| T0858 |
| ID: | 1405537830 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 494 (447) | ||
| Sequences: | 662 (535.1) | ||
| Seq/Len: | 1.481 | ||
| Nf(neff/√len): | 25.3 |
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: 1.481).
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 | 4.740 | 1.00 |
| 262_G | 305_Y | 4.090 | 1.00 |
| 428_A | 448_N | 3.846 | 1.00 |
| 214_F | 231_V | 3.150 | 1.00 |
| 457_L | 488_Y | 2.945 | 1.00 |
| 220_A | 223_A | 2.786 | 1.00 |
| 143_I | 209_D | 2.674 | 1.00 |
| 79_M | 365_I | 2.615 | 1.00 |
| 215_V | 268_A | 2.604 | 1.00 |
| 262_G | 266_K | 2.442 | 1.00 |
| 478_Y | 488_Y | 2.383 | 1.00 |
| 212_T | 264_Q | 2.241 | 0.99 |
| 152_E | 224_E | 2.206 | 0.99 |
| 86_I | 121_I | 2.187 | 0.99 |
| 325_H | 368_W | 2.186 | 0.99 |
| 428_A | 452_T | 2.170 | 0.99 |
| 75_Q | 447_E | 2.164 | 0.99 |
| 265_M | 270_L | 2.143 | 0.99 |
| 448_N | 452_T | 2.072 | 0.98 |
| 334_L | 371_G | 2.061 | 0.98 |
| 322_L | 367_N | 2.039 | 0.98 |
| 101_D | 104_A | 2.038 | 0.98 |
| 208_Q | 260_A | 2.005 | 0.98 |
| 258_K | 301_A | 2.002 | 0.98 |
| 157_L | 226_I | 1.997 | 0.98 |
| 258_K | 299_D | 1.973 | 0.98 |
| 125_I | 174_A | 1.937 | 0.97 |
| 208_Q | 264_Q | 1.902 | 0.97 |
| 216_K | 220_A | 1.881 | 0.97 |
| 176_P | 234_Q | 1.877 | 0.97 |
| 138_C | 143_I | 1.872 | 0.97 |
| 125_I | 214_F | 1.812 | 0.96 |
| 175_A | 232_T | 1.807 | 0.96 |
| 107_T | 166_I | 1.803 | 0.96 |
| 98_K | 406_K | 1.799 | 0.95 |
| 181_K | 197_W | 1.787 | 0.95 |
| 102_R | 162_E | 1.780 | 0.95 |
| 108_E | 410_R | 1.774 | 0.95 |
| 119_S | 426_P | 1.768 | 0.95 |
| 177_W | 184_K | 1.754 | 0.95 |
| 480_V | 486_T | 1.747 | 0.94 |
| 212_T | 215_V | 1.732 | 0.94 |
| 266_K | 304_Q | 1.728 | 0.94 |
| 75_Q | 429_V | 1.707 | 0.93 |
| 364_T | 372_V | 1.687 | 0.93 |
| 143_I | 212_T | 1.656 | 0.92 |
| 173_I | 373_I | 1.639 | 0.92 |
| 428_A | 450_D | 1.638 | 0.92 |
| 78_T | 429_V | 1.622 | 0.91 |
| 469_V | 476_F | 1.564 | 0.89 |
| 248_M | 253_Q | 1.557 | 0.89 |
| 441_I | 457_L | 1.545 | 0.88 |
| 313_N | 338_T | 1.512 | 0.87 |
| 222_K | 227_D | 1.510 | 0.86 |
| 215_V | 264_Q | 1.504 | 0.86 |
| 103_H | 162_E | 1.501 | 0.86 |
| 106_L | 163_I | 1.488 | 0.85 |
| 425_K | 428_A | 1.478 | 0.85 |
| 254_R | 299_D | 1.474 | 0.85 |
| 86_I | 160_L | 1.473 | 0.85 |
| 445_A | 455_F | 1.469 | 0.84 |
| 74_E | 432_A | 1.455 | 0.84 |
| 423_V | 487_S | 1.448 | 0.83 |
| 76_Y | 430_R | 1.448 | 0.83 |
| 148_L | 152_E | 1.445 | 0.83 |
| 264_Q | 268_A | 1.444 | 0.83 |
