What are these new families with _2, _3, _4 endings?

January 19, 2012

Some users have been contacting us about the new families that are appeared in Pfam release 26.0.

As pointed out by one of our users:

Pfam v26 includes, in addition to DDE_Tnp_1, the following new families:

DDE_Tnp_1_2
DDE_Tnp_1_3
DDE_Tnp_1_4
DDE_Tnp_1_5
DDE_Tnp_1_6
DDE_Tnp_1_7

These extra new families with the name_2, name_3, name_4 etc, have been constructed to increase the coverage of Pfam.  Many of our existing large diverse families are not well modelled by a single HMM and there are many true members that are not matched. So by building multiple models we can match more things.  Each of these models will be in the same Pfam clan, the RNaseH clan in this case.  For the most part these models do not represent any particular subfamily or classification group.  Essentially you should think of a match to any of the above seven DDE_TnP_1 families as being the same thing.  Because of the way  Pfam is built any particular region of a protein may only belong to one of these families.  We have a step in building clans called competition which means that if a region of a protein matches to both DDE_Tnp_1 and DDE_Tnp_1_2 for example then the region will be assigned to the family with the highest score.  This means that a match to DDE_Tnp_1 in release 25.0 may now end up in a different family such as DDE_Tnp_1_2.  You shouldn’t read too much into these changes.

The reason that many of these new families are appearing in Pfam release 26.0 is due to a change in strategy in how we are building many new Pfam families.  The new strategy consists of taking complete genomes and taking each protein that does not match Pfam and using it as a starting point for a Jackhmmer search.  Jackhmmer is an iterative search tool like PSI-blast.  If we find that the Jackhmmer search finds lots of homologues but has some overlaps with an existing family then we may build one of these new additional families to increase coverage of known sequences. Rather than give these families completely new names we simply call them the same as the existing family and append a number to them to show that they are closely related to each other.

 

Posted by Alex

2 Responses to “What are these new families with _2, _3, _4 endings?”


  1. Could you create a more formal list of families that are equivalent? I did a quick experiment with Pfam 25 and I found 117 clusters where each one had a family with name N and it could be associated with other families of name N_\d+ (in pseudo-regex), but I also found 205 groups where families looked like N_\d+ for a given N but N itself is not a family (an example is HTH_1). Is this a good working definition of equivalent families (N_\d+ are the same as N when N exists)? Or is this not always the case?

  2. alexbateman Says:

    Thanks for the comment. We don’t currently store a list of families which are equivalent and as you point out simply using your regex method isn’t enough. THere are naming schemes such as for HTH, peptidases and glycosyl hydrolases where sequential numbering is used for non-homologous families. If you do come up with a formal list then please do let us know.


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