| sdsdf |
| ID: | 1498382147 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 317 (280) | ||
| Sequences: | 21721 (11898.2) | ||
| Seq/Len: | 77.575 | ||
| Nf(neff/√len): | 711.1 |
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: 77.575).
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 |
| 52_S | 88_S | 5.301 | 1.00 |
| 79_C | 169_W | 3.968 | 1.00 |
| 205_V | 209_H | 3.245 | 1.00 |
| 79_C | 134_F | 2.939 | 1.00 |
| 143_Y | 148_Y | 2.538 | 1.00 |
| 159_P | 163_R | 2.428 | 1.00 |
| 137_A | 168_I | 2.340 | 1.00 |
| 208_V | 212_A | 2.323 | 1.00 |
| 143_Y | 209_H | 2.231 | 1.00 |
| 60_V | 78_C | 2.226 | 1.00 |
| 126_S | 173_V | 2.154 | 1.00 |
| 83_S | 130_S | 2.143 | 1.00 |
| 86_L | 127_S | 2.125 | 1.00 |
| 242_T | 301_H | 2.112 | 1.00 |
| 115_Q | 119_V | 2.107 | 1.00 |
| 202_L | 206_L | 2.048 | 1.00 |
| 114_Q | 118_N | 2.028 | 1.00 |
| 130_S | 172_S | 2.007 | 1.00 |
| 137_A | 164_A | 1.947 | 1.00 |
| 110_A | 113_L | 1.926 | 1.00 |
| 79_C | 165_V | 1.892 | 1.00 |
| 75_C | 165_V | 1.881 | 1.00 |
| 209_H | 213_R | 1.881 | 1.00 |
| 63_I | 78_C | 1.874 | 1.00 |
| 143_Y | 147_F | 1.870 | 1.00 |
| 122_V | 126_S | 1.864 | 1.00 |
| 148_Y | 151_R | 1.843 | 1.00 |
| 147_F | 213_R | 1.842 | 1.00 |
| 209_H | 212_A | 1.808 | 1.00 |
| 259_L | 263_L | 1.770 | 1.00 |
| 163_R | 167_A | 1.762 | 1.00 |
| 84_D | 294_D | 1.719 | 1.00 |
| 66_N | 308_T | 1.719 | 1.00 |
| 52_S | 292_I | 1.712 | 1.00 |
| 134_F | 165_V | 1.700 | 1.00 |
| 57_A | 61_A | 1.670 | 1.00 |
| 136_G | 206_L | 1.668 | 1.00 |
| 53_L | 85_L | 1.659 | 1.00 |
| 162_R | 166_A | 1.657 | 1.00 |
| 143_Y | 206_L | 1.652 | 1.00 |
| 76_F | 161_A | 1.615 | 1.00 |
| 212_A | 216_Q | 1.597 | 1.00 |
| 75_C | 162_R | 1.587 | 1.00 |
| 249_I | 297_I | 1.585 | 1.00 |
| 53_L | 88_S | 1.563 | 1.00 |
| 157_T | 160_R | 1.562 | 1.00 |
| 84_D | 131_S | 1.559 | 1.00 |
| 136_G | 202_L | 1.501 | 1.00 |
| 213_R | 216_Q | 1.487 | 1.00 |
| 254_W | 287_I | 1.474 | 1.00 |
| 144_I | 155_I | 1.465 | 1.00 |
| 177_T | 181_A | 1.450 | 1.00 |
| 78_C | 82_L | 1.449 | 1.00 |
| 69_L | 74_Y | 1.438 | 1.00 |
| 279_N | 283_F | 1.416 | 1.00 |
| 308_T | 311_E | 1.416 | 1.00 |
| 57_A | 85_L | 1.411 | 1.00 |
| 55_E | 292_I | 1.408 | 1.00 |
| 151_R | 155_I | 1.402 | 0.99 |
| 211_L | 215_C | 1.391 | 0.99 |
| 134_F | 169_W | 1.387 | 0.99 |
| 159_P | 162_R | 1.379 | 0.99 |
| 158_L | 162_R | 1.372 | 0.99 |
| 140_V | 206_L | 1.371 | 0.99 |
| 113_L | 117_D | 1.358 | 0.99 |
| 141_D | 145_S | 1.344 | 0.99 |
| 289_C | 293_I | 1.343 | 0.99 |
| 76_F | 138_I | 1.338 | 0.99 |
| 145_S | 149_A | 1.334 | 0.99 |
| 164_A | 168_I | 1.332 | 0.99 |
| 278_K | 282_L | 1.324 | 0.99 |
| 39_S | 43_G | 1.315 | 0.99 |
| 87_V | 291_A | 1.299 | 0.99 |
| 130_S | 134_F | 1.284 | 0.99 |
| 217_H | 221_I | 1.284 | 0.99 |
| 80_L | 134_F | 1.271 | 0.99 |
| 61_A | 312_V | 1.267 | 0.99 |
