| fred0 |
| ID: | 1440604475 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 395 (351) | ||
| Sequences: | 1489 (805) | ||
| Seq/Len: | 4.242 | ||
| Nf(neff/√len): | 43.0 |
HHblits Results: (2015_06)
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: 4.242).
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 |
| 124_L | 138_L | 3.655 | 1.00 |
| 297_R | 301_E | 3.368 | 1.00 |
| 208_A | 240_V | 3.325 | 1.00 |
| 93_F | 107_F | 2.847 | 1.00 |
| 268_F | 272_F | 2.731 | 1.00 |
| 152_T | 155_V | 2.556 | 1.00 |
| 91_E | 344_S | 2.423 | 1.00 |
| 321_E | 324_E | 2.365 | 1.00 |
| 382_W | 393_W | 2.224 | 1.00 |
| 124_L | 173_M | 2.179 | 1.00 |
| 110_L | 207_L | 2.139 | 1.00 |
| 107_F | 127_L | 2.134 | 1.00 |
| 86_N | 119_Q | 2.125 | 1.00 |
| 268_F | 274_E | 2.008 | 1.00 |
| 32_F | 275_G | 1.982 | 1.00 |
| 22_G | 26_Q | 1.967 | 1.00 |
| 124_L | 175_V | 1.939 | 1.00 |
| 106_R | 201_G | 1.915 | 1.00 |
| 85_A | 210_N | 1.914 | 1.00 |
| 207_L | 236_L | 1.897 | 1.00 |
| 180_R | 197_D | 1.843 | 1.00 |
| 316_A | 319_S | 1.806 | 1.00 |
| 83_V | 351_V | 1.750 | 0.99 |
| 123_L | 127_L | 1.720 | 0.99 |
| 110_L | 236_L | 1.700 | 0.99 |
| 22_G | 31_Y | 1.696 | 0.99 |
| 22_G | 27_K | 1.693 | 0.99 |
| 134_E | 175_V | 1.655 | 0.99 |
| 324_E | 332_R | 1.627 | 0.99 |
| 48_L | 51_L | 1.622 | 0.99 |
| 168_K | 171_R | 1.599 | 0.99 |
| 315_P | 319_S | 1.539 | 0.98 |
| 130_R | 133_D | 1.538 | 0.98 |
| 310_D | 316_A | 1.531 | 0.98 |
| 87_G | 350_D | 1.528 | 0.98 |
| 240_V | 341_V | 1.509 | 0.98 |
| 315_P | 322_R | 1.505 | 0.98 |
| 93_F | 208_A | 1.480 | 0.98 |
| 111_D | 120_W | 1.474 | 0.98 |
| 153_A | 156_Q | 1.474 | 0.98 |
| 151_P | 154_A | 1.467 | 0.97 |
| 162_I | 165_R | 1.466 | 0.97 |
| 94_L | 103_E | 1.426 | 0.97 |
| 227_D | 332_R | 1.404 | 0.96 |
| 89_I | 123_L | 1.402 | 0.96 |
| 170_A | 378_V | 1.391 | 0.96 |
| 152_T | 158_V | 1.390 | 0.96 |
| 174_G | 318_E | 1.385 | 0.96 |
| 387_L | 393_W | 1.377 | 0.96 |
| 85_A | 89_I | 1.374 | 0.96 |
| 86_N | 139_S | 1.374 | 0.96 |
| 131_S | 134_E | 1.357 | 0.95 |
| 88_A | 240_V | 1.348 | 0.95 |
| 244_V | 390_A | 1.345 | 0.95 |
| 382_W | 391_S | 1.341 | 0.95 |
| 155_V | 158_V | 1.330 | 0.95 |
| 119_Q | 210_N | 1.316 | 0.94 |
| 282_Y | 357_R | 1.309 | 0.94 |
| 77_W | 285_S | 1.308 | 0.94 |
| 152_T | 156_Q | 1.308 | 0.94 |
| 114_N | 117_C | 1.306 | 0.94 |
| 287_E | 292_K | 1.297 | 0.94 |
| 170_A | 392_A | 1.266 | 0.93 |
| 310_D | 315_P | 1.264 | 0.93 |
| 208_A | 242_T | 1.261 | 0.92 |
| 143_V | 196_L | 1.260 | 0.92 |
| 114_N | 140_I | 1.241 | 0.92 |
| 154_A | 158_V | 1.240 | 0.92 |
| 332_R | 336_A | 1.232 | 0.91 |
| 279_F | 308_I | 1.230 | 0.91 |
| 23_K | 26_Q | 1.222 | 0.91 |
| 380_L | 393_W | 1.215 | 0.91 |
| 178_R | 338_F | 1.197 | 0.90 |
| 297_R | 300_L | 1.195 | 0.90 |
| 153_A | 158_V | 1.193 | 0.89 |
| 271_V | 319_S | 1.190 | 0.89 |
| 316_A | 321_E | 1.190 | 0.89 |
| 31_Y | 34_Q | 1.190 | 0.89 |
| 298_L | 301_E | 1.189 | 0.89 |
| 33_L | 77_W | 1.187 | 0.89 |
| 64_T | 299_A | 1.183 | 0.89 |
| 86_N | 210_N | 1.183 | 0.89 |
| 110_L | 394_R | 1.182 | 0.89 |
| 81_G | 87_G | 1.182 | 0.89 |
| 211_C | 241_V | 1.179 | 0.89 |
