| BMSP |
| ID: | 1515265724 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 574 (548) | ||
| Sequences: | 5552 (3788.7) | ||
| Seq/Len: | 10.131 | ||
| Nf(neff/√len): | 161.8 |
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: 10.131).
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 |
| 321_M | 524_S | 4.706 | 1.00 |
| 16_N | 167_D | 4.675 | 1.00 |
| 114_G | 125_I | 4.294 | 1.00 |
| 263_Q | 339_K | 3.911 | 1.00 |
| 105_R | 112_E | 3.898 | 1.00 |
| 113_I | 130_L | 3.880 | 1.00 |
| 209_T | 254_S | 3.685 | 1.00 |
| 20_N | 56_R | 3.682 | 1.00 |
| 92_R | 126_E | 3.640 | 1.00 |
| 308_A | 339_K | 3.640 | 1.00 |
| 82_H | 135_E | 3.404 | 1.00 |
| 109_N | 136_N | 3.384 | 1.00 |
| 97_F | 140_I | 3.254 | 1.00 |
| 239_E | 247_K | 3.224 | 1.00 |
| 100_V | 164_I | 3.166 | 1.00 |
| 211_S | 254_S | 3.081 | 1.00 |
| 212_I | 264_I | 3.068 | 1.00 |
| 91_K | 172_T | 2.986 | 1.00 |
| 108_L | 113_I | 2.949 | 1.00 |
| 213_P | 252_I | 2.888 | 1.00 |
| 108_L | 138_I | 2.848 | 1.00 |
| 239_E | 245_N | 2.828 | 1.00 |
| 304_E | 332_Y | 2.823 | 1.00 |
| 384_Y | 445_V | 2.755 | 1.00 |
| 100_V | 104_C | 2.633 | 1.00 |
| 374_K | 411_L | 2.605 | 1.00 |
| 80_A | 137_F | 2.534 | 1.00 |
| 254_S | 259_R | 2.522 | 1.00 |
| 242_S | 245_N | 2.509 | 1.00 |
| 93_Q | 131_L | 2.431 | 1.00 |
| 373_I | 408_G | 2.431 | 1.00 |
| 242_S | 281_K | 2.415 | 1.00 |
| 210_V | 253_V | 2.397 | 1.00 |
| 91_K | 174_P | 2.356 | 1.00 |
| 211_S | 252_I | 2.353 | 1.00 |
| 100_V | 142_V | 2.310 | 1.00 |
| 243_S | 343_I | 2.273 | 1.00 |
| 182_F | 377_Q | 2.266 | 1.00 |
| 312_N | 316_A | 2.260 | 1.00 |
| 215_L | 247_K | 2.247 | 1.00 |
| 18_K | 56_R | 2.222 | 1.00 |
| 97_F | 100_V | 2.217 | 1.00 |
| 308_A | 312_N | 2.199 | 1.00 |
| 235_I | 266_F | 2.198 | 1.00 |
| 405_L | 409_K | 2.185 | 1.00 |
| 370_S | 407_T | 2.180 | 1.00 |
| 187_K | 240_R | 2.179 | 1.00 |
| 122_P | 375_R | 2.147 | 1.00 |
| 366_Q | 403_S | 2.121 | 1.00 |
| 93_Q | 172_T | 2.119 | 1.00 |
| 322_I | 342_F | 2.114 | 1.00 |
| 178_L | 197_V | 2.095 | 1.00 |
| 407_T | 411_L | 2.085 | 1.00 |
| 409_K | 417_Y | 2.081 | 1.00 |
| 271_V | 416_L | 2.056 | 1.00 |
| 285_M | 383_G | 2.049 | 1.00 |
| 250_E | 263_Q | 2.034 | 1.00 |
| 108_L | 127_V | 2.033 | 1.00 |
| 369_L | 408_G | 2.032 | 1.00 |
| 105_R | 115_S | 2.018 | 1.00 |
| 250_E | 261_E | 1.982 | 1.00 |
| 61_G | 66_Q | 1.982 | 1.00 |
| 95_L | 106_V | 1.956 | 1.00 |
| 15_L | 83_F | 1.956 | 1.00 |
| 412_D | 415_R | 1.945 | 1.00 |
| 252_I | 259_R | 1.936 | 1.00 |
| 251_V | 264_I | 1.935 | 1.00 |
| 94_F | 126_E | 1.935 | 1.00 |
