| ogt |
| ID: | 1497452441 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 1000 (468) | ||
| Sequences: | 68510 (46337.1) | ||
| Seq/Len: | 146.389 | ||
| Nf(neff/√len): | 2141.9 |
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: 146.389).
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 |
| 288_S | 291_E | 3.886 | 1.00 |
| 356_K | 359_E | 3.811 | 1.00 |
| 152_R | 155_E | 3.772 | 1.00 |
| 322_N | 325_E | 3.755 | 1.00 |
| 390_D | 393_G | 3.696 | 1.00 |
| 254_L | 257_L | 3.664 | 1.00 |
| 424_N | 427_E | 3.530 | 1.00 |
| 118_D | 121_G | 3.446 | 1.00 |
| 84_Q | 87_E | 3.372 | 1.00 |
| 220_I | 223_R | 3.292 | 1.00 |
| 186_E | 189_L | 3.237 | 1.00 |
| 50_R | 53_R | 2.231 | 1.00 |
| 280_A | 296_Y | 2.148 | 1.00 |
| 344_H | 363_H | 2.140 | 1.00 |
| 378_Y | 397_C | 2.073 | 1.00 |
| 412_H | 431_S | 2.059 | 1.00 |
| 276_Y | 295_C | 1.964 | 1.00 |
| 16_D | 19_A | 1.955 | 1.00 |
| 348_A | 364_Y | 1.951 | 1.00 |
| 347_L | 363_H | 1.943 | 1.00 |
| 381_M | 397_C | 1.927 | 1.00 |
| 242_H | 261_T | 1.924 | 1.00 |
| 157_K | 161_L | 1.923 | 1.00 |
| 314_A | 330_Y | 1.919 | 1.00 |
| 313_L | 329_L | 1.916 | 1.00 |
| 382_G | 398_Y | 1.910 | 1.00 |
| 263_R | 279_L | 1.904 | 1.00 |
| 246_A | 262_Y | 1.857 | 1.00 |
| 279_L | 295_C | 1.840 | 1.00 |
| 293_E | 297_N | 1.825 | 1.00 |
| 327_V | 331_R | 1.823 | 1.00 |
| 245_L | 261_T | 1.821 | 1.00 |
| 395_L | 399_T | 1.817 | 1.00 |
| 212_G | 228_Y | 1.801 | 1.00 |
| 297_N | 313_L | 1.771 | 1.00 |
| 361_L | 365_K | 1.737 | 1.00 |
| 110_A | 126_Y | 1.735 | 1.00 |
| 174_W | 193_H | 1.729 | 1.00 |
| 259_I | 263_R | 1.721 | 1.00 |
| 310_L | 329_L | 1.721 | 1.00 |
| 365_K | 381_M | 1.711 | 1.00 |
| 89_I | 93_R | 1.695 | 1.00 |
| 211_L | 227_A | 1.688 | 1.00 |
| 177_L | 193_H | 1.682 | 1.00 |
| 76_G | 92_Y | 1.675 | 1.00 |
| 331_R | 347_L | 1.669 | 1.00 |
| 123_V | 127_V | 1.666 | 1.00 |
| 279_L | 283_L | 1.666 | 1.00 |
| 208_Y | 227_A | 1.664 | 1.00 |
| 229_L | 245_L | 1.653 | 1.00 |
| 416_A | 432_Y | 1.645 | 1.00 |
| 144_G | 160_Y | 1.636 | 1.00 |
| 347_L | 351_L | 1.627 | 1.00 |
| 415_L | 431_S | 1.617 | 1.00 |
| 178_G | 194_F | 1.611 | 1.00 |
| 195_E | 211_L | 1.578 | 1.00 |
| 257_L | 260_D | 1.573 | 1.00 |
| 429_I | 433_R | 1.567 | 1.00 |
| 72_Y | 91_H | 1.565 | 1.00 |
| 93_R | 109_L | 1.564 | 1.00 |
| 351_L | 359_E | 1.538 | 1.00 |
| 399_T | 415_L | 1.532 | 1.00 |
| 291_E | 294_D | 1.526 | 1.00 |
| 109_L | 113_L | 1.523 | 1.00 |
| 109_L | 125_A | 1.520 | 1.00 |
| 225_V | 229_L | 1.487 | 1.00 |
| 317_K | 325_E | 1.486 | 1.00 |
| 143_L | 147_L | 1.471 | 1.00 |
| 381_M | 385_L | 1.470 | 1.00 |
| 283_L | 291_E | 1.468 | 1.00 |
| 325_E | 328_R | 1.459 | 1.00 |
| 161_L | 177_L | 1.455 | 1.00 |
| 277_C | 309_S | 1.452 | 1.00 |
| 191_I | 195_E | 1.435 | 1.00 |
| 127_V | 143_L | 1.430 | 1.00 |
| 249_Y | 257_L | 1.428 | 1.00 |
