Table 1.
FR3D search results for the five-nucleotide sarcin/ricin query motif shown with yellow letters in Fig. 7a from the PDB file 1s72. The query motif is shown in the first row. Candidate motifs are listed in order of increasing discrepancy, with bases of each candidate motif placed in the same column as the corresponding bases of the query motif. Yellow background indicates bona fide sarcin/ricin motifs confirmed by visual inspection. In the last column, L represents a local motif, C represents a composite motif, and C* represents a case where an intercalated base (A2302) comes from a third strand and forms a trans Hoogsteen/Hoogsteen basepair
| Discrepancy | Motifs found by FR3D | Type | ||||||
|---|---|---|---|---|---|---|---|---|
| Query Motif (Sarcin): | 0.0000 | A2694 | G2701 | U2693 | A2702 | G2692 | L | |
| PDB File: | 1S72 | 0.0712 | A1372 | G2053 | U1371 | A2054 | G1370 | L |
| Number of Search Nucleotides: | 5 | 0.1080 | A 383 | G 406 | U 382 | A 407 | G 381 | L |
| Motifs Identified: | 12 (All) | 0.1275 | A 590 | G 568 | U 589 | A 569 | G 588 | L |
| Basepairs Constrained: | None | 0.1784 | A 177 | G 159 | U 176 | A 160 | G 175 | L |
| Guaranteed Cutoff D0: | 0.5 | 0.1844 | A 466 | G 475 | U 465 | A 476 | G 464 | L |
| Relaxed Cutoff D1: | 0.5 | 0.1976 | A 360 | G 292 | U 359 | A 293 | G 358 | L |
| Exclude Redundant Candidates: | Yes | 0.2284 | A 215 | G 225 | U 214 | A 226 | G 213 | L |
| 0.2374 | A 80 | G 102 | U 79 | A 103 | G 78 | L | ||
| 0.2391 | A1973 | G2009 | U1972 | A2010 | G1971 | C | ||
| 0.2491 | A1294 | G 911 | U1293 | A 912 | G1292 | C | ||
| 0.2714 | A 955 | A1012 | U 954 | A1013 | G 953 | C* | ||
| Highest Scoring non-sarcin motif: | 0.4395 | C1545 | C1640 | U1544 | A1641 | G1543 | L | |