| nox |
| ID: | 1444462018 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 564 (510) | ||
| Sequences: | 1649 (983.5) | ||
| Seq/Len: | 3.233 | ||
| Nf(neff/√len): | 43.6 |
HHblits Results: (2015_06)
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: 3.233).
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 |
| 325_I | 353_I | 3.454 | 1.00 |
| 22_N | 63_N | 3.057 | 1.00 |
| 340_F | 362_T | 2.975 | 1.00 |
| 116_I | 182_T | 2.918 | 1.00 |
| 509_M | 512_N | 2.812 | 1.00 |
| 395_Y | 558_Y | 2.811 | 1.00 |
| 117_I | 121_F | 2.437 | 1.00 |
| 310_L | 355_I | 2.434 | 1.00 |
| 113_A | 186_I | 2.408 | 1.00 |
| 407_V | 435_F | 2.384 | 1.00 |
| 24_F | 28_D | 2.381 | 1.00 |
| 307_V | 405_I | 2.289 | 1.00 |
| 212_I | 216_L | 2.227 | 1.00 |
| 510_W | 536_L | 2.216 | 1.00 |
| 355_I | 365_L | 2.156 | 1.00 |
| 438_I | 508_P | 2.122 | 1.00 |
| 274_L | 278_I | 2.102 | 1.00 |
| 188_M | 191_S | 2.099 | 1.00 |
| 53_A | 118_A | 2.093 | 1.00 |
| 112_T | 116_I | 1.981 | 1.00 |
| 18_W | 63_N | 1.959 | 1.00 |
| 56_S | 114_I | 1.930 | 1.00 |
| 403_A | 533_P | 1.901 | 0.99 |
| 109_C | 189_V | 1.771 | 0.99 |
| 185_L | 214_Y | 1.750 | 0.99 |
| 329_C | 361_W | 1.745 | 0.99 |
| 333_S | 336_E | 1.659 | 0.98 |
| 21_L | 25_L | 1.652 | 0.98 |
| 327_V | 353_I | 1.640 | 0.98 |
| 405_I | 408_T | 1.632 | 0.98 |
| 312_M | 353_I | 1.618 | 0.98 |
| 362_T | 365_L | 1.602 | 0.98 |
| 532_G | 564_F | 1.582 | 0.97 |
| 403_A | 536_L | 1.575 | 0.97 |
| 64_S | 214_Y | 1.559 | 0.97 |
| 113_A | 117_I | 1.557 | 0.97 |
| 328_N | 337_W | 1.550 | 0.97 |
| 473_F | 513_E | 1.542 | 0.97 |
| 216_L | 220_I | 1.532 | 0.97 |
| 354_H | 405_I | 1.531 | 0.97 |
| 298_T | 310_L | 1.528 | 0.97 |
| 444_A | 447_W | 1.518 | 0.97 |
| 184_A | 213_F | 1.509 | 0.96 |
| 59_C | 111_H | 1.506 | 0.96 |
| 16_V | 20_G | 1.503 | 0.96 |
| 530_L | 540_L | 1.498 | 0.96 |
| 411_A | 448_F | 1.492 | 0.96 |
| 529_F | 532_G | 1.480 | 0.96 |
| 60_L | 112_T | 1.454 | 0.95 |
| 281_I | 285_I | 1.453 | 0.95 |
| 70_P | 97_N | 1.452 | 0.95 |
| 416_S | 420_K | 1.441 | 0.95 |
| 19_L | 23_V | 1.435 | 0.95 |
| 532_G | 562_E | 1.429 | 0.95 |
| 527_G | 560_N | 1.412 | 0.94 |
| 184_A | 214_Y | 1.399 | 0.94 |
| 98_L | 102_K | 1.396 | 0.94 |
