Skip to main content

Table 1 Analysis of the association of Insertion Sequence elements with REP sequences. Table 1 shows the results of the analysis of the presence of REP sequences in the extragenic spaces flanking mobile elements. The fifth column shows the association ratio between the number of mobile elements containing REP sequences in the flanking extragenic spaces and the total number of mobile elements in the analyzed genome. The canonical REP sequence for each analyzed species is in the additional material [see Additional file 15]

From: Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements

Genomes GenBank Accession IS copies Mobile elements Assoc. ratio Assoc. % REPs number
Pseudomonas syringae pv. tomato str. DC3000 [5] AE016853 128 ISPsy8 5/5 100% 323
    ISPsy7 6/10 60%  
    ISPsy 9 1/1 100%  
    ISPsy6 1/13 7.7%  
    ISPsy5 3/36 8.3%  
Pseudomonas aeruginosa PAO1 [1] AE004091 6 ISPa11 6/6 100% 157
Pseudomonas putida KT2440 [3] AE015451 51 ISPpu9 7/7 100% 938
    ISPpu10 7/7 100%  
    ISPpu11 1/2 50%  
    ISPpu15 1/4 25%  
    ISPpu14 1/5 20%  
    Group II intron 2/9 22.2%  
Escherichia coli CFT073 [17] AE014075 45 IS1397 1/2 50% 227
    IS150 1/2 50%  
Escherichia coli K12 [17] U00096 44 Transp. (169aa) 1/7 14.3% 290
Escherichia coli O157:H7[17] BA000007 47 IS5 1/11 9.1% 212
Escherichia coli O157:H7 EDL933[17] AE005174 39 --- --- --- 209
Salmonella enterica subsp. enterica serovar Typhi str. CT18 [55] AL513382 29 --- --- --- 228
Salmonella typhimurium LT2 [55] AL513382 16 IS200 1/25 4% 207
Shigella flexneri 2a str. 2457T [55] AE014073 266 --- --- --- 189
    IS1 6/101 6%  
    IS4 3/11 27.3%  
    IS2 2/37 5.4%  
    IS91 1/7 14.3%  
    IS3 1/6 16.7%  
Shigella flexneri 2a str. 301 [55] AE005674 84 ISSfl4 1/4 25% 193
    Transposase(insB) 1/1 100%  
    IS1106 5/9 55.5%  
Neisseria meningitidis MC58 [56] AE002098 32 IS1655 2/13 15.4% 747
    Transposase and PivNM COG3547 3/5 60%  
Neisseria meningitidis Z2491 [56] AL157959 51 IS1016C2 1/3 33.3% 673
    IS1106 7/15 46.7%  
    IS1655 2/6 33.3%  
    IS1016 2/17 11.8%  
Agrobacterium tumefaciens str. C58 UWash [1] AE008688
AE008689
6 Transposase and PivNM COG3547 1/5 20% 116
Agrobacterium tumefaciens str. C58 Cereon[1] AE007869
AE007870
5 --- --- --- 121
Sinorhizobium meliloti 1021 [1, 57] AL591688 53 --- --- --- 294
    ISRm22 9/9 100%  
    ISRm19 2/2 100%  
    ISRm11 1/6 16.6%  
    ISRm5 5/7 71.4%  
  AL591985 (pSymB) 11 ISRm21 2/3 66.6%  
    ISRm22 1/1 100%  
    ISRm19 2/2 100%  
    ISRm2011 1/2 50%  
    ISRm17 1/1 100%  
Deinococcus radiodurans R1 [58] AE000513 31 --- --- --- 149
Rickettsia conorii str. Malish 7 [59] AE006914 0 --- --- --- 237
Mycobacterium tuberculosis CDC1551 [1] AE000516 37 IS1558 1/2 50% 64
13 species 19 genomes 981 36 mobile elem. 107/981 11%