| ints13 -force run |
| ID: | 1517002015 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 706 (651) | ||
| Sequences: | 62 (41.5) | ||
| Seq/Len: | 0.095 | ||
| Nf(neff/√len): | 1.6 |
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: 0.095).
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 |
| 69_I | 351_T | 1.852 | 0.33 |
| 130_V | 386_L | 1.834 | 0.32 |
| 262_I | 311_K | 1.723 | 0.28 |
| 79_I | 449_K | 1.695 | 0.27 |
| 239_A | 359_S | 1.689 | 0.26 |
| 361_L | 378_S | 1.603 | 0.23 |
| 259_S | 313_T | 1.600 | 0.23 |
| 252_Q | 284_L | 1.582 | 0.22 |
| 67_Y | 255_F | 1.563 | 0.22 |
| 218_V | 239_A | 1.549 | 0.21 |
| 348_S | 352_N | 1.544 | 0.21 |
| 582_D | 633_K | 1.529 | 0.21 |
| 4_F | 328_L | 1.523 | 0.20 |
| 683_A | 689_L | 1.523 | 0.20 |
| 361_L | 495_Q | 1.506 | 0.20 |
| 427_L | 456_T | 1.495 | 0.20 |
| 345_R | 349_C | 1.479 | 0.19 |
| 672_F | 686_Y | 1.477 | 0.19 |
| 632_K | 674_G | 1.466 | 0.19 |
| 672_F | 689_L | 1.457 | 0.18 |
| 183_I | 364_Q | 1.452 | 0.18 |
| 459_W | 527_E | 1.446 | 0.18 |
| 297_G | 456_T | 1.445 | 0.18 |
| 460_P | 494_C | 1.424 | 0.17 |
| 130_V | 339_P | 1.423 | 0.17 |
| 158_G | 530_R | 1.406 | 0.17 |
| 672_F | 683_A | 1.400 | 0.17 |
| 632_K | 686_Y | 1.396 | 0.17 |
| 17_C | 351_T | 1.385 | 0.16 |
| 69_I | 160_I | 1.384 | 0.16 |
| 199_I | 276_S | 1.379 | 0.16 |
| 259_S | 316_L | 1.379 | 0.16 |
| 293_F | 486_L | 1.372 | 0.16 |
| 30_F | 557_L | 1.369 | 0.16 |
| 179_V | 215_D | 1.365 | 0.16 |
| 141_H | 145_T | 1.359 | 0.16 |
| 137_T | 490_D | 1.351 | 0.15 |
| 674_G | 686_Y | 1.348 | 0.15 |
| 444_P | 477_L | 1.334 | 0.15 |
| 475_V | 478_A | 1.334 | 0.15 |
| 80_V | 108_V | 1.330 | 0.15 |
| 313_T | 321_P | 1.317 | 0.15 |
| 284_L | 457_R | 1.317 | 0.15 |
| 7_S | 351_T | 1.307 | 0.14 |
| 426_R | 457_R | 1.304 | 0.14 |
| 674_G | 683_A | 1.301 | 0.14 |
| 477_L | 487_T | 1.294 | 0.14 |
| 421_F | 504_M | 1.294 | 0.14 |
| 251_V | 351_T | 1.294 | 0.14 |
| 424_E | 457_R | 1.294 | 0.14 |
| 417_D | 427_L | 1.287 | 0.14 |
| 290_H | 382_G | 1.284 | 0.14 |
| 210_Y | 236_S | 1.278 | 0.14 |
| 24_C | 47_I | 1.277 | 0.14 |
| 274_N | 361_L | 1.276 | 0.14 |
| 385_F | 456_T | 1.269 | 0.13 |
| 313_T | 316_L | 1.266 | 0.13 |
| 20_M | 386_L | 1.262 | 0.13 |
| 419_G | 463_I | 1.262 | 0.13 |
| 243_L | 486_L | 1.261 | 0.13 |
| 449_K | 463_I | 1.261 | 0.13 |
| 457_R | 506_R | 1.260 | 0.13 |
| 449_K | 532_M | 1.258 | 0.13 |
| 632_K | 683_A | 1.254 | 0.13 |
| 674_G | 689_L | 1.253 | 0.13 |
| 58_S | 146_L | 1.252 | 0.13 |
| 234_V | 547_S | 1.252 | 0.13 |