| 53_A | 57_A | 1.392 | 0.94 |
| 516_T | 520_S | 1.384 | 0.93 |
| 26_F | 56_S | 1.376 | 0.93 |
| 517_I | 526_V | 1.369 | 0.93 |
| 472_L | 501_Q | 1.365 | 0.93 |
| 109_C | 182_T | 1.358 | 0.93 |
| 399_V | 514_F | 1.352 | 0.92 |
| 21_L | 62_F | 1.351 | 0.92 |
| 180_I | 217_G | 1.348 | 0.92 |
| 280_Y | 284_R | 1.348 | 0.92 |
| 298_T | 379_I | 1.333 | 0.92 |
| 528_V | 562_E | 1.332 | 0.92 |
| 399_V | 436_Y | 1.330 | 0.92 |
| 54_R | 58_L | 1.319 | 0.91 |
| 401_V | 540_L | 1.317 | 0.91 |
| 452_L | 499_L | 1.308 | 0.91 |
| 434_Y | 471_R | 1.305 | 0.90 |
| 98_L | 326_F | 1.301 | 0.90 |
| 440_R | 476_G | 1.301 | 0.90 |
| 534_R | 538_K | 1.294 | 0.90 |
| 61_N | 218_L | 1.288 | 0.90 |
| 193_T | 196_I | 1.288 | 0.90 |
| 15_L | 19_L | 1.285 | 0.90 |
| 187_L | 274_L | 1.276 | 0.89 |
| 402_G | 410_F | 1.272 | 0.89 |
| 514_F | 528_V | 1.270 | 0.89 |
| 327_V | 467_F | 1.269 | 0.89 |
| 473_F | 504_S | 1.268 | 0.89 |
| 112_T | 182_T | 1.264 | 0.89 |
| 320_E | 323_Q | 1.263 | 0.88 |
| 12_V | 16_V | 1.262 | 0.88 |
| 543_C | 547_Y | 1.260 | 0.88 |
| 203_V | 207_T | 1.259 | 0.88 |
| 324_Y | 518_A | 1.253 | 0.88 |
| 407_V | 448_F | 1.252 | 0.88 |
| 20_G | 24_F | 1.250 | 0.88 |
| 438_I | 447_W | 1.248 | 0.88 |
| 68_L | 100_F | 1.247 | 0.88 |
| 184_A | 217_G | 1.245 | 0.88 |
| 300_V | 310_L | 1.245 | 0.88 |
| 191_S | 210_L | 1.243 | 0.87 |
| 363_E | 367_R | 1.241 | 0.87 |
| 187_L | 210_L | 1.232 | 0.87 |
| 401_V | 510_W | 1.231 | 0.87 |
| 177_T | 217_G | 1.222 | 0.86 |
| 269_S | 273_I | 1.221 | 0.86 |
| 186_I | 278_I | 1.216 | 0.86 |
| 119_H | 122_N | 1.213 | 0.86 |
| 325_I | 357_A | 1.211 | 0.86 |
| 283_E | 290_R | 1.211 | 0.86 |
| 514_F | 540_L | 1.206 | 0.85 |
| 392_V | 413_I | 1.202 | 0.85 |
| 437_W | 448_F | 1.202 | 0.85 |
| 312_M | 327_V | 1.201 | 0.85 |
| 64_S | 276_P | 1.200 | 0.85 |
| 528_V | 544_C | 1.195 | 0.84 |
| 528_V | 531_C | 1.191 | 0.84 |
| 340_F | 355_I | 1.191 | 0.84 |
| 388_A | 401_V | 1.189 | 0.84 |
| 472_L | 513_E | 1.189 | 0.84 |
| 354_H | 448_F | 1.189 | 0.84 |
| 107_M | 111_H | 1.188 | 0.84 |
| 22_N | 111_H | 1.187 | 0.84 |
| 323_Q | 386_G | 1.186 | 0.84 |
| 437_W | 447_W | 1.186 | 0.84 |
| 110_L | 114_I | 1.186 | 0.84 |
