| RCD1 -force run |
| ID: | 1464074317 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 589 (581) | ||
| Sequences: | 82 (57.6) | ||
| Seq/Len: | 0.141 | ||
| Nf(neff/√len): | 2.4 |
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: 0.141).
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 |
| 190_D | 542_T | 2.148 | 0.59 |
| 378_Y | 422_D | 1.899 | 0.45 |
| 86_T | 140_R | 1.815 | 0.41 |
| 80_Y | 83_F | 1.788 | 0.39 |
| 334_P | 365_H | 1.638 | 0.32 |
| 416_Y | 536_L | 1.614 | 0.30 |
| 165_I | 431_V | 1.567 | 0.28 |
| 348_L | 365_H | 1.540 | 0.27 |
| 114_E | 435_N | 1.531 | 0.27 |
| 368_A | 402_L | 1.522 | 0.26 |
| 331_A | 361_G | 1.514 | 0.26 |
| 166_Y | 499_S | 1.471 | 0.24 |
| 516_A | 562_T | 1.471 | 0.24 |
| 296_D | 325_D | 1.470 | 0.24 |
| 151_L | 418_N | 1.464 | 0.24 |
| 468_G | 542_T | 1.459 | 0.24 |
| 83_F | 323_R | 1.456 | 0.24 |
| 381_V | 548_R | 1.455 | 0.24 |
| 108_I | 431_V | 1.452 | 0.23 |
| 115_L | 296_D | 1.440 | 0.23 |
| 86_T | 198_D | 1.439 | 0.23 |
| 375_S | 390_V | 1.435 | 0.23 |
| 27_S | 92_V | 1.428 | 0.23 |
| 562_T | 566_L | 1.427 | 0.23 |
| 111_I | 150_P | 1.413 | 0.22 |
| 507_W | 547_V | 1.409 | 0.22 |
| 534_Q | 547_V | 1.403 | 0.22 |
| 192_K | 368_A | 1.394 | 0.21 |
| 331_A | 408_Q | 1.389 | 0.21 |
| 409_F | 529_I | 1.387 | 0.21 |
| 368_A | 537_R | 1.378 | 0.21 |
| 115_L | 141_L | 1.372 | 0.20 |
| 131_F | 444_F | 1.369 | 0.20 |
| 77_V | 416_Y | 1.356 | 0.20 |
| 29_A | 242_S | 1.353 | 0.20 |
| 536_L | 543_R | 1.352 | 0.20 |
| 23_K | 326_A | 1.348 | 0.20 |
| 87_G | 528_L | 1.348 | 0.20 |
| 536_L | 556_D | 1.343 | 0.19 |
| 22_R | 396_M | 1.342 | 0.19 |
| 118_K | 348_L | 1.341 | 0.19 |
| 361_G | 408_Q | 1.326 | 0.19 |
| 154_I | 550_L | 1.325 | 0.19 |
| 142_D | 563_I | 1.322 | 0.19 |
| 503_P | 553_I | 1.321 | 0.19 |
| 360_Y | 409_F | 1.319 | 0.19 |
| 328_V | 507_W | 1.317 | 0.19 |
| 389_M | 427_K | 1.317 | 0.19 |
| 526_M | 563_I | 1.314 | 0.18 |
| 85_K | 448_F | 1.310 | 0.18 |
| 422_D | 561_S | 1.309 | 0.18 |
| 52_I | 364_I | 1.308 | 0.18 |
| 325_D | 451_S | 1.306 | 0.18 |
| 20_K | 335_A | 1.305 | 0.18 |
| 111_I | 450_L | 1.305 | 0.18 |
| 333_L | 506_P | 1.301 | 0.18 |
| 23_K | 104_P | 1.301 | 0.18 |
| 83_F | 416_Y | 1.300 | 0.18 |
| 205_P | 483_S | 1.298 | 0.18 |
| 86_T | 177_H | 1.298 | 0.18 |
| 446_V | 562_T | 1.290 | 0.18 |
| 211_E | 215_E | 1.288 | 0.18 |