| 294_D | 298_Y | 1.266 | 0.99 |
| 172_S | 176_S | 1.263 | 0.99 |
| 60_V | 82_L | 1.261 | 0.99 |
| 122_V | 180_I | 1.260 | 0.99 |
| 90_S | 93_L | 1.258 | 0.99 |
| 49_G | 88_S | 1.251 | 0.99 |
| 236_G | 240_A | 1.250 | 0.99 |
| 204_A | 208_V | 1.241 | 0.98 |
| 275_C | 279_N | 1.236 | 0.98 |
| 190_L | 194_V | 1.235 | 0.98 |
| 129_L | 172_S | 1.234 | 0.98 |
| 133_C | 199_M | 1.227 | 0.98 |
| 179_F | 182_Y | 1.227 | 0.98 |
| 60_V | 85_L | 1.221 | 0.98 |
| 141_D | 156_V | 1.209 | 0.98 |
| 200_L | 251_F | 1.207 | 0.98 |
| 83_S | 169_W | 1.195 | 0.98 |
| 55_E | 296_L | 1.188 | 0.98 |
| 61_A | 65_K | 1.188 | 0.98 |
| 133_C | 171_A | 1.184 | 0.98 |
| 168_I | 172_S | 1.182 | 0.98 |
| 83_S | 131_S | 1.176 | 0.98 |
| 144_I | 148_Y | 1.165 | 0.97 |
| 255_G | 259_L | 1.164 | 0.97 |
| 72_P | 161_A | 1.162 | 0.97 |
| 130_S | 169_W | 1.161 | 0.97 |
| 113_L | 116_L | 1.151 | 0.97 |
| 133_C | 168_I | 1.146 | 0.97 |
| 59_V | 63_I | 1.137 | 0.97 |
| 54_V | 57_A | 1.137 | 0.97 |
| 93_L | 96_A | 1.135 | 0.97 |
| 160_R | 163_R | 1.125 | 0.97 |
| 139_A | 207_Y | 1.125 | 0.97 |
| 245_I | 301_H | 1.123 | 0.97 |
| 140_V | 144_I | 1.121 | 0.97 |
| 80_L | 84_D | 1.116 | 0.96 |
| 139_A | 206_L | 1.108 | 0.96 |
| 76_F | 137_A | 1.102 | 0.96 |
| 76_F | 134_F | 1.094 | 0.96 |
| 63_I | 69_L | 1.093 | 0.96 |
| 64_A | 78_C | 1.093 | 0.96 |
| 60_V | 81_A | 1.093 | 0.96 |
| 249_I | 293_I | 1.092 | 0.96 |
| 145_S | 150_L | 1.087 | 0.96 |
| 81_A | 84_D | 1.084 | 0.96 |
| 83_S | 127_S | 1.080 | 0.95 |
| 211_L | 240_A | 1.079 | 0.95 |
| 126_S | 176_S | 1.079 | 0.95 |
| 71_S | 74_Y | 1.078 | 0.95 |
| 66_N | 69_L | 1.066 | 0.95 |
| 91_N | 95_T | 1.066 | 0.95 |
| 143_Y | 205_V | 1.064 | 0.95 |
| 147_F | 209_H | 1.061 | 0.95 |
| 135_L | 203_M | 1.056 | 0.95 |
| 58_L | 62_T | 1.040 | 0.94 |
| 260_H | 283_F | 1.038 | 0.94 |
| 136_G | 203_M | 1.038 | 0.94 |
| 145_S | 152_Y | 1.037 | 0.94 |
| 132_L | 250_F | 1.035 | 0.94 |
| 51_V | 54_V | 1.031 | 0.94 |
| 141_D | 152_Y | 1.017 | 0.93 |
| 163_R | 166_A | 1.016 | 0.93 |
| 132_L | 136_G | 1.015 | 0.93 |
| 134_F | 168_I | 1.015 | 0.93 |
| 79_C | 83_S | 1.012 | 0.93 |
| 245_I | 297_I | 1.006 | 0.93 |
| 151_R | 154_S | 1.004 | 0.93 |
| 59_V | 81_A | 1.003 | 0.93 |
| 214_A | 239_G | 1.002 | 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 | |
| 4iarA | 1 | 0.8738 | 100 | 0.184 | Contact Map |
| 3vw7A | 1 | 0.8454 | 100 | 0.19 | Contact Map |
| 4pxzA | 1 | 0.8391 | 100 | 0.191 | Contact Map |
| 3uonA | 1 | 0.8517 | 100 | 0.193 | Contact Map |
| 2rh1A | 1 | 0.8549 | 100 | 0.193 | Contact Map |
| 3oduA | 2 | 0.8927 | 100 | 0.193 | Contact Map |
| 3emlA | 1 | 0.8612 | 100 | 0.201 | Contact Map |
| 3pblA | 2 | 0.8423 | 100 | 0.206 | Contact Map |
| 4grvA | 1 | 0.8644 | 100 | 0.207 | Contact Map |
| 4eiyA | 1 | 0.8738 | 100 | 0.215 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)