| 2wsw |
| ID: | 1380612111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 500 (495) | ||
| Sequences: | 1501 (1063.9) | ||
| Seq/Len: | 3.032 | ||
| Nf(neff/√len): | 47.8 |
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: 3.032).
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 |
| 59_A | 489_F | 3.401 | 1.00 |
| 202_L | 439_T | 3.285 | 1.00 |
| 87_E | 345_K | 3.119 | 1.00 |
| 83_R | 88_K | 3.092 | 1.00 |
| 277_W | 412_T | 2.912 | 1.00 |
| 180_L | 197_V | 2.824 | 1.00 |
| 442_S | 445_E | 2.793 | 1.00 |
| 277_W | 281_V | 2.778 | 1.00 |
| 238_A | 466_I | 2.575 | 1.00 |
| 91_F | 257_Q | 2.540 | 1.00 |
| 379_I | 385_N | 2.303 | 1.00 |
| 32_W | 36_R | 2.253 | 1.00 |
| 22_P | 199_N | 2.234 | 1.00 |
| 374_N | 406_L | 2.226 | 1.00 |
| 24_L | 456_G | 2.208 | 1.00 |
| 428_I | 461_V | 2.207 | 1.00 |
| 52_V | 486_C | 2.197 | 1.00 |
| 221_T | 236_L | 2.175 | 1.00 |
| 235_Q | 239_I | 2.151 | 1.00 |
| 37_D | 40_A | 2.105 | 1.00 |
| 70_G | 496_T | 2.098 | 1.00 |
| 245_I | 462_G | 2.037 | 1.00 |
| 250_I | 254_F | 2.028 | 1.00 |
| 279_F | 370_I | 1.976 | 1.00 |
| 67_M | 492_N | 1.970 | 1.00 |
| 132_S | 135_A | 1.964 | 1.00 |
| 291_F | 369_T | 1.945 | 1.00 |
| 191_G | 194_G | 1.942 | 1.00 |
| 254_F | 262_I | 1.940 | 1.00 |
| 75_V | 354_L | 1.923 | 0.99 |
| 33_L | 40_A | 1.914 | 0.99 |
| 251_C | 429_N | 1.898 | 0.99 |
| 95_S | 265_D | 1.892 | 0.99 |
| 66_I | 493_I | 1.891 | 0.99 |
| 426_T | 430_A | 1.851 | 0.99 |
| 77_G | 80_A | 1.832 | 0.99 |
| 278_V | 406_L | 1.830 | 0.99 |
| 331_I | 481_I | 1.822 | 0.99 |
| 279_F | 288_V | 1.821 | 0.99 |
| 275_L | 370_I | 1.812 | 0.99 |
| 63_Y | 67_M | 1.807 | 0.99 |
| 72_F | 76_F | 1.799 | 0.99 |
| 75_V | 353_C | 1.794 | 0.99 |
| 177_S | 195_T | 1.787 | 0.99 |
| 242_S | 466_I | 1.774 | 0.99 |
| 490_F | 494_M | 1.767 | 0.99 |
| 63_Y | 489_F | 1.764 | 0.99 |
| 221_T | 232_H | 1.760 | 0.99 |
| 144_L | 365_W | 1.752 | 0.99 |
| 271_S | 423_A | 1.745 | 0.99 |
| 432_S | 458_S | 1.740 | 0.99 |
| 233_T | 236_L | 1.721 | 0.99 |
| 118_Y | 379_I | 1.716 | 0.99 |
| 290_Y | 373_G | 1.711 | 0.98 |
| 64_M | 154_T | 1.710 | 0.98 |
| 221_T | 240_I | 1.685 | 0.98 |
| 118_Y | 386_I | 1.683 | 0.98 |
