A) Five ORFs have been clearly detected (a sixth ORF could exist, but it has not been considered since the homology search results in partial, short matches)

Four of these ORFs (shown in green) have been assigned to taxa (Fusobacteriaceae). The best hit for the second ORF (shown in red) is a short protein found in (Gamma-proteobacteria), and no hits with Fusobacteriales have been found in that zone. This can be indicative of a putative foreign origin of that ORF. B) The zone also shows atypical composition, which is very apparent and easily seen in the compositional diagram. C) Clustering of the distance matrix of compositional correlations. A clustering parameter indicates the point at which the groups of compositionally similar ORFs are extracted. The lower the value, the fewer the transitions found, since rather dissimilar ORFs are allowed to fall into the same cluster. In this example, the DNA composition of ORF 2 is so different that it will be recognised as being atypical at all values of the clustering parameter.<p><b>Copyright information:</b></p><p>Taken from "Estimating the extent of horizontal gene transfer in metagenomic sequences"</p><p>http://www.biomedcentral.com/1471-2164/9/136</p><p>BMC Genomics 2008;9():136-136.</p><p>Published online 24 Mar 2008</p><p>PMCID:PMC2324111.</p><p></p

Density map of the role of the nodes in the network that are conserved or deleted in , according to the procedure described in 23

<p><b>Copyright information:</b></p><p>Taken from "Modular organization in the reductive evolution of protein-protein interaction networks"</p><p>http://genomebiology.com/2007/8/5/R94</p><p>Genome Biology 2007;8(5):R94-R94.</p><p>Published online 28 May 2007</p><p>PMCID:PMC1929161.</p><p></p> The degree of participation measures the connection of a given node with the nodes from modules other than its own. The within-module degree measures the connection of the node with other nodes within its own module. Peripheral nodes show both low participation and low within-module degree. Non-hub connectors participate significantly and with a low degree of within-module connections, while connector hubs have both high participation and high degree of within-module connections [23]. Connector hubs and non-hub connectors are mainly conserved in the network, while the deletion of nodes mainly affects peripheral nodes. The measures are calculated as in [23], based on the modular division of the network obtained from the Butland dataset. The scale refers to the number of nodes in each position

Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein-3

<p><b>Copyright information:</b></p><p>Taken from "Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein"</p><p>http://www.biomedcentral.com/1471-2164/9/14</p><p>BMC Genomics 2008;9():14-14.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2257941.</p><p></p>espondent colours (see legend)

Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein-2

<p><b>Copyright information:</b></p><p>Taken from "Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein"</p><p>http://www.biomedcentral.com/1471-2164/9/14</p><p>BMC Genomics 2008;9():14-14.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2257941.</p><p></p> described regions sharing a nucleotide similarity higher than 70%. Green boxes represent gene positions and strand. Rtx 5' and 3' regions are shaded in red. For an easy visualization, the Corby sequence was complemented and reversed. For a more detailed view see additional fil

Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein-0

<p><b>Copyright information:</b></p><p>Taken from "Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein"</p><p>http://www.biomedcentral.com/1471-2164/9/14</p><p>BMC Genomics 2008;9():14-14.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2257941.</p><p></p>espondent colours (see legend)

Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein-1

<p><b>Copyright information:</b></p><p>Taken from "Virulence factor rtx in , evidence suggesting it is a modular multifunctional protein"</p><p>http://www.biomedcentral.com/1471-2164/9/14</p><p>BMC Genomics 2008;9():14-14.</p><p>Published online 14 Jan 2008</p><p>PMCID:PMC2257941.</p><p></p>0% (500 replicates)

Analysis of and function predictions for previously conserved hypothetical or putative proteins in -0

<p><b>Copyright information:</b></p><p>Taken from "Analysis of and function predictions for previously conserved hypothetical or putative proteins in "</p><p>BMC Microbiology 2006;6():1-1.</p><p>Published online 9 Jan 2006</p><p>PMCID:PMC1360075.</p><p>Copyright © 2006 Gaudermann et al; licensee BioMed Central Ltd.</p>nclude: a MFS family transporter (Bfl240, IolF-like, top right; exact substrate specificity not known), ADP-heptose synthase (Bfl063, IolC-like), an acetolactate synthase II, large subunit (Bfl593; IolD-like) and its small subunit, neighbouring protein Bfl 592 (both proteins should physically interact), fructose 1,6-bisphosphate aldolase (Bfl255, IolJ-like; this enzyme is also involved in glycolysis) and predicted myo-inositol-1(or 4)-monophosphatase (Bfl535; related to the Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family). Bfl601 (triosephosphate isomerase) finishes the pathway converting created dihydroxyacetone phosphate into glyceraldehyde 3-phosphate

Analysis of and function predictions for previously conserved hypothetical or putative proteins in -3

<p><b>Copyright information:</b></p><p>Taken from "Analysis of and function predictions for previously conserved hypothetical or putative proteins in "</p><p>BMC Microbiology 2006;6():1-1.</p><p>Published online 9 Jan 2006</p><p>PMCID:PMC1360075.</p><p>Copyright © 2006 Gaudermann et al; licensee BioMed Central Ltd.</p> the homology model (starting from residue 1, a Met in Bfl341). Important predicted catalytic residues outline the substrate cleft. These are His 130, Arg 180, Glu 217 and Arg 281 of Bfl341 corresponding to His 148, Arg 196, Glu 212, and Arg 274 in the template structure (four from five conserved residues known for the family and those checked from by mutagenesis to be important for catalysis in vitro [24]). Kajander et al. [24] did not know yet the accurate molecular function of the structure they solved. However, regarding the high sequence similarity of Bfl341 (38% identical, 57% similar residues) to recently characterized Pgl protein [25], the actual activity of Bfl341 we now predict to be a 6-phosphogluconolactonase