| 247_L | 370_D | 1.288 | 0.18 |
| 313_Q | 378_Y | 1.286 | 0.18 |
| 311_L | 435_N | 1.284 | 0.17 |
| 393_R | 517_I | 1.280 | 0.17 |
| 111_I | 365_H | 1.276 | 0.17 |
| 110_A | 388_Y | 1.268 | 0.17 |
| 385_G | 420_V | 1.268 | 0.17 |
| 433_N | 457_E | 1.267 | 0.17 |
| 279_K | 492_S | 1.266 | 0.17 |
| 2_E | 87_G | 1.265 | 0.17 |
| 118_K | 516_A | 1.264 | 0.17 |
| 113_N | 444_F | 1.263 | 0.17 |
| 48_G | 60_E | 1.257 | 0.17 |
| 537_R | 560_R | 1.253 | 0.17 |
| 344_M | 348_L | 1.252 | 0.17 |
| 402_L | 416_Y | 1.252 | 0.17 |
| 10_D | 365_H | 1.245 | 0.16 |
| 145_T | 564_T | 1.241 | 0.16 |
| 144_E | 151_L | 1.240 | 0.16 |
| 428_N | 541_M | 1.239 | 0.16 |
| 339_V | 430_I | 1.236 | 0.16 |
| 312_F | 363_G | 1.235 | 0.16 |
| 320_K | 360_Y | 1.234 | 0.16 |
| 282_F | 448_F | 1.233 | 0.16 |
| 190_D | 444_F | 1.232 | 0.16 |
| 196_E | 448_F | 1.232 | 0.16 |
| 337_R | 541_M | 1.231 | 0.16 |
| 86_T | 297_V | 1.230 | 0.16 |
| 95_Y | 272_V | 1.228 | 0.16 |
| 119_S | 221_M | 1.226 | 0.16 |
| 326_A | 449_K | 1.223 | 0.16 |
| 79_Y | 547_V | 1.221 | 0.16 |
| 89_A | 138_M | 1.217 | 0.15 |
| 517_I | 558_L | 1.215 | 0.15 |
| 279_K | 424_E | 1.214 | 0.15 |
| 119_S | 548_R | 1.212 | 0.15 |
| 408_Q | 551_R | 1.211 | 0.15 |
| 123_E | 384_N | 1.209 | 0.15 |
| 431_V | 445_V | 1.208 | 0.15 |
| 436_M | 456_A | 1.208 | 0.15 |
| 82_Y | 406_K | 1.205 | 0.15 |
| 246_K | 431_V | 1.198 | 0.15 |
| 274_D | 399_M | 1.198 | 0.15 |
| 67_A | 291_H | 1.193 | 0.15 |
| 551_R | 556_D | 1.191 | 0.15 |
| 325_D | 358_S | 1.190 | 0.15 |
| 335_A | 386_V | 1.190 | 0.15 |
| 102_D | 553_I | 1.189 | 0.15 |
| 384_N | 550_L | 1.188 | 0.15 |
| 281_M | 302_S | 1.183 | 0.15 |
| 514_F | 517_I | 1.182 | 0.14 |
| 31_Y | 455_N | 1.180 | 0.14 |
| 323_R | 400_E | 1.178 | 0.14 |
| 392_C | 443_E | 1.177 | 0.14 |
| 114_E | 348_L | 1.175 | 0.14 |
| 298_G | 449_K | 1.175 | 0.14 |
| 102_D | 344_M | 1.174 | 0.14 |
| 224_V | 409_F | 1.173 | 0.14 |
| 8_V | 508_M | 1.173 | 0.14 |
| 55_K | 448_F | 1.172 | 0.14 |
| 257_T | 509_P | 1.171 | 0.14 |
| 126_L | 444_F | 1.167 | 0.14 |
| 153_W | 163_P | 1.167 | 0.14 |
| 505_S | 558_L | 1.164 | 0.14 |
| 507_W | 543_R | 1.164 | 0.14 |
| 512_T | 536_L | 1.163 | 0.14 |
| 102_D | 509_P | 1.162 | 0.14 |
| 90_K | 289_L | 1.162 | 0.14 |
| 404_G | 413_G | 1.160 | 0.14 |
| 82_Y | 336_K | 1.158 | 0.14 |
| 160_C | 196_E | 1.157 | 0.14 |
