| T0788 - T0787 GP120 - GP41 |
| ID: | 1400696379 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 634 (629) | ||
| Sequences: | 5400 (331.3) | ||
| Seq/Len: | 8.585 | ||
| Nf(neff/√len): | 13.2 |
Jackhmmer Results: (2014_04_16)
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: 8.585).
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 |
| 253_N | 421_I | 5.451 | 1.00 |
| 470_K | 577_N | 3.286 | 1.00 |
| 317_Q | 320_K | 3.048 | 1.00 |
| 537_K | 599_L | 3.021 | 1.00 |
| 299_H | 303_S | 2.987 | 1.00 |
| 628_Q | 632_A | 2.903 | 1.00 |
| 181_E | 348_G | 2.856 | 1.00 |
| 84_Q | 172_T | 2.848 | 1.00 |
| 602_D | 606_S | 2.780 | 1.00 |
| 67_K | 245_E | 2.463 | 1.00 |
| 247_I | 321_H | 2.402 | 1.00 |
| 202_K | 238_E | 2.396 | 1.00 |
| 200_D | 210_P | 2.371 | 1.00 |
| 239_E | 317_Q | 2.366 | 1.00 |
| 19_E | 69_N | 2.295 | 1.00 |
| 140_R | 165_N | 2.289 | 1.00 |
| 263_Q | 306_T | 2.275 | 1.00 |
| 393_N | 400_Q | 2.264 | 1.00 |
| 201_K | 237_E | 2.262 | 1.00 |
| 245_E | 248_T | 2.261 | 1.00 |
| 301_N | 305_A | 2.139 | 1.00 |
| 17_D | 599_L | 2.038 | 1.00 |
| 611_I | 614_G | 1.980 | 1.00 |
| 55_H | 199_K | 1.926 | 1.00 |
| 329_R | 433_T | 1.913 | 1.00 |
| 168_T | 172_T | 1.906 | 1.00 |
| 240_V | 247_I | 1.897 | 1.00 |
| 121_F | 136_S | 1.881 | 1.00 |
| 590_S | 594_D | 1.879 | 1.00 |
| 485_I | 489_F | 1.873 | 1.00 |
| 297_Q | 303_S | 1.851 | 1.00 |
| 600_Q | 603_K | 1.847 | 1.00 |
| 323_G | 326_T | 1.837 | 1.00 |
| 202_K | 210_P | 1.802 | 1.00 |
| 270_N | 410_V | 1.801 | 1.00 |
| 537_K | 602_D | 1.785 | 1.00 |
| 365_I | 369_S | 1.771 | 1.00 |
| 16_K | 460_E | 1.757 | 1.00 |
| 572_L | 624_E | 1.751 | 1.00 |
| 400_Q | 537_K | 1.735 | 1.00 |
| 72_E | 444_R | 1.734 | 1.00 |
| 625_K | 628_Q | 1.718 | 1.00 |
| 35_K | 178_V | 1.713 | 1.00 |
| 602_D | 605_I | 1.708 | 1.00 |
| 278_R | 284_A | 1.698 | 1.00 |
| 338_L | 342_T | 1.687 | 1.00 |
| 278_R | 283_Q | 1.659 | 1.00 |
| 172_T | 393_N | 1.658 | 1.00 |
| 315_V | 364_W | 1.657 | 1.00 |
| 599_L | 602_D | 1.650 | 1.00 |
| 200_D | 535_L | 1.648 | 1.00 |
| 129_D | 162_R | 1.633 | 1.00 |
| 389_K | 392_I | 1.628 | 1.00 |
| 621_N | 628_Q | 1.616 | 1.00 |
| 16_K | 19_E | 1.615 | 1.00 |