| 317_L | 560_A | 1.929 | 1.00 |
| 374_K | 377_Q | 1.925 | 1.00 |
| 311_L | 342_F | 1.923 | 1.00 |
| 278_L | 343_I | 1.913 | 1.00 |
| 402_T | 406_E | 1.913 | 1.00 |
| 278_L | 283_T | 1.895 | 1.00 |
| 111_A | 130_L | 1.891 | 1.00 |
| 272_K | 277_Y | 1.881 | 1.00 |
| 210_V | 251_V | 1.867 | 1.00 |
| 92_R | 175_Q | 1.860 | 1.00 |
| 338_E | 379_R | 1.848 | 1.00 |
| 20_N | 80_A | 1.846 | 1.00 |
| 105_R | 141_E | 1.822 | 1.00 |
| 84_D | 135_E | 1.818 | 1.00 |
| 465_A | 517_I | 1.799 | 1.00 |
| 296_Q | 534_P | 1.793 | 1.00 |
| 80_A | 139_A | 1.784 | 1.00 |
| 252_I | 261_E | 1.781 | 1.00 |
| 98_G | 169_L | 1.776 | 1.00 |
| 337_A | 344_L | 1.760 | 1.00 |
| 186_D | 268_N | 1.754 | 1.00 |
| 276_I | 383_G | 1.753 | 1.00 |
| 235_I | 238_L | 1.749 | 1.00 |
| 78_W | 141_E | 1.745 | 1.00 |
| 12_I | 169_L | 1.743 | 1.00 |
| 82_H | 137_F | 1.732 | 1.00 |
| 181_Y | 253_V | 1.727 | 1.00 |
| 310_L | 555_G | 1.716 | 1.00 |
| 311_L | 340_M | 1.704 | 1.00 |
| 95_L | 127_V | 1.677 | 1.00 |
| 85_A | 131_L | 1.670 | 1.00 |
| 14_S | 167_D | 1.636 | 1.00 |
| 366_Q | 407_T | 1.636 | 1.00 |
| 51_F | 80_A | 1.630 | 1.00 |
| 269_I | 276_I | 1.628 | 1.00 |
| 63_W | 77_V | 1.619 | 1.00 |
| 76_T | 141_E | 1.619 | 1.00 |
| 94_F | 173_T | 1.615 | 1.00 |
| 322_I | 333_T | 1.604 | 1.00 |
| 186_D | 194_I | 1.600 | 1.00 |
| 194_I | 232_V | 1.588 | 1.00 |
| 55_L | 66_Q | 1.577 | 1.00 |
| 406_E | 410_Q | 1.563 | 1.00 |
| 294_I | 306_D | 1.543 | 1.00 |
| 213_P | 221_M | 1.538 | 1.00 |
| 346_Q | 372_M | 1.537 | 1.00 |
| 244_E | 315_K | 1.537 | 1.00 |
| 298_M | 303_S | 1.536 | 1.00 |
| 370_S | 411_L | 1.530 | 1.00 |
| 196_K | 230_E | 1.528 | 1.00 |
| 346_Q | 376_D | 1.516 | 1.00 |
| 527_I | 531_F | 1.514 | 1.00 |
| 176_T | 205_G | 1.509 | 1.00 |
| 309_M | 312_N | 1.506 | 1.00 |
| 112_E | 115_S | 1.505 | 1.00 |
| 244_E | 281_K | 1.498 | 1.00 |
| 212_I | 251_V | 1.495 | 1.00 |
| 405_L | 417_Y | 1.480 | 1.00 |
| 268_N | 280_G | 1.470 | 1.00 |
| 270_T | 277_Y | 1.467 | 1.00 |
| 243_S | 283_T | 1.466 | 1.00 |
| 183_I | 262_E | 1.464 | 1.00 |
| 96_Y | 124_Q | 1.459 | 1.00 |
| 303_S | 306_D | 1.457 | 1.00 |
| 180_D | 377_Q | 1.455 | 1.00 |
| 369_L | 404_L | 1.452 | 1.00 |
| 179_E | 200_S | 1.451 | 1.00 |
| 33_K | 36_R | 1.445 | 1.00 |
| 193_M | 264_I | 1.444 | 1.00 |
| 215_L | 219_I | 1.444 | 1.00 |
| 298_M | 301_A | 1.444 | 1.00 |
| 407_T | 410_Q | 1.441 | 1.00 |
| 343_I | 383_G | 1.439 | 1.00 |
| 508_R | 512_R | 1.433 | 1.00 |
| 92_R | 177_Y | 1.432 | 1.00 |
| 78_W | 139_A | 1.429 | 1.00 |
| 263_Q | 335_R | 1.423 | 1.00 |
| 116_H | 123_F | 1.419 | 1.00 |
