| Eric |
| ID: | 1427987208 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 462 (459) | ||
| Sequences: | 4029 (2495.5) | ||
| Seq/Len: | 8.778 | ||
| Nf(neff/√len): | 116.5 |
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: 8.778).
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 |
| 54_L | 255_V | 3.809 | 1.00 |
| 89_V | 261_G | 3.631 | 1.00 |
| 99_G | 251_R | 3.288 | 1.00 |
| 12_V | 291_V | 2.801 | 1.00 |
| 50_I | 259_V | 2.638 | 1.00 |
| 278_N | 288_S | 2.618 | 1.00 |
| 346_V | 359_I | 2.618 | 1.00 |
| 90_L | 218_A | 2.582 | 1.00 |
| 260_T | 265_G | 2.556 | 1.00 |
| 345_A | 349_F | 2.462 | 1.00 |
| 104_A | 247_N | 2.348 | 1.00 |
| 439_M | 449_V | 2.329 | 1.00 |
| 8_P | 12_V | 2.281 | 1.00 |
| 236_I | 275_S | 2.242 | 1.00 |
| 15_G | 291_V | 2.241 | 1.00 |
| 175_V | 179_T | 2.182 | 1.00 |
| 421_L | 424_A | 2.137 | 1.00 |
| 174_V | 178_V | 2.111 | 1.00 |
| 148_G | 317_A | 2.103 | 1.00 |
| 416_R | 450_E | 2.053 | 1.00 |
| 291_V | 295_F | 2.046 | 1.00 |
| 49_L | 290_F | 2.026 | 1.00 |
| 94_L | 215_F | 1.996 | 1.00 |
| 43_A | 268_G | 1.986 | 1.00 |
| 49_L | 293_G | 1.976 | 1.00 |
| 149_L | 317_A | 1.959 | 1.00 |
| 50_I | 255_V | 1.949 | 1.00 |
| 97_V | 101_A | 1.948 | 1.00 |
| 342_A | 363_L | 1.916 | 1.00 |
| 134_F | 145_V | 1.908 | 1.00 |
| 352_D | 355_L | 1.892 | 1.00 |
| 401_T | 430_S | 1.857 | 1.00 |
| 451_L | 454_L | 1.844 | 1.00 |
| 143_A | 147_A | 1.832 | 1.00 |
| 149_L | 321_V | 1.830 | 1.00 |
| 97_V | 100_W | 1.828 | 1.00 |
| 64_A | 69_A | 1.821 | 1.00 |
| 89_V | 258_I | 1.790 | 1.00 |
| 240_T | 279_V | 1.776 | 1.00 |
| 93_V | 97_V | 1.763 | 1.00 |
| 68_M | 221_L | 1.761 | 1.00 |
| 11_D | 284_R | 1.754 | 1.00 |
| 53_F | 290_F | 1.747 | 1.00 |
| 26_A | 65_T | 1.736 | 1.00 |
| 172_L | 314_A | 1.724 | 1.00 |
| 343_T | 360_G | 1.709 | 1.00 |
| 96_V | 258_I | 1.677 | 1.00 |
| 35_V | 266_M | 1.670 | 1.00 |
| 283_G | 288_S | 1.648 | 1.00 |
| 387_T | 418_V | 1.634 | 1.00 |
| 8_P | 287_L | 1.617 | 1.00 |
| 54_L | 252_G | 1.613 | 1.00 |
| 91_T | 221_L | 1.605 | 1.00 |
| 52_A | 290_F | 1.588 | 1.00 |
| 439_M | 443_M | 1.577 | 1.00 |
| 147_A | 175_V | 1.572 | 1.00 |
| 414_A | 447_T | 1.564 | 1.00 |
| 99_G | 104_A | 1.564 | 1.00 |
| 440_L | 444_R | 1.563 | 1.00 |
| 185_T | 188_D | 1.558 | 1.00 |
| 93_V | 258_I | 1.553 | 1.00 |
| 21_A | 277_I | 1.550 | 1.00 |
| 173_T | 176_A | 1.542 | 1.00 |
| 75_L | 87_A | 1.537 | 1.00 |
| 98_F | 103_L | 1.530 | 1.00 |
| 259_V | 263_F | 1.527 | 1.00 |
| 144_M | 183_V | 1.514 | 1.00 |
| 47_I | 268_G | 1.483 | 1.00 |
| 298_V | 302_A | 1.482 | 1.00 |
| 346_V | 350_T | 1.482 | 1.00 |
| 152_I | 168_A | 1.479 | 1.00 |
| 16_I | 295_F | 1.478 | 1.00 |
| 176_A | 181_A | 1.473 | 1.00 |