| 345_R | 350_L | 1.250 | 0.13 |
| 347_S | 350_L | 1.250 | 0.13 |
| 329_H | 339_P | 1.247 | 0.13 |
| 47_I | 379_S | 1.246 | 0.13 |
| 332_T | 343_N | 1.245 | 0.13 |
| 417_D | 456_T | 1.243 | 0.13 |
| 17_C | 127_V | 1.239 | 0.13 |
| 396_L | 404_E | 1.237 | 0.13 |
| 66_M | 423_R | 1.236 | 0.13 |
| 275_T | 526_D | 1.232 | 0.13 |
| 230_L | 382_G | 1.231 | 0.13 |
| 463_I | 519_R | 1.225 | 0.12 |
| 14_V | 20_M | 1.224 | 0.12 |
| 124_H | 175_L | 1.223 | 0.12 |
| 80_V | 158_G | 1.221 | 0.12 |
| 376_M | 509_D | 1.220 | 0.12 |
| 141_H | 144_R | 1.219 | 0.12 |
| 158_G | 169_D | 1.218 | 0.12 |
| 632_K | 689_L | 1.215 | 0.12 |
| 20_M | 371_K | 1.214 | 0.12 |
| 59_S | 177_D | 1.214 | 0.12 |
| 290_H | 377_L | 1.211 | 0.12 |
| 71_P | 263_T | 1.211 | 0.12 |
| 75_L | 417_D | 1.210 | 0.12 |
| 101_L | 185_E | 1.210 | 0.12 |
| 527_E | 547_S | 1.209 | 0.12 |
| 601_E | 671_E | 1.208 | 0.12 |
| 65_I | 313_T | 1.208 | 0.12 |
| 293_F | 468_I | 1.207 | 0.12 |
| 490_D | 549_K | 1.206 | 0.12 |
| 136_I | 468_I | 1.203 | 0.12 |
| 283_L | 560_C | 1.203 | 0.12 |
| 10_T | 65_I | 1.203 | 0.12 |
| 368_S | 530_R | 1.202 | 0.12 |
| 28_V | 262_I | 1.202 | 0.12 |
| 256_D | 373_I | 1.200 | 0.12 |
| 427_L | 476_P | 1.198 | 0.12 |
| 261_T | 282_E | 1.197 | 0.12 |
| 316_L | 320_T | 1.195 | 0.12 |
| 284_L | 502_V | 1.194 | 0.12 |
| 259_S | 318_W | 1.193 | 0.12 |
| 11_V | 476_P | 1.192 | 0.12 |
| 59_S | 161_I | 1.192 | 0.12 |
| 137_T | 486_L | 1.192 | 0.12 |
| 106_A | 541_R | 1.191 | 0.12 |
| 686_Y | 689_L | 1.190 | 0.12 |
| 154_V | 495_Q | 1.187 | 0.12 |
| 632_K | 672_F | 1.187 | 0.12 |
| 316_L | 321_P | 1.186 | 0.12 |
| 335_Y | 339_P | 1.183 | 0.12 |
| 130_V | 395_I | 1.182 | 0.12 |
| 38_T | 379_S | 1.181 | 0.12 |
| 172_V | 181_E | 1.181 | 0.12 |
| 283_L | 351_T | 1.179 | 0.12 |
| 175_L | 525_R | 1.178 | 0.11 |
| 160_I | 283_L | 1.176 | 0.11 |
| 3_I | 69_I | 1.176 | 0.11 |
| 346_P | 349_C | 1.176 | 0.11 |
| 20_M | 132_T | 1.175 | 0.11 |
| 94_E | 297_G | 1.173 | 0.11 |
| 29_E | 144_R | 1.169 | 0.11 |
| 349_C | 353_F | 1.166 | 0.11 |
| 97_N | 150_N | 1.164 | 0.11 |
| 167_K | 174_M | 1.164 | 0.11 |
| 255_F | 364_Q | 1.162 | 0.11 |
| 130_V | 308_G | 1.161 | 0.11 |
| 142_E | 198_Q | 1.161 | 0.11 |
| 653_L | 672_F | 1.161 | 0.11 |
| 584_S | 627_P | 1.160 | 0.11 |
| 671_E | 686_Y | 1.160 | 0.11 |
| 376_M | 485_S | 1.159 | 0.11 |
| 126_L | 250_L | 1.159 | 0.11 |
| 345_R | 353_F | 1.158 | 0.11 |
| 347_S | 353_F | 1.158 | 0.11 |
| 79_I | 532_M | 1.158 | 0.11 |
| 261_T | 313_T | 1.156 | 0.11 |
