There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli et al. for their iTOL project.
This tree is based on a concatenated set of conserved protein and not 16S rRNA (cf. Branching order of bacterial phyla (Woese, 1987)

Branching order of bacterial phyla (Woese, 1987)

There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all preceding models were based on discussions of morphology....

).
The arrangement of the various phyla differs from that of 16S, but may be due to long branch attraction

Long branch attraction

Long branch attraction is a phenomenon in phylogenetic analyses when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships. For example, in DNA sequence-based analyses, the problem arises when sequences from two lineages evolve rapidly...

 and due to the limited sampling (many phyla have a sole sequenced representative, whereas the Firmicutes and the Proteobacteria are over-represented). The Proteobacteria is not monophyletic in this phylogram, but this may be erroneous given the large amount of literature in favour of basal Acidobacteria. Contrary to 16S trees, the deepest branching clade is the Firmicutes

Firmicutes

The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...

. Nevertheless, the last common ancestor was between Bacteria and Archaea+Eukarya.

See also

• Branching order of bacterial phyla (Woese, 1987)
  Branching order of bacterial phyla (Woese, 1987)
  There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all preceding models were based on discussions of morphology....
  
  
• Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
  Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
  There are several models of the Branching order of bacterial phyla, the most cited of these was proposed in 1987 paper by Carl Woese. This cladogram was later expanded by Rappe and Giovanoni in 2003 to include newly discovered phyla.-See also:...
  
  
• Branching order of bacterial phyla after ARB Silva Living Tree
• Branching order of bacterial phyla (Ciccarelli et al., 2006)
  Branching order of bacterial phyla (Ciccarelli et al., 2006)
  There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli et al. for their iTOL project.This tree is based on a concatenated set of conserved protein and not 16S rRNA There are several models of the Branching order of bacterial phyla, one of...
  
  
• Branching order of bacterial phyla (Battistuzzi et al.,2004)
  Branching order of bacterial phyla (Battistuzzi et al.,2004)
  There are several models of the Branching order of bacterial phyla, one of these was proposed in 2004 by Battistuzzi and Hedges,, note the coinage of the taxa Terrabacteria and Hydrobacteria.-See also:* Branching order of bacterial phyla...
  
  
• Branching order of bacterial phyla (Gupta, 2001)
  Branching order of bacterial phyla (Gupta, 2001)
  There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved...
  
  
• Branching order of bacterial phyla (Cavalier-Smith, 2002)
  Branching order of bacterial phyla (Cavalier-Smith, 2002)
  There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure,...