| Morgan Nance |
| ID: | 1498585813 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 220 (203) | ||
| Sequences: | 12047 (7585.6) | ||
| Seq/Len: | 59.345 | ||
| Nf(neff/√len): | 532.4 |
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: 59.345).
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 |
| 41_P | 44_V | 3.462 | 1.00 |
| 47_N | 160_A | 3.305 | 1.00 |
| 42_L | 70_S | 2.893 | 1.00 |
| 42_L | 46_E | 2.611 | 1.00 |
| 66_F | 149_A | 2.497 | 1.00 |
| 48_I | 157_I | 2.431 | 1.00 |
| 67_V | 124_F | 2.338 | 1.00 |
| 38_R | 195_Y | 2.325 | 1.00 |
| 163_V | 196_P | 2.292 | 1.00 |
| 154_L | 164_A | 2.205 | 1.00 |
| 44_V | 160_A | 2.200 | 1.00 |
| 65_T | 215_V | 2.138 | 1.00 |
| 124_F | 185_E | 2.109 | 1.00 |
| 77_K | 178_I | 2.066 | 1.00 |
| 66_F | 121_I | 1.932 | 1.00 |
| 44_V | 162_L | 1.925 | 1.00 |
| 72_P | 76_A | 1.875 | 1.00 |
| 162_L | 195_Y | 1.848 | 1.00 |
| 28_H | 158_H | 1.845 | 1.00 |
| 176_Q | 187_P | 1.844 | 1.00 |
| 154_L | 166_T | 1.810 | 1.00 |
| 79_R | 115_E | 1.779 | 1.00 |
| 50_M | 53_S | 1.773 | 1.00 |
| 36_S | 197_A | 1.759 | 1.00 |
| 24_Q | 28_H | 1.752 | 1.00 |
| 76_A | 115_E | 1.718 | 1.00 |
| 34_E | 197_A | 1.690 | 1.00 |
| 44_V | 195_Y | 1.650 | 1.00 |
| 48_I | 153_L | 1.646 | 1.00 |
| 144_E | 147_G | 1.642 | 1.00 |
| 51_T | 156_A | 1.624 | 1.00 |
| 122_V | 187_P | 1.613 | 1.00 |
| 208_K | 212_A | 1.587 | 1.00 |
| 154_L | 191_V | 1.584 | 1.00 |
| 21_E | 24_Q | 1.581 | 1.00 |
| 68_V | 119_Y | 1.576 | 1.00 |
| 46_E | 211_A | 1.572 | 1.00 |
| 150_C | 189_L | 1.541 | 1.00 |
| 81_A | 178_I | 1.534 | 1.00 |
| 171_P | 174_F | 1.531 | 1.00 |
| 148_I | 151_G | 1.529 | 1.00 |
| 122_V | 190_L | 1.524 | 1.00 |
| 121_I | 153_L | 1.500 | 1.00 |
| 157_I | 193_V | 1.469 | 1.00 |
| 49_V | 214_M | 1.468 | 1.00 |
| 70_S | 119_Y | 1.463 | 1.00 |
| 123_V | 150_C | 1.459 | 1.00 |
| 22_Y | 26_M | 1.449 | 1.00 |
| 124_F | 181_R | 1.421 | 1.00 |
| 36_S | 195_Y | 1.420 | 1.00 |
| 123_V | 191_V | 1.419 | 1.00 |
| 69_V | 122_V | 1.413 | 1.00 |
| 52_A | 153_L | 1.412 | 1.00 |
| 65_T | 185_E | 1.406 | 0.99 |
| 20_A | 24_Q | 1.397 | 0.99 |
| 150_C | 191_V | 1.394 | 0.99 |
| 174_F | 177_K | 1.378 | 0.99 |
| 158_H | 163_V | 1.351 | 0.99 |
| 44_V | 47_N | 1.331 | 0.99 |
| 210_K | 214_M | 1.323 | 0.99 |
| 27_D | 54_T | 1.319 | 0.99 |
| 70_S | 216_V | 1.311 | 0.99 |
| 53_S | 213_V | 1.311 | 0.99 |
| 123_V | 153_L | 1.310 | 0.99 |