| 290_H | 374_S | 1.153 | 0.11 |
| 222_S | 326_I | 1.152 | 0.11 |
| 77_N | 311_K | 1.152 | 0.11 |
| 311_K | 364_Q | 1.152 | 0.11 |
| 66_M | 255_F | 1.150 | 0.11 |
| 102_M | 367_K | 1.150 | 0.11 |
| 185_E | 385_F | 1.149 | 0.11 |
| 213_G | 504_M | 1.145 | 0.11 |
| 259_S | 311_K | 1.144 | 0.11 |
| 137_T | 361_L | 1.143 | 0.11 |
| 77_N | 206_L | 1.141 | 0.11 |
| 683_A | 686_Y | 1.140 | 0.11 |
| 11_V | 47_I | 1.140 | 0.11 |
| 63_C | 322_R | 1.140 | 0.11 |
| 179_V | 213_G | 1.137 | 0.11 |
| 75_L | 456_T | 1.134 | 0.11 |
| 119_C | 123_L | 1.133 | 0.11 |
| 249_I | 490_D | 1.133 | 0.11 |
| 421_F | 502_V | 1.130 | 0.11 |
| 172_V | 182_T | 1.128 | 0.11 |
| 132_T | 142_E | 1.128 | 0.11 |
| 141_H | 544_I | 1.127 | 0.10 |
| 260_T | 265_I | 1.127 | 0.10 |
| 260_T | 266_P | 1.127 | 0.10 |
| 260_T | 267_M | 1.127 | 0.10 |
| 284_L | 292_D | 1.125 | 0.10 |
| 144_R | 147_L | 1.125 | 0.10 |
| 41_I | 419_G | 1.120 | 0.10 |
| 74_K | 89_N | 1.119 | 0.10 |
| 137_T | 495_Q | 1.119 | 0.10 |
| 53_T | 164_T | 1.118 | 0.10 |
| 380_H | 486_L | 1.118 | 0.10 |
| 255_F | 530_R | 1.115 | 0.10 |
| 243_L | 373_I | 1.114 | 0.10 |
| 30_F | 527_E | 1.114 | 0.10 |
| 448_A | 457_R | 1.113 | 0.10 |
| 137_T | 305_S | 1.112 | 0.10 |
| 181_E | 386_L | 1.112 | 0.10 |
| 346_P | 354_L | 1.111 | 0.10 |
| 130_V | 510_P | 1.111 | 0.10 |
| 66_M | 201_K | 1.111 | 0.10 |
| 8_H | 18_P | 1.111 | 0.10 |
| 73_K | 366_R | 1.111 | 0.10 |
| 270_E | 387_H | 1.110 | 0.10 |
| 335_Y | 351_T | 1.109 | 0.10 |
| 188_K | 234_V | 1.108 | 0.10 |
| 69_I | 208_H | 1.108 | 0.10 |
| 131_E | 234_V | 1.107 | 0.10 |
| 293_F | 361_L | 1.107 | 0.10 |
| 111_P | 470_N | 1.107 | 0.10 |
| 46_P | 419_G | 1.107 | 0.10 |
| 476_P | 480_V | 1.106 | 0.10 |
| 19_Y | 47_I | 1.106 | 0.10 |
| 332_T | 342_V | 1.106 | 0.10 |
| 586_K | 666_S | 1.104 | 0.10 |
| 106_A | 510_P | 1.100 | 0.10 |
| 133_L | 158_G | 1.099 | 0.10 |
| 7_S | 376_M | 1.099 | 0.10 |
| 422_M | 527_E | 1.097 | 0.10 |
| 627_P | 674_G | 1.097 | 0.10 |
| 427_L | 460_P | 1.096 | 0.10 |
| 427_L | 494_C | 1.096 | 0.10 |
| 380_H | 459_W | 1.095 | 0.10 |
| 377_L | 382_G | 1.095 | 0.10 |
| 149_E | 243_L | 1.094 | 0.10 |
| 212_V | 379_S | 1.094 | 0.10 |
| 232_S | 293_F | 1.094 | 0.10 |
| 417_D | 452_L | 1.093 | 0.10 |
| 12_F | 413_Y | 1.093 | 0.10 |
| 385_F | 392_S | 1.093 | 0.10 |
| 56_V | 313_T | 1.093 | 0.10 |
| 627_P | 632_K | 1.092 | 0.10 |
| 125_G | 129_A | 1.092 | 0.10 |
| 125_G | 360_V | 1.092 | 0.10 |
| 129_A | 360_V | 1.092 | 0.10 |
| 144_R | 461_M | 1.091 | 0.10 |
| 123_L | 135_K | 1.090 | 0.10 |
