| P450BM3 |
| ID: | 1494103159 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 464 (450) | ||
| Sequences: | 24120 (16557.5) | ||
| Seq/Len: | 53.600 | ||
| Nf(neff/√len): | 780.5 |
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: 53.600).
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 |
| 317_M | 381_E | 4.648 | 1.00 |
| 371_D | 374_E | 3.955 | 1.00 |
| 371_D | 376_R | 3.679 | 1.00 |
| 280_F | 326_W | 3.441 | 1.00 |
| 277_A | 415_L | 3.353 | 1.00 |
| 290_K | 378_E | 3.316 | 1.00 |
| 293_E | 297_R | 3.239 | 1.00 |
| 289_Q | 293_E | 3.207 | 1.00 |
| 287_V | 314_Y | 3.162 | 1.00 |
| 423_D | 450_K | 3.131 | 1.00 |
| 277_A | 322_A | 2.997 | 1.00 |
| 363_R | 373_E | 2.882 | 1.00 |
| 149_L | 414_V | 2.777 | 1.00 |
| 273_L | 411_A | 2.762 | 1.00 |
| 316_G | 412_T | 2.757 | 1.00 |
| 225_K | 252_D | 2.743 | 1.00 |
| 349_E | 352_D | 2.731 | 1.00 |
| 291_A | 318_V | 2.651 | 1.00 |
| 31_M | 35_D | 2.630 | 1.00 |
| 146_M | 278_L | 2.559 | 1.00 |
| 339_D | 350_K | 2.523 | 1.00 |
| 224_R | 233_D | 2.500 | 1.00 |
| 292_A | 452_K | 2.459 | 1.00 |
| 222_A | 252_D | 2.405 | 1.00 |
| 292_A | 423_D | 2.375 | 1.00 |
| 218_D | 222_A | 2.361 | 1.00 |
| 132_E | 451_S | 2.351 | 1.00 |
| 292_A | 296_A | 2.310 | 1.00 |
| 132_E | 421_H | 2.309 | 1.00 |
| 291_A | 419_L | 2.300 | 1.00 |
| 369_G | 372_V | 2.289 | 1.00 |
| 40_I | 53_L | 2.276 | 1.00 |
| 290_K | 314_Y | 2.275 | 1.00 |
| 277_A | 318_V | 2.262 | 1.00 |
| 341_V | 347_P | 2.257 | 1.00 |
| 222_A | 226_A | 2.250 | 1.00 |
| 218_D | 256_R | 2.239 | 1.00 |
| 125_V | 417_M | 2.221 | 1.00 |
| 339_D | 347_P | 2.172 | 1.00 |
| 289_Q | 423_D | 2.155 | 1.00 |
| 288_L | 292_A | 2.132 | 1.00 |
| 291_A | 315_V | 2.095 | 1.00 |
| 319_L | 411_A | 2.083 | 1.00 |
| 218_D | 252_D | 2.040 | 1.00 |
| 365_K | 372_V | 2.034 | 1.00 |
| 146_M | 274_L | 2.027 | 1.00 |
| 296_A | 452_K | 2.010 | 1.00 |
| 325_L | 363_R | 1.952 | 1.00 |
| 122_D | 156_L | 1.952 | 1.00 |
| 29_A | 32_K | 1.948 | 1.00 |
| 365_K | 370_D | 1.929 | 1.00 |
| 418_M | 424_F | 1.918 | 1.00 |
| 289_Q | 292_A | 1.912 | 1.00 |
| 215_D | 219_K | 1.910 | 1.00 |
| 288_L | 423_D | 1.889 | 1.00 |
| 359_P | 363_R | 1.858 | 1.00 |
| 284_N | 287_V | 1.853 | 1.00 |
| 280_F | 284_N | 1.849 | 1.00 |
| 305_S | 308_Q | 1.844 | 1.00 |
| 132_E | 422_F | 1.840 | 1.00 |
| 277_A | 281_L | 1.823 | 1.00 |
| 12_F | 15_L | 1.821 | 1.00 |
| 53_L | 62_A | 1.802 | 1.00 |
| 365_K | 373_E | 1.780 | 1.00 |
| 68_F | 340_T | 1.765 | 1.00 |
| 400_A | 404_Q | 1.760 | 1.00 |
| 336_A | 348_L | 1.755 | 1.00 |
| 274_L | 414_V | 1.744 | 1.00 |
| 280_F | 325_L | 1.730 | 1.00 |
| 318_V | 375_F | 1.693 | 1.00 |
| 32_K | 36_E | 1.690 | 1.00 |
| 287_V | 318_V | 1.672 | 1.00 |
| 211_K | 215_D | 1.672 | 1.00 |
| 219_K | 223_D | 1.670 | 1.00 |
| 100_A | 258_Q | 1.658 | 1.00 |
