| capri_target |
| ID: | 1502917306 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 421 (399) | ||
| Sequences: | 18871 (12507.4) | ||
| Seq/Len: | 47.296 | ||
| Nf(neff/√len): | 626.2 |
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: 47.296).
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 |
| 8_E | 40_N | 4.080 | 1.00 |
| 83_L | 303_P | 3.884 | 1.00 |
| 215_I | 394_E | 3.564 | 1.00 |
| 137_T | 271_E | 3.513 | 1.00 |
| 392_S | 395_E | 3.497 | 1.00 |
| 222_A | 226_N | 3.344 | 1.00 |
| 219_Q | 223_D | 3.161 | 1.00 |
| 136_K | 273_D | 3.115 | 1.00 |
| 8_E | 38_K | 3.029 | 1.00 |
| 34_H | 308_E | 2.989 | 1.00 |
| 84_D | 119_N | 2.856 | 1.00 |
| 24_K | 28_K | 2.777 | 1.00 |
| 10_T | 40_N | 2.712 | 1.00 |
| 37_V | 305_E | 2.692 | 1.00 |
| 30_F | 308_E | 2.683 | 1.00 |
| 394_E | 398_K | 2.660 | 1.00 |
| 154_T | 157_E | 2.595 | 1.00 |
| 134_Y | 273_D | 2.532 | 1.00 |
| 223_D | 227_K | 2.496 | 1.00 |
| 398_K | 402_P | 2.486 | 1.00 |
| 137_T | 141_K | 2.467 | 1.00 |
| 31_E | 38_K | 2.444 | 1.00 |
| 29_K | 312_Y | 2.436 | 1.00 |
| 308_E | 311_L | 2.378 | 1.00 |
| 29_K | 32_E | 2.334 | 1.00 |
| 401_K | 405_Q | 2.327 | 1.00 |
| 139_F | 253_F | 2.297 | 1.00 |
| 159_I | 223_D | 2.286 | 1.00 |
| 160_D | 164_K | 2.242 | 1.00 |
| 212_P | 216_E | 2.232 | 1.00 |
| 99_D | 335_K | 2.196 | 1.00 |
| 109_R | 120_L | 2.177 | 1.00 |
| 144_I | 161_V | 2.176 | 1.00 |
| 136_K | 140_E | 2.175 | 1.00 |
| 385_P | 390_K | 2.161 | 1.00 |
| 28_K | 32_E | 2.161 | 1.00 |
| 219_Q | 393_A | 2.153 | 1.00 |
| 6_K | 38_K | 2.150 | 1.00 |
| 315_A | 319_G | 2.131 | 1.00 |
| 25_N | 28_K | 2.123 | 1.00 |
| 210_D | 398_K | 2.108 | 1.00 |
| 66_F | 297_S | 2.108 | 1.00 |
| 302_H | 305_E | 2.108 | 1.00 |
| 391_M | 399_K | 2.103 | 1.00 |
| 157_E | 160_D | 2.086 | 1.00 |
| 64_D | 302_H | 2.057 | 1.00 |
| 27_V | 31_E | 2.037 | 1.00 |
| 163_K | 227_K | 2.033 | 1.00 |
| 102_E | 106_N | 2.008 | 1.00 |
| 27_V | 309_L | 1.968 | 1.00 |
| 163_K | 167_K | 1.962 | 1.00 |
| 10_T | 42_V | 1.960 | 1.00 |
| 48_Q | 51_T | 1.945 | 1.00 |
| 160_D | 163_K | 1.909 | 1.00 |
| 216_E | 219_Q | 1.859 | 1.00 |
| 385_P | 391_M | 1.816 | 1.00 |
| 405_Q | 409_D | 1.814 | 1.00 |
| 395_E | 399_K | 1.810 | 1.00 |
| 215_I | 393_A | 1.805 | 1.00 |
| 86_T | 119_N | 1.798 | 1.00 |
| 88_Y | 307_V | 1.797 | 1.00 |
| 304_K | 308_E | 1.779 | 1.00 |
| 29_K | 322_A | 1.772 | 1.00 |
| 134_Y | 275_I | 1.753 | 1.00 |
| 138_M | 252_G | 1.749 | 1.00 |
| 296_V | 310_A | 1.721 | 1.00 |
| 402_P | 406_K | 1.710 | 1.00 |
| 156_Q | 159_I | 1.709 | 1.00 |
| 238_Q | 241_D | 1.696 | 1.00 |
| 82_L | 295_G | 1.685 | 1.00 |
| 164_K | 168_D | 1.683 | 1.00 |
| 352_Q | 356_D | 1.669 | 1.00 |