| 141_L | 425_S | 1.156 | 0.14 |
| 19_G | 86_T | 1.155 | 0.14 |
| 53_P | 428_N | 1.155 | 0.14 |
| 293_P | 542_T | 1.155 | 0.14 |
| 344_M | 516_A | 1.155 | 0.14 |
| 94_M | 447_R | 1.154 | 0.14 |
| 315_Q | 445_V | 1.154 | 0.14 |
| 196_E | 511_P | 1.154 | 0.14 |
| 378_Y | 547_V | 1.152 | 0.14 |
| 91_R | 395_I | 1.149 | 0.14 |
| 334_P | 348_L | 1.146 | 0.14 |
| 496_V | 501_T | 1.145 | 0.14 |
| 503_P | 507_W | 1.145 | 0.14 |
| 119_S | 336_K | 1.145 | 0.14 |
| 316_V | 367_T | 1.145 | 0.14 |
| 317_E | 371_C | 1.143 | 0.13 |
| 86_T | 324_G | 1.142 | 0.13 |
| 507_W | 514_F | 1.141 | 0.13 |
| 343_V | 375_S | 1.141 | 0.13 |
| 7_K | 357_K | 1.140 | 0.13 |
| 103_L | 405_D | 1.138 | 0.13 |
| 152_A | 435_N | 1.137 | 0.13 |
| 331_A | 360_Y | 1.137 | 0.13 |
| 142_D | 526_M | 1.135 | 0.13 |
| 283_A | 544_A | 1.135 | 0.13 |
| 136_L | 448_F | 1.134 | 0.13 |
| 78_R | 529_I | 1.132 | 0.13 |
| 467_S | 529_I | 1.131 | 0.13 |
| 348_L | 391_L | 1.128 | 0.13 |
| 411_S | 569_Q | 1.127 | 0.13 |
| 252_S | 548_R | 1.126 | 0.13 |
| 84_K | 194_R | 1.126 | 0.13 |
| 123_E | 445_V | 1.124 | 0.13 |
| 88_I | 102_D | 1.124 | 0.13 |
| 55_K | 379_C | 1.124 | 0.13 |
| 388_Y | 436_M | 1.123 | 0.13 |
| 191_I | 216_S | 1.122 | 0.13 |
| 141_L | 221_M | 1.121 | 0.13 |
| 516_A | 525_D | 1.120 | 0.13 |
| 93_M | 338_E | 1.120 | 0.13 |
| 416_Y | 512_T | 1.117 | 0.13 |
| 83_F | 474_P | 1.117 | 0.13 |
| 365_H | 435_N | 1.116 | 0.13 |
| 207_L | 368_A | 1.115 | 0.13 |
| 310_A | 428_N | 1.113 | 0.13 |
| 5_I | 218_D | 1.113 | 0.13 |
| 289_L | 335_A | 1.112 | 0.13 |
| 404_G | 411_S | 1.111 | 0.13 |
| 29_A | 194_R | 1.110 | 0.13 |
| 325_D | 399_M | 1.109 | 0.13 |
| 141_L | 345_M | 1.108 | 0.13 |
| 22_R | 135_F | 1.107 | 0.13 |
| 82_Y | 405_D | 1.107 | 0.13 |
| 384_N | 408_Q | 1.107 | 0.13 |
| 394_V | 400_E | 1.106 | 0.13 |
| 88_I | 328_V | 1.105 | 0.13 |
| 400_E | 446_V | 1.105 | 0.13 |
| 83_F | 94_M | 1.103 | 0.12 |
| 201_G | 399_M | 1.102 | 0.12 |
| 151_L | 211_E | 1.102 | 0.12 |
| 410_F | 424_E | 1.102 | 0.12 |
| 103_L | 146_G | 1.102 | 0.12 |
| 314_K | 402_L | 1.101 | 0.12 |
| 118_K | 344_M | 1.100 | 0.12 |
| 542_T | 545_E | 1.098 | 0.12 |
| 413_G | 536_L | 1.096 | 0.12 |
| 115_L | 221_M | 1.094 | 0.12 |
| 115_L | 245_R | 1.091 | 0.12 |
| 142_D | 444_F | 1.091 | 0.12 |
| 329_R | 398_N | 1.090 | 0.12 |
| 121_A | 296_D | 1.085 | 0.12 |
