| CHANDRU JAYASANKARAN |
| ID: | 1476722415 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 420 (401) | ||
| Sequences: | 7588 (3687.7) | ||
| Seq/Len: | 18.923 | ||
| Nf(neff/√len): | 184.2 |
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: 18.923).
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 |
| 117_G | 299_I | 4.473 | 1.00 |
| 152_V | 188_G | 3.868 | 1.00 |
| 107_L | 309_G | 3.811 | 1.00 |
| 39_T | 307_F | 3.427 | 1.00 |
| 43_F | 303_I | 3.389 | 1.00 |
| 180_T | 185_F | 3.218 | 1.00 |
| 401_V | 413_A | 2.975 | 1.00 |
| 192_I | 365_A | 2.731 | 1.00 |
| 176_N | 179_D | 2.676 | 1.00 |
| 192_I | 369_A | 2.648 | 1.00 |
| 308_S | 313_C | 2.623 | 1.00 |
| 326_Q | 336_A | 2.596 | 1.00 |
| 181_N | 184_D | 2.574 | 1.00 |
| 146_V | 170_L | 2.474 | 1.00 |
| 122_G | 295_N | 2.462 | 1.00 |
| 108_L | 266_S | 2.454 | 1.00 |
| 38_L | 341_A | 2.415 | 1.00 |
| 401_V | 405_L | 2.406 | 1.00 |
| 115_I | 119_L | 2.375 | 1.00 |
| 400_I | 404_I | 2.355 | 1.00 |
| 107_L | 306_I | 2.335 | 1.00 |
| 223_A | 362_V | 2.298 | 1.00 |
| 38_L | 338_I | 2.275 | 1.00 |
| 58_S | 314_F | 2.259 | 1.00 |
| 397_F | 417_F | 2.243 | 1.00 |
| 191_T | 219_V | 2.218 | 1.00 |
| 225_A | 229_G | 2.046 | 1.00 |
| 191_T | 365_A | 2.008 | 1.00 |
| 398_T | 414_G | 1.889 | 1.00 |
| 112_I | 263_L | 1.817 | 1.00 |
| 116_F | 121_I | 1.810 | 1.00 |
| 115_I | 118_G | 1.787 | 1.00 |
| 52_G | 322_R | 1.783 | 1.00 |
| 110_G | 306_I | 1.770 | 1.00 |
| 111_I | 306_I | 1.757 | 1.00 |
| 32_S | 316_A | 1.754 | 1.00 |
| 145_L | 368_I | 1.752 | 1.00 |
| 184_D | 361_S | 1.749 | 1.00 |
| 288_Y | 327_E | 1.741 | 1.00 |
| 112_I | 266_S | 1.739 | 1.00 |
| 382_P | 386_R | 1.732 | 1.00 |
| 39_T | 303_I | 1.726 | 1.00 |
| 36_P | 316_A | 1.715 | 1.00 |
| 193_V | 197_A | 1.694 | 1.00 |
| 346_I | 350_A | 1.677 | 1.00 |
| 284_Y | 323_T | 1.677 | 1.00 |
| 112_I | 270_A | 1.673 | 1.00 |
| 117_G | 122_G | 1.641 | 1.00 |
| 191_T | 362_V | 1.636 | 1.00 |
| 188_G | 365_A | 1.622 | 1.00 |
| 141_A | 371_L | 1.618 | 1.00 |
| 331_G | 336_A | 1.605 | 1.00 |
| 186_T | 190_L | 1.605 | 1.00 |
| 40_Y | 51_V | 1.601 | 1.00 |
| 106_T | 309_G | 1.593 | 1.00 |
| 402_S | 410_G | 1.590 | 1.00 |
| 195_C | 219_V | 1.587 | 1.00 |
| 153_L | 173_I | 1.586 | 1.00 |
| 396_V | 400_I | 1.584 | 1.00 |
| 152_V | 364_A | 1.576 | 1.00 |
| 339_I | 343_I | 1.530 | 1.00 |
| 139_A | 403_I | 1.526 | 1.00 |
| 24_V | 314_F | 1.520 | 1.00 |
| 189_L | 193_V | 1.516 | 1.00 |
| 228_Y | 357_P | 1.513 | 1.00 |
| 171_V | 175_Q | 1.504 | 1.00 |
| 41_F | 337_G | 1.485 | 1.00 |
