| NmeIPMS_Coevolution |
| ID: | 1483938089 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 517 (515) | ||
| Sequences: | 1601 (728.1) | ||
| Seq/Len: | 3.109 | ||
| Nf(neff/√len): | 32.1 |
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: 3.109).
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 |
| 50_A | 74_S | 5.652 | 1.00 |
| 84_R | 130_I | 4.027 | 1.00 |
| 317_S | 320_S | 3.992 | 1.00 |
| 183_E | 222_G | 3.980 | 1.00 |
| 112_K | 143_E | 3.512 | 1.00 |
| 304_D | 308_K | 3.484 | 1.00 |
| 195_N | 199_V | 3.381 | 1.00 |
| 109_M | 117_P | 3.295 | 1.00 |
| 339_F | 359_A | 3.221 | 1.00 |
| 106_P | 117_P | 3.164 | 1.00 |
| 8_I | 44_I | 2.964 | 1.00 |
| 115_M | 123_A | 2.920 | 1.00 |
| 187_R | 191_V | 2.889 | 1.00 |
| 435_I | 492_A | 2.877 | 1.00 |
| 5_N | 225_R | 2.862 | 1.00 |
| 264_D | 267_Q | 2.860 | 1.00 |
| 452_Y | 491_T | 2.768 | 1.00 |
| 25_M | 278_I | 2.717 | 1.00 |
| 124_A | 160_V | 2.624 | 1.00 |
| 61_N | 65_K | 2.600 | 1.00 |
| 343_L | 382_V | 2.592 | 1.00 |
| 109_M | 152_F | 2.558 | 1.00 |
| 38_E | 69_K | 2.481 | 1.00 |
| 38_E | 70_S | 2.439 | 1.00 |
| 33_V | 275_V | 2.433 | 1.00 |
| 6_R | 262_G | 2.425 | 1.00 |
| 65_K | 92_P | 2.398 | 1.00 |
| 196_G | 201_W | 2.352 | 1.00 |
| 157_C | 168_I | 2.337 | 1.00 |
| 146_L | 177_S | 2.325 | 1.00 |
| 188_E | 192_K | 2.306 | 1.00 |
| 61_N | 92_P | 2.286 | 1.00 |
| 80_E | 126_K | 2.279 | 1.00 |
| 130_I | 134_Y | 2.224 | 1.00 |
| 103_A | 143_E | 2.206 | 1.00 |
| 125_V | 160_V | 2.206 | 1.00 |
| 84_R | 134_Y | 2.194 | 1.00 |
| 157_C | 170_I | 2.192 | 1.00 |
| 118_K | 121_I | 2.174 | 1.00 |
| 103_A | 112_K | 2.168 | 1.00 |
| 360_F | 364_K | 2.163 | 1.00 |
| 306_V | 326_N | 2.149 | 1.00 |
| 106_P | 109_M | 2.139 | 1.00 |
| 150_I | 188_E | 2.138 | 1.00 |
| 142_C | 157_C | 2.111 | 1.00 |
| 50_A | 60_V | 2.101 | 1.00 |
| 71_T | 95_K | 2.098 | 1.00 |
| 158_G | 195_N | 2.094 | 1.00 |
| 25_M | 33_V | 2.094 | 1.00 |
| 125_V | 159_A | 2.078 | 1.00 |
| 151_D | 154_A | 2.075 | 1.00 |
| 124_A | 156_I | 2.070 | 1.00 |
| 426_A | 441_S | 2.061 | 1.00 |
| 429_S | 485_T | 2.051 | 1.00 |
| 51_A | 85_Q | 2.032 | 1.00 |
| 154_A | 189_L | 2.029 | 1.00 |
| 80_E | 130_I | 2.006 | 1.00 |
| 106_P | 149_E | 1.992 | 1.00 |
