| mbp |
| ID: | 1414201490 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 370 (366) | ||
| Sequences: | 5336 (4136.8) | ||
| Seq/Len: | 14.579 | ||
| Nf(neff/√len): | 216.2 |
HHblits Results: (2013_03)
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: 14.579).
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 |
| 356_T | 359_E | 4.166 | 1.00 |
| 189_K | 358_D | 3.996 | 1.00 |
| 193_T | 197_D | 3.931 | 1.00 |
| 31_T | 278_E | 3.915 | 1.00 |
| 77_A | 273_K | 3.859 | 1.00 |
| 120_D | 241_N | 3.787 | 1.00 |
| 196_V | 200_K | 3.770 | 1.00 |
| 6_K | 36_T | 3.620 | 1.00 |
| 21_A | 25_K | 3.488 | 1.00 |
| 27_F | 278_E | 3.235 | 1.00 |
| 184_D | 362_K | 3.172 | 1.00 |
| 358_D | 362_K | 3.100 | 1.00 |
| 119_K | 243_G | 3.037 | 1.00 |
| 33_I | 275_L | 2.966 | 1.00 |
| 272_N | 275_L | 2.827 | 1.00 |
| 28_E | 34_K | 2.657 | 1.00 |
| 78_E | 102_K | 2.626 | 1.00 |
| 98_R | 103_L | 2.568 | 1.00 |
| 26_K | 282_N | 2.524 | 1.00 |
| 133_P | 197_D | 2.497 | 1.00 |
| 137_K | 201_N | 2.480 | 1.00 |
| 122_L | 224_M | 2.476 | 1.00 |
| 362_K | 366_T | 2.467 | 1.00 |
| 26_K | 29_K | 2.413 | 1.00 |
| 22_E | 25_K | 2.372 | 1.00 |
| 59_I | 280_L | 2.343 | 1.00 |
| 278_E | 281_E | 2.333 | 1.00 |
| 6_K | 34_K | 2.331 | 1.00 |
| 134_A | 138_E | 2.322 | 1.00 |
| 117_Y | 243_G | 2.296 | 1.00 |
| 91_P | 95_D | 2.287 | 1.00 |
| 27_F | 33_I | 2.283 | 1.00 |
| 88_K | 304_L | 2.279 | 1.00 |
| 355_Q | 363_D | 2.225 | 1.00 |
| 197_D | 201_N | 2.214 | 1.00 |
| 285_L | 288_E | 2.196 | 1.00 |
| 25_K | 29_K | 2.176 | 1.00 |
| 365_Q | 369_T | 2.167 | 1.00 |
| 318_A | 322_E | 2.154 | 1.00 |
| 24_G | 279_F | 2.125 | 1.00 |
| 24_G | 28_E | 2.114 | 1.00 |
| 186_A | 190_A | 2.078 | 1.00 |
| 128_T | 131_E | 2.053 | 1.00 |
| 193_T | 358_D | 2.017 | 1.00 |
| 270_S | 273_K | 1.996 | 1.00 |
| 131_E | 134_A | 1.980 | 1.00 |
| 42_K | 45_E | 1.941 | 1.00 |
| 60_I | 267_N | 1.922 | 1.00 |
| 4_E | 34_K | 1.919 | 1.00 |
| 349_N | 355_Q | 1.835 | 1.00 |
| 51_A | 56_G | 1.827 | 1.00 |
| 359_E | 363_D | 1.822 | 1.00 |
| 97_V | 263_S | 1.804 | 1.00 |
| 58_D | 272_N | 1.802 | 1.00 |
| 33_I | 278_E | 1.795 | 1.00 |
| 119_K | 123_P | 1.792 | 1.00 |
| 350_A | 360_A | 1.782 | 1.00 |
| 76_L | 265_G | 1.774 | 1.00 |
| 134_A | 137_K | 1.765 | 1.00 |
| 140_K | 146_A | 1.745 | 1.00 |
