edu/pro/entry/PR%3A000027512/

It isn't clear to me how I find this. If I search on pombe and cdc25 here http://pir.georgetown.edu/cgi-bin/textsearch.pl?sitesearch=on&submit.x=0&submit.y=0&query0=cdc25&field0=ALL&search=1

I get 2 proteins and neither is cdc25?

Original comment by: ValWood

[nataled]

I found it, I needed to search on 'gene name'

So from here http://research.bioinformatics.udel.edu/pro/entry/PR%3A000027506/

I see that there are exisitng PRO modification terms, but I can't link to them...

and when I follow the other link to here http://research.bioinformatics.udel.edu/pro/entry/PR%3AP06652/ no existing modifications are listed?

Original comment by: ValWood

[nataled]

I found another link to here: http://pir.georgetown.edu/cgi-bin/ipcEntry?id=P06652

and the ID is listed under "ontologies" Its pretty easy to miss...

Original comment by: ValWood

[nataled]

but thats a link back to this page: http://research.bioinformatics.udel.edu/pro/entry/PR%3A000027506/

...I still didn't find the link to the modifications....

Original comment by: ValWood

[nataled]

First, I need to point out that the search you used originally was NOT through PRO, but through iProClass, a database that (nowadays) basically contains UniProtKB data with some extra stuff. This is the default search if you use the search box at the very top of the page in the banner with PIR logo in it. However, oddly, I cannot reproduce your result. If I click the link you provided in the first comment, I get over 700 proteins (it searches only for cdc25 and not pombe). Looking at that table of results, I can add pombe in the second search box near where cdc25 appears, and I get 4 results. The top hit is the specific strain of S. pombe that is in UniProtKB, and you can see there are two PRO terms associated with it. One looks like a UniProtKB accession and that goes to the PRO term corresponding to the strain-specific protein. The other goes to the parent term, which represents any 1:1 ortholog of that strain protein. So, when you look at the strain-specific term (as per your second comment) you won't find any modified children because none were defined for it--pretty much all the modified forms for pombe are underneath the species umbrella and not the strain.

Looking at the entry for PR:000027506 (again, second comment) you said you see there are modification terms but you cannot link to them. I assume by this you mean you see in the table "Terms by PRO category" that there are such terms, but you cannot click the numbers? Hmm, I believe they are supposed to be clickable. I'll put in a request to have it fixed. In the meantime, you can click the triangle in the bottom box for "Protein Forms" (again, I think this is supposed to show by default; we recently switched the host server for PRO and some things are a bit wonky). The resulting list does indeed show the child term you wanted.

Your third comment refers to the iPROclass view of the entry. This is organized in the same way as UniProtKB, and PRO is listed under 'ontologies' in that database. We agree that it is easy to miss, but without changing UniProt policy... :(

I guess that brings us full circle back to PR:000027506. Hopefully you can now see the forms you wanted! I'll have a discussion about the pitfalls you noticed in your search. Thanks!

Original comment by: nataled