| 186_F | 203_A | 1.967 | 1.00 |
| 31_I | 63_I | 1.964 | 1.00 |
| 122_E | 126_K | 1.947 | 1.00 |
| 109_M | 120_V | 1.926 | 1.00 |
| 154_A | 188_E | 1.923 | 0.99 |
| 160_V | 168_I | 1.923 | 0.99 |
| 154_A | 192_K | 1.914 | 0.99 |
| 484_D | 489_V | 1.906 | 0.99 |
| 125_V | 129_K | 1.887 | 0.99 |
| 60_V | 74_S | 1.870 | 0.99 |
| 435_I | 488_L | 1.868 | 0.99 |
| 74_S | 86_A | 1.856 | 0.99 |
| 269_V | 323_W | 1.825 | 0.99 |
| 8_I | 167_T | 1.818 | 0.99 |
| 78_A | 100_T | 1.806 | 0.99 |
| 170_I | 189_L | 1.774 | 0.99 |
| 150_I | 185_F | 1.742 | 0.99 |
| 298_E | 333_L | 1.737 | 0.99 |
| 8_I | 200_V | 1.729 | 0.99 |
| 78_A | 127_A | 1.727 | 0.99 |
| 180_Y | 221_K | 1.721 | 0.99 |
| 119_Q | 122_E | 1.711 | 0.99 |
| 23_A | 275_V | 1.706 | 0.99 |
| 124_A | 159_A | 1.684 | 0.98 |
| 80_E | 84_R | 1.678 | 0.98 |
| 125_V | 163_A | 1.673 | 0.98 |
| 85_Q | 88_E | 1.671 | 0.98 |
| 351_E | 355_A | 1.664 | 0.98 |
| 109_M | 148_S | 1.663 | 0.98 |
| 241_A | 246_I | 1.630 | 0.98 |
| 359_A | 381_L | 1.626 | 0.98 |
| 23_A | 33_V | 1.618 | 0.98 |
| 337_N | 341_T | 1.598 | 0.97 |
| 187_R | 222_G | 1.596 | 0.97 |
| 410_R | 427_T | 1.596 | 0.97 |
| 361_A | 365_E | 1.585 | 0.97 |
| 340_K | 353_E | 1.582 | 0.97 |
| 23_A | 281_Y | 1.579 | 0.97 |
| 234_L | 275_V | 1.565 | 0.97 |
| 220_L | 227_V | 1.555 | 0.97 |
| 333_L | 371_R | 1.552 | 0.97 |
| 54_P | 85_Q | 1.549 | 0.97 |
| 339_F | 378_L | 1.541 | 0.97 |
| 341_T | 345_D | 1.539 | 0.97 |
| 109_M | 149_E | 1.539 | 0.97 |
| 397_I | 416_S | 1.530 | 0.96 |
| 452_Y | 487_V | 1.525 | 0.96 |
| 329_S | 333_L | 1.523 | 0.96 |
| 170_I | 185_F | 1.515 | 0.96 |
| 341_T | 344_A | 1.515 | 0.96 |
| 207_N | 284_Q | 1.510 | 0.96 |
| 148_S | 157_C | 1.510 | 0.96 |
| 115_M | 119_Q | 1.510 | 0.96 |
| 90_V | 96_K | 1.503 | 0.96 |
| 113_L | 143_E | 1.500 | 0.96 |
| 395_K | 416_S | 1.497 | 0.96 |
| 57_F | 85_Q | 1.492 | 0.96 |
| 71_T | 137_D | 1.491 | 0.96 |
| 216_S | 229_C | 1.488 | 0.96 |
| 104_T | 156_I | 1.487 | 0.96 |
| 200_V | 225_R | 1.482 | 0.96 |
| 450_Q | 472_A | 1.478 | 0.95 |
| 51_A | 81_R | 1.477 | 0.95 |
| 116_K | 119_Q | 1.472 | 0.95 |
| 298_E | 331_G | 1.467 | 0.95 |
| 190_I | 201_W | 1.465 | 0.95 |
| 439_I | 492_A | 1.440 | 0.95 |
| 33_V | 278_I | 1.438 | 0.95 |
