Table 4 Motifs in C6706 and CV2 as determined by SMRT sequencing
From: A mobile restriction modification system consisting of methylases on the IncA/C plasmid
Types | Motif | nGenomea | m6A | m4C | Modified_base | Undetected modification sites | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
C6707 | CV2 | C6707 | CV2 | C6707 | CV2 | C6707 | CV2 | C6707 | CV2 | ||
Common (6 types) | AAGNNNNNNCATC | 454 | 532 | 452 (99.6%) | 528 (99.2%) | 0 | 0 | 1 (0.2%) | 0 | 1 (0.2%) | 4 (0.8%) |
AKDTRGCA | 386 | 476 | 181 (46.9%) | 244 (51.3%) | 0 | 0 | 168 (43.5%) | 186 (39.1%) | 37 (9.6%) | 46 (9.7%) | |
AKGYANYA | 755 | 456 | 300 (39.7%) | 171 (37.5%) | 0 | 0 | 260 (34.4%) | 93 (20.4%) | 195 (25.8%) | 192 (42.1%) | |
GATC | 37,401 | 34,375 | 37,070 (99.1%) | 33,991 (98.9%) | 0 | 0 | 71 (0.2%) | 95 (0.3%) | 260 (0.7%) | 289 (0.8%) | |
GATGNNNNNNCTT | 613 | 562 | 609 (99.3%) | 558 (99.3%) | 0 | 0 | 4 (0.7%) | 3 (0.5%) | 0 | 1 (0.2%) | |
TNNNNNNH | 348,498 | 334,917 | 0 | 0 | 0 | 0 | 220,207 (63.2%) | 213,464 (63.7%) | 128,291 (36.8%) | 121,453 (36.3%) | |
C6707 specific (5 types) | AGKNNNNW | 5445 | 0 | 2795 (51.33%) | 0 | 0 | 0 | 1727 (31.7%) | 0 | 923 (17.0%) | 0 |
GADNDGCG | 2993 | 0 | 0 | 0 | 0 | 0 | 1403 (46.9%) | 0 | 1590 (53.1%) | 0 | |
GARVNNDG | 13,031 | 0 | 0 | 0 | 0 | 0 | 8830 (67.8%) | 0 | 4201 (32.2%) | 0 | |
TVVVNNDG | 26,727 | 0 | 0 | 0 | 0 | 0 | 15,684 (58.7%) | 0 | 11,043 (41.3%) | 0 | |
DCAGVHRNG | 1490 | 0 | 0 | 0 | 476 (31.9%) | 0 | 665 (44.6%) | 0 | 349 (23.4%) | 0 | |
CV2 specific (4 types) | ABNBMVBW | 0 | 10,259 | 0 | 6318 (61.8%) | 0 | 0 | 0 | 2596 (25.3%) | 0 | 1345 (13.1%) |
GANNDBBG | 0 | 14,158 | 0 | 0 | 0 | 0 | 0 | 8130 (57.4%) | 0 | 6028 (42.6%) | |
GARVNRNG | 0 | 7699 | 0 | 0 | 0 | 0 | 0 | 4448 (57.8%) | 0 | 3251 (42.2%) | |
TNVVNNDG | 0 | 27,441 | 0 | 0 | 0 | 0 | 0 | 16,388 (59.7%) | 0 | 11,053 (40.3%) | |