Comments for Xfam Blog

Comment on Proposed Pfam release changes by Pfam 27.0 is now available! | Xfam Blog

Pfam 27.0 is now available! | Xfam Blog — Fri, 22 Mar 2013 18:42:28 +0000

[...] a blog post published just over a year ago, I proposed a number of changes to the content of Pfam to improve [...]

Comment on Does my family of interest have a determined 3D protein structure? by Shyam

Shyam — Fri, 18 Jan 2013 01:29:10 +0000

Thank you. This was very helpful.

Shyam

Comment on Does my family of interest have a determined 3D protein structure? by rdfinn

rdfinn — Fri, 18 Jan 2013 00:50:53 +0000

Dear Shyam,

The difference is due to the fact that the mappings are obtained in two very different ways. The matches you obtained from RCSB come from running each sequence in the PDB file against the Pfam HMM library. The mappings to PDB on the Pfam website are considerably more detail as they are actually a residue by residue mapping between the PDB entry sequence and a UniProt sequence – we then cross reference or project our Pfam matches to UniProt on to the PDB structure/sequence. In the case of PF00002 (assuming you mean this accession), the structure, 3L2J only represents a subregion on the UniProt sequence. In fact, it only maps to four residues of the UniProt sequence (PTH1R_HUMAN/184-187). In this case the projection approach works, but there is simply insufficient sequence to obtain a significant match using the PDB sequence to HMM approach (i.e. RCSB).

I hope this helps,

Rob

Comment on Does my family of interest have a determined 3D protein structure? by Shyam

Shyam — Thu, 17 Jan 2013 23:55:05 +0000

Hi,

I downloaded all Pfam domains in tab delimited file via

http://www.rcsb.org/pdb/rest/hmmer?file=hmmer_pdb_all.txt

A quick look doesn’t show PF0002 with any structures.

However looking online shows 2 structrures —
http://pfam.sanger.ac.uk/family/7tm_2#tabview=tab9

Could you help me understand what’s going on?

Thanks,
Shyam

Comment on What’s new in AntiFam? by ppgardne

ppgardne — Tue, 11 Dec 2012 03:39:05 +0000

WordPress seems to have dropped the link I added:
http://en.wikipedia.org/wiki/NcRNA#Bifunctional_RNA

Comment on What’s new in AntiFam? by ppgardne

ppgardne — Mon, 10 Dec 2012 20:19:55 +0000

Good point Kelly, Thanks! There are definitely a few other Rfam families that are legitimately translated. The are worth checking too. If we had full length group I & II intron models then these would be a concern too (fortunately we don't).

Comment on What’s new in AntiFam? by kelly_williams

kelly_williams — Mon, 10 Dec 2012 19:27:38 +0000

Another anti-AntiFam is ANF00030. For most of its seed proteins (the ones ending “AA”), the last 10-11 amino acids are the legitimate translation product of tmRNA.

Comment on R-chie arc diagrams now available in our secondary structure galleries by Sarah

Sarah — Tue, 27 Nov 2012 09:20:11 +0000

UPDATE: there’s now a colour key describing what the colours in the Rchie diagrams mean. Enjoy!

Comment on What’s new in AntiFam? by ppgardne

ppgardne — Thu, 15 Nov 2012 11:25:09 +0000

There’s Ribin too [5].

[5] Ribin, a protein encoded by a message complementary to rRNA, modulates ribosomal transcription and cell proliferation.
Kermekchiev M, Ivanova L.
Mol Cell Biol. 2001 Dec;21(24):8255-63.
http://www.ncbi.nlm.nih.gov/pubmed/11713263

Comment on We’re on the move by ppgardne

ppgardne — Wed, 14 Nov 2012 21:32:32 +0000

I assume your twitter account will change to Xfam_EBI now too.