| 418_N | 423_I | 1.085 | 0.12 |
| 340_L | 537_R | 1.085 | 0.12 |
| 152_A | 539_K | 1.083 | 0.12 |
| 64_K | 391_L | 1.082 | 0.12 |
| 282_F | 379_C | 1.081 | 0.12 |
| 112_Q | 475_K | 1.080 | 0.12 |
| 334_P | 435_N | 1.080 | 0.12 |
| 93_M | 549_K | 1.079 | 0.12 |
| 5_I | 115_L | 1.078 | 0.12 |
| 24_R | 334_P | 1.078 | 0.12 |
| 22_R | 399_M | 1.078 | 0.12 |
| 357_K | 524_N | 1.077 | 0.12 |
| 331_A | 384_N | 1.077 | 0.12 |
| 389_M | 545_E | 1.077 | 0.12 |
| 72_S | 83_F | 1.075 | 0.12 |
| 442_P | 447_R | 1.075 | 0.12 |
| 44_P | 515_A | 1.073 | 0.12 |
| 93_M | 449_K | 1.072 | 0.12 |
| 323_R | 327_N | 1.072 | 0.12 |
| 107_V | 133_L | 1.072 | 0.12 |
| 400_E | 411_S | 1.069 | 0.12 |
| 507_W | 541_M | 1.068 | 0.12 |
| 79_Y | 340_L | 1.068 | 0.12 |
| 201_G | 274_D | 1.068 | 0.12 |
| 540_K | 567_Q | 1.065 | 0.12 |
| 52_I | 402_L | 1.064 | 0.12 |
| 543_R | 566_L | 1.063 | 0.12 |
| 311_L | 521_V | 1.063 | 0.12 |
| 107_V | 328_V | 1.062 | 0.12 |
| 150_P | 164_E | 1.062 | 0.12 |
| 152_A | 328_V | 1.062 | 0.12 |
| 343_V | 414_E | 1.061 | 0.11 |
| 68_Y | 372_P | 1.061 | 0.11 |
| 442_P | 445_V | 1.060 | 0.11 |
| 130_S | 227_A | 1.059 | 0.11 |
| 278_V | 366_L | 1.059 | 0.11 |
| 466_N | 532_D | 1.059 | 0.11 |
| 405_D | 418_N | 1.058 | 0.11 |
| 197_I | 436_M | 1.058 | 0.11 |
| 136_L | 143_M | 1.058 | 0.11 |
| 510_F | 529_I | 1.058 | 0.11 |
| 116_E | 522_A | 1.057 | 0.11 |
| 433_N | 519_H | 1.057 | 0.11 |
| 116_E | 512_T | 1.056 | 0.11 |
| 293_P | 545_E | 1.056 | 0.11 |
| 119_S | 381_V | 1.055 | 0.11 |
| 115_L | 139_Q | 1.054 | 0.11 |
| 3_A | 444_F | 1.053 | 0.11 |
| 98_G | 144_E | 1.052 | 0.11 |
| 528_L | 540_K | 1.051 | 0.11 |
| 146_G | 340_L | 1.050 | 0.11 |
| 294_V | 325_D | 1.049 | 0.11 |
| 276_D | 511_P | 1.047 | 0.11 |
| 194_R | 286_T | 1.047 | 0.11 |
| 481_L | 484_N | 1.046 | 0.11 |
| 56_R | 437_N | 1.044 | 0.11 |
| 120_A | 436_M | 1.044 | 0.11 |
| 65_L | 92_V | 1.044 | 0.11 |
| 23_K | 540_K | 1.042 | 0.11 |
| 87_G | 505_S | 1.039 | 0.11 |
| 216_S | 504_K | 1.039 | 0.11 |
| 120_A | 387_R | 1.039 | 0.11 |
| 146_G | 331_A | 1.039 | 0.11 |
| 229_R | 422_D | 1.038 | 0.11 |
| 360_Y | 391_L | 1.036 | 0.11 |
| 216_S | 468_G | 1.035 | 0.11 |
| 110_A | 221_M | 1.034 | 0.11 |
| 94_M | 192_K | 1.034 | 0.11 |
| 435_N | 526_M | 1.034 | 0.11 |
| 67_A | 74_K | 1.034 | 0.11 |
| 507_W | 517_I | 1.034 | 0.11 |