| 539_S | 543_C | 1.178 | 0.83 |
| 528_V | 532_G | 1.178 | 0.83 |
| 395_Y | 527_G | 1.175 | 0.83 |
| 23_V | 27_V | 1.163 | 0.82 |
| 219_G | 277_V | 1.159 | 0.82 |
| 73_R | 283_E | 1.158 | 0.82 |
| 292_Q | 330_P | 1.155 | 0.82 |
| 538_K | 561_K | 1.154 | 0.82 |
| 393_F | 416_S | 1.151 | 0.81 |
| 109_C | 113_A | 1.147 | 0.81 |
| 402_G | 413_I | 1.142 | 0.81 |
| 50_L | 55_A | 1.141 | 0.81 |
| 50_L | 54_R | 1.139 | 0.80 |
| 164_T | 167_Y | 1.138 | 0.80 |
| 15_L | 326_F | 1.137 | 0.80 |
| 68_L | 215_I | 1.136 | 0.80 |
| 407_V | 437_W | 1.136 | 0.80 |
| 446_S | 449_N | 1.135 | 0.80 |
| 410_F | 435_F | 1.135 | 0.80 |
| 105_A | 356_R | 1.134 | 0.80 |
| 439_C | 474_L | 1.133 | 0.80 |
| 511_D | 546_R | 1.132 | 0.80 |
| 135_G | 154_W | 1.130 | 0.80 |
| 368_A | 371_Q | 1.127 | 0.79 |
| 27_V | 216_L | 1.126 | 0.79 |
| 74_N | 382_D | 1.123 | 0.79 |
| 302_M | 369_F | 1.120 | 0.79 |
| 3_N | 6_V | 1.116 | 0.78 |
| 190_T | 207_T | 1.114 | 0.78 |
| 278_I | 282_C | 1.107 | 0.78 |
| 400_L | 529_F | 1.107 | 0.78 |
| 159_Q | 162_N | 1.106 | 0.78 |
| 77_S | 80_R | 1.106 | 0.78 |
| 397_V | 434_Y | 1.106 | 0.78 |
| 497_T | 503_T | 1.105 | 0.78 |
| 397_V | 432_K | 1.104 | 0.77 |
| 396_E | 431_K | 1.103 | 0.77 |
| 439_C | 445_F | 1.103 | 0.77 |
| 188_M | 211_F | 1.103 | 0.77 |
| 86_C | 97_N | 1.102 | 0.77 |
| 170_F | 179_V | 1.102 | 0.77 |
| 470_Y | 501_Q | 1.101 | 0.77 |
| 503_T | 506_G | 1.101 | 0.77 |
| 531_C | 562_E | 1.100 | 0.77 |
| 530_L | 559_F | 1.099 | 0.77 |
| 403_A | 438_I | 1.096 | 0.77 |
| 311_Q | 418_W | 1.096 | 0.77 |
| 303_H | 309_E | 1.092 | 0.76 |
| 368_A | 372_Q | 1.091 | 0.76 |
| 288_F | 518_A | 1.089 | 0.76 |
| 357_A | 366_I | 1.086 | 0.76 |
| 434_Y | 469_N | 1.086 | 0.76 |
| 128_R | 132_A | 1.085 | 0.76 |
| 439_C | 472_L | 1.084 | 0.76 |
| 515_S | 547_Y | 1.083 | 0.75 |
| 537_A | 559_F | 1.082 | 0.75 |
| 413_I | 527_G | 1.082 | 0.75 |
| 471_R | 504_S | 1.076 | 0.75 |
| 499_L | 506_G | 1.073 | 0.75 |
| 113_A | 193_T | 1.073 | 0.75 |
| 282_C | 286_L | 1.071 | 0.74 |
| 64_S | 218_L | 1.071 | 0.74 |
| 306_K | 363_E | 1.068 | 0.74 |
| 187_L | 281_I | 1.067 | 0.74 |
| 110_L | 187_L | 1.066 | 0.74 |
| 226_I | 230_Q | 1.064 | 0.74 |
| 206_Y | 336_E | 1.063 | 0.74 |
