| ubiquitin |
| ID: | 1405072149 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (76) | ||
| Sequences: | 2128 (1497.8) | ||
| Seq/Len: | 28.000 | ||
| Nf(neff/√len): | 171.8 |
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: 28.000).
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 |
| 27_K | 52_D | 4.084 | 1.00 |
| 21_D | 29_K | 2.637 | 1.00 |
| 24_E | 28_A | 2.060 | 1.00 |
| 21_D | 25_N | 2.009 | 1.00 |
| 55_T | 58_D | 1.977 | 1.00 |
| 54_R | 58_D | 1.973 | 1.00 |
| 54_R | 59_Y | 1.824 | 1.00 |
| 36_I | 41_Q | 1.776 | 1.00 |
| 37_P | 41_Q | 1.655 | 1.00 |
| 25_N | 28_A | 1.589 | 1.00 |
| 1_M | 16_E | 1.574 | 1.00 |
| 51_E | 54_R | 1.573 | 1.00 |
| 29_K | 32_D | 1.563 | 1.00 |
| 62_Q | 65_S | 1.546 | 1.00 |
| 44_I | 70_V | 1.531 | 1.00 |
| 31_Q | 38_P | 1.518 | 1.00 |
| 3_I | 17_V | 1.494 | 1.00 |
| 21_D | 26_V | 1.494 | 1.00 |
| 18_E | 21_D | 1.471 | 1.00 |
| 30_I | 43_L | 1.453 | 1.00 |
| 24_E | 52_D | 1.405 | 0.99 |
| 4_F | 14_T | 1.327 | 0.99 |
| 44_I | 49_Q | 1.300 | 0.99 |
| 22_T | 25_N | 1.243 | 0.98 |
| 44_I | 68_H | 1.240 | 0.98 |
| 73_L | 76_G | 1.197 | 0.98 |
| 61_I | 67_L | 1.174 | 0.98 |
| 17_V | 21_D | 1.162 | 0.97 |
| 2_Q | 14_T | 1.160 | 0.97 |
| 23_I | 56_L | 1.152 | 0.97 |
| 4_F | 66_T | 1.144 | 0.97 |
| 29_K | 33_K | 1.127 | 0.97 |
| 45_F | 65_S | 1.122 | 0.97 |
| 45_F | 48_K | 1.102 | 0.96 |
| 3_I | 26_V | 1.084 | 0.96 |
| 2_Q | 63_K | 1.079 | 0.95 |
| 19_P | 57_S | 1.070 | 0.95 |
| 50_L | 59_Y | 1.042 | 0.94 |
| 6_K | 47_G | 1.037 | 0.94 |
| 15_L | 26_V | 1.035 | 0.94 |
| 31_Q | 41_Q | 1.033 | 0.94 |
| 55_T | 59_Y | 1.033 | 0.94 |
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 | |
| 3u5cf | 1 | 0 | 99.6 | 0.025 | Contact Map |
| 4k95A | 12 | 0.9605 | 99.6 | 0.035 | Contact Map |
| 3u5em | 1 | 0 | 99.6 | 0.049 | Contact Map |
| 3q3fA | 1 | 1 | 99.6 | 0.05 | Contact Map |
| 3ai5A | 1 | 0.9342 | 99.6 | 0.054 | Contact Map |
| 3l0wB | 1 | 0.9868 | 99.6 | 0.058 | Contact Map |
| 1oqyA | 1 | 1 | 99.6 | 0.063 | Contact Map |
| 2uyzB | 1 | 0.9868 | 99.6 | 0.066 | Contact Map |
| 1se9A | 1 | 1 | 99.6 | 0.067 | Contact Map |
| 1wywB | 1 | 1 | 99.6 | 0.068 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)