| 313_L | 317_K | 1.424 | 1.00 |
| 400_R | 403_Q | 1.416 | 1.00 |
| 75_L | 91_H | 1.411 | 1.00 |
| 385_L | 393_G | 1.411 | 1.00 |
| 317_K | 322_N | 1.409 | 1.00 |
| 434_T | 437_K | 1.408 | 1.00 |
| 228_Y | 244_N | 1.403 | 0.99 |
| 106_Y | 125_A | 1.402 | 0.99 |
| 283_L | 295_C | 1.400 | 0.99 |
| 364_Y | 380_N | 1.393 | 0.99 |
| 262_Y | 278_N | 1.388 | 0.99 |
| 211_L | 215_L | 1.380 | 0.99 |
| 393_G | 396_Q | 1.374 | 0.99 |
| 177_L | 181_F | 1.371 | 0.99 |
| 415_L | 419_H | 1.366 | 0.99 |
| 311_N | 346_N | 1.364 | 0.99 |
| 427_E | 430_A | 1.363 | 0.99 |
| 419_H | 427_E | 1.357 | 0.99 |
| 75_L | 79_Y | 1.352 | 0.99 |
| 385_L | 390_D | 1.340 | 0.99 |
| 245_L | 249_Y | 1.332 | 0.99 |
| 351_L | 356_K | 1.331 | 0.99 |
| 249_Y | 254_L | 1.328 | 0.99 |
| 359_E | 362_M | 1.326 | 0.99 |
| 160_Y | 176_N | 1.324 | 0.99 |
| 366_E | 369_R | 1.321 | 0.99 |
| 155_E | 158_A | 1.320 | 0.99 |
| 140_R | 159_C | 1.319 | 0.99 |
| 121_G | 124_Q | 1.313 | 0.99 |
| 317_K | 329_L | 1.311 | 0.99 |
| 92_Y | 108_N | 1.308 | 0.99 |
| 189_L | 192_H | 1.303 | 0.99 |
| 419_H | 424_N | 1.297 | 0.99 |
| 379_S | 414_N | 1.286 | 0.99 |
| 243_G | 278_N | 1.286 | 0.99 |
| 87_E | 90_E | 1.284 | 0.99 |
| 296_Y | 312_N | 1.282 | 0.99 |
| 277_C | 312_N | 1.281 | 0.99 |
| 330_Y | 346_N | 1.281 | 0.99 |
| 283_L | 288_S | 1.280 | 0.99 |
| 223_R | 226_A | 1.277 | 0.99 |
| 113_L | 121_G | 1.271 | 0.99 |
| 79_Y | 87_E | 1.270 | 0.99 |
| 293_E | 317_K | 1.256 | 0.99 |
| 249_Y | 261_T | 1.253 | 0.99 |
| 126_Y | 142_D | 1.248 | 0.99 |
| 327_V | 347_L | 1.248 | 0.99 |
| 351_L | 363_H | 1.238 | 0.98 |
| 113_L | 118_D | 1.233 | 0.98 |
| 416_A | 435_A | 1.221 | 0.98 |
| 401_A | 411_A | 1.221 | 0.98 |
| 113_L | 125_A | 1.220 | 0.98 |
| 361_L | 381_M | 1.220 | 0.98 |
| 332_K | 335_E | 1.218 | 0.98 |
| 345_S | 377_A | 1.217 | 0.98 |
| 311_N | 343_A | 1.206 | 0.98 |
| 225_V | 248_V | 1.200 | 0.98 |
| 259_I | 282_A | 1.198 | 0.98 |
| 194_F | 210_N | 1.194 | 0.98 |
| 147_L | 152_R | 1.192 | 0.98 |
| 345_S | 380_N | 1.190 | 0.98 |
| 230_R | 233_S | 1.189 | 0.98 |
| 385_L | 397_C | 1.186 | 0.98 |
| 215_L | 227_A | 1.181 | 0.98 |
| 79_Y | 91_H | 1.180 | 0.98 |
| 327_V | 350_V | 1.180 | 0.98 |
| 215_L | 223_R | 1.174 | 0.98 |
| 293_E | 320_Q | 1.173 | 0.98 |
| 243_G | 275_A | 1.170 | 0.97 |
| 306_H | 309_S | 1.166 | 0.97 |
| 398_Y | 414_N | 1.164 | 0.97 |
| 395_L | 418_I | 1.164 | 0.97 |
| 143_L | 159_C | 1.162 | 0.97 |
| 333_A | 343_A | 1.161 | 0.97 |
| 367_A | 377_A | 1.158 | 0.97 |
| 405_N | 408_F | 1.158 | 0.97 |
| 79_Y | 84_Q | 1.157 | 0.97 |
| 73_S | 105_G | 1.157 | 0.97 |
| 371_S | 374_F | 1.154 | 0.97 |
| 215_L | 220_I | 1.153 | 0.97 |
| 181_F | 186_E | 1.149 | 0.97 |
| 327_V | 354_Q | 1.144 | 0.97 |
| 181_F | 189_L | 1.142 | 0.97 |
| 408_F | 411_A | 1.137 | 0.97 |
| 439_K | 442_F | 1.136 | 0.97 |