| 384_P | 506_G | 1.058 | 0.73 |
| 153_S | 158_I | 1.058 | 0.73 |
| 155_L | 159_Q | 1.056 | 0.73 |
| 67_I | 72_C | 1.056 | 0.73 |
| 69_L | 72_C | 1.055 | 0.73 |
| 185_L | 189_V | 1.054 | 0.73 |
| 289_Y | 519_T | 1.052 | 0.72 |
| 307_V | 447_W | 1.050 | 0.72 |
| 93_Q | 198_R | 1.047 | 0.72 |
| 135_G | 155_L | 1.046 | 0.72 |
| 314_K | 319_M | 1.044 | 0.72 |
| 67_I | 108_I | 1.041 | 0.71 |
| 301_V | 311_Q | 1.040 | 0.71 |
| 152_G | 155_L | 1.036 | 0.71 |
| 325_I | 342_L | 1.035 | 0.71 |
| 336_E | 434_Y | 1.035 | 0.71 |
| 19_L | 282_C | 1.034 | 0.71 |
| 343_T | 354_H | 1.034 | 0.71 |
| 152_G | 158_I | 1.033 | 0.71 |
| 544_C | 559_F | 1.031 | 0.70 |
| 346_P | 352_S | 1.028 | 0.70 |
| 448_F | 451_L | 1.027 | 0.70 |
| 63_N | 111_H | 1.025 | 0.70 |
| 3_N | 81_G | 1.025 | 0.70 |
| 355_I | 359_G | 1.025 | 0.70 |
| 107_M | 435_F | 1.024 | 0.70 |
| 351_F | 398_A | 1.023 | 0.69 |
| 452_L | 455_L | 1.023 | 0.69 |
| 358_A | 361_W | 1.020 | 0.69 |
| 531_C | 564_F | 1.019 | 0.69 |
| 135_G | 152_G | 1.019 | 0.69 |
| 417_I | 433_I | 1.018 | 0.69 |
| 489_F | 513_E | 1.018 | 0.69 |
| 8_H | 11_S | 1.017 | 0.69 |
| 18_W | 528_V | 1.017 | 0.69 |
| 416_S | 470_Y | 1.017 | 0.69 |
| 154_W | 159_Q | 1.014 | 0.68 |
| 217_G | 220_I | 1.008 | 0.68 |
| 312_M | 336_E | 1.008 | 0.68 |
| 355_I | 417_I | 1.006 | 0.68 |
| 3_N | 8_H | 1.006 | 0.68 |
| 95_D | 408_T | 1.006 | 0.68 |
| 295_V | 378_R | 1.006 | 0.68 |
| 405_I | 409_P | 1.006 | 0.68 |
| 52_C | 55_A | 1.006 | 0.68 |
| 449_N | 455_L | 1.004 | 0.67 |
| 170_F | 175_G | 1.004 | 0.67 |
| 537_A | 541_R | 1.001 | 0.67 |
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 | |
| 3a1fA | 1 | 0.289 | 100 | 0.772 | Contact Map |
| 1fdrA | 1 | 0.4131 | 100 | 0.786 | Contact Map |
| 4eh1A | 2 | 0.3936 | 100 | 0.79 | Contact Map |
| 1qfjA | 4 | 0.3901 | 100 | 0.791 | Contact Map |
| 2r6hA | 4 | 0.4202 | 100 | 0.792 | Contact Map |
| 3jqqA | 6 | 0.4415 | 100 | 0.792 | Contact Map |
| 1tvcA | 1 | 0.4131 | 100 | 0.793 | Contact Map |
| 2qdxA | 1 | 0.4238 | 100 | 0.798 | Contact Map |
| 4u9uA | 2 | 0.4113 | 100 | 0.799 | Contact Map |
| 2eixA | 2 | 0.4184 | 100 | 0.8 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)