| T0788 GP120 |
| ID: | 1400694995 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 481 (470) | ||
| Sequences: | 6129 (981.1) | ||
| Seq/Len: | 13.040 | ||
| Nf(neff/√len): | 45.3 |
HHblits Results: (2013_03)
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: 13.040).
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 | 6.792 | 1.00 |
| 263_Q | 306_T | 3.788 | 1.00 |
| 317_Q | 320_K | 3.610 | 1.00 |
| 67_K | 245_E | 3.401 | 1.00 |
| 201_K | 237_E | 3.383 | 1.00 |
| 247_I | 321_H | 3.240 | 1.00 |
| 202_K | 238_E | 3.160 | 1.00 |
| 278_R | 284_A | 3.119 | 1.00 |
| 245_E | 248_T | 2.998 | 1.00 |
| 200_D | 210_P | 2.951 | 1.00 |
| 329_R | 433_T | 2.939 | 1.00 |
| 35_K | 178_V | 2.878 | 1.00 |
| 329_R | 435_T | 2.873 | 1.00 |
| 19_E | 69_N | 2.872 | 1.00 |
| 189_A | 195_I | 2.810 | 1.00 |
| 55_H | 199_K | 2.739 | 1.00 |
| 260_T | 313_K | 2.729 | 1.00 |
| 62_E | 208_P | 2.602 | 1.00 |
| 299_H | 303_S | 2.591 | 1.00 |
| 294_D | 387_R | 2.582 | 1.00 |
| 129_D | 162_R | 2.534 | 1.00 |
| 260_T | 306_T | 2.357 | 1.00 |
| 121_F | 136_S | 2.340 | 1.00 |
| 259_N | 313_K | 2.339 | 1.00 |
| 270_N | 410_V | 2.327 | 1.00 |
| 260_T | 309_E | 2.324 | 1.00 |
| 201_K | 238_E | 2.308 | 1.00 |
| 32_E | 35_K | 2.279 | 1.00 |
| 245_E | 252_K | 2.248 | 1.00 |
| 16_K | 19_E | 2.241 | 1.00 |
| 301_N | 305_A | 2.233 | 1.00 |
| 239_E | 317_Q | 2.207 | 1.00 |
| 389_K | 392_I | 2.193 | 1.00 |
| 278_R | 283_Q | 2.192 | 1.00 |
| 181_E | 348_G | 2.137 | 1.00 |
| 84_Q | 172_T | 2.037 | 1.00 |
| 140_R | 165_N | 2.022 | 1.00 |
| 393_N | 400_Q | 2.022 | 1.00 |
| 326_T | 329_R | 2.021 | 1.00 |
| 202_K | 210_P | 2.000 | 1.00 |
| 91_K | 397_R | 1.987 | 1.00 |
| 265_N | 414_V | 1.948 | 1.00 |
| 263_Q | 267_T | 1.942 | 1.00 |
| 245_E | 249_N | 1.929 | 1.00 |
| 394_M | 397_R | 1.925 | 1.00 |
| 279_I | 283_Q | 1.911 | 1.00 |
| 358_G | 385_P | 1.907 | 1.00 |
| 206_T | 245_E | 1.868 | 1.00 |
| 338_L | 342_T | 1.854 | 1.00 |
| 439_G | 442_D | 1.851 | 1.00 |
| 274_R | 290_D | 1.803 | 1.00 |
| 202_K | 206_T | 1.792 | 1.00 |
| 476_R | 479_R | 1.789 | 1.00 |
| 279_I | 285_F | 1.784 | 1.00 |
| 134_V | 275_K | 1.773 | 1.00 |
| 204_N | 208_P | 1.773 | 1.00 |
| 257_Q | 261_P | 1.770 | 1.00 |
| 123_M | 134_V | 1.756 | 1.00 |
| 202_K | 239_E | 1.746 | 1.00 |
| 263_Q | 414_V | 1.740 | 1.00 |
| 162_R | 394_M | 1.729 | 1.00 |
| 126_E | 165_N | 1.708 | 1.00 |
| 76_T | 136_S | 1.691 | 1.00 |
| 315_V | 362_S | 1.681 | 1.00 |
| 397_R | 400_Q | 1.681 | 1.00 |
| 129_D | 139_Y | 1.656 | 1.00 |
| 240_V | 247_I | 1.644 | 1.00 |
| 140_R | 164_I | 1.628 | 1.00 |
| 240_V | 310_T | 1.615 | 1.00 |
| 275_K | 287_A | 1.602 | 1.00 |
| 470_K | 475_G | 1.596 | 1.00 |