| 76_A | 80_Q | 1.306 | 0.99 |
| 126_K | 184_N | 1.304 | 0.99 |
| 164_A | 191_V | 1.293 | 0.99 |
| 66_F | 123_V | 1.289 | 0.99 |
| 121_I | 193_V | 1.276 | 0.99 |
| 48_I | 193_V | 1.266 | 0.99 |
| 68_V | 214_M | 1.254 | 0.99 |
| 127_A | 186_R | 1.247 | 0.99 |
| 22_Y | 25_F | 1.246 | 0.98 |
| 23_Y | 47_N | 1.233 | 0.98 |
| 74_I | 77_K | 1.232 | 0.98 |
| 77_K | 80_Q | 1.229 | 0.98 |
| 125_R | 142_V | 1.223 | 0.98 |
| 157_I | 164_A | 1.222 | 0.98 |
| 23_Y | 27_D | 1.218 | 0.98 |
| 68_V | 216_V | 1.216 | 0.98 |
| 73_Q | 77_K | 1.212 | 0.98 |
| 24_Q | 27_D | 1.209 | 0.98 |
| 74_I | 217_Y | 1.198 | 0.98 |
| 68_V | 121_I | 1.195 | 0.98 |
| 31_T | 165_L | 1.192 | 0.98 |
| 42_L | 216_V | 1.188 | 0.98 |
| 151_G | 155_A | 1.177 | 0.98 |
| 67_V | 217_Y | 1.175 | 0.98 |
| 166_T | 189_L | 1.175 | 0.98 |
| 45_I | 119_Y | 1.172 | 0.98 |
| 55_A | 152_F | 1.167 | 0.97 |
| 71_D | 74_I | 1.161 | 0.97 |
| 81_A | 174_F | 1.152 | 0.97 |
| 27_D | 50_M | 1.151 | 0.97 |
| 70_S | 217_Y | 1.144 | 0.97 |
| 119_Y | 193_V | 1.138 | 0.97 |
| 35_F | 192_P | 1.133 | 0.97 |
| 72_P | 75_K | 1.130 | 0.97 |
| 26_M | 152_F | 1.114 | 0.96 |
| 146_V | 188_F | 1.104 | 0.96 |
| 141_Y | 168_T | 1.102 | 0.96 |
| 162_L | 193_V | 1.097 | 0.96 |
| 22_Y | 155_A | 1.096 | 0.96 |
| 80_Q | 84_K | 1.089 | 0.96 |
| 143_Q | 188_F | 1.085 | 0.96 |
| 156_A | 160_A | 1.083 | 0.96 |
| 128_Y | 184_N | 1.083 | 0.96 |
| 123_V | 146_V | 1.083 | 0.96 |
| 120_L | 190_L | 1.083 | 0.96 |
| 174_F | 178_I | 1.078 | 0.95 |
| 67_V | 185_E | 1.073 | 0.95 |
| 43_E | 46_E | 1.060 | 0.95 |
| 48_I | 162_L | 1.060 | 0.95 |
| 78_I | 175_L | 1.051 | 0.94 |
| 51_T | 160_A | 1.043 | 0.94 |
| 170_S | 190_L | 1.035 | 0.94 |
| 173_N | 176_Q | 1.025 | 0.93 |
| 40_I | 162_L | 1.020 | 0.93 |
| 164_A | 193_V | 1.011 | 0.93 |
| 125_R | 146_V | 1.003 | 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 | |
| 3gb5A | 1 | 0.8364 | 100 | 0.215 | Contact Map |
| 1noxA | 1 | 0.7818 | 100 | 0.272 | Contact Map |
| 3eo8A | 6 | 0.8909 | 100 | 0.276 | Contact Map |
| 1icrA | 2 | 0.8 | 100 | 0.277 | Contact Map |
| 3n2sA | 4 | 0.7864 | 100 | 0.278 | Contact Map |
| 3of4A | 3 | 0.7818 | 100 | 0.28 | Contact Map |
| 1zchA | 1 | 0.7909 | 100 | 0.28 | Contact Map |
| 1f5vA | 2 | 0.7909 | 100 | 0.28 | Contact Map |
| 4qlxA | 2 | 0.8318 | 100 | 0.28 | Contact Map |
| 2freA | 2 | 0.85 | 100 | 0.282 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)