| T0858 |
| ID: | 1440615076 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 494 (433) | ||
| Sequences: | 1285 (959.9) | ||
| Seq/Len: | 2.968 | ||
| Nf(neff/√len): | 46.1 |
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: 2.968).
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 |
| 179_C | 246_L | 5.467 | 1.00 |
| 428_A | 448_N | 3.968 | 1.00 |
| 262_G | 305_Y | 3.862 | 1.00 |
| 79_M | 365_I | 3.365 | 1.00 |
| 262_G | 266_K | 3.115 | 1.00 |
| 214_F | 231_V | 3.079 | 1.00 |
| 152_E | 224_E | 2.902 | 1.00 |
| 215_V | 268_A | 2.860 | 1.00 |
| 220_A | 223_A | 2.842 | 1.00 |
| 75_Q | 447_E | 2.836 | 1.00 |
| 212_T | 264_Q | 2.732 | 1.00 |
| 265_M | 270_L | 2.669 | 1.00 |
| 143_I | 209_D | 2.665 | 1.00 |
| 325_H | 368_W | 2.597 | 1.00 |
| 457_L | 488_Y | 2.589 | 1.00 |
| 478_Y | 488_Y | 2.584 | 1.00 |
| 365_I | 424_V | 2.518 | 1.00 |
| 219_Q | 268_A | 2.434 | 1.00 |
| 102_R | 162_E | 2.345 | 1.00 |
| 108_E | 410_R | 2.315 | 1.00 |
| 86_I | 121_I | 2.284 | 1.00 |
| 119_S | 426_P | 2.253 | 1.00 |
| 322_L | 367_N | 2.244 | 1.00 |
| 208_Q | 260_A | 2.233 | 1.00 |
| 222_K | 227_D | 2.230 | 1.00 |
| 448_N | 452_T | 2.227 | 1.00 |
| 208_Q | 264_Q | 2.206 | 1.00 |
| 78_T | 429_V | 2.182 | 1.00 |
| 101_D | 104_A | 2.162 | 1.00 |
| 266_K | 304_Q | 2.156 | 1.00 |
| 76_Y | 430_R | 2.153 | 1.00 |
| 125_I | 214_F | 2.130 | 1.00 |
| 334_L | 371_G | 2.127 | 1.00 |
| 125_I | 174_A | 2.052 | 1.00 |
| 175_A | 232_T | 2.046 | 1.00 |
| 428_A | 452_T | 2.043 | 1.00 |
| 313_N | 338_T | 2.028 | 1.00 |
| 441_I | 457_L | 2.027 | 1.00 |
| 107_T | 166_I | 2.024 | 1.00 |
| 143_I | 212_T | 2.005 | 1.00 |
| 216_K | 220_A | 2.004 | 1.00 |
| 74_E | 432_A | 1.985 | 1.00 |
| 457_L | 467_I | 1.914 | 0.99 |
| 107_T | 111_S | 1.914 | 0.99 |
| 428_A | 450_D | 1.911 | 0.99 |
| 215_V | 264_Q | 1.865 | 0.99 |
| 103_H | 162_E | 1.830 | 0.99 |
| 116_F | 418_A | 1.827 | 0.99 |
| 173_I | 373_I | 1.824 | 0.99 |
| 75_Q | 429_V | 1.780 | 0.99 |
| 80_D | 332_E | 1.775 | 0.99 |
| 208_Q | 212_T | 1.757 | 0.99 |
| 72_P | 431_I | 1.746 | 0.99 |
| 258_K | 299_D | 1.744 | 0.99 |
| 264_Q | 268_A | 1.743 | 0.99 |
| 464_S | 479_D | 1.695 | 0.98 |
| 480_V | 486_T | 1.688 | 0.98 |
| 238_L | 277_F | 1.615 | 0.97 |
| 172_V | 226_I | 1.589 | 0.97 |
| 255_D | 259_T | 1.581 | 0.97 |
| 176_P | 234_Q | 1.578 | 0.97 |
| 431_I | 447_E | 1.575 | 0.97 |
| 212_T | 215_V | 1.574 | 0.97 |
| 445_A | 455_F | 1.566 | 0.97 |
| 322_L | 326_Q | 1.565 | 0.97 |
| 157_L | 226_I | 1.528 | 0.96 |
| 462_E | 483_K | 1.517 | 0.96 |
