| Jiangfeng_NorM |
| ID: | 1493999305 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 472 (422) | ||
| Sequences: | 8101 (6730.9) | ||
| Seq/Len: | 19.197 | ||
| Nf(neff/√len): | 327.7 |
Jackhmmer Results: (2016_04)
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: 19.197).
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 |
| 135_E | 197_E | 3.061 | 1.00 |
| 337_F | 340_Y | 2.964 | 1.00 |
| 56_G | 276_Q | 2.872 | 1.00 |
| 162_D | 165_T | 2.852 | 1.00 |
| 342_V | 355_A | 2.760 | 1.00 |
| 81_A | 301_G | 2.663 | 1.00 |
| 350_E | 353_E | 2.557 | 1.00 |
| 308_N | 311_G | 2.512 | 1.00 |
| 214_Y | 218_L | 2.394 | 1.00 |
| 139_P | 197_E | 2.328 | 1.00 |
| 237_F | 241_R | 2.286 | 1.00 |
| 233_P | 237_F | 2.195 | 1.00 |
| 117_L | 121_K | 2.133 | 1.00 |
| 134_K | 138_T | 2.122 | 1.00 |
| 115_F | 118_F | 2.046 | 1.00 |
| 143_F | 146_I | 2.007 | 1.00 |
| 413_S | 416_V | 1.999 | 1.00 |
| 50_S | 128_T | 1.992 | 1.00 |
| 274_A | 354_W | 1.991 | 1.00 |
| 24_I | 28_V | 1.990 | 1.00 |
| 182_Y | 188_K | 1.979 | 1.00 |
| 132_L | 135_E | 1.968 | 1.00 |
| 187_G | 192_P | 1.945 | 1.00 |
| 182_Y | 185_I | 1.933 | 1.00 |
| 173_M | 177_H | 1.905 | 1.00 |
| 43_L | 185_I | 1.877 | 1.00 |
| 146_I | 208_I | 1.852 | 1.00 |
| 203_I | 207_E | 1.846 | 1.00 |
| 114_D | 117_L | 1.815 | 1.00 |
| 338_P | 356_S | 1.814 | 1.00 |
| 339_H | 343_Y | 1.809 | 1.00 |
| 304_Y | 382_M | 1.803 | 1.00 |
| 43_L | 181_A | 1.792 | 1.00 |
| 183_T | 191_L | 1.783 | 1.00 |
| 312_M | 316_V | 1.776 | 1.00 |
| 338_P | 360_Q | 1.770 | 1.00 |
| 17_K | 21_K | 1.750 | 1.00 |
| 349_P | 353_E | 1.734 | 1.00 |
| 164_K | 168_K | 1.732 | 1.00 |
| 139_P | 200_G | 1.728 | 1.00 |
| 339_H | 356_S | 1.726 | 1.00 |
| 117_L | 134_K | 1.702 | 1.00 |
| 403_P | 408_L | 1.692 | 1.00 |
| 183_T | 188_K | 1.686 | 1.00 |
| 176_T | 209_L | 1.670 | 1.00 |
| 88_K | 91_S | 1.668 | 1.00 |
| 224_P | 227_L | 1.666 | 1.00 |
| 340_Y | 343_Y | 1.665 | 1.00 |
| 197_E | 201_W | 1.663 | 1.00 |
| 405_Y | 408_L | 1.650 | 1.00 |
| 353_E | 357_Y | 1.650 | 1.00 |
| 214_Y | 217_L | 1.647 | 1.00 |
| 128_T | 269_D | 1.634 | 1.00 |
| 296_S | 319_S | 1.627 | 1.00 |
| 181_A | 184_L | 1.625 | 1.00 |
| 179_G | 183_T | 1.606 | 1.00 |
| 402_I | 405_Y | 1.594 | 1.00 |
| 175_L | 179_G | 1.588 | 1.00 |
| 177_H | 181_A | 1.581 | 1.00 |
| 340_Y | 344_P | 1.574 | 1.00 |
| 126_S | 269_D | 1.573 | 1.00 |
| 188_K | 191_L | 1.568 | 1.00 |
| 109_F | 113_K | 1.554 | 1.00 |
| 317_N | 321_H | 1.554 | 1.00 |
| 323_T | 327_M | 1.551 | 1.00 |
| 131_S | 135_E | 1.546 | 1.00 |
| 113_K | 117_L | 1.545 | 1.00 |
| 191_L | 194_L | 1.543 | 1.00 |
| 270_K | 350_E | 1.531 | 1.00 |
| 313_V | 317_N | 1.528 | 1.00 |
| 54_A | 132_L | 1.516 | 1.00 |
| 143_F | 147_G | 1.503 | 1.00 |
