| YELAB |
| ID: | 1426068759 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 379 (370) | ||
| Sequences: | 2235 (1723.3) | ||
| Seq/Len: | 6.041 | ||
| Nf(neff/√len): | 89.6 |
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: 6.041).
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 |
| 57_Q | 297_D | 4.468 | 1.00 |
| 298_M | 306_F | 3.969 | 1.00 |
| 186_R | 200_P | 3.743 | 1.00 |
| 228_Y | 333_T | 3.712 | 1.00 |
| 39_V | 322_Q | 2.980 | 1.00 |
| 224_L | 273_L | 2.967 | 1.00 |
| 72_A | 117_F | 2.923 | 1.00 |
| 51_G | 308_S | 2.755 | 1.00 |
| 57_Q | 296_T | 2.641 | 1.00 |
| 141_K | 149_S | 2.528 | 1.00 |
| 251_T | 375_Q | 2.487 | 1.00 |
| 124_V | 132_A | 2.450 | 1.00 |
| 58_I | 295_M | 2.444 | 1.00 |
| 279_S | 327_E | 2.416 | 1.00 |
| 53_E | 297_D | 2.404 | 1.00 |
| 18_R | 63_G | 2.390 | 1.00 |
| 99_V | 105_L | 2.384 | 1.00 |
| 278_F | 328_V | 2.357 | 1.00 |
| 283_E | 323_K | 2.204 | 1.00 |
| 285_D | 319_L | 2.182 | 1.00 |
| 130_E | 133_R | 2.157 | 1.00 |
| 204_Q | 208_F | 2.131 | 1.00 |
| 128_E | 131_R | 2.116 | 1.00 |
| 45_M | 113_F | 2.076 | 1.00 |
| 47_Q | 59_Q | 2.074 | 1.00 |
| 209_N | 225_E | 2.021 | 1.00 |
| 92_S | 145_K | 2.000 | 1.00 |
| 225_E | 365_N | 1.994 | 1.00 |
| 281_E | 323_K | 1.951 | 1.00 |
| 188_L | 198_S | 1.928 | 1.00 |
| 192_S | 195_S | 1.924 | 1.00 |
| 186_R | 198_S | 1.902 | 1.00 |
| 354_I | 376_V | 1.900 | 1.00 |
| 237_I | 354_I | 1.885 | 1.00 |
| 360_F | 374_G | 1.884 | 1.00 |
| 187_R | 274_V | 1.855 | 1.00 |
| 51_G | 305_D | 1.825 | 1.00 |
| 212_E | 241_Y | 1.821 | 1.00 |
| 141_K | 146_G | 1.788 | 1.00 |
| 191_K | 194_G | 1.782 | 1.00 |
| 274_V | 353_I | 1.762 | 1.00 |
| 140_V | 151_L | 1.742 | 1.00 |
| 235_M | 362_V | 1.712 | 1.00 |
| 20_F | 251_T | 1.711 | 1.00 |
| 326_I | 360_F | 1.707 | 1.00 |
| 122_K | 135_I | 1.699 | 1.00 |
| 133_R | 152_L | 1.674 | 1.00 |
| 46_L | 317_V | 1.674 | 1.00 |
| 287_R | 319_L | 1.668 | 1.00 |
| 152_L | 157_V | 1.660 | 1.00 |
| 48_L | 72_A | 1.658 | 1.00 |
| 235_M | 328_V | 1.652 | 1.00 |
| 106_V | 311_D | 1.646 | 1.00 |
| 203_A | 274_V | 1.640 | 1.00 |
| 275_L | 354_I | 1.608 | 0.99 |
| 43_L | 62_M | 1.608 | 0.99 |
| 114_F | 120_T | 1.608 | 0.99 |
| 224_L | 352_I | 1.599 | 0.99 |
| 94_T | 168_A | 1.568 | 0.99 |
| 300_R | 303_Q | 1.565 | 0.99 |
| 225_E | 234_S | 1.557 | 0.99 |
