Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

Additional file 1:

The list of 315 adjacent pairs of COGs. This file contains the list of 315 adjacent pairs of COGs that were further analyzed on a case by case basis for prediction of TAS (approach 1) as described in the Methods section.

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Additional file 2:

Multiple alignment of representative sequences of COG5606. The alignment supports the analysis and description of the predicted RelE-COG5606 TAS

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Additional file 3:

Multiple alignment of truncated members of the MerR-like family. The alignment supports the analysis and description of the predicted PIN-MerR TAS

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Additional file 4:

Multiple alignment of representative sequences of the XF1663 family. The alignment supports the analysis and description of the predicted MazF-XF1663 TAS

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Additional file 5:

Multiple alignment of representative sequences of the YhfG family. The alignment supports the analysis and description of the predicted YhfG-Fic/Doc TAS

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Additional file 6:

Multiple alignment of representative sequences of the DUF397 family. The alignment supports the analysis and description of the predicted DUF397-HTH TAS

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Additional file 7:

Multiple alignment of representative sequences of the YgiU family. The alignment supports the analysis and description of the predicted YgiU-xre TAS

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Additional file 8:

Multiple alignment of representative sequences of COG3832. The alignment supports the analysis and description of the predicted COG3832-ArsR TAS

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Additional file 9:

Multiple alignment of a representative set of GNAT family acetyltransferases. The alignment supports the analysis and description of the GNAT-xre and GNAT-RHH systems

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Additional file 10:

The representation of toxins, antitoxins and toxin-antitoxin pairs in 750 complete genomes of prokaryotes. This file contains the counts of solo toxin and antitoxin genes as well as TA-pairs for all 750 prokaryotic genomes analyzed in this work. Phenotypic characteristics and the total number of protein coding genes are given for each genome.

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Additional file 11:

Statistical Appendix for the Methods. The appendix contains additional details concerning the following procedures: i) the likelihood model used to estimate the scaling parameters for the number of TAS pairs relative to the genome size and ii) variability of abundance of different TAS pairs within ATGCs.

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Additional file 12:

Table S1. Distribution of TAS among prokaryotic taxa

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Additional file 13:

Species abbreviations used in the alignments in Figures 2, 4, 5, and 6. The provided table spells out the species abbreviations used in the alignments in Figures 2,4,5 and 6

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Additional file 14:

Complete list of GenBank identifiers for all predicted and known toxins and antitoxins. The table contains the GenBank identifiers (GI numbers) for all predicted and known toxins and antitoxins identified in this work in 750 complete prokaryotic genomes

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