| YELAB |
| ID: | 1426039072 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 394 (371) | ||
| Sequences: | 2218 (1687.1) | ||
| Seq/Len: | 5.978 | ||
| Nf(neff/√len): | 87.6 |
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: 5.978).
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 |
| 75_E | 310_K | 4.664 | 1.00 |
| 244_Y | 345_T | 3.966 | 1.00 |
| 205_E | 219_P | 3.902 | 1.00 |
| 311_V | 318_L | 3.820 | 1.00 |
| 93_H | 138_Y | 3.056 | 1.00 |
| 57_I | 334_H | 3.027 | 1.00 |
| 240_L | 286_L | 2.955 | 1.00 |
| 69_K | 320_G | 2.792 | 1.00 |
| 75_E | 309_T | 2.780 | 1.00 |
| 145_V | 153_A | 2.741 | 1.00 |
| 264_E | 387_K | 2.616 | 1.00 |
| 162_E | 170_V | 2.512 | 1.00 |
| 292_S | 339_T | 2.508 | 1.00 |
| 71_D | 310_K | 2.436 | 1.00 |
| 120_L | 126_L | 2.416 | 1.00 |
| 76_I | 308_I | 2.409 | 1.00 |
| 291_L | 340_I | 2.403 | 1.00 |
| 36_S | 81_N | 2.349 | 1.00 |
| 296_T | 335_K | 2.302 | 1.00 |
| 223_R | 227_F | 2.241 | 1.00 |
| 151_E | 154_K | 2.221 | 1.00 |
| 298_D | 331_K | 2.188 | 1.00 |
| 63_M | 134_V | 2.135 | 1.00 |
| 65_S | 77_L | 2.116 | 1.00 |
| 228_N | 241_L | 2.114 | 1.00 |
| 241_L | 377_Q | 2.055 | 1.00 |
| 294_T | 335_K | 2.042 | 1.00 |
| 113_T | 166_Q | 2.028 | 1.00 |
| 205_E | 217_K | 2.013 | 1.00 |
| 231_H | 256_D | 2.008 | 1.00 |
| 372_F | 386_G | 1.976 | 1.00 |
| 211_D | 214_T | 1.957 | 1.00 |
| 206_E | 287_H | 1.911 | 1.00 |
| 162_E | 167_G | 1.904 | 1.00 |
| 127_V | 323_E | 1.898 | 1.00 |
| 149_D | 152_E | 1.884 | 1.00 |
| 207_D | 217_K | 1.867 | 1.00 |
| 38_Y | 264_E | 1.833 | 1.00 |
| 161_V | 172_L | 1.821 | 1.00 |
| 366_F | 388_V | 1.806 | 1.00 |
| 210_V | 213_V | 1.801 | 1.00 |
| 287_H | 365_K | 1.769 | 1.00 |
| 69_K | 317_D | 1.752 | 1.00 |
| 154_K | 173_V | 1.746 | 1.00 |
| 222_K | 287_H | 1.740 | 1.00 |
| 173_V | 176_L | 1.737 | 1.00 |
| 143_F | 156_Q | 1.726 | 1.00 |
| 338_L | 372_F | 1.700 | 1.00 |
| 240_L | 364_V | 1.685 | 1.00 |
| 288_L | 366_F | 1.675 | 1.00 |
| 115_G | 187_Y | 1.660 | 1.00 |
| 373_L | 385_M | 1.640 | 1.00 |
| 300_K | 331_K | 1.636 | 1.00 |
| 64_L | 329_L | 1.608 | 0.99 |
| 66_L | 93_H | 1.599 | 0.99 |
| 135_K | 141_E | 1.583 | 0.99 |
| 61_F | 80_L | 1.573 | 0.99 |
| 286_L | 366_F | 1.563 | 0.99 |
| 207_D | 215_T | 1.548 | 0.99 |
| 376_E | 379_T | 1.535 | 0.99 |
| 61_F | 303_L | 1.524 | 0.99 |
| 51_F | 336_A | 1.503 | 0.99 |