| 47_I | 193_K | 1.493 | 1.00 |
| 194_L | 201_W | 1.487 | 1.00 |
| 311_G | 315_A | 1.476 | 1.00 |
| 238_K | 241_R | 1.469 | 1.00 |
| 200_G | 203_I | 1.462 | 1.00 |
| 180_T | 202_G | 1.451 | 1.00 |
| 48_S | 51_A | 1.451 | 1.00 |
| 69_M | 72_S | 1.438 | 1.00 |
| 405_Y | 409_K | 1.437 | 1.00 |
| 403_P | 406_F | 1.436 | 1.00 |
| 49_P | 348_D | 1.430 | 1.00 |
| 28_V | 167_M | 1.425 | 1.00 |
| 84_V | 302_Q | 1.419 | 1.00 |
| 23_S | 295_A | 1.417 | 1.00 |
| 200_G | 204_A | 1.413 | 1.00 |
| 324_A | 327_M | 1.408 | 1.00 |
| 216_F | 220_F | 1.398 | 0.99 |
| 412_H | 415_L | 1.395 | 0.99 |
| 180_T | 184_L | 1.390 | 0.99 |
| 179_G | 182_Y | 1.386 | 0.99 |
| 84_V | 160_A | 1.385 | 0.99 |
| 281_I | 341_L | 1.382 | 0.99 |
| 181_A | 185_I | 1.376 | 0.99 |
| 118_F | 122_V | 1.372 | 0.99 |
| 121_K | 130_R | 1.370 | 0.99 |
| 114_D | 118_F | 1.368 | 0.99 |
| 335_I | 360_Q | 1.363 | 0.99 |
| 204_A | 207_E | 1.361 | 0.99 |
| 127_E | 131_S | 1.357 | 0.99 |
| 312_M | 315_A | 1.355 | 0.99 |
| 310_R | 314_H | 1.354 | 0.99 |
| 404_S | 407_L | 1.350 | 0.99 |
| 356_S | 360_Q | 1.350 | 0.99 |
| 420_F | 424_E | 1.345 | 0.99 |
| 394_S | 398_L | 1.341 | 0.99 |
| 244_T | 248_L | 1.340 | 0.99 |
| 198_G | 203_I | 1.318 | 0.99 |
| 184_L | 191_L | 1.312 | 0.99 |
| 417_P | 420_F | 1.311 | 0.99 |
| 177_H | 180_T | 1.309 | 0.99 |
| 27_I | 291_G | 1.298 | 0.99 |
| 128_T | 131_S | 1.297 | 0.99 |
| 113_K | 116_V | 1.289 | 0.99 |
| 314_H | 318_T | 1.277 | 0.99 |
| 403_P | 409_K | 1.271 | 0.99 |
| 232_E | 235_L | 1.270 | 0.99 |
| 314_H | 317_N | 1.269 | 0.99 |
| 304_Y | 312_M | 1.263 | 0.99 |
| 82_Q | 383_G | 1.263 | 0.99 |
| 404_S | 408_L | 1.262 | 0.99 |
| 82_Q | 301_G | 1.262 | 0.99 |
| 197_E | 200_G | 1.257 | 0.99 |
| 168_K | 172_I | 1.252 | 0.99 |
| 162_D | 166_P | 1.246 | 0.98 |
| 32_L | 171_I | 1.241 | 0.98 |
| 39_I | 178_I | 1.238 | 0.98 |
| 92_P | 232_E | 1.235 | 0.98 |
| 118_F | 121_K | 1.234 | 0.98 |
| 180_T | 183_T | 1.231 | 0.98 |
| 221_F | 225_F | 1.226 | 0.98 |
| 109_F | 114_D | 1.211 | 0.98 |
| 232_E | 237_F | 1.209 | 0.98 |
| 180_T | 205_I | 1.209 | 0.98 |
| 258_N | 261_V | 1.207 | 0.98 |
| 386_H | 390_F | 1.202 | 0.98 |
| 183_T | 189_F | 1.200 | 0.98 |
| 130_R | 134_K | 1.200 | 0.98 |
| 120_M | 130_R | 1.199 | 0.98 |
| 412_H | 416_V | 1.198 | 0.98 |
| 111_Y | 114_D | 1.194 | 0.98 |
| 217_L | 221_F | 1.193 | 0.98 |
| 69_M | 73_Y | 1.193 | 0.98 |
| 390_F | 394_S | 1.190 | 0.98 |
| 424_E | 428_R | 1.189 | 0.98 |
| 335_I | 363_G | 1.185 | 0.98 |
| 70_A | 73_Y | 1.182 | 0.98 |
| 40_S | 203_I | 1.180 | 0.98 |
| 49_P | 270_K | 1.179 | 0.98 |
| 321_H | 325_L | 1.176 | 0.98 |
| 183_T | 186_N | 1.171 | 0.98 |
| 408_L | 411_I | 1.170 | 0.97 |
| 234_K | 237_F | 1.166 | 0.97 |
| 379_L | 384_K | 1.160 | 0.97 |
