| L23 50S Thermus Ribosome |
| ID: | 1377307531 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (94) | ||
| Sequences: | 1608 (971.4) | ||
| Seq/Len: | 17.106 | ||
| Nf(neff/√len): | 100.2 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 17.106).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 39_I | 56_T | 3.742 | 1.00 |
| 10_A | 29_W | 2.710 | 1.00 |
| 32_P | 58_H | 2.572 | 1.00 |
| 56_T | 77_K | 2.518 | 1.00 |
| 61_G | 75_D | 2.381 | 1.00 |
| 57_L | 80_I | 2.260 | 1.00 |
| 52_V | 84_A | 2.191 | 1.00 |
| 44_E | 50_K | 2.181 | 1.00 |
| 25_K | 80_I | 2.173 | 1.00 |
| 8_I | 46_A | 2.145 | 1.00 |
| 59_V | 78_K | 2.075 | 1.00 |
| 50_K | 84_A | 2.065 | 1.00 |
| 59_V | 76_R | 2.020 | 1.00 |
| 63_K | 72_K | 1.820 | 1.00 |
| 50_K | 87_Q | 1.771 | 1.00 |
| 9_L | 31_H | 1.769 | 1.00 |
| 63_K | 70_L | 1.743 | 1.00 |
| 12_V | 29_W | 1.639 | 1.00 |
| 38_E | 41_N | 1.625 | 1.00 |
| 55_N | 82_Q | 1.601 | 1.00 |
| 29_W | 76_R | 1.568 | 1.00 |
| 72_K | 75_D | 1.542 | 1.00 |
| 26_Y | 89_I | 1.540 | 1.00 |
| 41_N | 45_T | 1.517 | 1.00 |
| 66_L | 69_Y | 1.517 | 1.00 |
| 30_V | 39_I | 1.475 | 1.00 |
| 35_T | 38_E | 1.450 | 1.00 |
| 2_K | 38_E | 1.385 | 0.99 |
| 4_A | 45_T | 1.357 | 0.99 |
| 17_A | 27_T | 1.333 | 0.99 |
| 43_V | 51_V | 1.302 | 0.99 |
| 51_V | 84_A | 1.283 | 0.99 |
| 52_V | 82_Q | 1.254 | 0.99 |
| 37_T | 40_K | 1.250 | 0.99 |
| 43_V | 81_V | 1.248 | 0.99 |
| 25_K | 55_N | 1.248 | 0.99 |
| 32_P | 75_D | 1.230 | 0.98 |
| 52_V | 55_N | 1.223 | 0.98 |
| 27_T | 80_I | 1.220 | 0.98 |
| 37_T | 41_N | 1.186 | 0.98 |
| 24_G | 88_K | 1.126 | 0.97 |
| 90_E | 94_G | 1.120 | 0.96 |
| 56_T | 79_A | 1.111 | 0.96 |
| 43_V | 46_A | 1.077 | 0.95 |
| 12_V | 27_T | 1.073 | 0.95 |
| 29_W | 74_P | 1.072 | 0.95 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3j3wT | 1 | 0.9792 | 100 | 0.053 | Contact Map |
| 4btdX | 1 | 0.9583 | 100 | 0.06 | Contact Map |
| 2zjrQ | 1 | 0.9688 | 100 | 0.069 | Contact Map |
| 4kixT | 1 | 0.9271 | 100 | 0.085 | Contact Map |
| 3j39X | 1 | 0.8646 | 99.9 | 0.207 | Contact Map |
| 2go54 | 1 | 0.8229 | 99.9 | 0.226 | Contact Map |
| 4a17R | 1 | 0.8646 | 99.9 | 0.229 | Contact Map |
| 3u5eX | 1 | 0.8646 | 99.9 | 0.231 | Contact Map |
| 3bboV | 1 | 0.8438 | 99.9 | 0.232 | Contact Map |
| 3zf7X | 1 | 0.8646 | 99.9 | 0.235 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)