| 5_blade 2EXH_A |
| ID: | 1483621916 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 533 (521) | ||
| Sequences: | 2118 (1376.6) | ||
| Seq/Len: | 4.065 | ||
| Nf(neff/√len): | 60.3 |
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: 4.065).
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 |
| 22_D | 40_H | 7.839 | 1.00 |
| 136_R | 160_E | 5.765 | 1.00 |
| 195_Y | 217_T | 5.599 | 1.00 |
| 43_D | 46_N | 4.725 | 1.00 |
| 82_K | 108_D | 4.436 | 1.00 |
| 253_T | 257_E | 3.939 | 1.00 |
| 363_R | 524_D | 3.724 | 1.00 |
| 53_P | 85_L | 3.686 | 1.00 |
| 133_E | 191_K | 3.585 | 1.00 |
| 107_C | 113_A | 3.547 | 1.00 |
| 21_D | 42_K | 3.415 | 1.00 |
| 250_I | 293_L | 3.225 | 1.00 |
| 460_Y | 475_S | 3.158 | 1.00 |
| 76_L | 85_L | 2.978 | 1.00 |
| 358_R | 361_H | 2.943 | 1.00 |
| 199_L | 211_A | 2.721 | 1.00 |
| 36_V | 85_L | 2.717 | 1.00 |
| 82_K | 106_T | 2.681 | 1.00 |
| 22_D | 42_K | 2.643 | 1.00 |
| 219_L | 223_Y | 2.586 | 1.00 |
| 199_L | 213_I | 2.556 | 1.00 |
| 260_L | 302_V | 2.497 | 1.00 |
| 23_Y | 253_T | 2.443 | 1.00 |
| 462_R | 481_W | 2.403 | 1.00 |
| 71_V | 87_Y | 2.401 | 1.00 |
| 6_I | 261_V | 2.369 | 1.00 |
| 218_S | 223_Y | 2.344 | 1.00 |
| 393_K | 458_Y | 2.322 | 1.00 |
| 330_D | 341_F | 2.274 | 1.00 |
| 215_R | 299_W | 2.270 | 1.00 |
| 11_H | 39_Y | 2.264 | 1.00 |
| 158_L | 175_I | 2.260 | 1.00 |
| 36_V | 87_Y | 2.250 | 1.00 |
| 85_L | 105_V | 2.192 | 1.00 |
| 390_A | 528_F | 2.178 | 1.00 |
| 211_A | 248_A | 2.140 | 1.00 |
| 393_K | 460_Y | 2.078 | 1.00 |
| 342_Q | 508_F | 2.068 | 1.00 |
| 27_V | 186_G | 2.031 | 1.00 |
| 405_A | 523_A | 2.013 | 1.00 |
| 184_T | 200_T | 1.995 | 1.00 |
| 393_K | 526_D | 1.940 | 1.00 |
| 40_H | 48_R | 1.937 | 1.00 |
| 390_A | 407_L | 1.912 | 1.00 |
| 56_R | 59_Q | 1.900 | 1.00 |
| 331_D | 529_L | 1.885 | 1.00 |
| 408_V | 510_G | 1.875 | 1.00 |
| 58_S | 116_D | 1.871 | 1.00 |
| 358_R | 524_D | 1.870 | 1.00 |
| 86_I | 139_L | 1.868 | 1.00 |
| 176_F | 214_A | 1.868 | 1.00 |
| 173_K | 220_Y | 1.861 | 1.00 |
| 195_Y | 215_R | 1.852 | 1.00 |
| 389_V | 462_R | 1.840 | 1.00 |
| 109_T | 113_A | 1.835 | 1.00 |
| 475_S | 481_W | 1.812 | 1.00 |
| 26_A | 76_L | 1.812 | 1.00 |
| 354_T | 358_R | 1.797 | 1.00 |
| 213_I | 231_L | 1.760 | 0.99 |
| 2_I | 45_K | 1.758 | 0.99 |
| 262_H | 291_Q | 1.752 | 0.99 |
| 162_S | 167_K | 1.721 | 0.99 |
| 419_L | 484_L | 1.717 | 0.99 |
| 363_R | 522_Y | 1.705 | 0.99 |
| 329_K | 529_L | 1.705 | 0.99 |
| 54_L | 71_V | 1.697 | 0.99 |
| 392_T | 527_Y | 1.687 | 0.99 |
| 215_R | 224_E | 1.676 | 0.99 |
| 19_V | 83_F | 1.672 | 0.99 |
| 160_E | 169_V | 1.668 | 0.99 |
| 140_V | 158_L | 1.668 | 0.99 |
| 26_A | 85_L | 1.666 | 0.99 |
| 158_L | 223_Y | 1.657 | 0.99 |
| 252_H | 256_D | 1.654 | 0.99 |
| 391_E | 462_R | 1.644 | 0.99 |
| 80_D | 84_W | 1.629 | 0.99 |