| 221_F | 224_P | 1.159 | 0.97 |
| 332_L | 336_L | 1.155 | 0.97 |
| 117_L | 120_M | 1.149 | 0.97 |
| 403_P | 407_L | 1.147 | 0.97 |
| 82_Q | 86_A | 1.135 | 0.97 |
| 139_P | 201_W | 1.132 | 0.97 |
| 83_F | 86_A | 1.127 | 0.97 |
| 311_G | 314_H | 1.124 | 0.97 |
| 184_L | 187_G | 1.122 | 0.97 |
| 303_N | 311_G | 1.122 | 0.97 |
| 142_W | 146_I | 1.121 | 0.97 |
| 41_M | 52_V | 1.117 | 0.96 |
| 46_S | 347_R | 1.115 | 0.96 |
| 40_S | 44_V | 1.113 | 0.96 |
| 241_R | 386_H | 1.110 | 0.96 |
| 182_Y | 186_N | 1.107 | 0.96 |
| 92_P | 96_N | 1.105 | 0.96 |
| 111_Y | 115_F | 1.104 | 0.96 |
| 201_W | 205_I | 1.102 | 0.96 |
| 188_K | 193_K | 1.102 | 0.96 |
| 79_L | 83_F | 1.099 | 0.96 |
| 58_S | 137_L | 1.099 | 0.96 |
| 82_Q | 304_Y | 1.098 | 0.96 |
| 419_G | 422_T | 1.079 | 0.95 |
| 202_G | 207_E | 1.077 | 0.95 |
| 278_G | 358_Y | 1.073 | 0.95 |
| 44_V | 55_T | 1.071 | 0.95 |
| 53_A | 273_A | 1.070 | 0.95 |
| 353_E | 356_S | 1.069 | 0.95 |
| 312_M | 382_M | 1.064 | 0.95 |
| 43_L | 182_Y | 1.064 | 0.95 |
| 112_G | 116_V | 1.061 | 0.95 |
| 26_I | 294_I | 1.056 | 0.95 |
| 47_I | 51_A | 1.055 | 0.95 |
| 67_S | 70_A | 1.053 | 0.95 |
| 194_L | 198_G | 1.052 | 0.95 |
| 327_M | 331_G | 1.050 | 0.94 |
| 176_T | 180_T | 1.048 | 0.94 |
| 339_H | 353_E | 1.047 | 0.94 |
| 223_K | 226_P | 1.046 | 0.94 |
| 181_A | 202_G | 1.046 | 0.94 |
| 183_T | 187_G | 1.045 | 0.94 |
| 315_A | 318_T | 1.043 | 0.94 |
| 89_D | 92_P | 1.042 | 0.94 |
| 141_F | 145_P | 1.042 | 0.94 |
| 225_F | 228_H | 1.041 | 0.94 |
| 352_I | 355_A | 1.039 | 0.94 |
| 218_L | 222_K | 1.038 | 0.94 |
| 418_W | 421_M | 1.037 | 0.94 |
| 51_A | 132_L | 1.037 | 0.94 |
| 212_F | 216_F | 1.036 | 0.94 |
| 316_V | 375_Y | 1.033 | 0.94 |
| 327_M | 330_T | 1.032 | 0.94 |
| 55_T | 196_V | 1.031 | 0.94 |
| 218_L | 221_F | 1.027 | 0.94 |
| 300_A | 378_A | 1.024 | 0.93 |
| 408_L | 412_H | 1.020 | 0.93 |
| 400_R | 403_P | 1.020 | 0.93 |
| 320_A | 323_T | 1.014 | 0.93 |
| 50_S | 269_D | 1.013 | 0.93 |
| 63_W | 66_Y | 1.011 | 0.93 |
| 398_L | 402_I | 1.009 | 0.93 |
| 129_V | 133_A | 1.007 | 0.93 |
| 40_S | 45_S | 1.003 | 0.93 |
| 151_N | 154_Y | 1.001 | 0.92 |
| 216_F | 219_I | 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 | |
| 3mktA | 2 | 0.947 | 100 | 0.485 | Contact Map |
| 4humA | 1 | 0.9555 | 100 | 0.495 | Contact Map |
| 4lz6A | 1 | 0.9301 | 100 | 0.53 | Contact Map |
| 3w4tA | 1 | 0.9216 | 100 | 0.58 | Contact Map |
| 4tphA | 2 | 0.786 | 95.8 | 0.946 | Contact Map |
| 4pypA | 1 | 0.8114 | 92.4 | 0.954 | Contact Map |
| 3wdoA | 1 | 0.8602 | 90.2 | 0.957 | Contact Map |
| 4w6vA | 1 | 0 | 84.7 | 0.96 | Contact Map |
| 4ikvA | 1 | 0.8411 | 69.6 | 0.965 | Contact Map |
| 4m64A | 4 | 0.839 | 69.2 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)