From: Systematic identification of stem-loop containing sequence families in bacterial genomes
Species | Family | This work | Literature | Type | Notes | |||
---|---|---|---|---|---|---|---|---|
 |  | size | copies | size | copies | ref. |  |  |
B. anthracis | Bant-1 | 72 | 104(29) | Â | Â | Â | I | Â |
 | Bcr1 | 167 | 31(21) | 147 | 12 | [24] | I |  |
B. halodurans | Bhal-1 | 74 | 36(32) | Â | Â | Â | I | Â |
 | Bhal-2 | 76 | 50(41) |  |  |  | I | contains CRISPR repeats |
C. perfringens | Clop-1 | 93 | 44(28) | Â | Â | Â | I | Â |
C. tetani | Clot-1 | 74 | 19(16) | Â | Â | Â | I | Â |
 | Clot-2 | 31 | 34(32) |  |  |  |  | contains CRISPR repeats |
 | Clot-3 | 90 | 24(17) |  |  |  | I | contains CRISPR repeats |
E. faecalis | Efa-1 | 163 | 65 (18) | Â | Â | Â | I | Â |
 | Efa-2 | 292 | 11(9) |  |  |  | G |  |
L. johnsonii | Lac-1 | 231 | 34(6) | Â | Â | Â | G | Â |
S. aureus | Sta-1 | 105 | 25(25) | Â | Â | Â | I | Â |
 | Sta-2 | 460 | 9(8) |  |  |  | S |  |
 | Sta-3 | 136 | 24(15) |  |  |  | I |  |
 | Sta-4 | 99 | 46(27) |  |  |  | I |  |
S. pneumoniae | BOX | 84 | 205(105) | 100–200 | 127 | [25] | I |  |
 | RUP | 63 | 110(99) | 108 | 54 | [26] | I |  |
 | Stre-1 | 45 | 241(225) |  |  |  | G |  |
B. melithensis | Bru-RS | 118 | 222(69) | 103–105 | 35–40 | [27] | I |  |
R. conorii | Rpe-4 | 100 | 97(74) | 95 | 94 | [28] | I | Â |
 | Rpe-5 | 115 | 45(35) | 115 | 55 | [28] | I |  |
 | Rpe-6 | 108 | 123(74) | 136 | 168 | [28] |  |  |
 | Rpe-7 | 123 | 186 144) | 99 | 223 | [28] |  |  |
M. genitalium | Myg-1 | 259 | 10(7) | Â | Â | Â | I | Â |
M. pneumoniae | Myp-1 | 143 | 25(18) | Â | Â | Â | G | part of REPMP1 repeat |
 | Myp-2 | 158 | 42(16) |  |  |  | G | part of REPMP4 repeat |
 | Myp-3 | 558 | 11(8) |  |  |  | G | part of REPMP5 repeat |
 | Myp-4 | 364 | 8(7) |  |  |  | G | part of REPMP5 repeat |
 | Myp-5 | 426 | 8 (8) |  |  |  | G | part of REPMP5 repeat |
 | Myp-6 | 468 | 11(11) |  |  |  | G | part of REPMP2/3 repeat |
 | Myp-8 | 674 | 9(9) |  |  |  | G | part of REPMP2/3 repeat |
 | Myp-9 | 226 | 9(9) |  |  |  | G | part of REPMP2/3 repeat |
 | Myp-10 | 330 | 12 (12) |  |  |  | G | part of REPMP2/3 repeat |
 | Myp-7 | 131 | 42(22) |  |  |  | G |  |
C. diphtheriae | Cod-1 | 140 | 17(16) | Â | Â | Â | I | Â |
 | Cod-2 | 32 | 43(39) |  |  |  | G |  |
 | Cod-3 | 170 | 23(20) |  |  |  |  |  |
 | Cod-5 | 74 | 35(29) |  |  |  | I |  |
M. tuberculosis | Myt-1 | 72 | 75(70) | Â | Â | Â | Â | Â |
 | Myt-2 | 115 | 769(223) |  |  |  | G | located within PE genes |
 | Myt-3 | 81 | 81(77) |  |  |  | G | located within PE genes |
 | Myt-4 | 83 | 196(68) |  |  |  | G | located within PE genes |