| 32_E | 35_K | 1.609 | 1.00 |
| 62_E | 208_P | 1.609 | 1.00 |
| 260_T | 306_T | 1.587 | 1.00 |
| 392_I | 589_L | 1.572 | 1.00 |
| 341_T | 475_G | 1.562 | 1.00 |
| 84_Q | 168_T | 1.560 | 1.00 |
| 338_L | 393_N | 1.559 | 1.00 |
| 126_E | 165_N | 1.555 | 1.00 |
| 314_V | 358_G | 1.553 | 1.00 |
| 201_K | 238_E | 1.547 | 1.00 |
| 193_F | 458_K | 1.544 | 1.00 |
| 19_E | 602_D | 1.528 | 1.00 |
| 172_T | 589_L | 1.508 | 1.00 |
| 16_K | 606_S | 1.508 | 1.00 |
| 439_G | 442_D | 1.498 | 1.00 |
| 260_T | 313_K | 1.495 | 1.00 |
| 427_G | 434_E | 1.492 | 1.00 |
| 629_D | 632_A | 1.473 | 1.00 |
| 294_D | 387_R | 1.459 | 0.99 |
| 124_T | 165_N | 1.456 | 0.99 |
| 172_T | 599_L | 1.455 | 0.99 |
| 317_Q | 397_R | 1.447 | 0.99 |
| 260_T | 309_E | 1.444 | 0.99 |
| 338_L | 400_Q | 1.441 | 0.99 |
| 618_E | 625_K | 1.439 | 0.99 |
| 475_G | 582_S | 1.437 | 0.99 |
| 54_I | 488_V | 1.434 | 0.99 |
| 165_N | 170_A | 1.432 | 0.99 |
| 127_L | 162_R | 1.428 | 0.99 |
| 249_N | 357_S | 1.425 | 0.99 |
| 123_M | 134_V | 1.412 | 0.99 |
| 397_R | 400_Q | 1.411 | 0.99 |
| 426_G | 434_E | 1.405 | 0.99 |
| 263_Q | 267_T | 1.394 | 0.99 |
| 275_K | 287_A | 1.388 | 0.99 |
| 111_D | 114_G | 1.385 | 0.99 |
| 297_Q | 301_N | 1.377 | 0.99 |
| 535_L | 616_L | 1.374 | 0.99 |
| 258_F | 317_Q | 1.372 | 0.99 |
| 202_K | 239_E | 1.370 | 0.99 |
| 279_I | 285_F | 1.356 | 0.99 |
| 338_L | 392_I | 1.356 | 0.99 |
| 283_Q | 475_G | 1.347 | 0.99 |
| 318_L | 436_F | 1.344 | 0.99 |
| 283_Q | 321_H | 1.344 | 0.99 |
| 290_D | 392_I | 1.343 | 0.99 |
| 257_Q | 261_P | 1.337 | 0.99 |
| 76_T | 134_V | 1.330 | 0.99 |
| 42_H | 539_T | 1.326 | 0.99 |
| 302_V | 332_N | 1.324 | 0.99 |
| 156_N | 159_K | 1.314 | 0.99 |
| 193_F | 625_K | 1.313 | 0.99 |
| 126_E | 170_A | 1.301 | 0.99 |
| 35_K | 348_G | 1.297 | 0.98 |
| 299_H | 383_T | 1.296 | 0.98 |
| 168_T | 470_K | 1.295 | 0.98 |
| 126_E | 132_Q | 1.294 | 0.98 |
| 165_N | 400_Q | 1.292 | 0.98 |
| 204_N | 208_P | 1.289 | 0.98 |
| 488_V | 537_K | 1.288 | 0.98 |
| 62_E | 603_K | 1.285 | 0.98 |
| 275_K | 289_G | 1.283 | 0.98 |
| 172_T | 400_Q | 1.281 | 0.98 |
| 276_S | 289_G | 1.280 | 0.98 |
| 302_V | 310_T | 1.276 | 0.98 |