| 70_G | 500_I | 1.658 | 0.98 |
| 87_E | 168_V | 1.644 | 0.98 |
| 428_I | 432_S | 1.638 | 0.98 |
| 151_P | 329_W | 1.632 | 0.98 |
| 249_A | 253_A | 1.625 | 0.98 |
| 253_A | 455_I | 1.621 | 0.98 |
| 148_G | 361_T | 1.619 | 0.98 |
| 184_V | 193_F | 1.616 | 0.98 |
| 349_V | 503_A | 1.605 | 0.97 |
| 92_S | 95_S | 1.600 | 0.97 |
| 468_L | 480_A | 1.593 | 0.97 |
| 421_F | 425_V | 1.584 | 0.97 |
| 249_A | 458_S | 1.567 | 0.97 |
| 78_R | 81_K | 1.565 | 0.97 |
| 436_A | 453_V | 1.564 | 0.97 |
| 48_V | 483_A | 1.556 | 0.97 |
| 83_R | 86_D | 1.556 | 0.97 |
| 221_T | 237_D | 1.553 | 0.97 |
| 65_V | 307_F | 1.549 | 0.97 |
| 129_E | 132_S | 1.518 | 0.96 |
| 112_W | 115_I | 1.513 | 0.96 |
| 377_Q | 381_Q | 1.507 | 0.96 |
| 68_F | 72_F | 1.496 | 0.96 |
| 155_Y | 329_W | 1.496 | 0.96 |
| 269_Y | 273_L | 1.487 | 0.95 |
| 30_L | 207_L | 1.483 | 0.95 |
| 48_V | 51_Y | 1.475 | 0.95 |
| 90_E | 345_K | 1.468 | 0.95 |
| 121_I | 380_D | 1.461 | 0.95 |
| 217_T | 240_I | 1.455 | 0.95 |
| 98_F | 102_A | 1.452 | 0.95 |
| 401_E | 404_A | 1.449 | 0.95 |
| 230_I | 236_L | 1.448 | 0.95 |
| 105_T | 151_P | 1.446 | 0.95 |
| 215_L | 324_F | 1.445 | 0.94 |
| 403_W | 416_F | 1.439 | 0.94 |
| 102_A | 422_I | 1.436 | 0.94 |
| 121_I | 131_Y | 1.433 | 0.94 |
| 91_F | 342_R | 1.428 | 0.94 |
| 73_W | 500_I | 1.425 | 0.94 |
| 200_F | 491_V | 1.422 | 0.94 |
| 33_L | 41_S | 1.420 | 0.94 |
| 225_Q | 231_P | 1.407 | 0.93 |
| 161_A | 495_V | 1.403 | 0.93 |
| 263_A | 429_N | 1.400 | 0.93 |
| 74_L | 349_V | 1.394 | 0.93 |
| 158_L | 495_V | 1.394 | 0.93 |
| 193_F | 196_V | 1.393 | 0.93 |
| 291_F | 366_L | 1.384 | 0.93 |
| 239_I | 243_C | 1.372 | 0.92 |
| 231_P | 236_L | 1.371 | 0.92 |
| 177_S | 248_N | 1.367 | 0.92 |
| 292_T | 296_G | 1.366 | 0.92 |
| 35_V | 467_I | 1.350 | 0.91 |
| 93_T | 351_E | 1.343 | 0.91 |
| 192_L | 196_V | 1.343 | 0.91 |
| 245_I | 248_N | 1.328 | 0.91 |
| 141_A | 301_Y | 1.312 | 0.90 |
| 403_W | 412_T | 1.306 | 0.90 |
| 411_A | 414_W | 1.301 | 0.89 |
| 185_G | 191_G | 1.298 | 0.89 |
| 179_T | 495_V | 1.294 | 0.89 |
| 294_S | 369_T | 1.292 | 0.89 |
| 486_C | 490_F | 1.289 | 0.89 |
| 432_S | 461_V | 1.285 | 0.88 |
| 427_L | 430_A | 1.272 | 0.88 |
| 200_F | 484_G | 1.271 | 0.88 |