| 231_V | 274_I | 1.505 | 0.96 |
| 258_K | 301_A | 1.494 | 0.95 |
| 71_N | 74_E | 1.494 | 0.95 |
| 469_V | 476_F | 1.467 | 0.95 |
| 148_L | 220_A | 1.464 | 0.95 |
| 106_L | 163_I | 1.461 | 0.95 |
| 276_A | 296_I | 1.458 | 0.95 |
| 181_K | 189_T | 1.440 | 0.94 |
| 218_I | 228_I | 1.438 | 0.94 |
| 276_A | 306_L | 1.430 | 0.94 |
| 425_K | 428_A | 1.428 | 0.94 |
| 323_N | 326_Q | 1.428 | 0.94 |
| 130_F | 379_L | 1.420 | 0.94 |
| 431_I | 453_Y | 1.418 | 0.93 |
| 212_T | 268_A | 1.413 | 0.93 |
| 311_Y | 333_L | 1.408 | 0.93 |
| 455_F | 469_V | 1.405 | 0.93 |
| 82_F | 365_I | 1.405 | 0.93 |
| 161_K | 224_E | 1.403 | 0.93 |
| 174_A | 228_I | 1.390 | 0.93 |
| 98_K | 406_K | 1.388 | 0.93 |
| 248_M | 253_Q | 1.379 | 0.92 |
| 425_K | 448_N | 1.379 | 0.92 |
| 103_H | 107_T | 1.371 | 0.92 |
| 275_Y | 310_A | 1.370 | 0.92 |
| 310_A | 336_T | 1.357 | 0.91 |
| 172_V | 228_I | 1.356 | 0.91 |
| 174_A | 217_W | 1.349 | 0.91 |
| 215_V | 219_Q | 1.346 | 0.91 |
| 257_V | 306_L | 1.345 | 0.91 |
| 98_K | 101_D | 1.345 | 0.91 |
| 454_A | 489_R | 1.345 | 0.91 |
| 219_Q | 270_L | 1.337 | 0.91 |
| 94_L | 102_R | 1.329 | 0.90 |
| 210_Y | 214_F | 1.328 | 0.90 |
| 376_N | 379_L | 1.317 | 0.90 |
| 237_P | 314_Y | 1.317 | 0.90 |
| 332_E | 370_K | 1.313 | 0.89 |
| 79_M | 82_F | 1.312 | 0.89 |
| 111_S | 117_G | 1.309 | 0.89 |
| 418_A | 422_S | 1.293 | 0.89 |
| 307_A | 331_K | 1.280 | 0.88 |
| 298_E | 328_Y | 1.277 | 0.88 |
| 82_F | 421_S | 1.273 | 0.87 |
| 89_S | 379_L | 1.266 | 0.87 |
| 441_I | 480_V | 1.245 | 0.86 |
| 455_F | 490_W | 1.243 | 0.86 |
| 480_V | 484_S | 1.241 | 0.86 |
| 176_P | 214_F | 1.236 | 0.85 |
| 307_A | 332_E | 1.235 | 0.85 |
| 273_K | 307_A | 1.231 | 0.85 |
| 257_V | 262_G | 1.226 | 0.85 |
| 104_A | 108_E | 1.216 | 0.84 |
| 476_F | 488_Y | 1.213 | 0.84 |
| 364_T | 369_C | 1.210 | 0.84 |
| 374_V | 417_I | 1.207 | 0.83 |
| 151_E | 221_F | 1.205 | 0.83 |
| 94_L | 105_F | 1.201 | 0.83 |
| 86_I | 160_L | 1.200 | 0.83 |
| 76_Y | 431_I | 1.198 | 0.83 |
| 217_W | 221_F | 1.194 | 0.83 |
| 257_V | 305_Y | 1.192 | 0.82 |
| 138_C | 143_I | 1.188 | 0.82 |
| 216_K | 219_Q | 1.186 | 0.82 |
| 123_I | 228_I | 1.185 | 0.82 |
| 423_V | 487_S | 1.183 | 0.82 |
| 264_Q | 267_A | 1.183 | 0.82 |
| 203_N | 206_Y | 1.183 | 0.82 |
| 358_E | 458_I | 1.176 | 0.81 |
| 162_E | 165_A | 1.173 | 0.81 |
| 127_C | 244_A | 1.169 | 0.81 |
| 178_T | 181_K | 1.167 | 0.80 |
| 69_T | 470_S | 1.162 | 0.80 |
| 148_L | 224_E | 1.160 | 0.80 |
| 76_Y | 432_A | 1.159 | 0.80 |