| 172_V | 226_I | 1.438 | 0.83 |
| 130_F | 379_L | 1.435 | 0.82 |
| 366_N | 444_S | 1.434 | 0.82 |
| 149_Q | 152_E | 1.431 | 0.82 |
| 107_T | 114_D | 1.427 | 0.82 |
| 88_G | 124_S | 1.418 | 0.81 |
| 255_D | 259_T | 1.406 | 0.81 |
| 402_N | 407_T | 1.403 | 0.80 |
| 365_I | 424_V | 1.389 | 0.79 |
| 110_F | 163_I | 1.382 | 0.79 |
| 185_V | 203_N | 1.374 | 0.78 |
| 94_L | 105_F | 1.364 | 0.78 |
| 203_N | 206_Y | 1.363 | 0.78 |
| 116_F | 418_A | 1.363 | 0.78 |
| 464_S | 479_D | 1.360 | 0.77 |
| 86_I | 163_I | 1.357 | 0.77 |
| 431_I | 453_Y | 1.354 | 0.77 |
| 219_Q | 268_A | 1.352 | 0.77 |
| 455_F | 490_W | 1.342 | 0.76 |
| 257_V | 262_G | 1.342 | 0.76 |
| 476_F | 488_Y | 1.341 | 0.76 |
| 208_Q | 212_T | 1.333 | 0.75 |
| 237_P | 314_Y | 1.331 | 0.75 |
| 219_Q | 269_G | 1.327 | 0.75 |
| 107_T | 111_S | 1.327 | 0.75 |
| 111_S | 117_G | 1.320 | 0.74 |
| 161_K | 224_E | 1.317 | 0.74 |
| 148_L | 220_A | 1.317 | 0.74 |
| 455_F | 469_V | 1.317 | 0.74 |
| 136_T | 197_W | 1.302 | 0.73 |
| 94_L | 378_M | 1.291 | 0.72 |
| 79_M | 82_F | 1.288 | 0.72 |
| 76_Y | 431_I | 1.287 | 0.72 |
| 212_T | 268_A | 1.282 | 0.71 |
| 250_W | 295_K | 1.276 | 0.71 |
| 82_F | 421_S | 1.273 | 0.71 |
| 217_W | 221_F | 1.272 | 0.70 |
| 376_N | 379_L | 1.271 | 0.70 |
| 118_F | 374_V | 1.266 | 0.70 |
| 322_L | 326_Q | 1.257 | 0.69 |
| 218_I | 228_I | 1.257 | 0.69 |
| 374_V | 397_A | 1.248 | 0.68 |
| 256_F | 263_P | 1.245 | 0.68 |
| 176_P | 214_F | 1.237 | 0.67 |
| 185_V | 200_G | 1.236 | 0.67 |
| 238_L | 277_F | 1.229 | 0.67 |
| 124_S | 244_A | 1.224 | 0.66 |
| 466_K | 479_D | 1.212 | 0.65 |
| 130_F | 376_N | 1.211 | 0.65 |
| 87_T | 385_P | 1.210 | 0.65 |
| 123_I | 228_I | 1.208 | 0.65 |
| 46_L | 49_D | 1.202 | 0.64 |
| 275_Y | 310_A | 1.195 | 0.63 |
| 109_T | 397_A | 1.189 | 0.63 |
| 89_S | 130_F | 1.187 | 0.63 |
| 462_E | 483_K | 1.181 | 0.62 |
| 40_Y | 423_V | 1.179 | 0.62 |
| 402_N | 405_Y | 1.174 | 0.61 |
| 425_K | 448_N | 1.172 | 0.61 |
| 355_E | 483_K | 1.170 | 0.61 |
| 431_I | 447_E | 1.167 | 0.61 |
| 148_L | 224_E | 1.163 | 0.60 |
| 418_A | 422_S | 1.162 | 0.60 |
| 77_Q | 430_R | 1.150 | 0.59 |
| 232_T | 278_D | 1.149 | 0.59 |
| 123_I | 217_W | 1.144 | 0.58 |
| 361_A | 398_V | 1.141 | 0.58 |
| 41_T | 53_D | 1.140 | 0.58 |
| 80_D | 332_E | 1.137 | 0.58 |
| 37_V | 55_V | 1.134 | 0.57 |
| 276_A | 296_I | 1.134 | 0.57 |
| 94_L | 102_R | 1.128 | 0.57 |
| 172_V | 228_I | 1.121 | 0.56 |
| 374_V | 417_I | 1.119 | 0.56 |
| 260_A | 263_P | 1.115 | 0.56 |
| 280_N | 394_C | 1.114 | 0.55 |
