| Ethan HHblits Aligment |
| ID: | 1490308412 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 335 (251) | ||
| Sequences: | 88042 (53936.6) | ||
| Seq/Len: | 350.765 | ||
| Nf(neff/√len): | 3404.4 |
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: 350.765).
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 |
| 320_C | 325_H | 3.298 | 1.00 |
| 187_H | 272_H | 3.094 | 1.00 |
| 213_E | 223_E | 3.003 | 1.00 |
| 91_E | 103_E | 2.776 | 1.00 |
| 103_E | 111_E | 2.579 | 1.00 |
| 92_E | 100_E | 2.558 | 1.00 |
| 265_H | 318_H | 2.400 | 1.00 |
| 195_H | 199_H | 2.389 | 1.00 |
| 141_C | 144_E | 2.290 | 1.00 |
| 104_E | 114_E | 2.221 | 1.00 |
| 162_C | 216_C | 2.213 | 1.00 |
| 317_H | 327_C | 2.210 | 1.00 |
| 92_E | 95_E | 2.209 | 1.00 |
| 215_C | 219_E | 2.200 | 1.00 |
| 180_H | 308_C | 2.179 | 1.00 |
| 189_H | 220_E | 2.133 | 1.00 |
| 189_H | 219_E | 2.103 | 1.00 |
| 104_E | 112_E | 2.084 | 1.00 |
| 208_C | 245_C | 2.068 | 1.00 |
| 195_H | 330_H | 2.044 | 1.00 |
| 167_H | 210_H | 1.977 | 1.00 |
| 159_E | 221_E | 1.958 | 1.00 |
| 194_H | 268_H | 1.931 | 1.00 |
| 191_H | 268_H | 1.922 | 1.00 |
| 190_H | 212_E | 1.897 | 1.00 |
| 322_C | 325_H | 1.894 | 1.00 |
| 88_E | 105_E | 1.876 | 1.00 |
| 88_E | 107_C | 1.799 | 1.00 |
| 212_E | 220_E | 1.796 | 1.00 |
| 179_C | 182_H | 1.788 | 1.00 |
| 269_H | 318_H | 1.727 | 1.00 |
| 250_C | 263_H | 1.723 | 1.00 |
| 103_E | 160_E | 1.721 | 1.00 |
| 244_C | 249_C | 1.708 | 1.00 |
| 86_E | 106_E | 1.697 | 1.00 |
| 139_C | 143_C | 1.692 | 1.00 |
| 90_E | 105_E | 1.660 | 1.00 |
| 207_C | 271_H | 1.643 | 1.00 |
| 215_C | 221_E | 1.624 | 1.00 |
| 165_C | 168_H | 1.614 | 1.00 |
| 92_E | 102_E | 1.572 | 1.00 |
| 142_C | 145_E | 1.570 | 1.00 |
| 194_H | 207_C | 1.566 | 1.00 |
| 130_H | 133_H | 1.548 | 1.00 |
| 193_H | 222_E | 1.529 | 1.00 |
| 137_C | 141_C | 1.509 | 1.00 |
| 276_H | 311_H | 1.501 | 1.00 |
| 183_H | 276_H | 1.493 | 1.00 |
| 140_C | 143_C | 1.484 | 1.00 |
| 191_H | 332_H | 1.476 | 1.00 |
| 187_H | 268_H | 1.464 | 1.00 |
| 140_C | 145_E | 1.460 | 1.00 |
| 140_C | 144_E | 1.448 | 1.00 |
| 105_E | 111_E | 1.445 | 1.00 |
| 141_C | 146_E | 1.443 | 1.00 |
| 202_C | 228_C | 1.443 | 1.00 |
| 138_C | 142_C | 1.434 | 1.00 |
| 187_H | 275_H | 1.428 | 1.00 |
| 128_H | 131_H | 1.425 | 1.00 |
| 95_E | 100_E | 1.420 | 1.00 |
| 318_H | 332_H | 1.419 | 1.00 |
| 106_E | 109_C | 1.417 | 1.00 |
| 137_C | 143_C | 1.410 | 1.00 |
| 188_H | 192_H | 1.406 | 0.99 |
| 138_C | 144_E | 1.405 | 0.99 |
| 137_C | 140_C | 1.401 | 0.99 |
| 185_H | 189_H | 1.394 | 0.99 |
| 272_H | 314_H | 1.392 | 0.99 |
| 127_H | 130_H | 1.382 | 0.99 |
| 167_H | 171_H | 1.359 | 0.99 |
| 114_E | 157_E | 1.352 | 0.99 |