| 511_M | 525_F | 1.628 | 0.99 |
| 159_Q | 168_L | 1.624 | 0.99 |
| 158_L | 220_Y | 1.619 | 0.99 |
| 244_K | 265_G | 1.616 | 0.99 |
| 358_R | 395_S | 1.612 | 0.99 |
| 36_V | 53_P | 1.602 | 0.99 |
| 333_D | 526_D | 1.587 | 0.99 |
| 158_L | 219_L | 1.578 | 0.98 |
| 404_S | 512_H | 1.574 | 0.98 |
| 29_T | 37_R | 1.559 | 0.98 |
| 2_I | 259_F | 1.539 | 0.98 |
| 26_A | 53_P | 1.532 | 0.98 |
| 36_V | 71_V | 1.524 | 0.98 |
| 162_S | 166_K | 1.519 | 0.98 |
| 213_I | 300_P | 1.508 | 0.98 |
| 104_L | 166_K | 1.508 | 0.98 |
| 130_F | 196_Y | 1.507 | 0.98 |
| 107_C | 111_D | 1.506 | 0.98 |
| 39_Y | 49_L | 1.505 | 0.98 |
| 253_T | 259_F | 1.504 | 0.98 |
| 192_I | 252_H | 1.498 | 0.98 |
| 36_V | 74_P | 1.497 | 0.98 |
| 194_G | 217_T | 1.486 | 0.97 |
| 395_S | 458_Y | 1.477 | 0.97 |
| 354_T | 357_A | 1.469 | 0.97 |
| 53_P | 105_V | 1.468 | 0.97 |
| 191_K | 194_G | 1.449 | 0.97 |
| 248_A | 260_L | 1.448 | 0.97 |
| 291_Q | 302_V | 1.444 | 0.97 |
| 195_Y | 216_S | 1.433 | 0.97 |
| 391_E | 527_Y | 1.432 | 0.97 |
| 473_S | 483_D | 1.431 | 0.97 |
| 15_S | 76_L | 1.428 | 0.97 |
| 49_L | 52_R | 1.426 | 0.97 |
| 252_H | 258_W | 1.422 | 0.96 |
| 330_D | 338_N | 1.419 | 0.96 |
| 245_A | 264_T | 1.413 | 0.96 |
| 224_E | 299_W | 1.408 | 0.96 |
| 141_N | 159_Q | 1.407 | 0.96 |
| 156_I | 200_T | 1.407 | 0.96 |
| 133_E | 194_G | 1.399 | 0.96 |
| 215_R | 295_W | 1.396 | 0.96 |
| 36_V | 105_V | 1.394 | 0.96 |
| 216_S | 223_Y | 1.393 | 0.96 |
| 264_T | 289_A | 1.389 | 0.96 |
| 231_L | 302_V | 1.386 | 0.96 |
| 259_F | 292_R | 1.383 | 0.96 |
| 26_A | 74_P | 1.375 | 0.95 |
| 162_S | 165_Q | 1.375 | 0.95 |
| 52_R | 342_Q | 1.366 | 0.95 |
| 16_I | 261_V | 1.360 | 0.95 |
| 361_H | 524_D | 1.360 | 0.95 |
| 460_Y | 481_W | 1.355 | 0.95 |
| 18_R | 252_H | 1.346 | 0.95 |
| 340_H | 381_R | 1.345 | 0.95 |
| 18_R | 21_D | 1.339 | 0.95 |
| 19_V | 78_Y | 1.338 | 0.95 |
| 295_W | 300_P | 1.337 | 0.94 |
| 18_R | 254_H | 1.334 | 0.94 |
| 130_F | 189_L | 1.332 | 0.94 |
| 261_V | 288_T | 1.328 | 0.94 |
| 332_F | 362_L | 1.325 | 0.94 |
| 175_I | 219_L | 1.320 | 0.94 |
| 361_H | 526_D | 1.316 | 0.94 |
| 54_L | 105_V | 1.312 | 0.94 |
| 131_H | 137_K | 1.305 | 0.94 |
| 393_K | 527_Y | 1.305 | 0.94 |
| 6_I | 16_I | 1.281 | 0.93 |
| 19_V | 22_D | 1.276 | 0.93 |
| 242_L | 289_A | 1.272 | 0.92 |
| 366_G | 515_D | 1.256 | 0.92 |
| 161_Y | 166_K | 1.249 | 0.91 |
| 259_F | 290_I | 1.248 | 0.91 |
| 26_A | 36_V | 1.244 | 0.91 |
| 364_L | 377_A | 1.232 | 0.91 |
| 45_K | 315_P | 1.229 | 0.91 |
| 20_G | 40_H | 1.228 | 0.91 |
| 355_L | 358_R | 1.228 | 0.91 |
| 27_V | 39_Y | 1.224 | 0.90 |
| 462_R | 473_S | 1.211 | 0.90 |
| 191_K | 196_Y | 1.203 | 0.89 |
| 56_R | 116_D | 1.200 | 0.89 |
| 338_N | 341_F | 1.196 | 0.89 |
| 192_I | 258_W | 1.196 | 0.89 |
| 390_A | 509_V | 1.191 | 0.89 |
| 1_K | 313_D | 1.191 | 0.89 |