| 144_V | 391_I | 1.595 | 1.00 |
| 315_V | 364_W | 1.576 | 1.00 |
| 240_V | 257_Q | 1.565 | 1.00 |
| 272_N | 276_S | 1.557 | 1.00 |
| 276_S | 290_D | 1.541 | 1.00 |
| 238_E | 259_N | 1.540 | 1.00 |
| 126_E | 132_Q | 1.520 | 1.00 |
| 127_L | 162_R | 1.519 | 1.00 |
| 16_K | 460_E | 1.514 | 1.00 |
| 127_L | 165_N | 1.505 | 1.00 |
| 439_G | 444_R | 1.499 | 1.00 |
| 165_N | 170_A | 1.492 | 1.00 |
| 271_N | 292_I | 1.484 | 1.00 |
| 129_D | 394_M | 1.476 | 1.00 |
| 304_K | 380_D | 1.475 | 1.00 |
| 276_S | 289_G | 1.474 | 1.00 |
| 276_S | 292_I | 1.443 | 1.00 |
| 103_N | 117_K | 1.436 | 1.00 |
| 309_E | 313_K | 1.436 | 1.00 |
| 35_K | 348_G | 1.428 | 1.00 |
| 123_M | 127_L | 1.425 | 1.00 |
| 271_N | 276_S | 1.423 | 1.00 |
| 249_N | 442_D | 1.415 | 1.00 |
| 139_Y | 162_R | 1.405 | 0.99 |
| 200_D | 206_T | 1.398 | 0.99 |
| 323_G | 326_T | 1.387 | 0.99 |
| 126_E | 170_A | 1.360 | 0.99 |
| 239_E | 259_N | 1.355 | 0.99 |
| 273_T | 276_S | 1.345 | 0.99 |
| 378_S | 381_S | 1.341 | 0.99 |
| 193_F | 458_K | 1.341 | 0.99 |
| 32_E | 38_V | 1.335 | 0.99 |
| 370_V | 375_S | 1.331 | 0.99 |
| 274_R | 292_I | 1.328 | 0.99 |
| 144_V | 162_R | 1.324 | 0.99 |
| 245_E | 251_A | 1.322 | 0.99 |
| 287_A | 290_D | 1.321 | 0.99 |
| 302_V | 358_G | 1.317 | 0.99 |
| 240_V | 315_V | 1.317 | 0.99 |
| 72_E | 444_R | 1.313 | 0.99 |
| 319_R | 362_S | 1.300 | 0.99 |
| 240_V | 262_V | 1.299 | 0.99 |
| 304_K | 308_N | 1.298 | 0.99 |
| 348_G | 411_I | 1.298 | 0.99 |
| 165_N | 171_I | 1.294 | 0.99 |
| 340_V | 344_S | 1.291 | 0.99 |
| 315_V | 319_R | 1.286 | 0.99 |
| 424_R | 427_G | 1.274 | 0.99 |
| 55_H | 200_D | 1.272 | 0.99 |
| 103_N | 114_G | 1.272 | 0.99 |
| 275_K | 289_G | 1.270 | 0.99 |
| 126_E | 131_K | 1.264 | 0.99 |
| 117_K | 143_V | 1.260 | 0.99 |
| 259_N | 263_Q | 1.259 | 0.99 |
| 316_K | 320_K | 1.257 | 0.99 |
| 162_R | 165_N | 1.254 | 0.99 |
| 338_L | 393_N | 1.243 | 0.98 |
| 267_T | 414_V | 1.241 | 0.98 |
| 116_L | 291_I | 1.233 | 0.98 |
| 35_K | 179_S | 1.231 | 0.98 |
| 199_K | 202_K | 1.229 | 0.98 |
| 302_V | 332_N | 1.228 | 0.98 |
| 30_A | 35_K | 1.227 | 0.98 |
| 261_P | 313_K | 1.225 | 0.98 |
| 306_T | 309_E | 1.224 | 0.98 |
| 84_Q | 168_T | 1.219 | 0.98 |
| 168_T | 172_T | 1.219 | 0.98 |
| 239_E | 320_K | 1.208 | 0.98 |
| 91_K | 172_T | 1.207 | 0.98 |
| 35_K | 38_V | 1.202 | 0.98 |
| 294_D | 297_Q | 1.201 | 0.98 |
| 114_G | 117_K | 1.201 | 0.98 |
| 312_G | 316_K | 1.184 | 0.98 |
| 265_N | 412_R | 1.182 | 0.98 |
| 273_T | 408_Q | 1.181 | 0.98 |
| 155_N | 159_K | 1.179 | 0.98 |
| 314_V | 421_I | 1.166 | 0.97 |
| 131_K | 170_A | 1.164 | 0.97 |
| 57_E | 210_P | 1.159 | 0.97 |
| 290_D | 408_Q | 1.151 | 0.97 |
