RDFs are small accessory proteins that play an architecural role in controling directionality in integrase-mediated site-specific recombination. An analysis of the RDF proteins has revealed several interesting characteristics of this class of proteins. Sequence comparison have shown that the proteins distibute into several different clusters of related proteins. (View Tree) Ten of these clusters are persistant through multiple rounds of analysis and have been clasified as families (Families: L5, pSAM2, SLP1, P22, HP1, P2, Lambda, L54a, Tn5276 and Tn916) Two groups of families show similarities within the group and between different families and are likely to be related (L5-pSam2-SLP1 and HP1-P2). These superfamilies can further be defined by shared protien characteristic. The HP1 and P2 families consist of Cox proteins, and unlike most excisionases, they have a transcriptional regulatory activity in addition to the excisionase activity. The presence of Helix-Turn-Helix DNA binding(HTH) motif has been reported in several excisionases. Analysis of the entire list shows that 28 of the excisionases have an HTH motif. Of these, 13 are in the L5, pSam2 and SLP1 families, while in contrast, the Lambda family has no members with an HTH motif. Analysis of the charge of the protein indicates that the majority of the protein have a basic charge and that only 10 of the 63 protein have an isoelectric focusing point that is less than 7. ( View pI Histogram) Half of these acidic proteins are either in the L54a excisionase family or have a cognate integrase that is in the L54a family. This data suggests that it is unlikely that excisionase have one ancestral path. In fact, it is likely that at least four (cox, HTH, acidic and others) and possible more exist.
Families: L5, pSAM2, SLP1, P22, HP1, P2, Lambda, L54, and Tn5276
Phylogenetic Tree
Charge Histogram