| 431_I | 441_I | 1.113 | 0.55 |
| 257_V | 306_L | 1.111 | 0.55 |
| 278_D | 362_L | 1.110 | 0.55 |
| 111_S | 307_A | 1.110 | 0.55 |
| 231_V | 274_I | 1.109 | 0.55 |
| 110_F | 121_I | 1.105 | 0.54 |
| 430_R | 446_F | 1.101 | 0.54 |
| 103_H | 107_T | 1.100 | 0.54 |
| 178_T | 184_K | 1.099 | 0.54 |
| 89_S | 379_L | 1.096 | 0.54 |
| 299_D | 325_H | 1.093 | 0.53 |
| 126_G | 244_A | 1.087 | 0.53 |
| 127_C | 244_A | 1.087 | 0.53 |
| 239_N | 293_P | 1.082 | 0.52 |
| 408_I | 419_H | 1.081 | 0.52 |
| 218_I | 270_L | 1.075 | 0.51 |
| 176_P | 184_K | 1.066 | 0.50 |
| 308_G | 376_N | 1.058 | 0.50 |
| 335_F | 338_T | 1.057 | 0.50 |
| 56_N | 59_P | 1.054 | 0.49 |
| 462_E | 469_V | 1.052 | 0.49 |
| 97_M | 105_F | 1.051 | 0.49 |
| 125_I | 423_V | 1.050 | 0.49 |
| 297_Y | 309_A | 1.050 | 0.49 |
| 466_K | 480_V | 1.049 | 0.49 |
| 296_I | 306_L | 1.045 | 0.48 |
| 278_D | 380_D | 1.043 | 0.48 |
| 262_G | 302_A | 1.038 | 0.48 |
| 215_V | 219_Q | 1.037 | 0.47 |
| 84_A | 397_A | 1.035 | 0.47 |
| 109_T | 118_F | 1.034 | 0.47 |
| 457_L | 480_V | 1.033 | 0.47 |
| 257_V | 305_Y | 1.029 | 0.47 |
| 38_A | 52_R | 1.025 | 0.46 |
| 397_A | 413_H | 1.023 | 0.46 |
| 143_I | 227_D | 1.023 | 0.46 |
| 278_D | 312_H | 1.023 | 0.46 |
| 211_A | 256_F | 1.022 | 0.46 |
| 88_G | 135_Y | 1.022 | 0.46 |
| 140_T | 143_I | 1.022 | 0.46 |
| 332_E | 370_K | 1.019 | 0.46 |
| 201_Q | 252_E | 1.019 | 0.46 |
| 118_F | 419_H | 1.018 | 0.46 |
| 70_L | 196_S | 1.016 | 0.45 |
| 480_V | 484_S | 1.016 | 0.45 |
| 389_G | 394_C | 1.016 | 0.45 |
| 43_T | 46_L | 1.016 | 0.45 |
| 341_G | 422_S | 1.013 | 0.45 |
| 398_V | 469_V | 1.006 | 0.44 |
| 163_I | 170_I | 1.006 | 0.44 |
| 274_I | 400_I | 1.006 | 0.44 |
| 424_V | 456_V | 1.005 | 0.44 |
| 174_A | 217_W | 1.003 | 0.44 |
| 210_Y | 214_F | 1.002 | 0.44 |
| 471_D | 490_W | 1.002 | 0.44 |
| 279_H | 394_C | 1.000 | 0.44 |
| 51_T | 57_F | 1.000 | 0.44 |
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 | 0.9575 | 100 | 0.228 | Contact Map |
| 2wnwA | 2 | 0.8826 | 100 | 0.29 | Contact Map |
| 4ccdA | 1 | 0.749 | 100 | 0.357 | Contact Map |
| 3clwA | 6 | 0.8117 | 100 | 0.362 | Contact Map |
| 3kl0A | 4 | 0.7308 | 100 | 0.424 | Contact Map |
| 4fmvA | 1 | 0.7126 | 100 | 0.441 | Contact Map |
| 2y24A | 1 | 0.7146 | 100 | 0.45 | Contact Map |
| 4m29A | 1 | 0.7429 | 100 | 0.749 | Contact Map |
| 1w91A | 8 | 0.753 | 100 | 0.775 | Contact Map |
| 1uhvA | 4 | 0.753 | 100 | 0.782 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)