| 502_V | 540_V | 1.088 | 0.10 |
| 486_L | 543_H | 1.088 | 0.10 |
| 69_I | 504_M | 1.087 | 0.10 |
| 28_V | 314_I | 1.087 | 0.10 |
| 58_S | 115_A | 1.086 | 0.10 |
| 313_T | 318_W | 1.086 | 0.10 |
| 25_R | 351_T | 1.085 | 0.10 |
| 29_E | 193_S | 1.084 | 0.10 |
| 10_T | 358_R | 1.084 | 0.10 |
| 29_E | 141_H | 1.081 | 0.10 |
| 102_M | 392_S | 1.079 | 0.10 |
| 137_T | 378_S | 1.079 | 0.10 |
| 177_D | 221_R | 1.079 | 0.10 |
| 283_L | 395_I | 1.079 | 0.10 |
| 35_K | 355_L | 1.078 | 0.10 |
| 25_R | 251_V | 1.076 | 0.10 |
| 339_P | 386_L | 1.075 | 0.10 |
| 270_E | 414_R | 1.075 | 0.10 |
| 585_E | 654_L | 1.074 | 0.10 |
| 39_Q | 189_L | 1.073 | 0.10 |
| 487_T | 552_R | 1.071 | 0.09 |
| 231_T | 493_N | 1.071 | 0.09 |
| 197_M | 423_R | 1.071 | 0.09 |
| 259_S | 486_L | 1.070 | 0.09 |
| 387_H | 414_R | 1.070 | 0.09 |
| 259_S | 282_E | 1.069 | 0.09 |
| 7_S | 239_A | 1.068 | 0.09 |
| 255_F | 311_K | 1.067 | 0.09 |
| 255_F | 465_Q | 1.065 | 0.09 |
| 197_M | 461_M | 1.065 | 0.09 |
| 284_L | 555_E | 1.064 | 0.09 |
| 121_S | 300_H | 1.064 | 0.09 |
| 332_T | 340_V | 1.062 | 0.09 |
| 93_Q | 145_T | 1.061 | 0.09 |
| 43_P | 399_P | 1.060 | 0.09 |
| 386_L | 477_L | 1.060 | 0.09 |
| 456_T | 491_V | 1.060 | 0.09 |
| 209_T | 234_V | 1.059 | 0.09 |
| 41_I | 194_D | 1.059 | 0.09 |
| 627_P | 686_Y | 1.058 | 0.09 |
| 459_W | 525_R | 1.057 | 0.09 |
| 172_V | 385_F | 1.057 | 0.09 |
| 119_C | 228_P | 1.055 | 0.09 |
| 21_A | 109_G | 1.055 | 0.09 |
| 422_M | 486_L | 1.054 | 0.09 |
| 137_T | 146_L | 1.054 | 0.09 |
| 496_K | 562_S | 1.053 | 0.09 |
| 68_D | 357_G | 1.052 | 0.09 |
| 270_E | 363_E | 1.052 | 0.09 |
| 226_L | 292_D | 1.052 | 0.09 |
| 209_T | 475_V | 1.047 | 0.09 |
| 195_H | 379_S | 1.046 | 0.09 |
| 124_H | 385_F | 1.046 | 0.09 |
| 21_A | 351_T | 1.045 | 0.09 |
| 208_H | 262_I | 1.045 | 0.09 |
| 3_I | 379_S | 1.045 | 0.09 |
| 282_E | 486_L | 1.043 | 0.09 |
| 131_E | 290_H | 1.042 | 0.09 |
| 677_N | 680_N | 1.042 | 0.09 |
| 653_L | 668_K | 1.042 | 0.09 |
| 101_L | 145_T | 1.042 | 0.09 |
| 167_K | 351_T | 1.042 | 0.09 |
| 171_H | 351_T | 1.040 | 0.09 |
| 493_N | 526_D | 1.040 | 0.09 |
| 616_E | 628_E | 1.038 | 0.09 |
| 315_T | 322_R | 1.038 | 0.09 |
| 423_R | 488_E | 1.038 | 0.09 |
| 374_S | 382_G | 1.037 | 0.09 |
| 389_L | 415_I | 1.037 | 0.09 |
| 381_G | 497_T | 1.037 | 0.09 |
| 197_M | 328_L | 1.036 | 0.09 |
| 75_L | 313_T | 1.036 | 0.09 |
| 295_K | 459_W | 1.036 | 0.09 |
| 259_S | 320_T | 1.035 | 0.09 |
| 168_S | 523_P | 1.035 | 0.09 |
| 491_V | 540_V | 1.035 | 0.09 |