| 386_V | 396_Y | 1.668 | 1.00 |
| 27_V | 41_I | 1.661 | 1.00 |
| 108_Y | 293_G | 1.653 | 1.00 |
| 139_F | 144_I | 1.635 | 1.00 |
| 28_K | 31_E | 1.634 | 1.00 |
| 222_A | 386_V | 1.626 | 1.00 |
| 378_E | 403_K | 1.624 | 1.00 |
| 7_I | 305_E | 1.622 | 1.00 |
| 219_Q | 394_E | 1.606 | 1.00 |
| 395_E | 398_K | 1.604 | 1.00 |
| 153_Y | 157_E | 1.603 | 1.00 |
| 399_K | 402_P | 1.602 | 1.00 |
| 57_I | 62_I | 1.602 | 1.00 |
| 132_L | 275_I | 1.597 | 1.00 |
| 382_N | 399_K | 1.595 | 1.00 |
| 30_F | 37_V | 1.593 | 1.00 |
| 25_N | 29_K | 1.587 | 1.00 |
| 156_Q | 160_D | 1.586 | 1.00 |
| 165_L | 252_G | 1.580 | 1.00 |
| 30_F | 309_L | 1.569 | 1.00 |
| 245_R | 250_Q | 1.554 | 1.00 |
| 132_L | 253_F | 1.553 | 1.00 |
| 300_T | 303_P | 1.551 | 1.00 |
| 106_N | 109_R | 1.529 | 1.00 |
| 68_F | 295_G | 1.525 | 1.00 |
| 83_L | 298_S | 1.525 | 1.00 |
| 399_K | 403_K | 1.518 | 1.00 |
| 6_K | 36_N | 1.512 | 1.00 |
| 391_M | 396_Y | 1.502 | 1.00 |
| 20_Q | 24_K | 1.494 | 1.00 |
| 136_K | 271_E | 1.491 | 1.00 |
| 30_F | 312_Y | 1.485 | 1.00 |
| 321_K | 325_D | 1.485 | 1.00 |
| 159_I | 163_K | 1.484 | 1.00 |
| 298_S | 303_P | 1.468 | 1.00 |
| 29_K | 33_K | 1.456 | 1.00 |
| 7_I | 302_H | 1.453 | 1.00 |
| 377_D | 381_R | 1.445 | 1.00 |
| 45_S | 48_Q | 1.440 | 1.00 |
| 122_G | 293_G | 1.437 | 1.00 |
| 215_I | 219_Q | 1.435 | 1.00 |
| 138_M | 165_L | 1.434 | 1.00 |
| 65_V | 310_A | 1.430 | 1.00 |
| 246_W | 272_Y | 1.417 | 1.00 |
| 77_V | 121_Y | 1.415 | 1.00 |
| 31_E | 35_P | 1.403 | 0.99 |
| 296_V | 306_A | 1.385 | 0.99 |
| 322_A | 326_Q | 1.372 | 0.99 |
| 382_N | 391_M | 1.371 | 0.99 |
| 159_I | 224_M | 1.355 | 0.99 |
| 140_E | 146_L | 1.347 | 0.99 |
| 84_D | 87_K | 1.345 | 0.99 |
| 37_V | 308_E | 1.345 | 0.99 |
| 220_F | 223_D | 1.341 | 0.99 |
| 382_N | 385_P | 1.340 | 0.99 |
| 27_V | 39_V | 1.338 | 0.99 |
| 403_K | 406_K | 1.330 | 0.99 |
| 31_E | 34_H | 1.324 | 0.99 |
| 386_V | 393_A | 1.323 | 0.99 |
| 53_L | 66_F | 1.312 | 0.99 |
| 131_A | 354_F | 1.304 | 0.99 |
| 398_K | 401_K | 1.304 | 0.99 |
| 30_F | 305_E | 1.299 | 0.99 |
| 21_T | 24_K | 1.296 | 0.99 |
| 30_F | 34_H | 1.295 | 0.99 |
| 356_D | 360_D | 1.291 | 0.99 |
| 65_V | 306_A | 1.284 | 0.99 |
| 309_L | 313_L | 1.282 | 0.99 |
| 142_A | 165_L | 1.281 | 0.99 |
| 317_P | 321_K | 1.281 | 0.99 |
| 319_G | 322_A | 1.271 | 0.99 |
| 162_C | 253_F | 1.268 | 0.99 |
| 144_I | 164_K | 1.259 | 0.99 |
| 213_K | 216_E | 1.248 | 0.99 |
| 201_D | 205_T | 1.243 | 0.98 |
| 131_A | 274_L | 1.237 | 0.98 |
| 12_M | 56_A | 1.237 | 0.98 |
| 307_V | 311_L | 1.232 | 0.98 |
| 99_D | 333_S | 1.228 | 0.98 |
| 309_L | 312_Y | 1.222 | 0.98 |
| 223_D | 226_N | 1.219 | 0.98 |
| 312_Y | 319_G | 1.210 | 0.98 |
