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Open Access Research article

IS4 family goes genomic

Daniel De Palmenaer1, Patricia Siguier2 and Jacques Mahillon1*

Author Affiliations

1 Laboratoire de microbiologie alimentaire et environnementale, Université catholique de Louvain, Croix du Sud 2/12, B-1348 Louvain-la-Neuve, Belgium

2 Laboratoire de microbiologie et génétique moléculaires, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse cedex 9, France

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BMC Evolutionary Biology 2008, 8:18  doi:10.1186/1471-2148-8-18

Published: 23 January 2008

Additional files

Additional file 1:

Subgroup IS231. A. Dendrogram displaying relative distances of transposases from subgroup IS231. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Additional file 2:

Subgroup ISH8. A. Dendrogram displaying relative distances of transposases from subgroup ISH8. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Additional file 3:

Subgroup IS4Sa. A. Dendrogram displaying relative distances of transposases from subgroup IS4Sa. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 4:

Subgroup IS4. A. Dendrogram displaying relative distances of transposases from subgroup IS4. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 5:

Subgroup IS10. A. Dendrogram displaying relative distances of transposases from subgroup IS10. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 6:

Subgroup IS50. A. Dendrogram displaying relative distances of transposases from subgroup IS50. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 7:

Subgroup ISPepr1. A. Dendrogram displaying relative distances of transposases from subgroup ISPepr1. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 8:

Family IS701. A. Dendrogram displaying relative distances of transposases from family IS701. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Three distinct alignments, corresponding to three different DNA end signatures, are shown in this case. Names of corresponding elements are listed in the same order as in A. Blue color scheme represents percentage of nucleotide identity per column in each alignment, and is represented by black bars for the upper alignment only. Minimal (black line) and maximal (dashed line) extent of TIRs is given in each case. IRL, left TIR; IRR, right TIR.

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Additional file 9:

Family ISH3. A. Dendrogram displaying relative distances of transposases from family ISH3. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 10:

Family IS1634. A. Dendrogram displaying relative distances of transposases from family IS1634. Each tree leave indicates the name of the associated element, followed by the host organism and prokaryotic phylum in which the IS was found originally. For a complete description of individual elements please refer to the ISfinder database [15]. B. and C. Alignment of left and right DNA extremities, respectively. Names of corresponding elements are listed in the same order as in A. The blue color scheme represents the percentage of nucleotide identity per column as displayed by black bars. The DNA extremity consensus used in Figure 1 is shown in bottom, together with minimal (black line) and maximal (dashed line) extent of TIRs. IRL, left TIR; IRR, right TIR.

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Open Data

Additional file 11:

Combining alignment data from subgroup IS50 with functional data from transposons Tn5. The black sequence is the consensus obtained after multiple alignments of 19 members of the IS50 subgroup with MCOFFEE. Interrupting dashes indicate alignment gaps. The conservation percentage is represented by black bars over each position. The dotted line stands for 70% residue conservation. Residues of the IS50R transposase with known functional data are shown together with their position coordinates. They are grouped and color-coded following the function they carry out in regulation or during the transposition mechanism. Aspartate and glutamate residues of the DDE motif are pointed out by white triangles among the conservation bars. The YREK motif is highlighted by white 'V'. The transpososome formation step (i) is divided into successive stages including initial cis-binding, dimerization, 3'-end & 5'-end trans binding, trans-binding via the β hairpin clamp and additional trans contacts. Target capture residues are displayed by (ii), while integration and transposase release are not shown. Residues annotated as intramolecular inhibition are supposed to inhibit dimerization of full length transposases. For further details about these mechanistic concepts, see references [9,25,59]. Each residue is linked by colored lines to the corresponding position in the alignment consensus. Their designation is colored and bold if the residue is conserved at least at 70%, gray if it is less or not conserved. Conserved positions with unknown function are pointed out by asterisks (*).

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