| 213_V | 246_I | 1.426 | 0.94 |
| 393_S | 418_K | 1.418 | 0.94 |
| 87_G | 96_K | 1.402 | 0.94 |
| 159_A | 162_E | 1.384 | 0.93 |
| 7_V | 225_R | 1.384 | 0.93 |
| 396_F | 496_L | 1.382 | 0.93 |
| 36_Q | 267_Q | 1.380 | 0.93 |
| 178_I | 257_F | 1.372 | 0.93 |
| 344_A | 349_E | 1.368 | 0.92 |
| 117_P | 152_F | 1.366 | 0.92 |
| 414_V | 423_R | 1.351 | 0.92 |
| 25_M | 275_V | 1.343 | 0.91 |
| 35_R | 66_T | 1.338 | 0.91 |
| 62_A | 66_T | 1.334 | 0.91 |
| 186_F | 201_W | 1.332 | 0.91 |
| 7_V | 250_L | 1.330 | 0.91 |
| 465_G | 487_V | 1.328 | 0.91 |
| 95_K | 137_D | 1.315 | 0.90 |
| 117_P | 149_E | 1.312 | 0.90 |
| 213_V | 241_A | 1.307 | 0.90 |
| 87_G | 135_T | 1.303 | 0.90 |
| 275_V | 278_I | 1.293 | 0.89 |
| 266_T | 320_S | 1.290 | 0.89 |
| 227_V | 246_I | 1.286 | 0.89 |
| 251_K | 320_S | 1.284 | 0.89 |
| 36_Q | 271_S | 1.275 | 0.88 |
| 54_P | 365_E | 1.272 | 0.88 |
| 118_K | 155_E | 1.270 | 0.88 |
| 142_C | 153_L | 1.270 | 0.88 |
| 343_L | 378_L | 1.267 | 0.88 |
| 111_Y | 309_H | 1.266 | 0.88 |
| 168_I | 195_N | 1.266 | 0.88 |
| 100_T | 138_V | 1.265 | 0.88 |
| 103_A | 148_S | 1.265 | 0.88 |
| 92_P | 96_K | 1.260 | 0.88 |
| 207_N | 211_L | 1.260 | 0.88 |
| 137_D | 167_T | 1.255 | 0.87 |
| 84_R | 87_G | 1.248 | 0.87 |
| 428_G | 438_A | 1.246 | 0.87 |
| 117_P | 155_E | 1.244 | 0.87 |
| 88_E | 91_A | 1.243 | 0.87 |
| 95_K | 136_D | 1.242 | 0.87 |
| 143_E | 313_Y | 1.238 | 0.86 |
| 332_K | 364_K | 1.219 | 0.85 |
| 229_C | 246_I | 1.218 | 0.85 |
| 87_G | 92_P | 1.218 | 0.85 |
| 87_G | 134_Y | 1.215 | 0.85 |
| 102_I | 120_V | 1.215 | 0.85 |
| 472_A | 475_N | 1.201 | 0.84 |
| 130_I | 133_E | 1.200 | 0.84 |
| 392_E | 395_K | 1.196 | 0.84 |
| 182_T | 203_A | 1.194 | 0.84 |
| 180_Y | 184_E | 1.186 | 0.83 |
| 103_A | 113_L | 1.181 | 0.83 |
| 448_T | 472_A | 1.179 | 0.82 |
| 397_I | 414_V | 1.177 | 0.82 |
| 207_N | 212_A | 1.177 | 0.82 |
| 218_A | 221_K | 1.176 | 0.82 |
| 185_F | 189_L | 1.175 | 0.82 |
| 100_T | 128_V | 1.155 | 0.81 |
| 142_C | 170_I | 1.144 | 0.80 |
| 157_C | 193_T | 1.140 | 0.79 |
| 417_I | 442_V | 1.135 | 0.79 |
| 229_C | 247_V | 1.134 | 0.79 |
| 167_T | 200_V | 1.132 | 0.79 |
| 478_V | 502_L | 1.129 | 0.79 |
| 86_A | 90_V | 1.122 | 0.78 |