| 182_L | 186_T | 1.484 | 1.00 |
| 10_V | 325_V | 1.480 | 1.00 |
| 57_V | 269_I | 1.474 | 1.00 |
| 326_Q | 331_G | 1.474 | 1.00 |
| 296_Q | 299_I | 1.467 | 1.00 |
| 412_L | 416_I | 1.465 | 1.00 |
| 1_V | 339_I | 1.464 | 1.00 |
| 111_I | 115_I | 1.460 | 1.00 |
| 142_F | 399_C | 1.457 | 1.00 |
| 406_G | 409_L | 1.439 | 1.00 |
| 379_C | 382_P | 1.437 | 1.00 |
| 338_I | 342_A | 1.433 | 1.00 |
| 342_A | 346_I | 1.431 | 1.00 |
| 114_L | 299_I | 1.428 | 1.00 |
| 48_H | 327_E | 1.419 | 1.00 |
| 35_F | 311_F | 1.413 | 1.00 |
| 117_G | 302_G | 1.409 | 1.00 |
| 405_L | 409_L | 1.407 | 0.99 |
| 347_A | 351_L | 1.402 | 0.99 |
| 108_L | 262_M | 1.395 | 0.99 |
| 196_M | 369_A | 1.390 | 0.99 |
| 61_V | 315_V | 1.368 | 0.99 |
| 138_T | 399_C | 1.365 | 0.99 |
| 151_I | 364_A | 1.348 | 0.99 |
| 112_I | 267_F | 1.347 | 0.99 |
| 105_L | 269_I | 1.347 | 0.99 |
| 4_G | 8_G | 1.346 | 0.99 |
| 152_V | 368_I | 1.337 | 0.99 |
| 69_A | 101_I | 1.332 | 0.99 |
| 185_F | 189_L | 1.330 | 0.99 |
| 277_A | 281_G | 1.319 | 0.99 |
| 231_N | 234_K | 1.296 | 0.99 |
| 194_V | 219_V | 1.285 | 0.99 |
| 307_F | 311_F | 1.283 | 0.99 |
| 195_C | 365_A | 1.282 | 0.99 |
| 114_L | 306_I | 1.282 | 0.99 |
| 221_I | 225_A | 1.270 | 0.99 |
| 62_G | 66_L | 1.270 | 0.99 |
| 192_I | 196_M | 1.266 | 0.99 |
| 3_S | 7_T | 1.256 | 0.99 |
| 335_V | 339_I | 1.248 | 0.99 |
| 224_T | 227_S | 1.245 | 0.98 |
| 51_V | 301_F | 1.245 | 0.98 |
| 225_A | 228_Y | 1.241 | 0.98 |
| 106_T | 315_V | 1.238 | 0.98 |
| 222_I | 226_I | 1.236 | 0.98 |
| 299_I | 303_I | 1.233 | 0.98 |
| 100_L | 252_E | 1.231 | 0.98 |
| 187_A | 238_A | 1.227 | 0.98 |
| 104_A | 259_F | 1.224 | 0.98 |
| 109_V | 269_I | 1.220 | 0.98 |
| 103_S | 309_G | 1.220 | 0.98 |
| 15_G | 54_F | 1.217 | 0.98 |
| 120_Q | 295_N | 1.216 | 0.98 |
| 392_A | 396_V | 1.212 | 0.98 |
| 183_A | 186_T | 1.208 | 0.98 |
| 319_A | 322_R | 1.189 | 0.98 |
| 48_H | 290_Y | 1.186 | 0.98 |
| 226_I | 230_A | 1.186 | 0.98 |
| 54_F | 319_A | 1.182 | 0.98 |
| 266_S | 270_A | 1.179 | 0.98 |
| 41_F | 338_I | 1.179 | 0.98 |
| 105_L | 262_M | 1.178 | 0.98 |
| 325_V | 329_T | 1.177 | 0.98 |
| 146_V | 149_L | 1.172 | 0.98 |
| 118_G | 299_I | 1.171 | 0.98 |
| 34_F | 341_A | 1.170 | 0.97 |
| 141_A | 375_F | 1.164 | 0.97 |
| 97_A | 100_L | 1.159 | 0.97 |
| 43_F | 300_A | 1.156 | 0.97 |
| 8_G | 343_I | 1.154 | 0.97 |
| 285_A | 292_I | 1.153 | 0.97 |
| 116_F | 270_A | 1.151 | 0.97 |
| 409_L | 412_L | 1.145 | 0.97 |
| 263_L | 267_F | 1.142 | 0.97 |
| 110_G | 302_G | 1.141 | 0.97 |
| 188_G | 368_I | 1.141 | 0.97 |