| 139_C | 144_E | 1.348 | 0.99 |
| 143_C | 146_E | 1.339 | 0.99 |
| 328_C | 331_H | 1.319 | 0.99 |
| 212_E | 271_H | 1.309 | 0.99 |
| 144_E | 147_E | 1.306 | 0.99 |
| 265_H | 329_H | 1.304 | 0.99 |
| 209_H | 248_C | 1.297 | 0.99 |
| 195_H | 333_H | 1.294 | 0.99 |
| 201_C | 261_C | 1.288 | 0.99 |
| 315_H | 319_C | 1.283 | 0.99 |
| 248_C | 274_H | 1.279 | 0.99 |
| 312_H | 316_H | 1.268 | 0.99 |
| 90_E | 103_E | 1.261 | 0.99 |
| 186_H | 220_E | 1.259 | 0.99 |
| 161_C | 215_C | 1.256 | 0.99 |
| 194_H | 329_H | 1.254 | 0.99 |
| 138_C | 141_C | 1.252 | 0.99 |
| 164_C | 172_H | 1.238 | 0.98 |
| 129_H | 132_H | 1.236 | 0.98 |
| 327_C | 332_H | 1.207 | 0.98 |
| 140_C | 146_E | 1.202 | 0.98 |
| 161_C | 221_E | 1.201 | 0.98 |
| 313_H | 317_H | 1.198 | 0.98 |
| 329_H | 332_H | 1.197 | 0.98 |
| 250_C | 253_H | 1.196 | 0.98 |
| 196_H | 200_C | 1.195 | 0.98 |
| 183_H | 275_H | 1.189 | 0.98 |
| 143_C | 147_E | 1.187 | 0.98 |
| 139_C | 142_C | 1.177 | 0.98 |
| 262_H | 328_C | 1.171 | 0.98 |
| 141_C | 145_E | 1.169 | 0.97 |
| 314_H | 318_H | 1.155 | 0.97 |
| 314_H | 327_C | 1.152 | 0.97 |
| 101_E | 113_E | 1.150 | 0.97 |
| 209_H | 271_H | 1.146 | 0.97 |
| 139_C | 146_E | 1.143 | 0.97 |
| 167_H | 274_H | 1.135 | 0.97 |
| 199_H | 330_H | 1.133 | 0.97 |
| 190_H | 220_E | 1.132 | 0.97 |
| 317_H | 320_C | 1.124 | 0.97 |
| 279_C | 282_C | 1.120 | 0.96 |
| 206_C | 211_H | 1.113 | 0.96 |
| 204_C | 207_C | 1.111 | 0.96 |
| 205_C | 259_C | 1.108 | 0.96 |
| 102_E | 116_E | 1.107 | 0.96 |
| 112_E | 157_E | 1.098 | 0.96 |
| 96_C | 99_E | 1.097 | 0.96 |
| 192_H | 333_H | 1.096 | 0.96 |
| 314_H | 332_H | 1.095 | 0.96 |
| 259_C | 263_H | 1.089 | 0.96 |
| 253_H | 263_H | 1.088 | 0.96 |
| 139_C | 147_E | 1.071 | 0.95 |
| 116_E | 155_E | 1.069 | 0.95 |
| 192_H | 195_H | 1.064 | 0.95 |
| 126_H | 129_H | 1.063 | 0.95 |
| 116_E | 153_C | 1.060 | 0.95 |
| 185_H | 219_E | 1.033 | 0.94 |
| 138_C | 145_E | 1.032 | 0.94 |
| 274_H | 281_C | 1.023 | 0.93 |
| 161_C | 213_E | 1.019 | 0.93 |
| 137_C | 144_E | 1.014 | 0.93 |
| 211_H | 224_E | 1.013 | 0.93 |
| 270_H | 319_C | 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 | |
| 4ic7A | 2 | 0.7582 | 100 | 0.235 | Contact Map |
| 3pfqA | 1 | 0.8418 | 100 | 0.236 | Contact Map |
| 4gv1A | 1 | 0.7463 | 100 | 0.245 | Contact Map |
| 1nxkA | 4 | 0.7672 | 100 | 0.246 | Contact Map |
| 5a46A | 2 | 0 | 100 | 0.249 | Contact Map |
| 4g3fA | 1 | 0.8448 | 100 | 0.249 | Contact Map |
| 4bkyA | 1 | 0.6985 | 100 | 0.251 | Contact Map |
| 4c0tA | 1 | 0.7493 | 100 | 0.253 | Contact Map |
| 4aojA | 3 | 0.7313 | 100 | 0.253 | Contact Map |
| 2h8hA | 1 | 0.9045 | 100 | 0.253 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)