| 382_N | 400_A | 1.207 | 0.98 |
| 159_I | 227_K | 1.206 | 0.98 |
| 158_F | 180_T | 1.199 | 0.98 |
| 218_L | 386_V | 1.198 | 0.98 |
| 125_K | 294_I | 1.193 | 0.98 |
| 192_V | 214_F | 1.192 | 0.98 |
| 192_V | 197_A | 1.192 | 0.98 |
| 201_D | 206_K | 1.191 | 0.98 |
| 101_W | 334_V | 1.181 | 0.98 |
| 322_A | 325_D | 1.178 | 0.98 |
| 65_V | 309_L | 1.166 | 0.97 |
| 391_M | 395_E | 1.164 | 0.97 |
| 21_T | 25_N | 1.164 | 0.97 |
| 139_F | 161_V | 1.163 | 0.97 |
| 159_I | 220_F | 1.154 | 0.97 |
| 385_P | 399_K | 1.151 | 0.97 |
| 305_E | 308_E | 1.150 | 0.97 |
| 181_G | 251_L | 1.145 | 0.97 |
| 195_N | 216_E | 1.145 | 0.97 |
| 303_P | 307_V | 1.143 | 0.97 |
| 210_D | 401_K | 1.137 | 0.97 |
| 138_M | 141_K | 1.135 | 0.97 |
| 108_Y | 120_L | 1.134 | 0.97 |
| 39_V | 309_L | 1.133 | 0.97 |
| 102_E | 334_V | 1.127 | 0.97 |
| 161_V | 253_F | 1.126 | 0.97 |
| 219_Q | 222_A | 1.121 | 0.97 |
| 147_P | 152_P | 1.120 | 0.96 |
| 122_G | 295_G | 1.118 | 0.96 |
| 222_A | 393_A | 1.117 | 0.96 |
| 83_L | 300_T | 1.116 | 0.96 |
| 31_E | 36_N | 1.113 | 0.96 |
| 317_P | 335_K | 1.111 | 0.96 |
| 375_W | 404_M | 1.111 | 0.96 |
| 315_A | 318_E | 1.108 | 0.96 |
| 402_P | 405_Q | 1.104 | 0.96 |
| 9_L | 309_L | 1.103 | 0.96 |
| 152_P | 157_E | 1.095 | 0.96 |
| 161_V | 164_K | 1.095 | 0.96 |
| 138_M | 142_A | 1.089 | 0.96 |
| 215_I | 397_V | 1.084 | 0.96 |
| 25_N | 322_A | 1.081 | 0.95 |
| 7_I | 36_N | 1.079 | 0.95 |
| 245_R | 251_L | 1.079 | 0.95 |
| 52_K | 56_A | 1.070 | 0.95 |
| 26_V | 29_K | 1.069 | 0.95 |
| 198_D | 202_E | 1.067 | 0.95 |
| 80_N | 298_S | 1.063 | 0.95 |
| 244_Q | 248_R | 1.051 | 0.94 |
| 135_N | 138_M | 1.047 | 0.94 |
| 220_F | 224_M | 1.047 | 0.94 |
| 62_I | 297_S | 1.042 | 0.94 |
| 77_V | 116_G | 1.041 | 0.94 |
| 318_E | 321_K | 1.040 | 0.94 |
| 166_T | 179_G | 1.029 | 0.94 |
| 86_T | 120_L | 1.029 | 0.94 |
| 381_R | 403_K | 1.028 | 0.94 |
| 158_F | 162_C | 1.025 | 0.93 |
| 7_I | 37_V | 1.015 | 0.93 |
| 296_V | 307_V | 1.014 | 0.93 |
| 139_F | 165_L | 1.012 | 0.93 |
| 382_N | 396_Y | 1.007 | 0.93 |
| 133_G | 256_V | 1.003 | 0.93 |
| 57_I | 81_V | 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 | |
| 4r6kA | 1 | 0.9264 | 100 | 0.113 | Contact Map |
| 3uorA | 2 | 0.9287 | 100 | 0.123 | Contact Map |
| 3k01A | 1 | 0.9097 | 100 | 0.13 | Contact Map |
| 1eu8A | 1 | 0.924 | 100 | 0.13 | Contact Map |
| 5ci5A | 2 | 0 | 100 | 0.138 | Contact Map |
| 4r9fA | 1 | 0.9026 | 100 | 0.141 | Contact Map |
| 4ovjA | 1 | 0.905 | 100 | 0.146 | Contact Map |
| 4rjzA | 1 | 0.8836 | 100 | 0.146 | Contact Map |
| 4mfiA | 1 | 0.9406 | 100 | 0.15 | Contact Map |
| 4r2fA | 1 | 0.8812 | 100 | 0.154 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)