| 189_K | 357_V | 1.744 | 1.00 |
| 190_A | 193_T | 1.724 | 1.00 |
| 8_V | 36_T | 1.722 | 1.00 |
| 24_G | 37_V | 1.715 | 1.00 |
| 25_K | 28_E | 1.711 | 1.00 |
| 105_A | 265_G | 1.708 | 1.00 |
| 10_W | 50_V | 1.704 | 1.00 |
| 266_I | 280_L | 1.689 | 1.00 |
| 28_E | 31_T | 1.674 | 1.00 |
| 279_F | 283_Y | 1.645 | 1.00 |
| 193_T | 357_V | 1.607 | 1.00 |
| 130_E | 133_P | 1.603 | 1.00 |
| 26_K | 30_D | 1.583 | 1.00 |
| 184_D | 365_Q | 1.576 | 1.00 |
| 170_K | 180_D | 1.574 | 1.00 |
| 349_N | 354_R | 1.547 | 1.00 |
| 133_P | 201_N | 1.543 | 1.00 |
| 114_S | 320_T | 1.532 | 1.00 |
| 22_E | 26_K | 1.506 | 1.00 |
| 77_A | 270_S | 1.502 | 1.00 |
| 274_E | 278_E | 1.496 | 1.00 |
| 355_Q | 360_A | 1.494 | 1.00 |
| 35_V | 279_F | 1.476 | 1.00 |
| 346_A | 355_Q | 1.466 | 1.00 |
| 139_L | 223_A | 1.461 | 1.00 |
| 117_Y | 245_T | 1.455 | 1.00 |
| 17_Y | 21_A | 1.455 | 1.00 |
| 127_K | 131_E | 1.435 | 1.00 |
| 161_I | 166_G | 1.419 | 1.00 |
| 362_K | 365_Q | 1.399 | 0.99 |
| 77_A | 268_A | 1.396 | 0.99 |
| 115_L | 245_T | 1.396 | 0.99 |
| 363_D | 366_T | 1.392 | 0.99 |
| 138_E | 142_K | 1.391 | 0.99 |
| 82_D | 277_K | 1.384 | 0.99 |
| 197_D | 200_K | 1.378 | 0.99 |
| 322_E | 325_Q | 1.378 | 0.99 |
| 277_K | 281_E | 1.376 | 0.99 |
| 58_D | 270_S | 1.364 | 0.99 |
| 119_K | 241_N | 1.363 | 0.99 |
| 115_L | 224_M | 1.348 | 0.99 |
| 26_K | 291_E | 1.339 | 0.99 |
| 133_P | 198_L | 1.338 | 0.99 |
| 88_K | 302_V | 1.337 | 0.99 |
| 359_E | 362_K | 1.336 | 0.99 |
| 132_I | 147_L | 1.336 | 0.99 |
| 95_D | 98_R | 1.332 | 0.99 |
| 196_V | 350_A | 1.326 | 0.99 |
| 126_P | 131_E | 1.324 | 0.99 |
| 346_A | 364_A | 1.319 | 0.99 |
| 282_N | 288_E | 1.318 | 0.99 |
| 136_D | 224_M | 1.315 | 0.99 |
| 8_V | 38_E | 1.314 | 0.99 |
| 341_Y | 345_T | 1.299 | 0.99 |
| 27_F | 282_N | 1.292 | 0.99 |
| 121_L | 223_A | 1.292 | 0.99 |
| 130_E | 134_A | 1.286 | 0.99 |
| 28_E | 32_G | 1.280 | 0.99 |
| 346_A | 363_D | 1.271 | 0.99 |
| 133_P | 137_K | 1.269 | 0.99 |
| 266_I | 276_A | 1.269 | 0.99 |
| 187_G | 190_A | 1.265 | 0.99 |
| 5_G | 32_G | 1.264 | 0.99 |
| 189_K | 193_T | 1.257 | 0.99 |
| 350_A | 357_V | 1.251 | 0.99 |
| 27_F | 275_L | 1.248 | 0.99 |
| 170_K | 179_K | 1.245 | 0.98 |
| 4_E | 32_G | 1.233 | 0.98 |
| 363_D | 367_R | 1.232 | 0.98 |
| 137_K | 203_H | 1.228 | 0.98 |