| 94_F | 124_Q | 1.408 | 1.00 |
| 312_N | 340_M | 1.407 | 0.99 |
| 183_I | 251_V | 1.404 | 0.99 |
| 92_R | 129_D | 1.392 | 0.99 |
| 113_I | 125_I | 1.384 | 0.99 |
| 57_L | 66_Q | 1.377 | 0.99 |
| 179_E | 198_A | 1.376 | 0.99 |
| 64_N | 162_G | 1.372 | 0.99 |
| 20_N | 51_F | 1.367 | 0.99 |
| 556_I | 560_A | 1.363 | 0.99 |
| 96_Y | 169_L | 1.363 | 0.99 |
| 21_A | 77_V | 1.360 | 0.99 |
| 288_I | 319_V | 1.359 | 0.99 |
| 329_Q | 334_V | 1.358 | 0.99 |
| 367_R | 371_E | 1.358 | 0.99 |
| 238_L | 266_F | 1.357 | 0.99 |
| 338_E | 381_A | 1.354 | 0.99 |
| 184_Q | 196_K | 1.347 | 0.99 |
| 178_L | 255_S | 1.341 | 0.99 |
| 191_N | 266_F | 1.340 | 0.99 |
| 244_E | 283_T | 1.331 | 0.99 |
| 314_A | 342_F | 1.330 | 0.99 |
| 274_T | 277_Y | 1.329 | 0.99 |
| 96_Y | 171_V | 1.325 | 0.99 |
| 117_E | 364_K | 1.313 | 0.99 |
| 108_L | 130_L | 1.311 | 0.99 |
| 317_L | 561_W | 1.308 | 0.99 |
| 176_T | 201_D | 1.304 | 0.99 |
| 304_E | 308_A | 1.304 | 0.99 |
| 563_L | 567_Y | 1.303 | 0.99 |
| 15_L | 81_R | 1.300 | 0.99 |
| 183_I | 264_I | 1.293 | 0.99 |
| 178_L | 253_V | 1.287 | 0.99 |
| 94_F | 177_Y | 1.285 | 0.99 |
| 116_H | 371_E | 1.275 | 0.99 |
| 211_S | 221_M | 1.270 | 0.99 |
| 336_L | 340_M | 1.268 | 0.99 |
| 83_F | 138_I | 1.264 | 0.99 |
| 210_V | 231_T | 1.263 | 0.99 |
| 90_H | 175_Q | 1.261 | 0.99 |
| 529_F | 555_G | 1.251 | 0.99 |
| 92_R | 128_T | 1.247 | 0.99 |
| 103_R | 117_E | 1.244 | 0.98 |
| 221_M | 224_D | 1.242 | 0.98 |
| 311_L | 337_A | 1.234 | 0.98 |
| 277_Y | 282_P | 1.231 | 0.98 |
| 298_M | 306_D | 1.227 | 0.98 |
| 214_E | 220_D | 1.222 | 0.98 |
| 333_T | 337_A | 1.217 | 0.98 |
| 185_L | 191_N | 1.217 | 0.98 |
| 107_Y | 112_E | 1.217 | 0.98 |
| 58_N | 61_G | 1.216 | 0.98 |
| 213_P | 250_E | 1.209 | 0.98 |
| 290_F | 329_Q | 1.208 | 0.98 |
| 344_L | 381_A | 1.207 | 0.98 |
| 121_T | 371_E | 1.199 | 0.98 |
| 86_K | 172_T | 1.197 | 0.98 |
| 305_A | 308_A | 1.195 | 0.98 |
| 223_T | 233_F | 1.194 | 0.98 |
| 104_C | 116_H | 1.191 | 0.98 |
| 18_K | 58_N | 1.184 | 0.98 |
| 409_K | 444_D | 1.183 | 0.98 |
| 184_Q | 194_I | 1.182 | 0.98 |
| 527_I | 548_K | 1.172 | 0.98 |
| 314_A | 319_V | 1.169 | 0.97 |
| 214_E | 247_K | 1.162 | 0.97 |
| 399_E | 402_T | 1.162 | 0.97 |
| 58_N | 66_Q | 1.158 | 0.97 |
| 248_L | 263_Q | 1.155 | 0.97 |
| 13_R | 172_T | 1.153 | 0.97 |
| 294_I | 303_S | 1.147 | 0.97 |
| 182_F | 196_K | 1.145 | 0.97 |
| 185_L | 266_F | 1.143 | 0.97 |
| 140_I | 164_I | 1.138 | 0.97 |
| 370_S | 410_Q | 1.132 | 0.97 |
| 366_Q | 370_S | 1.131 | 0.97 |
| 214_E | 239_E | 1.131 | 0.97 |
| 208_I | 253_V | 1.130 | 0.97 |