| 309_E | 312_G | 1.147 | 0.97 |
| 299_H | 383_T | 1.141 | 0.97 |
| 319_R | 326_T | 1.136 | 0.97 |
| 122_N | 125_T | 1.135 | 0.97 |
| 249_N | 252_K | 1.133 | 0.97 |
| 317_Q | 338_L | 1.132 | 0.97 |
| 316_K | 319_R | 1.130 | 0.97 |
| 270_N | 385_P | 1.126 | 0.97 |
| 297_Q | 301_N | 1.122 | 0.97 |
| 350_E | 354_C | 1.117 | 0.96 |
| 247_I | 322_F | 1.116 | 0.96 |
| 278_R | 285_F | 1.113 | 0.96 |
| 131_K | 283_Q | 1.112 | 0.96 |
| 410_V | 414_V | 1.111 | 0.96 |
| 424_R | 434_E | 1.109 | 0.96 |
| 426_G | 434_E | 1.107 | 0.96 |
| 128_R | 131_K | 1.104 | 0.96 |
| 270_N | 292_I | 1.103 | 0.96 |
| 338_L | 397_R | 1.102 | 0.96 |
| 284_A | 287_A | 1.092 | 0.96 |
| 172_T | 400_Q | 1.092 | 0.96 |
| 2_E | 468_R | 1.087 | 0.96 |
| 408_Q | 412_R | 1.086 | 0.96 |
| 181_E | 193_F | 1.085 | 0.96 |
| 400_Q | 410_V | 1.085 | 0.96 |
| 317_Q | 397_R | 1.084 | 0.96 |
| 319_R | 364_W | 1.080 | 0.95 |
| 222_K | 261_P | 1.071 | 0.95 |
| 255_L | 421_I | 1.071 | 0.95 |
| 64_N | 245_E | 1.070 | 0.95 |
| 116_L | 270_N | 1.064 | 0.95 |
| 338_L | 400_Q | 1.060 | 0.95 |
| 338_L | 392_I | 1.060 | 0.95 |
| 472_R | 475_G | 1.052 | 0.95 |
| 272_N | 292_I | 1.050 | 0.94 |
| 131_K | 165_N | 1.047 | 0.94 |
| 1_A | 172_T | 1.047 | 0.94 |
| 276_S | 284_A | 1.045 | 0.94 |
| 343_H | 356_T | 1.043 | 0.94 |
| 347_C | 354_C | 1.043 | 0.94 |
| 469_C | 474_V | 1.040 | 0.94 |
| 64_N | 248_T | 1.039 | 0.94 |
| 193_F | 257_Q | 1.039 | 0.94 |
| 265_N | 306_T | 1.038 | 0.94 |
| 242_I | 247_I | 1.038 | 0.94 |
| 258_F | 317_Q | 1.035 | 0.94 |
| 136_S | 397_R | 1.034 | 0.94 |
| 283_Q | 475_G | 1.032 | 0.94 |
| 239_E | 313_K | 1.026 | 0.94 |
| 32_E | 179_S | 1.025 | 0.93 |
| 318_L | 436_F | 1.024 | 0.93 |
| 67_K | 252_K | 1.021 | 0.93 |
| 116_L | 139_Y | 1.015 | 0.93 |
| 403_Y | 413_C | 1.014 | 0.93 |
| 333_S | 340_V | 1.013 | 0.93 |
| 204_N | 245_E | 1.011 | 0.93 |
| 277_I | 284_A | 1.010 | 0.93 |
| 123_M | 162_R | 1.008 | 0.93 |
| 311_L | 315_V | 1.008 | 0.93 |
| 143_V | 391_I | 1.007 | 0.93 |
| 406_P | 413_C | 1.005 | 0.93 |
| 181_E | 222_K | 1.002 | 0.92 |
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 | 0.8732 | 100 | 0.005 | Contact Map |
| 4jzzA | 1 | 0.6965 | 100 | 0.243 | Contact Map |
| 3lqaG | 1 | 0.5967 | 100 | 0.345 | Contact Map |
| 2bf1A | 1 | 0.6175 | 100 | 0.355 | Contact Map |
| 4i3sG | 1 | 0.3742 | 100 | 0.672 | Contact Map |
| 3tygA | 1 | 0.3035 | 100 | 0.75 | Contact Map |
| 4jpkA | 1 | 0.3139 | 100 | 0.795 | Contact Map |
| 3u2sG | 2 | 0.183 | 100 | 0.836 | Contact Map |
| 1meqA | 1 | 0.0478 | 98.6 | 0.962 | Contact Map |
| 3mlzP | 1 | 0.0457 | 98.5 | 0.964 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)