| 37_R | 52_R | 1.190 | 0.89 |
| 50_V | 339_H | 1.190 | 0.89 |
| 137_K | 161_Y | 1.188 | 0.88 |
| 2_I | 290_I | 1.186 | 0.88 |
| 192_I | 295_W | 1.185 | 0.88 |
| 17_C | 83_F | 1.185 | 0.88 |
| 199_L | 293_L | 1.169 | 0.87 |
| 390_A | 463_V | 1.167 | 0.87 |
| 463_V | 472_Y | 1.165 | 0.87 |
| 199_L | 250_I | 1.159 | 0.87 |
| 249_S | 261_V | 1.157 | 0.87 |
| 401_F | 424_H | 1.152 | 0.86 |
| 293_L | 302_V | 1.150 | 0.86 |
| 401_F | 426_E | 1.150 | 0.86 |
| 24_Y | 111_D | 1.149 | 0.86 |
| 391_E | 460_Y | 1.149 | 0.86 |
| 396_F | 403_Q | 1.149 | 0.86 |
| 190_Y | 250_I | 1.138 | 0.85 |
| 161_Y | 169_V | 1.135 | 0.85 |
| 138_Y | 220_Y | 1.133 | 0.85 |
| 387_H | 466_Q | 1.121 | 0.84 |
| 136_R | 169_V | 1.121 | 0.84 |
| 355_L | 359_P | 1.120 | 0.84 |
| 21_D | 254_H | 1.118 | 0.84 |
| 471_K | 483_D | 1.112 | 0.84 |
| 80_D | 135_G | 1.109 | 0.83 |
| 105_V | 117_P | 1.107 | 0.83 |
| 409_N | 463_V | 1.100 | 0.83 |
| 219_L | 222_P | 1.100 | 0.83 |
| 50_V | 111_D | 1.097 | 0.82 |
| 367_R | 377_A | 1.095 | 0.82 |
| 406_G | 512_H | 1.095 | 0.82 |
| 395_S | 457_E | 1.091 | 0.82 |
| 192_I | 195_Y | 1.087 | 0.82 |
| 16_I | 251_V | 1.086 | 0.82 |
| 392_T | 525_F | 1.085 | 0.82 |
| 7_L | 11_H | 1.083 | 0.81 |
| 175_I | 198_L | 1.079 | 0.81 |
| 380_A | 508_F | 1.073 | 0.81 |
| 139_L | 186_G | 1.068 | 0.80 |
| 190_Y | 199_L | 1.059 | 0.79 |
| 23_Y | 254_H | 1.058 | 0.79 |
| 17_C | 76_L | 1.056 | 0.79 |
| 12_P | 30_F | 1.054 | 0.79 |
| 130_F | 219_L | 1.050 | 0.78 |
| 138_Y | 474_Y | 1.050 | 0.78 |
| 24_Y | 83_F | 1.048 | 0.78 |
| 405_A | 525_F | 1.043 | 0.78 |
| 388_F | 465_V | 1.037 | 0.77 |
| 190_Y | 249_S | 1.034 | 0.77 |
| 394_V | 523_A | 1.034 | 0.77 |
| 8_T | 385_H | 1.032 | 0.77 |
| 77_S | 249_S | 1.029 | 0.77 |
| 69_G | 91_K | 1.029 | 0.77 |
| 9_G | 14_P | 1.026 | 0.76 |
| 202_E | 212_T | 1.025 | 0.76 |
| 200_T | 212_T | 1.022 | 0.76 |
| 128_S | 140_V | 1.018 | 0.75 |
| 342_Q | 382_R | 1.014 | 0.75 |
| 296_K | 300_P | 1.011 | 0.75 |
| 143_Y | 157_V | 1.010 | 0.75 |
| 330_D | 526_D | 1.010 | 0.75 |
| 107_C | 112_G | 1.010 | 0.75 |
| 130_F | 134_D | 1.006 | 0.74 |
| 209_H | 246_G | 1.004 | 0.74 |
| 358_R | 363_R | 1.004 | 0.74 |
| 359_P | 524_D | 1.004 | 0.74 |
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 | |
| 3c2uA | 4 | 0.9981 | 100 | 0.271 | Contact Map |
| 1yifA | 4 | 0.9981 | 100 | 0.271 | Contact Map |
| 2exhA | 4 | 1 | 100 | 0.271 | Contact Map |
| 1yrzA | 2 | 0.9737 | 100 | 0.274 | Contact Map |
| 3zxkA | 2 | 0.8949 | 100 | 0.35 | Contact Map |
| 4kc7A | 3 | 0.6904 | 100 | 0.611 | Contact Map |
| 2x8sA | 2 | 0.6904 | 100 | 0.617 | Contact Map |
| 4kcaA | 2 | 0.7317 | 100 | 0.617 | Contact Map |
| 3akhA | 1 | 0.7655 | 100 | 0.642 | Contact Map |
| 3cu9A | 1 | 0.5141 | 100 | 0.645 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)