| 153_Y | 321_V | 1.457 | 0.99 |
| 236_I | 279_V | 1.457 | 0.99 |
| 438_V | 449_V | 1.451 | 0.99 |
| 45_F | 297_M | 1.448 | 0.99 |
| 14_A | 18_V | 1.447 | 0.99 |
| 148_G | 168_A | 1.445 | 0.99 |
| 387_T | 416_R | 1.430 | 0.99 |
| 215_F | 219_L | 1.426 | 0.99 |
| 88_T | 267_A | 1.423 | 0.99 |
| 61_I | 67_A | 1.419 | 0.99 |
| 408_F | 438_V | 1.416 | 0.99 |
| 147_A | 172_L | 1.414 | 0.99 |
| 92_G | 258_I | 1.393 | 0.99 |
| 405_L | 437_K | 1.384 | 0.99 |
| 149_L | 153_Y | 1.377 | 0.99 |
| 46_I | 259_V | 1.362 | 0.99 |
| 154_L | 158_V | 1.359 | 0.99 |
| 218_A | 222_S | 1.355 | 0.99 |
| 59_G | 283_G | 1.353 | 0.99 |
| 150_A | 154_L | 1.348 | 0.99 |
| 94_L | 222_S | 1.343 | 0.99 |
| 57_R | 63_A | 1.343 | 0.99 |
| 237_D | 244_S | 1.340 | 0.99 |
| 162_M | 167_V | 1.335 | 0.99 |
| 294_A | 298_V | 1.333 | 0.99 |
| 99_G | 254_G | 1.329 | 0.99 |
| 248_V | 251_R | 1.329 | 0.99 |
| 123_A | 323_A | 1.325 | 0.99 |
| 100_W | 251_R | 1.319 | 0.99 |
| 419_I | 451_L | 1.319 | 0.99 |
| 140_Q | 143_A | 1.311 | 0.99 |
| 94_L | 218_A | 1.309 | 0.99 |
| 299_L | 303_L | 1.306 | 0.99 |
| 177_V | 309_Q | 1.297 | 0.99 |
| 50_I | 252_G | 1.296 | 0.99 |
| 395_Q | 425_H | 1.290 | 0.98 |
| 341_L | 345_A | 1.287 | 0.98 |
| 8_P | 291_V | 1.281 | 0.98 |
| 10_K | 284_R | 1.280 | 0.98 |
| 90_L | 214_I | 1.274 | 0.98 |
| 50_I | 54_L | 1.270 | 0.98 |
| 63_A | 66_G | 1.269 | 0.98 |
| 386_G | 415_R | 1.267 | 0.98 |
| 419_I | 449_V | 1.267 | 0.98 |
| 187_G | 190_G | 1.259 | 0.98 |
| 278_N | 283_G | 1.254 | 0.98 |
| 67_A | 72_M | 1.253 | 0.98 |
| 51_T | 55_G | 1.252 | 0.98 |
| 46_I | 263_F | 1.249 | 0.98 |
| 336_E | 339_V | 1.244 | 0.98 |
| 418_V | 450_E | 1.237 | 0.98 |
| 277_I | 281_S | 1.235 | 0.98 |
| 256_A | 260_T | 1.233 | 0.98 |
| 23_I | 296_L | 1.232 | 0.98 |
| 347_T | 356_G | 1.226 | 0.98 |
| 45_F | 293_G | 1.219 | 0.98 |
| 47_I | 51_T | 1.217 | 0.98 |
| 102_K | 105_R | 1.216 | 0.98 |
| 41_L | 296_L | 1.213 | 0.98 |
| 210_T | 213_I | 1.205 | 0.97 |
| 228_E | 232_T | 1.204 | 0.97 |
| 51_T | 62_S | 1.204 | 0.97 |
| 251_R | 255_V | 1.203 | 0.97 |
| 416_R | 448_S | 1.202 | 0.97 |
| 145_V | 152_I | 1.201 | 0.97 |
| 19_A | 65_T | 1.201 | 0.97 |
| 96_V | 251_R | 1.199 | 0.97 |
| 151_I | 172_L | 1.192 | 0.97 |
| 127_F | 320_M | 1.192 | 0.97 |
| 226_L | 250_S | 1.184 | 0.97 |
| 159_F | 162_M | 1.169 | 0.97 |
| 102_K | 247_N | 1.169 | 0.97 |
| 393_R | 423_D | 1.168 | 0.97 |
| 166_L | 170_V | 1.164 | 0.97 |
| 52_A | 289_T | 1.160 | 0.97 |
| 183_V | 187_G | 1.159 | 0.96 |
| 392_V | 404_F | 1.156 | 0.96 |
| 401_T | 434_A | 1.156 | 0.96 |
| 199_F | 263_F | 1.153 | 0.96 |
| 91_T | 267_A | 1.150 | 0.96 |
| 343_T | 346_V | 1.146 | 0.96 |
| 66_G | 69_A | 1.145 | 0.96 |
