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Table 3 Analysis of potentially informative gene structures in korarchaeota and thaumarchaeota.

From: The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

Sequence Property Initially reported to support In Korarchaeota In Thaumarchaea Now Supports Notes
Split RpoA Holophyly X X Holophyly or paraphyly (Thaumarchaeota or Korarchaeota)  
7 AA Insert in EF-1 Paraphyly (Crenarchaea) 2 aa insert shared with thermoplasma X Paraphyly, but weakly Must be reversion in Euryarchaea
6 AA insert in RadA Paraphyly (Euryarchaea) ? ? ? There is probably an artifact in the original alignment.
1 AA insert in SecY Paraphyly (Crenarchaea) absent X Paraphyly (Crenarchaea or Thaumarchaeota) Single Glycine, but anchors are really nicely conserved
1 AA insert in proAS Holophyly X absent Probably holophyly, maybe paraphyly (Thaumarchaeota) BLAST reveals Thaumarchaeota may have HGT from Firmicutes.
7 AA insert in GatD Holophyly X X Inconclusive Completely conserved, but its not clear the Eukaryotes inherited this from Archaea
2 AA insert in PBG Holophyly Gene is absent Gene is absent Inconclusive (bacterial origin) This protein is present in bacteria, so the Thaumarchaeota and Korarchaeota probably lost it
2 AA insert in ribosomal S12 Holophyly X X Inconclusive It is conserved across the Eukaryotes and Archaea
  1. Each indel was analyzed by creating an alignment of archaeal sequences from BLAST searches. We consider these results to be inconclusive until thaumarchaeota and korarchaeota are sampled better.