| 80_A | 350_R | 1.269 | 0.88 |
| 82_K | 503_A | 1.265 | 0.87 |
| 60_F | 327_A | 1.263 | 0.87 |
| 223_C | 400_I | 1.253 | 0.87 |
| 459_V | 463_I | 1.252 | 0.87 |
| 181_V | 190_N | 1.250 | 0.87 |
| 76_F | 354_L | 1.249 | 0.87 |
| 182_P | 185_G | 1.236 | 0.86 |
| 160_V | 349_V | 1.232 | 0.86 |
| 77_G | 82_K | 1.227 | 0.85 |
| 76_F | 350_R | 1.223 | 0.85 |
| 41_S | 45_I | 1.222 | 0.85 |
| 183_L | 497_L | 1.217 | 0.85 |
| 184_V | 498_S | 1.214 | 0.84 |
| 110_L | 420_C | 1.214 | 0.84 |
| 143_S | 368_W | 1.214 | 0.84 |
| 252_V | 458_S | 1.212 | 0.84 |
| 316_G | 320_A | 1.209 | 0.84 |
| 475_K | 478_Q | 1.207 | 0.84 |
| 171_M | 181_V | 1.202 | 0.84 |
| 225_Q | 232_H | 1.201 | 0.83 |
| 455_I | 459_V | 1.199 | 0.83 |
| 174_I | 177_S | 1.192 | 0.83 |
| 165_F | 502_D | 1.192 | 0.83 |
| 300_M | 304_R | 1.188 | 0.83 |
| 168_V | 171_M | 1.185 | 0.82 |
| 112_W | 395_V | 1.183 | 0.82 |
| 184_V | 189_V | 1.182 | 0.82 |
| 221_T | 233_T | 1.182 | 0.82 |
| 248_N | 458_S | 1.177 | 0.82 |
| 66_I | 496_T | 1.177 | 0.82 |
| 51_Y | 55_V | 1.175 | 0.82 |
| 379_I | 384_L | 1.172 | 0.81 |
| 221_T | 231_P | 1.169 | 0.81 |
| 18_K | 22_P | 1.158 | 0.80 |
| 212_S | 216_A | 1.155 | 0.80 |
| 181_V | 189_V | 1.154 | 0.80 |
| 258_K | 262_I | 1.153 | 0.80 |
| 83_R | 348_T | 1.148 | 0.80 |
| 252_V | 256_L | 1.144 | 0.79 |
| 65_V | 306_L | 1.144 | 0.79 |
| 224_I | 228_F | 1.143 | 0.79 |
| 59_A | 63_Y | 1.136 | 0.79 |
| 44_V | 48_V | 1.129 | 0.78 |
| 279_F | 284_A | 1.126 | 0.78 |
| 43_E | 47_A | 1.125 | 0.78 |
| 177_S | 431_C | 1.125 | 0.78 |
| 291_F | 365_W | 1.122 | 0.77 |
| 236_L | 239_I | 1.121 | 0.77 |
| 62_W | 292_T | 1.117 | 0.77 |
| 43_E | 134_P | 1.115 | 0.77 |
| 68_F | 153_A | 1.113 | 0.77 |
| 18_K | 195_T | 1.113 | 0.77 |
| 67_M | 496_T | 1.112 | 0.76 |
| 246_L | 250_I | 1.112 | 0.76 |
| 95_S | 261_K | 1.111 | 0.76 |
| 33_L | 37_D | 1.110 | 0.76 |
| 79_Y | 504_K | 1.110 | 0.76 |
| 34_T | 41_S | 1.109 | 0.76 |
| 266_V | 269_Y | 1.108 | 0.76 |
| 249_A | 455_I | 1.099 | 0.75 |
| 369_T | 374_N | 1.095 | 0.75 |
| 21_F | 25_I | 1.095 | 0.75 |
| 91_F | 99_M | 1.094 | 0.75 |
| 263_A | 422_I | 1.093 | 0.75 |
| 283_G | 287_I | 1.091 | 0.74 |