| 375_S | 447_R | 1.033 | 0.11 |
| 375_S | 386_V | 1.032 | 0.11 |
| 333_L | 547_V | 1.032 | 0.11 |
| 426_P | 555_G | 1.032 | 0.11 |
| 391_L | 541_M | 1.028 | 0.11 |
| 77_V | 522_A | 1.027 | 0.11 |
| 138_M | 153_W | 1.026 | 0.11 |
| 357_K | 436_M | 1.025 | 0.11 |
| 514_F | 540_K | 1.025 | 0.11 |
| 80_Y | 540_K | 1.023 | 0.11 |
| 207_L | 379_C | 1.022 | 0.11 |
| 344_M | 550_L | 1.021 | 0.11 |
| 150_P | 365_H | 1.021 | 0.11 |
| 85_K | 131_F | 1.020 | 0.11 |
| 86_T | 186_N | 1.020 | 0.11 |
| 154_I | 400_E | 1.019 | 0.11 |
| 145_T | 533_Y | 1.018 | 0.11 |
| 91_R | 102_D | 1.016 | 0.11 |
| 11_S | 413_G | 1.016 | 0.11 |
| 151_L | 166_Y | 1.016 | 0.11 |
| 2_E | 505_S | 1.016 | 0.11 |
| 82_Y | 221_M | 1.016 | 0.11 |
| 108_I | 195_L | 1.014 | 0.10 |
| 52_I | 368_A | 1.014 | 0.10 |
| 167_E | 374_F | 1.014 | 0.10 |
| 278_V | 347_G | 1.014 | 0.10 |
| 221_M | 336_K | 1.013 | 0.10 |
| 150_P | 467_S | 1.013 | 0.10 |
| 245_R | 250_A | 1.013 | 0.10 |
| 402_L | 473_G | 1.013 | 0.10 |
| 83_F | 256_E | 1.013 | 0.10 |
| 278_V | 385_G | 1.012 | 0.10 |
| 438_T | 448_F | 1.012 | 0.10 |
| 344_M | 365_H | 1.011 | 0.10 |
| 324_G | 363_G | 1.010 | 0.10 |
| 54_D | 156_N | 1.009 | 0.10 |
| 391_L | 426_P | 1.009 | 0.10 |
| 40_L | 469_V | 1.009 | 0.10 |
| 428_N | 446_V | 1.008 | 0.10 |
| 102_D | 505_S | 1.008 | 0.10 |
| 512_T | 522_A | 1.006 | 0.10 |
| 97_N | 434_I | 1.005 | 0.10 |
| 283_A | 553_I | 1.005 | 0.10 |
| 245_R | 296_D | 1.005 | 0.10 |
| 154_I | 408_Q | 1.004 | 0.10 |
| 85_K | 438_T | 1.003 | 0.10 |
| 20_K | 289_L | 1.003 | 0.10 |
| 537_R | 546_F | 1.002 | 0.10 |
| 123_E | 550_L | 1.002 | 0.10 |
| 340_L | 368_A | 1.002 | 0.10 |
| 297_V | 406_K | 1.002 | 0.10 |
| 107_V | 497_G | 1.001 | 0.10 |
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 | |
| 3hkvA | 2 | 0.3124 | 100 | 0.878 | Contact Map |
| 3smjA | 2 | 0.3073 | 100 | 0.88 | Contact Map |
| 3bljA | 2 | 0.3243 | 100 | 0.883 | Contact Map |
| 2pqfA | 6 | 0.3073 | 100 | 0.884 | Contact Map |
| 2x5yA | 1 | 0.2903 | 100 | 0.893 | Contact Map |
| 4pnlA | 4 | 0.3039 | 99.9 | 0.901 | Contact Map |
| 4bueA | 2 | 0.3056 | 99.9 | 0.904 | Contact Map |
| 1efyA | 1 | 0.5195 | 99.9 | 0.907 | Contact Map |
| 4gv2A | 1 | 0.5042 | 99.9 | 0.91 | Contact Map |
| 4dqyC | 2 | 0.5976 | 99.9 | 0.91 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)