Figure 1

RecJ homologs in archaea. Color code: eukaryotes - red; bacteria - yellow; euryarchaea - dark blue; crenarchaea - light blue; deeply branched archaeal lineages (Thaumarchaeota, Korarchaeota, Nanoarchaeota) - purple. A. Phylogeny of the DHH superfamily, The tree was constructed using aligned blocks corresponding to DHH domain (229 sequences in total, 83 aligned positions; see Additional file 1 for details). arCOG or COG numbers or family name (for eukaryotes) are indicated for the corresponding branches. Three distinct major clades are shaded. The location of the GAN protein is indicated by green. B. Genomic context of the RecJ homologs in selected archaea, Orthologous genes are shown by arrows of the same color; genes shown approximately to scale. The arCOGs to which RecJ-like proteins are assigned are indicated in parenthesis. The protein IDs for this region in the corresponding genomes are provided. C. The phyletic patterns of RecJ-related arCOGs, The tree is a modified version of the consensus tree representing phylogeny of archaea [38] with Caldiarchaeum subterraneum included in the Thaumarchaeota branch and several branches with consistent distribution of RecJ-related subfamilies are collapsed. The phyletic patterns for indicated arCOGs (filled circles show presence and empty circles show absence) are superimposed over the phylogenetic tree of archaea. The circles for proteins implicated in replication are shaded. The number of paralogs is indicated inside the circles for arCOG00427 (all other subfamilies have one paralog for each genome). Abbreviations: Arcfu - Archaeoglobus fulgidus; Metsm - Methanobrevibacter smithii ATCC 35061; Metth - Methanothermobacter thermautotrophicus; Metst - Methanosphaera stadtmanae; Metmp - Methanococcus maripaludis S2; Metva - Methanococcus vannielii SB; Metae - Methanococcus aeolicus Nankai-3; Metja - Methanocaldococcus jannaschii; Metvu - Methanocaldococcus vulcanius M7; Metin - Methanocaldococcus infernus ME; Metka - Methanopyrus kandleri; Pyrae - Pyrobaculum aerophilum; Pyrar - Pyrobaculum arsenaticum DSM 13514; Pyris - Pyrobaculum islandicum DSM 4184; Thene - Thermoproteus neutrophilus V24Sta; Pyrca - Pyrobaculum calidifontis JCM 11548; Thete - Thermoproteus tenax; Calma - Caldivirga maquilingensis IC-167; Thepe - Thermofilum pendens Hrk 5; Censy - Cenarchaeum symbiosum; Nitma - Nitrosopumilus maritimus SCM1; Naneq - Nanoarchaeum equitans; Korcr - Candidatus Korarchaeum cryptofilum OPF8; Calte - Candidatus Caldiarchaeum subterraneum.