| 33_T | 170_A | 1.273 | 0.98 |
| 241_M | 261_P | 1.271 | 0.98 |
| 588_N | 591_E | 1.271 | 0.98 |
| 553_V | 602_D | 1.270 | 0.98 |
| 357_S | 475_G | 1.269 | 0.98 |
| 523_S | 632_A | 1.267 | 0.98 |
| 321_H | 341_T | 1.264 | 0.98 |
| 319_R | 362_S | 1.264 | 0.98 |
| 193_F | 257_Q | 1.264 | 0.98 |
| 412_R | 460_E | 1.263 | 0.98 |
| 16_K | 168_T | 1.262 | 0.98 |
| 534_H | 537_K | 1.261 | 0.98 |
| 116_L | 291_I | 1.260 | 0.98 |
| 35_K | 172_T | 1.258 | 0.98 |
| 263_Q | 414_V | 1.256 | 0.98 |
| 342_T | 357_S | 1.256 | 0.98 |
| 240_V | 257_Q | 1.256 | 0.98 |
| 240_V | 310_T | 1.253 | 0.98 |
| 304_K | 380_D | 1.253 | 0.98 |
| 400_Q | 599_L | 1.246 | 0.98 |
| 276_S | 290_D | 1.243 | 0.98 |
| 124_T | 129_D | 1.243 | 0.98 |
| 19_E | 629_D | 1.241 | 0.98 |
| 401_A | 539_T | 1.232 | 0.98 |
| 259_N | 313_K | 1.227 | 0.98 |
| 144_V | 162_R | 1.227 | 0.98 |
| 16_K | 32_E | 1.224 | 0.98 |
| 272_N | 292_I | 1.220 | 0.98 |
| 240_V | 364_W | 1.220 | 0.98 |
| 364_W | 408_Q | 1.218 | 0.97 |
| 324_N | 327_I | 1.214 | 0.97 |
| 202_K | 206_T | 1.213 | 0.97 |
| 537_K | 553_V | 1.210 | 0.97 |
| 183_I | 186_H | 1.210 | 0.97 |
| 319_R | 364_W | 1.209 | 0.97 |
| 19_E | 599_L | 1.207 | 0.97 |
| 110_D | 113_R | 1.206 | 0.97 |
| 317_Q | 338_L | 1.204 | 0.97 |
| 265_N | 414_V | 1.192 | 0.97 |
| 276_S | 292_I | 1.192 | 0.97 |
| 136_S | 602_D | 1.190 | 0.97 |
| 321_H | 582_S | 1.189 | 0.97 |
| 394_M | 397_R | 1.187 | 0.97 |
| 402_M | 619_S | 1.185 | 0.97 |
| 272_N | 276_S | 1.185 | 0.97 |
| 403_Y | 413_C | 1.185 | 0.97 |
| 19_E | 72_E | 1.183 | 0.97 |
| 602_D | 629_D | 1.179 | 0.97 |
| 170_A | 341_T | 1.174 | 0.97 |
| 199_K | 202_K | 1.170 | 0.97 |
| 404_A | 407_I | 1.169 | 0.97 |
| 483_V | 572_L | 1.168 | 0.97 |
| 134_V | 275_K | 1.164 | 0.96 |
| 424_R | 434_E | 1.163 | 0.96 |
| 386_C | 395_W | 1.160 | 0.96 |
| 316_K | 320_K | 1.160 | 0.96 |
| 131_K | 170_A | 1.157 | 0.96 |
| 505_M | 523_S | 1.152 | 0.96 |
| 309_E | 313_K | 1.149 | 0.96 |
| 165_N | 171_I | 1.148 | 0.96 |
| 128_R | 357_S | 1.145 | 0.96 |
| 395_W | 413_C | 1.139 | 0.96 |
| 202_K | 400_Q | 1.139 | 0.96 |
| 149_N | 376_T | 1.139 | 0.96 |
| 283_Q | 338_L | 1.136 | 0.96 |
| 364_W | 412_R | 1.132 | 0.96 |