| 146_V | 166_I | 1.140 | 0.97 |
| 253_L | 310_F | 1.139 | 0.97 |
| 269_I | 315_V | 1.135 | 0.97 |
| 37_I | 341_A | 1.134 | 0.97 |
| 382_P | 385_W | 1.131 | 0.97 |
| 142_F | 403_I | 1.131 | 0.97 |
| 39_T | 300_A | 1.128 | 0.97 |
| 388_N | 391_D | 1.126 | 0.97 |
| 6_S | 329_T | 1.125 | 0.97 |
| 129_A | 418_G | 1.112 | 0.96 |
| 18_Y | 55_P | 1.107 | 0.96 |
| 39_T | 43_F | 1.107 | 0.96 |
| 149_L | 170_L | 1.106 | 0.96 |
| 190_L | 223_A | 1.104 | 0.96 |
| 191_T | 223_A | 1.104 | 0.96 |
| 397_F | 400_I | 1.102 | 0.96 |
| 113_Q | 274_Y | 1.097 | 0.96 |
| 153_L | 185_F | 1.096 | 0.96 |
| 168_Y | 172_E | 1.094 | 0.96 |
| 109_V | 113_Q | 1.092 | 0.96 |
| 385_W | 392_A | 1.090 | 0.96 |
| 113_Q | 273_A | 1.090 | 0.96 |
| 28_Y | 314_F | 1.083 | 0.96 |
| 197_A | 200_E | 1.083 | 0.96 |
| 125_V | 128_L | 1.082 | 0.96 |
| 4_G | 339_I | 1.078 | 0.95 |
| 139_A | 399_C | 1.075 | 0.95 |
| 109_V | 270_A | 1.072 | 0.95 |
| 284_Y | 327_E | 1.070 | 0.95 |
| 165_S | 168_Y | 1.068 | 0.95 |
| 383_R | 386_R | 1.067 | 0.95 |
| 172_E | 176_N | 1.066 | 0.95 |
| 409_L | 413_A | 1.064 | 0.95 |
| 391_D | 394_I | 1.057 | 0.95 |
| 207_H | 210_P | 1.056 | 0.95 |
| 397_F | 401_V | 1.055 | 0.95 |
| 385_W | 389_K | 1.055 | 0.95 |
| 134_G | 380_D | 1.050 | 0.94 |
| 186_T | 189_L | 1.049 | 0.94 |
| 114_L | 118_G | 1.041 | 0.94 |
| 393_V | 397_F | 1.040 | 0.94 |
| 15_G | 19_A | 1.039 | 0.94 |
| 42_I | 338_I | 1.032 | 0.94 |
| 227_S | 240_I | 1.031 | 0.94 |
| 54_F | 320_L | 1.030 | 0.94 |
| 335_V | 338_I | 1.028 | 0.94 |
| 185_F | 188_G | 1.026 | 0.94 |
| 138_T | 141_A | 1.024 | 0.93 |
| 50_S | 337_G | 1.022 | 0.93 |
| 114_L | 302_G | 1.020 | 0.93 |
| 251_P | 311_F | 1.019 | 0.93 |
| 69_A | 98_R | 1.013 | 0.93 |
| 342_A | 345_M | 1.011 | 0.93 |
| 44_G | 49_I | 1.011 | 0.93 |
| 258_L | 261_E | 1.006 | 0.93 |
| 198_V | 215_I | 1.006 | 0.93 |
| 309_G | 313_C | 1.006 | 0.93 |
| 177_I | 180_T | 1.003 | 0.93 |
| 223_A | 227_S | 1.001 | 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 | |
| 3qe7A | 1 | 0.8571 | 100 | 0.521 | Contact Map |
| 1btsA | 1 | 0.05 | 16 | 0.964 | Contact Map |
| 1colA | 2 | 0.1357 | 4.6 | 0.972 | Contact Map |
| 3nd0A | 2 | 0.5738 | 4.5 | 0.972 | Contact Map |
| 1a87A | 1 | 0.1452 | 3.7 | 0.973 | Contact Map |
| 4eneA | 2 | 0.6048 | 3.5 | 0.974 | Contact Map |
| 1wazA | 1 | 0.1095 | 1.8 | 0.977 | Contact Map |
| 1kvdA | 2 | 0.0952 | 1.5 | 0.978 | Contact Map |
| 2kncA | 1 | 0.1238 | 1.5 | 0.978 | Contact Map |
| 2mwrA | 1 | 0.0548 | 1.5 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)