| 237_I | 275_L | 1.541 | 0.99 |
| 273_L | 354_I | 1.531 | 0.99 |
| 43_L | 290_L | 1.517 | 0.99 |
| 151_L | 338_S | 1.508 | 0.99 |
| 301_Q | 316_H | 1.505 | 0.99 |
| 361_V | 373_M | 1.477 | 0.99 |
| 246_P | 356_R | 1.466 | 0.99 |
| 169_L | 324_V | 1.465 | 0.99 |
| 188_L | 196_T | 1.453 | 0.99 |
| 94_T | 139_W | 1.441 | 0.99 |
| 232_T | 364_H | 1.439 | 0.99 |
| 20_F | 373_M | 1.418 | 0.98 |
| 33_V | 324_V | 1.404 | 0.98 |
| 54_T | 298_M | 1.398 | 0.98 |
| 107_Q | 111_P | 1.390 | 0.98 |
| 42_V | 341_V | 1.387 | 0.98 |
| 38_G | 167_N | 1.376 | 0.98 |
| 33_V | 326_I | 1.376 | 0.98 |
| 187_R | 201_M | 1.374 | 0.98 |
| 364_H | 367_T | 1.374 | 0.98 |
| 226_L | 273_L | 1.373 | 0.98 |
| 220_Y | 241_Y | 1.365 | 0.98 |
| 280_L | 360_F | 1.363 | 0.98 |
| 42_V | 322_Q | 1.359 | 0.98 |
| 175_W | 179_F | 1.357 | 0.98 |
| 134_F | 138_D | 1.354 | 0.98 |
| 95_D | 167_N | 1.354 | 0.98 |
| 223_I | 262_W | 1.350 | 0.98 |
| 210_Y | 222_D | 1.350 | 0.98 |
| 46_L | 341_V | 1.349 | 0.98 |
| 109_F | 113_F | 1.348 | 0.98 |
| 213_F | 221_Y | 1.345 | 0.98 |
| 191_K | 197_V | 1.342 | 0.98 |
| 273_L | 352_I | 1.341 | 0.98 |
| 277_K | 329_N | 1.335 | 0.97 |
| 328_V | 333_T | 1.335 | 0.97 |
| 287_R | 291_E | 1.327 | 0.97 |
| 190_H | 196_T | 1.301 | 0.97 |
| 226_L | 275_L | 1.299 | 0.97 |
| 239_A | 356_R | 1.292 | 0.97 |
| 277_K | 330_E | 1.286 | 0.97 |
| 222_D | 241_Y | 1.286 | 0.97 |
| 309_L | 315_L | 1.282 | 0.97 |
| 105_L | 309_L | 1.272 | 0.96 |
| 177_T | 204_Q | 1.271 | 0.96 |
| 179_F | 202_M | 1.265 | 0.96 |
| 55_Q | 59_Q | 1.265 | 0.96 |
| 138_D | 142_T | 1.264 | 0.96 |
| 306_F | 343_V | 1.262 | 0.96 |
| 335_A | 338_S | 1.259 | 0.96 |
| 179_F | 184_T | 1.256 | 0.96 |
| 54_T | 304_A | 1.254 | 0.96 |
| 174_Q | 178_P | 1.250 | 0.96 |
| 297_D | 303_Q | 1.245 | 0.96 |
| 105_L | 110_M | 1.238 | 0.96 |
| 191_K | 195_S | 1.229 | 0.95 |
| 153_G | 156_A | 1.224 | 0.95 |
| 147_M | 334_V | 1.222 | 0.95 |
| 48_L | 117_F | 1.218 | 0.95 |
| 174_Q | 229_H | 1.216 | 0.95 |
| 47_Q | 55_Q | 1.215 | 0.95 |
| 208_F | 273_L | 1.211 | 0.95 |
| 290_L | 320_A | 1.208 | 0.95 |
| 288_K | 291_E | 1.205 | 0.95 |
| 272_L | 351_E | 1.204 | 0.95 |
| 158_Q | 161_T | 1.200 | 0.94 |
| 329_N | 334_V | 1.198 | 0.94 |
| 295_M | 298_M | 1.192 | 0.94 |
| 43_L | 320_A | 1.190 | 0.94 |
| 342_I | 346_R | 1.183 | 0.94 |