| 293_E | 313_L | 1.134 | 0.97 |
| 265_A | 275_A | 1.133 | 0.97 |
| 298_T | 301_R | 1.133 | 0.97 |
| 181_F | 193_H | 1.124 | 0.97 |
| 235_S | 238_H | 1.122 | 0.97 |
| 276_Y | 299_A | 1.119 | 0.96 |
| 332_K | 336_V | 1.116 | 0.96 |
| 259_I | 279_L | 1.114 | 0.96 |
| 315_N | 346_N | 1.113 | 0.96 |
| 147_L | 155_E | 1.110 | 0.96 |
| 259_I | 286_K | 1.105 | 0.96 |
| 196_K | 199_T | 1.097 | 0.96 |
| 299_A | 309_S | 1.097 | 0.96 |
| 433_R | 449_L | 1.093 | 0.96 |
| 204_F | 207_A | 1.090 | 0.96 |
| 344_H | 366_E | 1.088 | 0.96 |
| 366_E | 370_I | 1.081 | 0.95 |
| 147_L | 159_C | 1.079 | 0.95 |
| 419_H | 431_S | 1.079 | 0.95 |
| 264_R | 267_E | 1.078 | 0.95 |
| 76_G | 95_A | 1.075 | 0.95 |
| 293_E | 316_I | 1.070 | 0.95 |
| 374_F | 377_A | 1.070 | 0.95 |
| 379_S | 411_A | 1.067 | 0.95 |
| 212_G | 231_A | 1.064 | 0.95 |
| 264_R | 268_L | 1.063 | 0.95 |
| 222_D | 252_Q | 1.063 | 0.95 |
| 361_L | 384_T | 1.062 | 0.95 |
| 281_N | 312_N | 1.061 | 0.95 |
| 256_D | 286_K | 1.060 | 0.95 |
| 289_V | 316_I | 1.054 | 0.95 |
| 458_D | 461_D | 1.053 | 0.95 |
| 348_A | 367_A | 1.052 | 0.95 |
| 280_A | 299_A | 1.049 | 0.94 |
| 400_R | 404_I | 1.049 | 0.94 |
| 303_C | 306_H | 1.046 | 0.94 |
| 89_I | 113_L | 1.044 | 0.94 |
| 73_S | 108_N | 1.042 | 0.94 |
| 246_A | 265_A | 1.040 | 0.94 |
| 242_H | 264_R | 1.039 | 0.94 |
| 146_L | 150_L | 1.036 | 0.94 |
| 128_S | 131_Q | 1.036 | 0.94 |
| 41_L | 45_H | 1.035 | 0.94 |
| 198_V | 208_Y | 1.035 | 0.94 |
| 259_I | 283_L | 1.035 | 0.94 |
| 247_C | 278_N | 1.031 | 0.94 |
| 298_T | 302_L | 1.029 | 0.94 |
| 77_N | 81_E | 1.028 | 0.94 |
| 340_F | 343_A | 1.024 | 0.93 |
| 157_K | 180_V | 1.022 | 0.93 |
| 250_Y | 282_A | 1.021 | 0.93 |
| 231_A | 241_V | 1.021 | 0.93 |
| 392_Q | 422_S | 1.016 | 0.93 |
| 94_H | 97_R | 1.016 | 0.93 |
| 386_K | 418_I | 1.014 | 0.93 |
| 396_Q | 400_R | 1.013 | 0.93 |
| 144_G | 163_A | 1.012 | 0.93 |
| 442_F | 445_A | 1.012 | 0.93 |
| 255_I | 282_A | 1.011 | 0.93 |
| 324_E | 354_Q | 1.010 | 0.93 |
| 209_I | 244_N | 1.010 | 0.93 |
| 395_L | 422_S | 1.007 | 0.93 |
| 157_K | 177_L | 1.006 | 0.93 |
| 201_D | 204_F | 1.006 | 0.93 |
| 266_I | 276_Y | 1.002 | 0.92 |
| 247_C | 251_E | 1.001 | 0.92 |
| 331_R | 359_E | 1.000 | 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 | |
| 4gywA | 2 | 0.678 | 100 | 0.385 | Contact Map |
| 2vsyA | 2 | 0.531 | 100 | 0.64 | Contact Map |
| 3q3eA | 2 | 0.578 | 100 | 0.732 | Contact Map |
| 1w3bA | 2 | 0.388 | 100 | 0.737 | Contact Map |
| 4ui9J | 1 | 0 | 100 | 0.739 | Contact Map |
| 2xpiA | 2 | 0.449 | 100 | 0.739 | Contact Map |
| 4rg9A | 2 | 0.428 | 100 | 0.743 | Contact Map |
| 4kvmA | 4 | 0.497 | 100 | 0.743 | Contact Map |
| 4ui9X | 2 | 0 | 100 | 0.748 | Contact Map |
| 4ui9C | 2 | 0 | 100 | 0.754 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)