| 315_V | 362_S | 1.129 | 0.96 |
| 168_T | 392_I | 1.128 | 0.96 |
| 302_V | 358_G | 1.126 | 0.95 |
| 131_K | 283_Q | 1.126 | 0.95 |
| 366_S | 369_S | 1.123 | 0.95 |
| 238_E | 259_N | 1.123 | 0.95 |
| 274_R | 290_D | 1.121 | 0.95 |
| 129_D | 139_Y | 1.120 | 0.95 |
| 424_R | 427_G | 1.119 | 0.95 |
| 338_L | 433_T | 1.118 | 0.95 |
| 17_D | 202_K | 1.118 | 0.95 |
| 602_D | 611_I | 1.116 | 0.95 |
| 320_K | 582_S | 1.115 | 0.95 |
| 193_F | 460_E | 1.115 | 0.95 |
| 35_K | 523_S | 1.115 | 0.95 |
| 558_R | 616_L | 1.115 | 0.95 |
| 577_N | 619_S | 1.111 | 0.95 |
| 193_F | 364_W | 1.111 | 0.95 |
| 245_E | 252_K | 1.110 | 0.95 |
| 241_M | 259_N | 1.110 | 0.95 |
| 403_Y | 409_G | 1.106 | 0.95 |
| 283_Q | 342_T | 1.106 | 0.95 |
| 395_W | 403_Y | 1.106 | 0.95 |
| 338_L | 632_A | 1.105 | 0.95 |
| 553_V | 558_R | 1.105 | 0.95 |
| 62_E | 136_S | 1.104 | 0.95 |
| 202_K | 535_L | 1.103 | 0.95 |
| 31_Y | 38_V | 1.102 | 0.95 |
| 323_G | 327_I | 1.096 | 0.95 |
| 374_N | 379_N | 1.093 | 0.94 |
| 537_K | 632_A | 1.092 | 0.94 |
| 464_V | 537_K | 1.092 | 0.94 |
| 62_E | 600_Q | 1.090 | 0.94 |
| 348_G | 411_I | 1.089 | 0.94 |
| 30_A | 35_K | 1.089 | 0.94 |
| 439_G | 619_S | 1.089 | 0.94 |
| 240_V | 262_V | 1.085 | 0.94 |
| 386_C | 390_Q | 1.083 | 0.94 |
| 245_E | 249_N | 1.081 | 0.94 |
| 530_E | 604_E | 1.080 | 0.94 |
| 565_I | 572_L | 1.080 | 0.94 |
| 103_N | 114_G | 1.079 | 0.94 |
| 239_E | 259_N | 1.078 | 0.94 |
| 33_T | 323_G | 1.078 | 0.94 |
| 562_L | 572_L | 1.076 | 0.94 |
| 35_K | 393_N | 1.074 | 0.94 |
| 311_L | 315_V | 1.073 | 0.94 |
| 19_E | 412_R | 1.073 | 0.94 |
| 247_I | 341_T | 1.073 | 0.94 |
| 408_Q | 412_R | 1.070 | 0.94 |
| 2_E | 468_R | 1.069 | 0.94 |
| 30_A | 535_L | 1.069 | 0.94 |
| 302_V | 408_Q | 1.066 | 0.93 |
| 394_M | 401_A | 1.066 | 0.93 |
| 240_V | 259_N | 1.064 | 0.93 |
| 78_I | 181_E | 1.064 | 0.93 |
| 76_T | 136_S | 1.063 | 0.93 |
| 409_G | 413_C | 1.063 | 0.93 |
| 458_K | 616_L | 1.062 | 0.93 |
| 122_N | 125_T | 1.062 | 0.93 |
| 33_T | 364_W | 1.061 | 0.93 |
| 172_T | 460_E | 1.059 | 0.93 |
| 430_N | 535_L | 1.057 | 0.93 |
| 193_F | 628_Q | 1.057 | 0.93 |
| 38_V | 462_L | 1.057 | 0.93 |