| 159_S | 164_Y | 1.089 | 0.74 |
| 50_S | 54_N | 1.088 | 0.74 |
| 503_A | 506_H | 1.087 | 0.74 |
| 149_P | 357_V | 1.087 | 0.74 |
| 461_V | 465_G | 1.086 | 0.74 |
| 409_S | 413_M | 1.083 | 0.74 |
| 131_Y | 135_A | 1.079 | 0.73 |
| 338_I | 437_M | 1.079 | 0.73 |
| 40_A | 44_V | 1.076 | 0.73 |
| 333_A | 492_N | 1.075 | 0.73 |
| 142_Y | 305_M | 1.071 | 0.73 |
| 262_I | 266_V | 1.070 | 0.72 |
| 136_K | 380_D | 1.057 | 0.71 |
| 332_Y | 427_L | 1.055 | 0.71 |
| 43_E | 233_T | 1.047 | 0.70 |
| 382_N | 386_I | 1.044 | 0.70 |
| 343_I | 495_V | 1.043 | 0.70 |
| 185_G | 194_G | 1.040 | 0.69 |
| 423_A | 427_L | 1.039 | 0.69 |
| 156_S | 356_M | 1.036 | 0.69 |
| 260_V | 430_A | 1.034 | 0.69 |
| 61_E | 318_P | 1.034 | 0.69 |
| 105_T | 109_V | 1.033 | 0.69 |
| 378_L | 405_A | 1.032 | 0.69 |
| 261_K | 265_D | 1.031 | 0.68 |
| 234_L | 238_A | 1.031 | 0.68 |
| 57_G | 124_P | 1.030 | 0.68 |
| 399_I | 416_F | 1.025 | 0.68 |
| 253_A | 451_L | 1.024 | 0.68 |
| 243_C | 247_L | 1.023 | 0.68 |
| 107_A | 216_A | 1.019 | 0.67 |
| 94_A | 98_F | 1.018 | 0.67 |
| 128_M | 132_S | 1.017 | 0.67 |
| 115_I | 317_F | 1.016 | 0.67 |
| 322_T | 326_W | 1.016 | 0.67 |
| 234_L | 470_A | 1.014 | 0.67 |
| 186_E | 190_N | 1.012 | 0.66 |
| 105_T | 364_T | 1.012 | 0.66 |
| 58_W | 62_W | 1.010 | 0.66 |
| 245_I | 424_T | 1.009 | 0.66 |
| 414_W | 418_I | 1.006 | 0.66 |
| 406_L | 411_A | 1.005 | 0.66 |
| 266_V | 422_I | 1.005 | 0.66 |
| 114_S | 118_Y | 1.004 | 0.65 |
| 428_I | 458_S | 1.004 | 0.65 |
| 134_P | 138_I | 1.002 | 0.65 |
| 283_G | 377_Q | 1.002 | 0.65 |
| 69_G | 73_W | 1.001 | 0.65 |
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 | |
| 2wswA | 1 | 0.998 | 100 | 0.025 | Contact Map |
| 4c7rA | 3 | 0.9548 | 100 | 0.08 | Contact Map |
| 2xq2A | 1 | 0.7525 | 97.3 | 0.956 | Contact Map |
| 3dh4A | 4 | 0.725 | 96.5 | 0.961 | Contact Map |
| 3giaA | 1 | 0.6699 | 95.1 | 0.965 | Contact Map |
| 2jlnA | 1 | 0.7289 | 94.8 | 0.966 | Contact Map |
| 3l1lA | 1 | 0.6719 | 91.7 | 0.969 | Contact Map |
| 4djkA | 2 | 0.664 | 81.7 | 0.974 | Contact Map |
| 4m48A | 1 | 0.3183 | 15.7 | 0.984 | Contact Map |
| 1q90L | 1 | 0.0629 | 11.6 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)