 | Myt-5 | 71 | 41(2) |  |  |  | G | contains CRISPR repeats |
 | Myt-7 | 136 | 278(68) |  |  |  | G | located within PE genes |
 | Myt-8 | 92 | 33(25) |  |  |  |  |  |
 | Myt-9 | 67 | 53(15) |  |  |  |  |  |
 | Myt-10 | 154 | 62(59) |  |  |  | G | located within PE genes |
 | Myt-11 | 65 | 56(21) |  |  |  |  | contains MIRU repeats |
M. leprae | REPLEP | 740 | 29(9) | 400–880 | 15 | [29] | I |  |
 | RLEP | 641 | 38(30) | 601–1075 | 37 | [29] | S |  |
 | Myl-1 | 371 | 7(4) |  |  |  | S | part of LEPREP repeat |
 | Myl-2 | 1979 | 9(7) |  |  |  | S | part of LEPREP repeat |
B. bronchiseptica | Bor-1 | 117 | 196(92) | Â | Â | Â | I | Â |
 | Bor-2 | 167 | 17(6) |  |  |  | I |  |
 | Bor-3 | 134 | 34(32) |  |  |  | G |  |
 | Bor-4 | 81 | 164(114) |  |  |  | G |  |
 | Bor-5 | 112 | 135(101) |  |  |  | G |  |
 | Bor-6 | 147 | 37(31) |  |  |  | G |  |
B. pertussis | Bor-1 | 93 | 128(78) | Â | Â | Â | I | Â |
N. meningitidis | ATR | 206 | 14(9) | 183 | 13 | [30] | I | Â |
 | Nem-2 | 341 | 11(7) |  |  |  |  |  |
 | Nem-3 | 127 | 10(9) |  |  |  | G |  |
 | Nem-4 | 36 | 412(362) |  |  |  | I | contains DUS repeats |
 | dRS3 | 33 | 755(708) | 20 | 770 | [30] | I |  |
 | NEMIS | 46 | 262(81) | 106–158 | 250 | [13] | I |  |
 | Rep2 | 65 | 22(18) | 59–154 | 26 | [30] | I |  |
P. multocida | Pam-1 | 155 | 12(12) | Â | Â | Â | S | contains DUS repeats |
E. coli | BoxC | 50 | 22(20) | 56 | 32 | [31] | Â | Â |
 | Eco-1 | 734 | 9(7) |  |  |  | G |  |
 | ERIC | 140 | 19(19) | 127 | 21 | [32] | S |  |
 | PU-BIME | 108 | 301(199) | 40 | 485 | [31] |  |  |
H. influenzae | Hin-1 | 31 | 53(51) | Â | Â | Â | I | contains DUS repeats |
P. aeruginosa | Pae-1 | 84 | 133(61) | Â | Â | Â | I | Â |
 | Pae-2 | 287 | 65(24) |  |  |  | G |  |
 | Pae-3 | 220 | 16(13) |  |  |  | G |  |
 | Pae-4 | 52 | 41(35) |  |  |  |  |  |
P. putida | Ppu-1 | 617 | 39(28) | Â | Â | Â | I | Â |
 | Ppu-2 | 2056 | 10(8) |  |  |  | S |  |
 | Ppu-3 | 251 | 27(23) |  |  |  | G |  |
 | Ppu-4 | 81 | 41(24) |  |  |  | I |  |
 | Ppu-9 | 124 | 57(31) |  |  |  | I |  |
 | REP | 39 | 588(496) | 30 | 804 | [33] | I |  |
S. typhi | PU-BIME | 43 | 146(126) | 40 | 100 | [31] | I | Â |
 | PU-BIME* | 80 | 59(37) | 40 | >100 | [31] |  |  |
S. typhimurium | PU-BIME | 78 | 142(94) | 40 | 82 | [31] | Â | Â |
 | Sal-1 | 115 | 27(17) |  |  |  | I |  |
 | Sal-2 | 120 | 33(3) |  |  |  | G | contains CRISPR repeats |
V. cholerae | ERIC | 103 | 97(66) | 127 | 80 | [31] | I | Â |
 | Vic-1 | 184 | 14(1) |  |  |  | I |  |
Y. pestis | ERIC | 115 | 241(128) | 69–127 | 167 | [16] | I |  |
 | YPAL | 168 | 101(68) | 169 | 30 | [17] | I |  |
 | YPAL* | 136 | 26(13) | 130 | 10 | [17] | I |  |