BMC Genomics 2002, 3 http://www.biomedcentral.com/1471-2164/3/8 ERF_ bIL67 ERF_c2 ERF orf364 SSB Met ERF_MM1 ORF7_ST7201 ERF orf364 SSB RusA Orf11 Orf12 Met ERF_P22 ERF_HK97 λcIII λcIII kil ARF ERF ABC1 kil gene42.1 ERF gene41 ABC1 Associated with a λ exonuclease BBL29_Bbcp32-8 BBO29_Bb BBR29_Bb BBC05_Bb ORF4 Bb orf216_φSLT orf100a Orf86 Orf178 ERF SSB EndoVII ERF_Unk_6015511 ERF SSB Orf52_D3 ERF λEXO HTH orf17_φPV83 Orf86 GP46 ERF SSB EndoVII lmo2318_Lm GP46 ERF DNAD Met Orf15 lmo2314 GP37 ORF244_BPmv4 Orf223_Lj771 orf364 ERF Figure 4 Maximum likelihood tree for the ERF superfamily of proteins. The designations, gene names and species abbreviations are as in Fig. 2A. The internal branches with RELL bootstrap support >70% are indicated by blue circles. The gene neighbor- hoods of the ERF proteins are shown whenever they contained gene coding for proteins with potential functional relevance. Gene abbreviations are as in Fig. 1B Additionally, in the loop between helices 4 and 5 of the ERF domain there is a universally conserved acidic motif of the form DXD. Analogous to the RecT superfamily, this acidic dyad might coordinate a divalent cation and under- go a conformational change dependent on metal-binding. However, the average size of the core domains, the pat- terns of conserved residues, and the predicted secondary structures of the RecT/Redβ and ERF domains show no correspondence to each other, implying that there is no direct evolutionary link between these protein groups. ERF homologs are encoded by the genomes of several temperate phages of Gram-positive bacteria and γ-proteo- bacteria; additionally, we detected members of this super- family in Listeria and in all the circular plasmids and one linear plasmid of Borrelia burgdorferi (Fig. 4). Thus, like the RecT/Redβ superfamily, the ERF family is likely to have emerged in the temperate phages, and was disseminated to the Borrelia circular plasmids and some bacterial ge- nomes via prophages. Detection of bacterial homologs of RAD52 and identifica- tion of an aberrant HhH domain in these proteins The baker's yeast protein RAD52 and its paralog RAD59 define a small family of proteins thus far represented in fungi, vertebrates and the early-branching ameboid eu- karyote, Entamoeba histolytica. Rad52 functions in con- junction with the RecA ortholog, the RAD51 recombinase in double-strand break repair and meiotic recombination [6]. RAD52 binds ssDNA during recombination and also Page 6 of 11 (page number not for citation purposes)