| 15_L | 19_P | 1.656 | 1.00 |
| 251_D | 254_N | 1.654 | 1.00 |
| 121_V | 417_M | 1.616 | 1.00 |
| 67_R | 338_E | 1.612 | 1.00 |
| 59_I | 361_L | 1.608 | 1.00 |
| 316_G | 320_N | 1.606 | 1.00 |
| 424_F | 449_A | 1.591 | 1.00 |
| 295_A | 416_G | 1.587 | 1.00 |
| 294_E | 312_L | 1.582 | 1.00 |
| 317_M | 378_E | 1.573 | 1.00 |
| 126_Q | 167_Y | 1.572 | 1.00 |
| 278_L | 418_M | 1.565 | 1.00 |
| 32_K | 35_D | 1.560 | 1.00 |
| 314_Y | 378_E | 1.559 | 1.00 |
| 281_L | 287_V | 1.550 | 1.00 |
| 338_E | 350_K | 1.539 | 1.00 |
| 31_M | 360_Q | 1.534 | 1.00 |
| 154_I | 266_G | 1.530 | 1.00 |
| 17_N | 20_L | 1.523 | 1.00 |
| 42_K | 49_V | 1.514 | 1.00 |
| 124_A | 149_L | 1.506 | 1.00 |
| 123_I | 126_Q | 1.506 | 1.00 |
| 339_D | 349_E | 1.505 | 1.00 |
| 298_V | 312_L | 1.491 | 1.00 |
| 273_L | 328_T | 1.487 | 1.00 |
| 321_E | 324_R | 1.484 | 1.00 |
| 223_D | 227_S | 1.476 | 1.00 |
| 95_K | 99_K | 1.468 | 1.00 |
| 55_S | 58_L | 1.465 | 1.00 |
| 282_V | 288_L | 1.459 | 1.00 |
| 161_Y | 223_D | 1.441 | 1.00 |
| 279_Y | 283_K | 1.438 | 1.00 |
| 296_A | 420_K | 1.434 | 1.00 |
| 407_A | 411_A | 1.431 | 1.00 |
| 222_A | 225_K | 1.422 | 1.00 |
| 281_L | 288_L | 1.412 | 1.00 |
| 141_E | 144_E | 1.385 | 0.99 |
| 39_E | 55_S | 1.380 | 0.99 |
| 41_F | 52_Y | 1.371 | 0.99 |
| 320_N | 408_L | 1.371 | 0.99 |
| 295_A | 312_L | 1.366 | 0.99 |
| 335_Y | 351_G | 1.365 | 0.99 |
| 318_V | 322_A | 1.359 | 0.99 |
| 290_K | 293_E | 1.359 | 0.99 |
| 13_G | 16_K | 1.355 | 0.99 |
| 220_I | 223_D | 1.353 | 0.99 |
| 123_I | 156_L | 1.351 | 0.99 |
| 95_K | 98_K | 1.351 | 0.99 |
| 236_T | 240_N | 1.336 | 0.99 |
| 44_E | 49_V | 1.336 | 0.99 |
| 130_K | 145_D | 1.336 | 0.99 |
| 362_H | 393_P | 1.330 | 0.99 |
| 149_L | 153_T | 1.309 | 0.99 |
| 322_A | 375_F | 1.304 | 0.99 |
| 121_V | 125_V | 1.304 | 0.99 |
| 278_L | 447_V | 1.302 | 0.99 |
| 280_F | 322_A | 1.302 | 0.99 |
| 299_L | 420_K | 1.300 | 0.99 |
| 323_L | 393_P | 1.295 | 0.99 |
| 176_T | 180_R | 1.292 | 0.99 |
| 51_R | 352_D | 1.290 | 0.99 |
| 131_W | 145_D | 1.282 | 0.99 |
| 341_V | 345_E | 1.280 | 0.99 |
| 274_L | 411_A | 1.276 | 0.99 |
| 292_A | 419_L | 1.269 | 0.99 |
| 164_N | 167_Y | 1.269 | 0.99 |
| 156_L | 162_R | 1.244 | 0.98 |
| 223_D | 226_A | 1.233 | 0.98 |
| 29_A | 33_I | 1.227 | 0.98 |
| 214_N | 256_R | 1.225 | 0.98 |
| 99_K | 254_N | 1.217 | 0.98 |
| 287_V | 378_E | 1.215 | 0.98 |
| 281_L | 291_A | 1.210 | 0.98 |
| 151_L | 267_H | 1.207 | 0.98 |
| 214_N | 218_D | 1.206 | 0.98 |
| 53_L | 58_L | 1.206 | 0.98 |
| 154_I | 158_G | 1.205 | 0.98 |
| 35_D | 365_K | 1.204 | 0.98 |
| 54_S | 364_D | 1.191 | 0.98 |
| 173_P | 212_V | 1.191 | 0.98 |
| 408_L | 412_T | 1.189 | 0.98 |
| 320_N | 391_F | 1.175 | 0.98 |
| 155_G | 163_F | 1.172 | 0.98 |
| 417_M | 421_H | 1.169 | 0.97 |
| 214_N | 253_E | 1.168 | 0.97 |