| 107_T | 114_D | 1.157 | 0.80 |
| 297_Y | 309_A | 1.154 | 0.79 |
| 116_F | 423_V | 1.152 | 0.79 |
| 464_S | 482_G | 1.149 | 0.79 |
| 429_V | 432_A | 1.149 | 0.79 |
| 433_T | 443_C | 1.144 | 0.79 |
| 178_T | 184_K | 1.135 | 0.78 |
| 177_W | 184_K | 1.133 | 0.78 |
| 267_A | 326_Q | 1.132 | 0.78 |
| 123_I | 217_W | 1.129 | 0.77 |
| 118_F | 374_V | 1.128 | 0.77 |
| 265_M | 272_T | 1.125 | 0.77 |
| 420_L | 424_V | 1.124 | 0.77 |
| 262_G | 302_A | 1.121 | 0.77 |
| 250_W | 295_K | 1.120 | 0.77 |
| 117_G | 425_K | 1.117 | 0.76 |
| 254_R | 299_D | 1.115 | 0.76 |
| 378_M | 408_I | 1.115 | 0.76 |
| 399_D | 411_N | 1.114 | 0.76 |
| 219_Q | 269_G | 1.102 | 0.75 |
| 449_T | 454_A | 1.102 | 0.75 |
| 335_F | 338_T | 1.100 | 0.75 |
| 84_A | 397_A | 1.099 | 0.75 |
| 171_K | 426_P | 1.097 | 0.74 |
| 94_L | 378_M | 1.097 | 0.74 |
| 125_I | 217_W | 1.095 | 0.74 |
| 88_G | 124_S | 1.093 | 0.74 |
| 362_L | 420_L | 1.089 | 0.74 |
| 424_V | 456_V | 1.086 | 0.73 |
| 124_S | 128_S | 1.086 | 0.73 |
| 120_Y | 371_G | 1.085 | 0.73 |
| 110_F | 163_I | 1.083 | 0.73 |
| 262_G | 304_Q | 1.082 | 0.73 |
| 255_D | 258_K | 1.077 | 0.73 |
| 254_R | 258_K | 1.073 | 0.72 |
| 136_T | 139_D | 1.070 | 0.72 |
| 80_D | 171_K | 1.070 | 0.72 |
| 116_F | 422_S | 1.069 | 0.72 |
| 109_T | 118_F | 1.069 | 0.72 |
| 126_G | 244_A | 1.064 | 0.71 |
| 160_L | 172_V | 1.061 | 0.71 |
| 124_S | 244_A | 1.059 | 0.71 |
| 311_Y | 369_C | 1.058 | 0.71 |
| 359_E | 460_N | 1.050 | 0.70 |
| 125_I | 231_V | 1.049 | 0.70 |
| 84_A | 377_L | 1.047 | 0.69 |
| 281_Y | 321_L | 1.046 | 0.69 |
| 78_T | 427_G | 1.044 | 0.69 |
| 149_Q | 152_E | 1.043 | 0.69 |
| 464_S | 481_P | 1.039 | 0.69 |
| 173_I | 310_A | 1.034 | 0.68 |
| 364_T | 372_V | 1.034 | 0.68 |
| 80_D | 334_L | 1.033 | 0.68 |
| 220_A | 224_E | 1.033 | 0.68 |
| 361_A | 365_I | 1.033 | 0.68 |
| 339_S | 395_Y | 1.026 | 0.67 |
| 401_N | 407_T | 1.025 | 0.67 |
| 77_Q | 430_R | 1.017 | 0.66 |
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 | |
| 2nt0A | 4 | 0.9676 | 100 | 0.134 | Contact Map |
| 2wnwA | 2 | 0.8846 | 100 | 0.281 | Contact Map |
| 3clwA | 6 | 0.8259 | 100 | 0.318 | Contact Map |
| 4ccdA | 1 | 0.7571 | 100 | 0.326 | Contact Map |
| 4qawA | 8 | 0.7267 | 100 | 0.4 | Contact Map |
| 4uqdA | 1 | 0 | 100 | 0.419 | Contact Map |
| 4fmvA | 1 | 0.7206 | 100 | 0.422 | Contact Map |
| 2y24A | 1 | 0.7166 | 100 | 0.43 | Contact Map |
| 4m29A | 1 | 0.7368 | 100 | 0.744 | Contact Map |
| 1w91A | 8 | 0.7652 | 100 | 0.759 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)