| 172_L | 350_A | 1.470 | 0.99 |
| 115_G | 160_Y | 1.466 | 0.99 |
| 248_A | 251_I | 1.461 | 0.99 |
| 56_S | 186_N | 1.457 | 0.99 |
| 206_E | 220_M | 1.437 | 0.99 |
| 300_K | 304_G | 1.434 | 0.99 |
| 188_I | 336_A | 1.433 | 0.99 |
| 38_Y | 385_M | 1.427 | 0.98 |
| 232_X | 237_S | 1.426 | 0.98 |
| 210_V | 216_V | 1.402 | 0.98 |
| 286_L | 364_V | 1.388 | 0.98 |
| 242_M | 288_L | 1.384 | 0.98 |
| 194_W | 198_F | 1.383 | 0.98 |
| 72_T | 311_V | 1.374 | 0.98 |
| 209_H | 215_T | 1.365 | 0.98 |
| 60_A | 334_H | 1.364 | 0.98 |
| 293_I | 372_F | 1.360 | 0.98 |
| 198_F | 203_T | 1.357 | 0.98 |
| 196_R | 223_R | 1.357 | 0.98 |
| 51_F | 338_L | 1.347 | 0.98 |
| 126_L | 321_V | 1.343 | 0.97 |
| 236_S | 256_D | 1.343 | 0.97 |
| 314_N | 328_K | 1.342 | 0.97 |
| 340_I | 345_T | 1.334 | 0.97 |
| 26_I | 30_L | 1.331 | 0.97 |
| 239_V | 275_F | 1.327 | 0.97 |
| 242_M | 286_L | 1.321 | 0.97 |
| 60_A | 353_L | 1.321 | 0.97 |
| 193_K | 197_P | 1.321 | 0.97 |
| 159_D | 163_K | 1.313 | 0.97 |
| 128_D | 132_E | 1.308 | 0.97 |
| 321_V | 327_L | 1.295 | 0.97 |
| 155_K | 159_D | 1.293 | 0.97 |
| 64_L | 353_L | 1.288 | 0.97 |
| 285_S | 363_E | 1.287 | 0.97 |
| 117_G | 143_F | 1.286 | 0.97 |
| 198_F | 221_M | 1.284 | 0.96 |
| 252_F | 366_F | 1.280 | 0.96 |
| 198_F | 208_F | 1.279 | 0.96 |
| 168_K | 346_E | 1.276 | 0.96 |
| 146_N | 149_D | 1.269 | 0.96 |
| 238_W | 256_D | 1.267 | 0.96 |
| 250_A | 374_M | 1.262 | 0.96 |
| 73_H | 77_L | 1.261 | 0.96 |
| 72_T | 316_A | 1.255 | 0.96 |
| 130_F | 134_V | 1.246 | 0.96 |
| 301_S | 304_G | 1.242 | 0.96 |
| 203_T | 221_M | 1.242 | 0.96 |
| 303_L | 332_A | 1.236 | 0.95 |
| 210_V | 214_T | 1.235 | 0.95 |
| 304_G | 309_T | 1.229 | 0.95 |
| 347_A | 351_M | 1.217 | 0.95 |
| 290_K | 341_D | 1.215 | 0.95 |
| 259_K | 368_K | 1.207 | 0.95 |
| 206_E | 365_K | 1.204 | 0.94 |
| 65_S | 73_H | 1.202 | 0.94 |
| 290_K | 342_E | 1.200 | 0.94 |
| 347_A | 350_A | 1.190 | 0.94 |
| 45_S | 48_T | 1.189 | 0.94 |
| 310_K | 315_G | 1.188 | 0.94 |
| 249_T | 252_F | 1.187 | 0.94 |
| 341_D | 346_E | 1.186 | 0.94 |
| 308_I | 311_V | 1.178 | 0.94 |
| 173_V | 352_F | 1.177 | 0.94 |
| 66_L | 138_Y | 1.176 | 0.93 |
| 293_I | 388_V | 1.174 | 0.93 |
| 193_K | 245_L | 1.172 | 0.93 |
| 203_T | 208_F | 1.170 | 0.93 |
| 177_D | 180_T | 1.166 | 0.93 |
| 224_L | 283_S | 1.164 | 0.93 |
| 119_F | 185_V | 1.152 | 0.93 |
| 126_L | 131_L | 1.150 | 0.92 |