| 147_L | 543_H | 1.034 | 0.09 |
| 96_Q | 202_C | 1.032 | 0.09 |
| 634_P | 653_L | 1.032 | 0.09 |
| 215_D | 385_F | 1.031 | 0.09 |
| 147_L | 461_M | 1.031 | 0.09 |
| 159_R | 394_S | 1.030 | 0.09 |
| 137_T | 143_A | 1.029 | 0.09 |
| 29_E | 41_I | 1.028 | 0.09 |
| 161_I | 334_A | 1.028 | 0.09 |
| 211_P | 458_Y | 1.028 | 0.09 |
| 69_I | 158_G | 1.027 | 0.09 |
| 189_L | 484_E | 1.027 | 0.09 |
| 295_K | 522_G | 1.026 | 0.09 |
| 29_E | 194_D | 1.025 | 0.09 |
| 427_L | 452_L | 1.025 | 0.09 |
| 54_C | 121_S | 1.024 | 0.09 |
| 203_E | 283_L | 1.024 | 0.09 |
| 159_R | 271_Q | 1.023 | 0.09 |
| 194_D | 463_I | 1.023 | 0.09 |
| 43_P | 505_E | 1.021 | 0.09 |
| 670_Q | 676_L | 1.020 | 0.09 |
| 131_E | 458_Y | 1.020 | 0.09 |
| 110_P | 283_L | 1.020 | 0.09 |
| 422_M | 470_N | 1.018 | 0.09 |
| 63_C | 467_T | 1.018 | 0.09 |
| 73_K | 283_L | 1.017 | 0.09 |
| 259_S | 321_P | 1.017 | 0.09 |
| 426_R | 555_E | 1.017 | 0.09 |
| 532_M | 557_L | 1.016 | 0.09 |
| 108_V | 170_S | 1.016 | 0.09 |
| 338_S | 531_I | 1.015 | 0.09 |
| 226_L | 286_H | 1.014 | 0.09 |
| 366_R | 469_F | 1.012 | 0.09 |
| 11_V | 477_L | 1.012 | 0.09 |
| 450_D | 527_E | 1.012 | 0.09 |
| 225_E | 236_S | 1.012 | 0.09 |
| 223_K | 467_T | 1.012 | 0.09 |
| 140_Q | 358_R | 1.011 | 0.09 |
| 94_E | 251_V | 1.011 | 0.09 |
| 14_V | 209_T | 1.010 | 0.09 |
| 211_P | 314_I | 1.010 | 0.09 |
| 262_I | 388_V | 1.010 | 0.09 |
| 468_I | 476_P | 1.009 | 0.08 |
| 261_T | 290_H | 1.009 | 0.08 |
| 531_I | 548_E | 1.008 | 0.08 |
| 133_L | 381_G | 1.008 | 0.08 |
| 29_E | 547_S | 1.007 | 0.08 |
| 318_W | 321_P | 1.005 | 0.08 |
| 70_F | 80_V | 1.005 | 0.08 |
| 130_V | 183_I | 1.005 | 0.08 |
| 197_M | 243_L | 1.004 | 0.08 |
| 208_H | 218_V | 1.003 | 0.08 |
| 174_M | 213_G | 1.002 | 0.08 |
| 119_C | 531_I | 1.001 | 0.08 |
| 243_L | 392_S | 1.001 | 0.08 |
| 149_E | 287_K | 1.001 | 0.08 |
| 276_S | 350_L | 1.001 | 0.08 |
| 160_I | 351_T | 1.000 | 0.08 |
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 | |
| 1q0pA | 1 | 0.2649 | 57.5 | 0.988 | Contact Map |
| 2x31A | 6 | 0.2521 | 30.5 | 0.99 | Contact Map |
| 1lngA | 1 | 0.1232 | 23.5 | 0.99 | Contact Map |
| 2x5nA | 1 | 0.2578 | 21.2 | 0.99 | Contact Map |
| 4igiA | 1 | 0.2606 | 20.1 | 0.99 | Contact Map |
| 1pt6A | 2 | 0.2705 | 18.9 | 0.991 | Contact Map |
| 4rckA | 2 | 0.2705 | 16.4 | 0.991 | Contact Map |
| 1n3yA | 1 | 0.2663 | 15.3 | 0.991 | Contact Map |
| 4jduA | 1 | 0.2493 | 13.7 | 0.991 | Contact Map |
| 3zqkA | 3 | 0.2564 | 11.3 | 0.991 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)