| eldelumab LC |
| ID: | 1454347316 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (118) | ||
| Sequences: | 4058 (2402.1) | ||
| Seq/Len: | 34.390 | ||
| Nf(neff/√len): | 221.1 |
HHblits Results: (2015_06)
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: 34.390).
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 |
| 12_V | 86_L | 2.599 | 1.00 |
| 115_G | 118_T | 2.453 | 1.00 |
| 110_G | 119_T | 2.157 | 1.00 |
| 62_D | 65_K | 1.892 | 1.00 |
| 68_F | 83_M | 1.859 | 1.00 |
| 118_T | 122_V | 1.836 | 1.00 |
| 38_R | 46_E | 1.822 | 1.00 |
| 38_R | 92_A | 1.807 | 1.00 |
| 13_Q | 16_R | 1.786 | 1.00 |
| 34_M | 79_L | 1.748 | 1.00 |
| 18_L | 120_V | 1.728 | 1.00 |
| 49_A | 70_I | 1.696 | 1.00 |
| 111_M | 119_T | 1.667 | 1.00 |
| 117_G | 120_V | 1.615 | 1.00 |
| 112_D | 119_T | 1.610 | 1.00 |
| 39_Q | 45_L | 1.592 | 1.00 |
| 24_A | 34_M | 1.589 | 1.00 |
| 12_V | 16_R | 1.570 | 1.00 |
| 48_V | 64_V | 1.528 | 1.00 |
| 114_W | 117_G | 1.495 | 1.00 |
| 111_M | 120_V | 1.471 | 1.00 |
| 33_G | 50_V | 1.465 | 1.00 |
| 113_V | 116_Q | 1.459 | 1.00 |
| 119_T | 123_S | 1.438 | 1.00 |
| 37_V | 47_W | 1.432 | 1.00 |
| 48_V | 68_F | 1.410 | 1.00 |
| 103_S | 109_Y | 1.380 | 0.99 |
| 114_W | 119_T | 1.360 | 0.99 |
| 12_V | 18_L | 1.350 | 0.99 |
| 36_W | 81_L | 1.334 | 0.99 |
| 19_R | 80_Y | 1.317 | 0.99 |
| 33_G | 52_W | 1.316 | 0.99 |
| 117_G | 122_V | 1.310 | 0.99 |
| 14_P | 88_A | 1.244 | 0.98 |
| 54_D | 57_N | 1.238 | 0.98 |
| 17_S | 86_L | 1.224 | 0.98 |
| 35_H | 50_V | 1.212 | 0.98 |
| 19_R | 82_E | 1.205 | 0.98 |
| 112_D | 121_T | 1.195 | 0.98 |
| 113_V | 123_S | 1.188 | 0.98 |
| 68_F | 81_L | 1.184 | 0.98 |
| 103_S | 110_G | 1.182 | 0.98 |
| 60_Y | 64_V | 1.171 | 0.98 |
| 110_G | 113_V | 1.169 | 0.97 |
| 113_V | 119_T | 1.156 | 0.97 |
| 116_Q | 123_S | 1.143 | 0.97 |
| 67_R | 90_D | 1.141 | 0.97 |
| 111_M | 121_T | 1.139 | 0.97 |
| 112_D | 116_Q | 1.131 | 0.97 |
| 35_H | 47_W | 1.128 | 0.97 |
| 12_V | 38_R | 1.127 | 0.97 |
| 113_V | 121_T | 1.126 | 0.97 |
| 67_R | 83_M | 1.119 | 0.96 |
| 40_A | 43_K | 1.117 | 0.96 |
| 111_M | 116_Q | 1.115 | 0.96 |
| 116_Q | 119_T | 1.090 | 0.96 |
| 115_G | 119_T | 1.079 | 0.95 |
| 43_K | 46_E | 1.061 | 0.95 |
| 50_V | 59_F | 1.052 | 0.95 |
| 110_G | 120_V | 1.044 | 0.94 |
| 110_G | 116_Q | 1.024 | 0.93 |
| 9_G | 18_L | 1.019 | 0.93 |
| 46_E | 63_S | 1.000 | 0.92 |
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 | |
| 4pfeA | 2 | 0 | 99.9 | 0.172 | Contact Map |
| 4ut7H | 1 | 0.9919 | 99.9 | 0.177 | Contact Map |
| 1dqtA | 4 | 0.9274 | 99.9 | 0.217 | Contact Map |
| 4qgyA | 2 | 1 | 99.8 | 0.221 | Contact Map |
| 3k3qA | 1 | 1 | 99.8 | 0.225 | Contact Map |
| 4i13B | 1 | 1 | 99.8 | 0.228 | Contact Map |
| 3lh2H | 4 | 0.9919 | 99.8 | 0.233 | Contact Map |
| 1zvyA | 1 | 0.9839 | 99.8 | 0.237 | Contact Map |
| 1yjdC | 1 | 0.9274 | 99.8 | 0.238 | Contact Map |
| 2vyrE | 8 | 1 | 99.8 | 0.24 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)