| 183_E | 187_R | 1.121 | 0.78 |
| 87_G | 91_A | 1.120 | 0.78 |
| 121_I | 155_E | 1.119 | 0.78 |
| 106_P | 110_E | 1.117 | 0.78 |
| 281_Y | 285_P | 1.113 | 0.77 |
| 117_P | 120_V | 1.113 | 0.77 |
| 162_E | 195_N | 1.107 | 0.77 |
| 398_S | 414_V | 1.104 | 0.76 |
| 182_T | 219_A | 1.102 | 0.76 |
| 38_E | 72_V | 1.088 | 0.75 |
| 251_K | 254_H | 1.082 | 0.74 |
| 336_R | 357_N | 1.077 | 0.74 |
| 353_E | 357_N | 1.073 | 0.73 |
| 39_K | 267_Q | 1.072 | 0.73 |
| 117_P | 148_S | 1.065 | 0.73 |
| 122_E | 155_E | 1.063 | 0.72 |
| 5_N | 200_V | 1.063 | 0.72 |
| 436_F | 469_V | 1.058 | 0.72 |
| 178_I | 256_L | 1.057 | 0.72 |
| 216_S | 220_L | 1.053 | 0.71 |
| 182_T | 186_F | 1.051 | 0.71 |
| 216_S | 227_V | 1.051 | 0.71 |
| 158_G | 161_I | 1.051 | 0.71 |
| 41_G | 69_K | 1.048 | 0.71 |
| 183_E | 218_A | 1.044 | 0.71 |
| 31_I | 66_T | 1.044 | 0.71 |
| 154_A | 158_G | 1.040 | 0.70 |
| 447_A | 471_L | 1.039 | 0.70 |
| 378_L | 382_V | 1.038 | 0.70 |
| 408_E | 412_D | 1.036 | 0.70 |
| 218_A | 222_G | 1.033 | 0.69 |
| 400_K | 404_E | 1.033 | 0.69 |
| 132_R | 166_T | 1.028 | 0.69 |
| 150_I | 192_K | 1.025 | 0.68 |
| 471_L | 502_L | 1.023 | 0.68 |
| 110_E | 116_K | 1.022 | 0.68 |
| 376_E | 379_H | 1.018 | 0.68 |
| 70_S | 95_K | 1.015 | 0.67 |
| 96_K | 135_T | 1.014 | 0.67 |
| 33_V | 276_S | 1.013 | 0.67 |
| 177_S | 181_K | 1.012 | 0.67 |
| 351_E | 354_E | 1.011 | 0.67 |
| 102_I | 142_C | 1.009 | 0.67 |
| 20_S | 23_A | 1.008 | 0.67 |
| 342_K | 346_L | 1.004 | 0.66 |
| 129_K | 163_A | 1.004 | 0.66 |
| 191_V | 222_G | 1.002 | 0.66 |
| 55_G | 332_K | 1.000 | 0.66 |
| 109_M | 116_K | 1.000 | 0.66 |
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 | |
| 3hq1A | 2 | 0.9323 | 100 | 0.448 | Contact Map |
| 4ov4A | 1 | 0.7079 | 100 | 0.54 | Contact Map |
| 3rmjA | 2 | 0.5977 | 100 | 0.547 | Contact Map |
| 2ztjA | 1 | 0.5996 | 100 | 0.558 | Contact Map |
| 3ivsA | 2 | 0.6944 | 100 | 0.569 | Contact Map |
| 3eegA | 2 | 0.528 | 100 | 0.645 | Contact Map |
| 3bleA | 1 | 0.5745 | 100 | 0.646 | Contact Map |
| 2qf7A | 2 | 0.8781 | 100 | 0.666 | Contact Map |
| 3ewbX | 1 | 0.5242 | 100 | 0.706 | Contact Map |
| 4qshA | 4 | 0.8646 | 100 | 0.708 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)