| 153_A | 157_I | 1.148 | 0.92 |
| 254_L | 368_K | 1.148 | 0.92 |
| 241_L | 249_T | 1.145 | 0.92 |
| 252_F | 288_L | 1.144 | 0.92 |
| 67_G | 321_V | 1.137 | 0.92 |
| 197_P | 343_K | 1.135 | 0.92 |
| 221_M | 342_E | 1.134 | 0.92 |
| 250_A | 253_F | 1.129 | 0.92 |
| 116_N | 186_N | 1.128 | 0.92 |
| 200_V | 343_K | 1.126 | 0.91 |
| 61_F | 332_A | 1.122 | 0.91 |
| 372_F | 388_V | 1.118 | 0.91 |
| 231_H | 238_W | 1.112 | 0.91 |
| 232_X | 239_V | 1.110 | 0.91 |
| 71_D | 74_D | 1.110 | 0.91 |
| 229_I | 238_W | 1.104 | 0.90 |
| 203_T | 342_E | 1.099 | 0.90 |
| 176_L | 183_A | 1.097 | 0.90 |
| 218_V | 221_M | 1.097 | 0.90 |
| 159_D | 162_E | 1.094 | 0.90 |
| 165_T | 169_I | 1.091 | 0.90 |
| 227_F | 243_K | 1.091 | 0.90 |
| 268_T | 271_I | 1.088 | 0.89 |
| 58_A | 387_K | 1.081 | 0.89 |
| 199_E | 202_D | 1.081 | 0.89 |
| 194_W | 344_G | 1.078 | 0.89 |
| 291_L | 338_L | 1.076 | 0.89 |
| 323_E | 326_P | 1.070 | 0.88 |
| 249_T | 253_F | 1.067 | 0.88 |
| 250_A | 340_I | 1.065 | 0.88 |
| 158_N | 169_I | 1.062 | 0.88 |
| 311_V | 329_L | 1.058 | 0.88 |
| 68_T | 76_I | 1.055 | 0.87 |
| 191_K | 343_K | 1.053 | 0.87 |
| 34_A | 58_A | 1.051 | 0.87 |
| 354_E | 358_M | 1.051 | 0.87 |
| 168_K | 337_V | 1.048 | 0.87 |
| 40_Q | 305_Q | 1.042 | 0.87 |
| 93_H | 96_F | 1.040 | 0.86 |
| 227_F | 286_L | 1.035 | 0.86 |
| 189_F | 346_E | 1.032 | 0.86 |
| 30_L | 58_A | 1.024 | 0.85 |
| 68_T | 72_T | 1.022 | 0.85 |
| 219_P | 290_K | 1.021 | 0.85 |
| 337_V | 346_E | 1.018 | 0.85 |
| 374_M | 384_F | 1.016 | 0.85 |
| 318_L | 329_L | 1.016 | 0.85 |
| 162_E | 172_L | 1.014 | 0.84 |
| 334_H | 349_G | 1.011 | 0.84 |
| 338_L | 345_T | 1.010 | 0.84 |
| 249_T | 259_K | 1.006 | 0.84 |
| 158_N | 165_T | 1.003 | 0.84 |
| 241_L | 251_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 | |
| 3ne4A | 1 | 0.9391 | 100 | 0.07 | Contact Map |
| 4if8A | 2 | 0.9365 | 100 | 0.093 | Contact Map |
| 4c41A | 1 | 0.9315 | 100 | 0.099 | Contact Map |
| 1qmnA | 1 | 0.9112 | 100 | 0.101 | Contact Map |
| 2ceoA | 2 | 0.9264 | 100 | 0.103 | Contact Map |
| 1yxaA | 2 | 0.9442 | 100 | 0.103 | Contact Map |
| 4ajtA | 1 | 0.9365 | 100 | 0.112 | Contact Map |
| 3f5nA | 5 | 0.9213 | 100 | 0.118 | Contact Map |
| 1uhgA | 4 | 0.9264 | 100 | 0.119 | Contact Map |
| 4ga7A | 2 | 0.901 | 100 | 0.122 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)