| 249_N | 442_D | 1.055 | 0.93 |
| 247_I | 582_S | 1.051 | 0.93 |
| 178_V | 442_D | 1.050 | 0.93 |
| 338_L | 341_T | 1.049 | 0.93 |
| 16_K | 602_D | 1.048 | 0.93 |
| 400_Q | 410_V | 1.047 | 0.93 |
| 114_G | 297_Q | 1.042 | 0.92 |
| 582_S | 599_L | 1.038 | 0.92 |
| 600_Q | 604_E | 1.038 | 0.92 |
| 344_S | 348_G | 1.035 | 0.92 |
| 589_L | 616_L | 1.034 | 0.92 |
| 468_R | 616_L | 1.031 | 0.92 |
| 289_G | 408_Q | 1.031 | 0.92 |
| 302_V | 558_R | 1.031 | 0.92 |
| 373_S | 376_T | 1.031 | 0.92 |
| 243_R | 257_Q | 1.027 | 0.92 |
| 326_T | 329_R | 1.027 | 0.92 |
| 488_V | 632_A | 1.025 | 0.92 |
| 32_E | 599_L | 1.022 | 0.91 |
| 17_D | 69_N | 1.021 | 0.91 |
| 91_K | 397_R | 1.021 | 0.91 |
| 488_V | 523_S | 1.018 | 0.91 |
| 18_A | 25_A | 1.018 | 0.91 |
| 124_T | 142_D | 1.018 | 0.91 |
| 242_I | 247_I | 1.017 | 0.91 |
| 475_G | 575_C | 1.016 | 0.91 |
| 7_T | 11_G | 1.014 | 0.91 |
| 8_V | 11_G | 1.012 | 0.91 |
| 495_A | 511_A | 1.012 | 0.91 |
| 136_S | 397_R | 1.011 | 0.91 |
| 181_E | 222_K | 1.011 | 0.91 |
| 35_K | 181_E | 1.011 | 0.91 |
| 105_T | 108_I | 1.010 | 0.91 |
| 279_I | 283_Q | 1.010 | 0.91 |
| 2_E | 210_P | 1.009 | 0.91 |
| 464_V | 602_D | 1.009 | 0.91 |
| 291_I | 297_Q | 1.008 | 0.91 |
| 285_F | 290_D | 1.007 | 0.91 |
| 247_I | 458_K | 1.007 | 0.91 |
| 364_W | 553_V | 1.006 | 0.91 |
| 247_I | 400_Q | 1.004 | 0.90 |
| 7_T | 15_W | 1.004 | 0.90 |
| 17_D | 537_K | 1.003 | 0.90 |
| 38_V | 535_L | 1.002 | 0.90 |
| 112_M | 116_L | 1.001 | 0.90 |
| 276_S | 287_A | 1.001 | 0.90 |
| 317_Q | 619_S | 1.000 | 0.90 |
| 69_N | 458_K | 1.000 | 0.90 |
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 | |
| 4ncoA | 3 | 0.6625 | 100 | 0.273 | Contact Map |
| 4jzzA | 1 | 0.5284 | 100 | 0.443 | Contact Map |
| 3lqaG | 1 | 0.4527 | 100 | 0.518 | Contact Map |
| 2bf1A | 1 | 0.4685 | 100 | 0.524 | Contact Map |
| 4i3sG | 1 | 0.2839 | 100 | 0.763 | Contact Map |
| 1qbzA | 3 | 0.1877 | 100 | 0.817 | Contact Map |
| 3tygA | 1 | 0.2303 | 100 | 0.82 | Contact Map |
| 4jpkA | 1 | 0.2397 | 100 | 0.852 | Contact Map |
| 1envA | 1 | 0.1767 | 100 | 0.857 | Contact Map |
| 3p30A | 1 | 0.1262 | 100 | 0.872 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)