| 382_W | 385_Q | 1.176 | 0.89 |
| 80_F | 380_L | 1.173 | 0.88 |
| 328_A | 335_S | 1.168 | 0.88 |
| 379_F | 389_W | 1.167 | 0.88 |
| 106_R | 137_H | 1.161 | 0.88 |
| 94_L | 174_G | 1.151 | 0.87 |
| 138_L | 170_A | 1.150 | 0.87 |
| 27_K | 36_L | 1.147 | 0.87 |
| 209_V | 233_L | 1.142 | 0.87 |
| 32_F | 35_G | 1.141 | 0.86 |
| 385_Q | 389_W | 1.135 | 0.86 |
| 297_R | 302_R | 1.133 | 0.86 |
| 231_A | 234_R | 1.132 | 0.86 |
| 107_F | 134_E | 1.132 | 0.86 |
| 36_L | 39_R | 1.126 | 0.85 |
| 339_S | 394_R | 1.120 | 0.85 |
| 73_E | 88_A | 1.118 | 0.85 |
| 104_T | 239_R | 1.115 | 0.85 |
| 35_G | 308_I | 1.114 | 0.85 |
| 143_V | 182_V | 1.112 | 0.85 |
| 111_D | 119_Q | 1.105 | 0.84 |
| 152_T | 243_V | 1.102 | 0.84 |
| 350_D | 353_S | 1.101 | 0.84 |
| 75_S | 285_S | 1.100 | 0.84 |
| 140_I | 295_N | 1.100 | 0.84 |
| 321_E | 332_R | 1.099 | 0.84 |
| 87_G | 354_L | 1.092 | 0.83 |
| 82_H | 122_T | 1.091 | 0.83 |
| 316_A | 322_R | 1.090 | 0.83 |
| 151_P | 155_V | 1.089 | 0.83 |
| 241_V | 333_M | 1.081 | 0.82 |
| 28_L | 303_G | 1.081 | 0.82 |
| 271_V | 315_P | 1.080 | 0.82 |
| 174_G | 237_D | 1.075 | 0.82 |
| 315_P | 320_M | 1.073 | 0.82 |
| 152_T | 157_R | 1.070 | 0.81 |
| 325_T | 331_R | 1.070 | 0.81 |
| 93_F | 127_L | 1.070 | 0.81 |
| 69_L | 172_L | 1.069 | 0.81 |
| 87_G | 91_E | 1.069 | 0.81 |
| 361_G | 390_A | 1.066 | 0.81 |
| 117_C | 169_F | 1.065 | 0.81 |
| 251_V | 315_P | 1.063 | 0.81 |
| 226_R | 332_R | 1.063 | 0.81 |
| 81_G | 244_V | 1.062 | 0.81 |
| 310_D | 319_S | 1.060 | 0.80 |
| 92_S | 208_A | 1.054 | 0.80 |
| 216_R | 323_R | 1.053 | 0.80 |
| 269_L | 272_F | 1.050 | 0.80 |
| 247_E | 386_P | 1.047 | 0.79 |
| 297_R | 305_G | 1.045 | 0.79 |
| 250_L | 323_R | 1.041 | 0.79 |
| 81_G | 122_T | 1.041 | 0.79 |
| 347_V | 351_V | 1.038 | 0.78 |
| 110_L | 320_M | 1.038 | 0.78 |
| 24_A | 34_Q | 1.038 | 0.78 |
| 206_A | 239_R | 1.036 | 0.78 |
| 86_N | 111_D | 1.034 | 0.78 |
| 142_T | 181_A | 1.030 | 0.78 |
| 88_A | 242_T | 1.028 | 0.78 |
| 315_P | 324_E | 1.023 | 0.77 |
| 92_S | 110_L | 1.021 | 0.77 |
| 74_L | 290_F | 1.016 | 0.76 |
| 271_V | 310_D | 1.014 | 0.76 |
| 310_D | 314_C | 1.011 | 0.76 |
| 282_Y | 290_F | 1.010 | 0.76 |
| 25_V | 29_A | 1.009 | 0.76 |
| 268_F | 276_L | 1.008 | 0.76 |
| 39_R | 227_D | 1.008 | 0.76 |
| 87_G | 351_V | 1.007 | 0.75 |
| 363_S | 366_E | 1.006 | 0.75 |
| 83_V | 234_R | 1.005 | 0.75 |
| 108_H | 141_T | 1.004 | 0.75 |
| 163_G | 177_F | 1.003 | 0.75 |
| 355_L | 364_M | 1.002 | 0.75 |
| 230_A | 282_Y | 1.001 | 0.75 |
| 306_R | 311_L | 1.000 | 0.75 |
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 | |
| 4obxA | 4 | 0.5747 | 95.4 | 0.947 | Contact Map |
| 2aotA | 1 | 0.6253 | 91.3 | 0.955 | Contact Map |
| 3g07A | 6 | 0.4582 | 90 | 0.956 | Contact Map |
| 4pneA | 2 | 0.638 | 89.6 | 0.957 | Contact Map |
| 1y8cA | 1 | 0.5975 | 88.7 | 0.957 | Contact Map |
| 1vl5A | 4 | 0.5772 | 87.9 | 0.958 | Contact Map |
| 4qdjA | 1 | 0.5013 | 87.5 | 0.958 | Contact Map |
| 3bxoA | 2 | 0.5797 | 86.9 | 0.958 | Contact Map |
| 3dtnA | 2 | 0.5595 | 85 | 0.96 | Contact Map |
| 3d2lA | 4 | 0.6025 | 83.8 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)