| 216_A | 221_E | 1.212 | 0.98 |
| 194_F | 198_L | 1.208 | 0.98 |
| 135_L | 138_E | 1.202 | 0.98 |
| 122_L | 139_L | 1.193 | 0.98 |
| 209_D | 212_I | 1.192 | 0.98 |
| 78_E | 81_P | 1.189 | 0.98 |
| 356_T | 360_A | 1.186 | 0.98 |
| 80_T | 102_K | 1.175 | 0.98 |
| 71_A | 104_I | 1.174 | 0.98 |
| 118_N | 240_V | 1.165 | 0.97 |
| 349_N | 363_D | 1.164 | 0.97 |
| 137_K | 141_A | 1.162 | 0.97 |
| 27_F | 31_T | 1.158 | 0.97 |
| 71_A | 99_Y | 1.156 | 0.97 |
| 291_E | 295_K | 1.154 | 0.97 |
| 24_G | 35_V | 1.151 | 0.97 |
| 266_I | 277_K | 1.144 | 0.97 |
| 342_A | 367_R | 1.143 | 0.97 |
| 198_L | 203_H | 1.126 | 0.97 |
| 164_D | 190_A | 1.125 | 0.97 |
| 192_L | 350_A | 1.124 | 0.97 |
| 140_K | 203_H | 1.117 | 0.96 |
| 148_M | 222_T | 1.107 | 0.96 |
| 62_W | 265_G | 1.094 | 0.96 |
| 133_P | 194_F | 1.084 | 0.96 |
| 266_I | 270_S | 1.082 | 0.96 |
| 59_I | 279_F | 1.075 | 0.95 |
| 268_A | 273_K | 1.071 | 0.95 |
| 193_T | 196_V | 1.066 | 0.95 |
| 23_V | 26_K | 1.064 | 0.95 |
| 161_I | 188_A | 1.062 | 0.95 |
| 5_G | 275_L | 1.062 | 0.95 |
| 11_I | 37_V | 1.060 | 0.95 |
| 108_I | 264_A | 1.059 | 0.95 |
| 44_E | 66_R | 1.055 | 0.95 |
| 135_L | 224_M | 1.054 | 0.95 |
| 32_G | 278_E | 1.051 | 0.94 |
| 286_T | 290_L | 1.051 | 0.94 |
| 51_A | 75_L | 1.050 | 0.94 |
| 139_L | 224_M | 1.044 | 0.94 |
| 264_A | 280_L | 1.043 | 0.94 |
| 192_L | 361_L | 1.040 | 0.94 |
| 181_V | 365_Q | 1.038 | 0.94 |
| 47_F | 60_I | 1.034 | 0.94 |
| 122_L | 135_L | 1.032 | 0.94 |
| 267_N | 270_S | 1.032 | 0.94 |
| 105_A | 263_S | 1.032 | 0.94 |
| 114_S | 244_V | 1.023 | 0.93 |
| 273_K | 277_K | 1.014 | 0.93 |
| 345_T | 367_R | 1.011 | 0.93 |
| 18_N | 22_E | 1.006 | 0.93 |
| 27_F | 279_F | 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 | |
| 2zyoA | 1 | 1 | 100 | 0.162 | Contact Map |
| 1hsjA | 2 | 1 | 100 | 0.182 | Contact Map |
| 4kegA | 1 | 1 | 100 | 0.182 | Contact Map |
| 3iotA | 3 | 1 | 100 | 0.185 | Contact Map |
| 4logA | 2 | 0.9946 | 100 | 0.185 | Contact Map |
| 3oaiA | 2 | 0.9919 | 100 | 0.185 | Contact Map |
| 4egcA | 1 | 1 | 100 | 0.185 | Contact Map |
| 3h4zA | 3 | 1 | 100 | 0.187 | Contact Map |
| 1y4cA | 1 | 0.9919 | 100 | 0.187 | Contact Map |
| 4irlA | 3 | 1 | 100 | 0.187 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)