| 234_S | 365_N | 1.182 | 0.94 |
| 8_V | 12_A | 1.177 | 0.94 |
| 53_E | 56_Q | 1.174 | 0.94 |
| 184_T | 330_E | 1.173 | 0.93 |
| 98_F | 166_V | 1.173 | 0.93 |
| 335_A | 339_T | 1.166 | 0.93 |
| 96_A | 122_K | 1.160 | 0.93 |
| 125_D | 128_E | 1.158 | 0.93 |
| 179_F | 189_F | 1.157 | 0.93 |
| 181_D | 331_S | 1.149 | 0.93 |
| 311_D | 314_P | 1.147 | 0.92 |
| 239_A | 352_I | 1.143 | 0.92 |
| 184_T | 189_F | 1.140 | 0.92 |
| 291_E | 296_T | 1.129 | 0.92 |
| 42_V | 339_T | 1.125 | 0.92 |
| 236_F | 263_K | 1.118 | 0.91 |
| 49_T | 309_L | 1.117 | 0.91 |
| 50_T | 58_I | 1.112 | 0.91 |
| 50_T | 54_T | 1.103 | 0.90 |
| 298_M | 317_V | 1.102 | 0.90 |
| 360_F | 376_V | 1.101 | 0.90 |
| 152_L | 340_A | 1.096 | 0.90 |
| 27_S | 30_R | 1.094 | 0.90 |
| 225_E | 236_F | 1.093 | 0.90 |
| 138_D | 141_K | 1.089 | 0.90 |
| 202_M | 330_E | 1.080 | 0.89 |
| 187_R | 353_I | 1.080 | 0.89 |
| 180_P | 183_S | 1.075 | 0.89 |
| 200_P | 277_K | 1.075 | 0.89 |
| 306_F | 317_V | 1.074 | 0.89 |
| 326_I | 335_A | 1.073 | 0.89 |
| 325_K | 334_V | 1.067 | 0.88 |
| 178_P | 331_S | 1.063 | 0.88 |
| 280_L | 376_V | 1.062 | 0.88 |
| 322_Q | 337_S | 1.060 | 0.88 |
| 133_R | 153_G | 1.055 | 0.88 |
| 40_A | 375_Q | 1.054 | 0.88 |
| 278_F | 326_I | 1.053 | 0.87 |
| 12_A | 40_A | 1.052 | 0.87 |
| 176_K | 231_D | 1.050 | 0.87 |
| 234_S | 237_I | 1.045 | 0.87 |
| 175_W | 332_G | 1.039 | 0.87 |
| 147_M | 325_K | 1.034 | 0.86 |
| 184_T | 202_M | 1.030 | 0.86 |
| 96_A | 139_W | 1.028 | 0.86 |
| 245_V | 250_L | 1.022 | 0.85 |
| 147_M | 336_S | 1.020 | 0.85 |
| 205_T | 270_P | 1.013 | 0.85 |
| 144_T | 148_I | 1.013 | 0.85 |
| 333_T | 337_S | 1.010 | 0.84 |
| 245_V | 356_R | 1.009 | 0.84 |
| 132_A | 136_I | 1.002 | 0.84 |
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 | |
| 1lj5A | 1 | 0.9894 | 100 | 0.014 | Contact Map |
| 1uhgA | 4 | 0.9631 | 100 | 0.02 | Contact Map |
| 3stoA | 1 | 0.9261 | 100 | 0.025 | Contact Map |
| 3ne4A | 1 | 0.9631 | 100 | 0.025 | Contact Map |
| 4dy0A | 2 | 0.9736 | 100 | 0.026 | Contact Map |
| 3f5nA | 5 | 0.9604 | 100 | 0.026 | Contact Map |
| 4ga7A | 2 | 0.9525 | 100 | 0.028 | Contact Map |
| 2arrA | 1 | 0.9208 | 100 | 0.03 | Contact Map |
| 4dteA | 2 | 0.9683 | 100 | 0.03 | Contact Map |
| 4kdsA | 1 | 0.9657 | 100 | 0.031 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)