| 295_A | 315_V | 1.168 | 0.97 |
| 51_R | 348_L | 1.168 | 0.97 |
| 157_C | 406_F | 1.167 | 0.97 |
| 142_V | 278_L | 1.164 | 0.97 |
| 280_F | 283_K | 1.163 | 0.97 |
| 39_E | 366_T | 1.160 | 0.97 |
| 286_H | 290_K | 1.159 | 0.97 |
| 96_N | 99_K | 1.158 | 0.97 |
| 282_V | 424_F | 1.157 | 0.97 |
| 302_P | 308_Q | 1.156 | 0.97 |
| 113_M | 409_H | 1.155 | 0.97 |
| 97_W | 101_H | 1.155 | 0.97 |
| 8_Q | 37_L | 1.148 | 0.97 |
| 57_R | 60_K | 1.148 | 0.97 |
| 90_S | 96_N | 1.148 | 0.97 |
| 404_Q | 408_L | 1.143 | 0.97 |
| 85_D | 96_N | 1.143 | 0.97 |
| 277_A | 319_L | 1.135 | 0.97 |
| 59_I | 356_V | 1.131 | 0.97 |
| 144_E | 148_R | 1.127 | 0.97 |
| 130_K | 133_R | 1.126 | 0.97 |
| 69_D | 337_K | 1.122 | 0.97 |
| 362_H | 391_F | 1.120 | 0.96 |
| 8_Q | 17_N | 1.116 | 0.96 |
| 139_H | 446_V | 1.115 | 0.96 |
| 129_Q | 132_E | 1.114 | 0.96 |
| 313_K | 317_M | 1.110 | 0.96 |
| 119_M | 156_L | 1.110 | 0.96 |
| 225_K | 242_K | 1.107 | 0.96 |
| 128_V | 422_F | 1.103 | 0.96 |
| 287_V | 376_R | 1.103 | 0.96 |
| 376_R | 382_N | 1.099 | 0.96 |
| 358_I | 392_K | 1.094 | 0.96 |
| 139_H | 448_K | 1.090 | 0.96 |
| 273_L | 322_A | 1.090 | 0.96 |
| 130_K | 134_L | 1.084 | 0.96 |
| 335_Y | 353_E | 1.073 | 0.95 |
| 287_V | 290_K | 1.071 | 0.95 |
| 86_G | 261_T | 1.070 | 0.95 |
| 87_L | 402_I | 1.070 | 0.95 |
| 33_I | 41_F | 1.066 | 0.95 |
| 282_V | 447_V | 1.060 | 0.95 |
| 124_A | 128_V | 1.058 | 0.95 |
| 291_A | 314_Y | 1.057 | 0.95 |
| 125_V | 129_Q | 1.050 | 0.94 |
| 60_K | 64_D | 1.048 | 0.94 |
| 123_I | 162_R | 1.047 | 0.94 |
| 285_P | 289_Q | 1.044 | 0.94 |
| 433_D | 443_E | 1.042 | 0.94 |
| 288_L | 419_L | 1.039 | 0.94 |
| 12_F | 19_P | 1.039 | 0.94 |
| 96_N | 254_N | 1.038 | 0.94 |
| 308_Q | 311_Q | 1.037 | 0.94 |
| 208_E | 212_V | 1.034 | 0.94 |
| 143_P | 275_S | 1.032 | 0.94 |
| 150_T | 270_T | 1.026 | 0.94 |
| 204_R | 208_E | 1.025 | 0.93 |
| 122_D | 126_Q | 1.024 | 0.93 |
| 278_L | 415_L | 1.024 | 0.93 |
| 177_S | 212_V | 1.022 | 0.93 |
| 373_E | 376_R | 1.021 | 0.93 |
| 112_A | 115_G | 1.021 | 0.93 |
| 233_D | 236_T | 1.014 | 0.93 |
| 212_V | 215_D | 1.010 | 0.93 |
| 284_N | 374_E | 1.010 | 0.93 |
| 128_V | 417_M | 1.009 | 0.93 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2ij2A | 2 | 0.9849 | 100 | 0.082 | Contact Map |
| 4r21A | 2 | 0.8815 | 100 | 0.167 | Contact Map |
| 3czhA | 2 | 0.9591 | 100 | 0.171 | Contact Map |
| 3k9vA | 2 | 0.9526 | 100 | 0.172 | Contact Map |
| 3dbgA | 2 | 0.8125 | 100 | 0.172 | Contact Map |
| 3tbgA | 4 | 0.9547 | 100 | 0.178 | Contact Map |
| 3nxuA | 2 | 0.9353 | 100 | 0.182 | Contact Map |
| 4y8wA | 3 | 0.9246 | 100 | 0.182 | Contact Map |
| 2ve3A | 2 | 0.9224 | 100 | 0.182 | Contact Map |
| 3pm0A | 1 | 0.9224 | 100 | 0.186 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)