| Amelie |
| ID: | 1454314609 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 218 (184) | ||
| Sequences: | 679 (456) | ||
| Seq/Len: | 3.690 | ||
| Nf(neff/√len): | 33.6 |
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: 3.690).
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 |
| 56_E | 178_F | 4.997 | 1.00 |
| 159_K | 177_D | 3.887 | 1.00 |
| 66_C | 75_F | 3.411 | 1.00 |
| 45_R | 181_F | 2.802 | 1.00 |
| 129_N | 156_K | 2.667 | 1.00 |
| 67_V | 146_L | 2.638 | 1.00 |
| 126_T | 154_N | 2.619 | 1.00 |
| 155_P | 158_V | 2.539 | 1.00 |
| 77_D | 191_Y | 2.261 | 1.00 |
| 57_M | 157_M | 2.204 | 1.00 |
| 49_L | 180_G | 2.198 | 1.00 |
| 62_I | 131_L | 2.174 | 1.00 |
| 55_K | 58_G | 2.092 | 1.00 |
| 147_L | 151_R | 2.064 | 1.00 |
| 50_A | 54_M | 2.056 | 1.00 |
| 45_R | 48_R | 1.998 | 1.00 |
| 64_A | 79_L | 1.991 | 1.00 |
| 67_V | 100_I | 1.984 | 1.00 |
| 129_N | 157_M | 1.981 | 1.00 |
| 64_A | 131_L | 1.931 | 1.00 |
| 72_Y | 97_V | 1.918 | 1.00 |
| 183_I | 188_V | 1.835 | 0.99 |
| 165_V | 170_R | 1.808 | 0.99 |
| 77_D | 80_D | 1.802 | 0.99 |
| 164_L | 205_V | 1.709 | 0.99 |
| 54_M | 83_K | 1.703 | 0.99 |
| 147_L | 160_V | 1.676 | 0.99 |
| 134_E | 137_I | 1.644 | 0.99 |
| 137_I | 162_S | 1.632 | 0.99 |
| 62_I | 128_K | 1.628 | 0.99 |
| 169_P | 185_D | 1.582 | 0.98 |
| 149_L | 153_Y | 1.558 | 0.98 |
| 38_P | 41_L | 1.525 | 0.97 |
| 72_Y | 76_A | 1.508 | 0.97 |
| 39_H | 43_M | 1.482 | 0.97 |
| 72_Y | 99_F | 1.481 | 0.97 |
| 144_Q | 148_S | 1.459 | 0.96 |
| 141_K | 171_S | 1.433 | 0.96 |
| 164_L | 188_V | 1.413 | 0.96 |
| 57_M | 129_N | 1.385 | 0.95 |
| 193_L | 208_I | 1.375 | 0.95 |
| 96_T | 128_K | 1.342 | 0.94 |
| 164_L | 183_I | 1.338 | 0.93 |
| 45_R | 52_D | 1.307 | 0.92 |
| 47_E | 81_Y | 1.296 | 0.92 |
| 54_M | 82_I | 1.268 | 0.91 |
| 134_E | 160_V | 1.267 | 0.91 |
| 52_D | 56_E | 1.251 | 0.90 |
| 132_I | 150_V | 1.246 | 0.90 |
| 73_K | 80_D | 1.245 | 0.90 |
| 76_A | 97_V | 1.240 | 0.90 |
| 148_S | 151_R | 1.227 | 0.89 |
| 63_V | 96_T | 1.218 | 0.88 |
| 187_F | 195_Y | 1.194 | 0.87 |
| 69_K | 197_E | 1.186 | 0.87 |
| 57_M | 131_L | 1.184 | 0.86 |
| 63_V | 128_K | 1.178 | 0.86 |
| 68_L | 99_F | 1.174 | 0.86 |
| 134_E | 162_S | 1.159 | 0.85 |
| 34_R | 209_S | 1.157 | 0.85 |
| 165_V | 182_E | 1.147 | 0.84 |
| 53_V | 82_I | 1.146 | 0.84 |
| 165_V | 169_P | 1.131 | 0.83 |
| 41_L | 45_R | 1.129 | 0.83 |
| 78_L | 133_V | 1.115 | 0.82 |
| 106_C | 196_N | 1.107 | 0.81 |
| 148_S | 152_Q | 1.090 | 0.80 |
| 132_I | 156_K | 1.081 | 0.79 |
| 50_A | 193_L | 1.071 | 0.78 |
| 69_K | 101_R | 1.051 | 0.76 |
| 167_R | 182_E | 1.038 | 0.75 |
| 52_D | 178_F | 1.037 | 0.75 |
| 50_A | 82_I | 1.036 | 0.75 |
| 43_M | 81_Y | 1.033 | 0.74 |
| 37_I | 183_I | 1.032 | 0.74 |
| 31_D | 199_F | 1.024 | 0.73 |
| 74_F | 161_A | 1.022 | 0.73 |
| 66_C | 71_G | 1.022 | 0.73 |
| 188_V | 193_L | 1.015 | 0.72 |
| 48_R | 181_F | 1.009 | 0.72 |
| 60_H | 156_K | 1.006 | 0.71 |
| 100_I | 116_V | 1.000 | 0.71 |
| 168_T | 184_P | 1.000 | 0.71 |
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 | |
| 2jbhA | 2 | 0.9908 | 100 | 0.395 | Contact Map |
| 4raoA | 4 | 0.9633 | 100 | 0.405 | Contact Map |
| 3ozfA | 4 | 0.9862 | 100 | 0.409 | Contact Map |
| 1fsgA | 2 | 0.9862 | 100 | 0.419 | Contact Map |
| 1pzmA | 2 | 0.7615 | 100 | 0.465 | Contact Map |
| 4qyiA | 1 | 0.7706 | 100 | 0.471 | Contact Map |
| 1tc1A | 2 | 0.8165 | 100 | 0.474 | Contact Map |
| 4pfqA | 8 | 0.8394 | 100 | 0.478 | Contact Map |
| 1hgxA | 2 | 0.7661 | 100 | 0.482 | Contact Map |
| 4qriA | 2 | 0.7248 | 100 | 0.485 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)