| 183_I | 195_A | 1.128 | 0.97 |
| 324_L | 329_Q | 1.128 | 0.97 |
| 76_T | 143_N | 1.127 | 0.97 |
| 106_V | 140_I | 1.113 | 0.96 |
| 10_R | 258_D | 1.110 | 0.96 |
| 197_V | 231_T | 1.103 | 0.96 |
| 83_F | 136_N | 1.102 | 0.96 |
| 561_W | 564_M | 1.100 | 0.96 |
| 334_V | 344_L | 1.100 | 0.96 |
| 215_L | 239_E | 1.099 | 0.96 |
| 127_V | 131_L | 1.097 | 0.96 |
| 315_K | 340_M | 1.092 | 0.96 |
| 190_P | 240_R | 1.089 | 0.96 |
| 305_A | 312_N | 1.088 | 0.96 |
| 283_T | 343_I | 1.087 | 0.96 |
| 336_L | 339_K | 1.087 | 0.96 |
| 468_E | 519_N | 1.085 | 0.96 |
| 302_F | 307_A | 1.083 | 0.96 |
| 307_A | 333_T | 1.078 | 0.95 |
| 92_R | 173_T | 1.074 | 0.95 |
| 116_H | 121_T | 1.073 | 0.95 |
| 373_I | 411_L | 1.072 | 0.95 |
| 290_F | 310_L | 1.068 | 0.95 |
| 24_D | 78_W | 1.068 | 0.95 |
| 362_R | 403_S | 1.067 | 0.95 |
| 476_I | 521_R | 1.066 | 0.95 |
| 253_V | 262_E | 1.066 | 0.95 |
| 270_T | 280_G | 1.065 | 0.95 |
| 356_F | 365_A | 1.065 | 0.95 |
| 348_I | 372_M | 1.063 | 0.95 |
| 194_I | 230_E | 1.063 | 0.95 |
| 308_A | 340_M | 1.057 | 0.95 |
| 195_A | 210_V | 1.056 | 0.95 |
| 193_M | 266_F | 1.056 | 0.95 |
| 531_F | 548_K | 1.053 | 0.95 |
| 387_I | 408_G | 1.051 | 0.94 |
| 308_A | 336_L | 1.048 | 0.94 |
| 86_K | 93_Q | 1.046 | 0.94 |
| 243_S | 278_L | 1.045 | 0.94 |
| 314_A | 551_V | 1.045 | 0.94 |
| 370_S | 374_K | 1.042 | 0.94 |
| 314_A | 528_L | 1.042 | 0.94 |
| 311_L | 333_T | 1.033 | 0.94 |
| 565_R | 568_Y | 1.031 | 0.94 |
| 418_V | 447_A | 1.030 | 0.94 |
| 525_P | 563_L | 1.030 | 0.94 |
| 489_S | 501_E | 1.021 | 0.93 |
| 275_D | 282_P | 1.020 | 0.93 |
| 372_M | 382_V | 1.019 | 0.93 |
| 104_C | 140_I | 1.018 | 0.93 |
| 77_V | 162_G | 1.017 | 0.93 |
| 13_R | 86_K | 1.017 | 0.93 |
| 334_V | 376_D | 1.015 | 0.93 |
| 304_E | 336_L | 1.015 | 0.93 |
| 103_R | 115_S | 1.015 | 0.93 |
| 173_T | 258_D | 1.012 | 0.93 |
| 345_W | 384_Y | 1.007 | 0.93 |
| 14_S | 169_L | 1.003 | 0.93 |
| 192_R | 232_V | 1.001 | 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 | |
| 1jz7A | 4 | 0.9042 | 100 | 0.254 | Contact Map |
| 1yq2A | 6 | 0.9059 | 100 | 0.264 | Contact Map |
| 3fn9A | 4 | 0.9338 | 100 | 0.269 | Contact Map |
| 3bgaA | 2 | 0.8937 | 100 | 0.269 | Contact Map |
| 3cmgA | 1 | 0.9164 | 100 | 0.271 | Contact Map |
| 3obaA | 4 | 0.8972 | 100 | 0.273 | Contact Map |
| 3gm8A | 1 | 0.8902 | 100 | 0.275 | Contact Map |
| 4ypjA | 2 | 0 | 100 | 0.278 | Contact Map |
| 4cu7A | 1 | 0.9355 | 100 | 0.3 | Contact Map |
| 3hn3A | 4 | 0.9495 | 100 | 0.3 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)