| Kristian Davidsen |
| ID: | 1500493862 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 125 (122) | ||
| Sequences: | 4845 (2641.5) | ||
| Seq/Len: | 39.713 | ||
| Nf(neff/√len): | 239.2 |
HHblits Results: (2016_02)
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: 39.713).
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 |
| 116_G | 119_T | 2.704 | 1.00 |
| 12_V | 86_L | 2.605 | 1.00 |
| 111_Y | 114_V | 2.306 | 1.00 |
| 13_H | 16_T | 2.205 | 1.00 |
| 62_D | 65_K | 2.195 | 1.00 |
| 114_V | 120_K | 2.140 | 1.00 |
| 12_V | 16_T | 2.105 | 1.00 |
| 68_F | 83_M | 2.046 | 1.00 |
| 105_E | 109_Y | 1.848 | 1.00 |
| 48_V | 68_F | 1.831 | 1.00 |
| 115_W | 118_G | 1.720 | 1.00 |
| 39_Q | 45_L | 1.630 | 1.00 |
| 33_G | 52_W | 1.623 | 1.00 |
| 19_R | 80_Y | 1.598 | 1.00 |
| 118_G | 121_V | 1.591 | 1.00 |
| 112_M | 120_K | 1.547 | 1.00 |
| 38_R | 46_E | 1.535 | 1.00 |
| 104_L | 110_Y | 1.532 | 1.00 |
| 24_A | 34_M | 1.529 | 1.00 |
| 36_W | 81_L | 1.477 | 1.00 |
| 35_H | 47_W | 1.464 | 1.00 |
| 90_D | 94_Y | 1.448 | 1.00 |
| 19_R | 82_Q | 1.442 | 1.00 |
| 104_L | 109_Y | 1.442 | 1.00 |
| 105_E | 108_Y | 1.432 | 1.00 |
| 110_Y | 114_V | 1.396 | 0.99 |
| 34_M | 79_L | 1.393 | 0.99 |
| 105_E | 110_Y | 1.381 | 0.99 |
| 49_A | 70_V | 1.360 | 0.99 |
| 6_E | 9_G | 1.347 | 0.99 |
| 112_M | 115_W | 1.347 | 0.99 |
| 119_T | 123_V | 1.336 | 0.99 |
| 111_Y | 120_K | 1.334 | 0.99 |
| 50_V | 59_Y | 1.305 | 0.99 |
| 18_L | 121_V | 1.282 | 0.99 |
| 115_W | 119_T | 1.272 | 0.99 |
| 24_A | 29_F | 1.270 | 0.99 |
| 38_R | 92_A | 1.267 | 0.99 |
| 90_D | 96_C | 1.264 | 0.99 |
| 114_V | 117_K | 1.262 | 0.99 |
| 115_W | 120_K | 1.262 | 0.99 |
| 33_G | 50_V | 1.259 | 0.99 |
| 118_G | 123_V | 1.209 | 0.98 |
| 102_G | 105_E | 1.209 | 0.98 |
| 113_D | 120_K | 1.203 | 0.98 |
| 115_W | 121_V | 1.191 | 0.98 |
| 109_Y | 112_M | 1.190 | 0.98 |
| 113_D | 122_T | 1.186 | 0.98 |
| 12_V | 18_L | 1.178 | 0.98 |
| 110_Y | 120_K | 1.163 | 0.97 |
| 104_L | 108_Y | 1.156 | 0.97 |
| 48_V | 64_V | 1.139 | 0.97 |
| 60_Y | 64_V | 1.121 | 0.97 |
| 103_R | 108_Y | 1.106 | 0.96 |
| 67_R | 83_M | 1.105 | 0.96 |
| 100_V | 103_R | 1.100 | 0.96 |
| 23_A | 78_T | 1.100 | 0.96 |
| 7_S | 10_G | 1.098 | 0.96 |
| 116_G | 121_V | 1.086 | 0.96 |
| 6_E | 10_G | 1.081 | 0.95 |
| 94_Y | 97_A | 1.054 | 0.95 |
| 37_V | 47_W | 1.051 | 0.94 |
| 10_G | 18_L | 1.039 | 0.94 |
| 35_H | 50_V | 1.033 | 0.94 |
| 102_G | 109_Y | 1.020 | 0.93 |
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 | |
| 4ut7H | 1 | 0.992 | 99.9 | 0.171 | Contact Map |
| 4pfeA | 2 | 0 | 99.9 | 0.183 | Contact Map |
| 4qgyA | 2 | 1 | 99.8 | 0.216 | Contact Map |
| 4i13B | 1 | 1 | 99.8 | 0.233 | Contact Map |
| 3g9aB | 1 | 0.976 | 99.8 | 0.236 | Contact Map |
| 3k3qA | 1 | 1 | 99.8 | 0.237 | Contact Map |
| 1dqtA | 4 | 0.92 | 99.8 | 0.238 | Contact Map |
| 1zvyA | 1 | 0.984 | 99.8 | 0.244 | Contact Map |
| 4qo1A | 1 | 0.976 | 99.8 | 0.246 | Contact Map |
| 2vyrE | 8 | 0.992 | 99.8 | 0.248 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)