| 237_D | 242_T | 1.144 | 0.96 |
| 68_M | 91_T | 1.143 | 0.96 |
| 228_E | 269_C | 1.139 | 0.96 |
| 225_G | 229_S | 1.134 | 0.96 |
| 19_A | 295_F | 1.129 | 0.96 |
| 201_F | 262_F | 1.126 | 0.96 |
| 442_F | 447_T | 1.125 | 0.96 |
| 148_G | 172_L | 1.124 | 0.96 |
| 455_N | 458_S | 1.116 | 0.95 |
| 389_T | 418_V | 1.116 | 0.95 |
| 133_Q | 316_V | 1.114 | 0.95 |
| 367_F | 371_K | 1.112 | 0.95 |
| 142_Y | 145_V | 1.111 | 0.95 |
| 88_T | 261_G | 1.111 | 0.95 |
| 187_G | 308_V | 1.109 | 0.95 |
| 232_T | 272_I | 1.109 | 0.95 |
| 395_Q | 424_A | 1.108 | 0.95 |
| 174_V | 177_V | 1.106 | 0.95 |
| 100_W | 103_L | 1.105 | 0.95 |
| 35_V | 76_V | 1.104 | 0.95 |
| 120_N | 123_A | 1.102 | 0.95 |
| 107_L | 110_V | 1.100 | 0.95 |
| 456_A | 460_T | 1.097 | 0.95 |
| 46_I | 260_T | 1.095 | 0.95 |
| 420_D | 452_R | 1.092 | 0.95 |
| 69_A | 72_M | 1.085 | 0.94 |
| 370_R | 374_Q | 1.085 | 0.94 |
| 147_A | 154_L | 1.084 | 0.94 |
| 25_E | 122_L | 1.084 | 0.94 |
| 64_A | 68_M | 1.082 | 0.94 |
| 134_F | 316_V | 1.082 | 0.94 |
| 11_D | 285_G | 1.082 | 0.94 |
| 440_L | 443_M | 1.072 | 0.94 |
| 83_Y | 86_A | 1.069 | 0.94 |
| 139_W | 143_A | 1.068 | 0.94 |
| 63_A | 72_M | 1.065 | 0.94 |
| 221_L | 267_A | 1.065 | 0.94 |
| 203_P | 207_T | 1.060 | 0.93 |
| 15_G | 19_A | 1.057 | 0.93 |
| 342_A | 359_I | 1.056 | 0.93 |
| 147_A | 151_I | 1.053 | 0.93 |
| 209_E | 212_A | 1.050 | 0.93 |
| 342_A | 346_V | 1.049 | 0.93 |
| 90_L | 94_L | 1.049 | 0.93 |
| 59_G | 63_A | 1.041 | 0.93 |
| 207_T | 210_T | 1.040 | 0.93 |
| 191_T | 194_T | 1.038 | 0.92 |
| 59_G | 64_A | 1.030 | 0.92 |
| 61_I | 65_T | 1.027 | 0.92 |
| 7_N | 284_R | 1.024 | 0.92 |
| 67_A | 70_L | 1.021 | 0.92 |
| 122_L | 231_L | 1.021 | 0.92 |
| 126_I | 278_N | 1.016 | 0.91 |
| 51_T | 252_G | 1.015 | 0.91 |
| 26_A | 29_F | 1.014 | 0.91 |
| 420_D | 453_G | 1.014 | 0.91 |
| 408_F | 442_F | 1.012 | 0.91 |
| 299_L | 307_L | 1.012 | 0.91 |
| 69_A | 266_M | 1.010 | 0.91 |
| 57_R | 64_A | 1.007 | 0.91 |
| 454_L | 458_S | 1.006 | 0.91 |
| 146_A | 150_A | 1.006 | 0.91 |
| 43_A | 273_G | 1.004 | 0.91 |
| 323_A | 326_T | 1.003 | 0.91 |
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 | 0.7792 | 100 | 0.59 | Contact Map |
| 3oizA | 1 | 0.1991 | 99.4 | 0.874 | Contact Map |
| 2klnA | 1 | 0.197 | 99.3 | 0.876 | Contact Map |
| 3ny7A | 1 | 0.1991 | 99.3 | 0.88 | Contact Map |
| 3lloA | 1 | 0.2186 | 99.2 | 0.881 | Contact Map |
| 4dgfA | 2 | 0.197 | 99.2 | 0.882 | Contact Map |
| 4qtpA | 4 | 0.1883 | 99.2 | 0.882 | Contact Map |
| 4dghA | 2 | 0.2056 | 99.2 | 0.882 | Contact Map |
| 3t6oA | 3 | 0.1905 | 99.2 | 0.884 | Contact Map |
| 2ka5A | 1 | 0.21 | 99.1 | 0.886 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)