| hk |
| ID: | 1500207321 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 371 (371) | ||
| Sequences: | 3179 (3152.8) | ||
| Seq/Len: | 8.569 | ||
| Nf(neff/√len): | 163.7 |
HHblits Results: (2016_02)
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: 8.569).
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 |
| 295_V | 304_C | 4.045 | 1.00 |
| 287_C | 345_L | 3.331 | 1.00 |
| 202_S | 223_V | 3.180 | 1.00 |
| 286_M | 289_K | 3.169 | 1.00 |
| 302_K | 322_D | 3.156 | 1.00 |
| 345_L | 364_M | 2.943 | 1.00 |
| 198_I | 227_A | 2.899 | 1.00 |
| 291_A | 362_L | 2.800 | 1.00 |
| 288_L | 317_I | 2.677 | 1.00 |
| 300_Q | 324_T | 2.659 | 1.00 |
| 314_E | 365_A | 2.559 | 1.00 |
| 206_R | 224_Q | 2.498 | 1.00 |
| 303_T | 322_D | 2.447 | 1.00 |
| 301_A | 322_D | 2.403 | 1.00 |
| 320_S | 361_K | 2.323 | 1.00 |
| 205_A | 220_L | 2.281 | 1.00 |
| 277_S | 282_N | 2.259 | 1.00 |
| 210_Y | 217_A | 2.240 | 1.00 |
| 242_K | 343_E | 2.216 | 1.00 |
| 291_A | 319_V | 2.214 | 1.00 |
| 284_L | 315_V | 2.180 | 1.00 |
| 291_A | 341_M | 2.091 | 1.00 |
| 295_V | 299_S | 2.027 | 1.00 |
| 318_T | 363_T | 2.014 | 1.00 |
| 284_L | 317_I | 2.002 | 1.00 |
| 321_D | 359_G | 2.000 | 1.00 |
| 341_M | 352_L | 1.988 | 1.00 |
| 278_L | 282_N | 1.984 | 1.00 |
| 292_V | 304_C | 1.973 | 1.00 |
| 199_G | 227_A | 1.930 | 1.00 |
| 264_M | 267_Y | 1.925 | 1.00 |
| 198_I | 223_V | 1.918 | 1.00 |
| 248_K | 252_I | 1.906 | 1.00 |
| 247_L | 251_L | 1.861 | 1.00 |
| 251_L | 258_L | 1.849 | 1.00 |
| 202_S | 220_L | 1.837 | 1.00 |
| 318_T | 361_K | 1.837 | 1.00 |
| 191_L | 234_V | 1.835 | 1.00 |
| 345_L | 350_G | 1.822 | 1.00 |
| 245_I | 249_D | 1.780 | 1.00 |
| 250_E | 255_K | 1.779 | 1.00 |
| 325_F | 356_T | 1.771 | 1.00 |
| 263_I | 266_I | 1.763 | 1.00 |
| 292_V | 296_V | 1.760 | 1.00 |
| 249_D | 254_I | 1.741 | 1.00 |
| 250_E | 257_I | 1.739 | 1.00 |
| 276_I | 281_E | 1.723 | 1.00 |
| 252_I | 259_E | 1.723 | 1.00 |
| 265_F | 268_E | 1.719 | 1.00 |
| 175_V | 179_E | 1.701 | 1.00 |
| 206_R | 221_K | 1.678 | 1.00 |
| 248_K | 253_N | 1.668 | 1.00 |
| 354_I | 360_T | 1.668 | 1.00 |
| 285_S | 289_K | 1.664 | 1.00 |
| 316_V | 363_T | 1.647 | 1.00 |
| 325_F | 360_T | 1.645 | 1.00 |
| 203_D | 224_Q | 1.642 | 1.00 |
| 351_S | 365_A | 1.633 | 1.00 |
| 246_R | 250_E | 1.632 | 1.00 |
| 345_L | 352_L | 1.627 | 1.00 |
| 277_S | 281_E | 1.622 | 1.00 |
| 249_D | 256_Q | 1.610 | 1.00 |
| 276_I | 282_N | 1.607 | 1.00 |
| 250_E | 254_I | 1.606 | 1.00 |
| 251_L | 256_Q | 1.601 | 1.00 |
| 212_D | 215_Q | 1.599 | 1.00 |
| 252_I | 256_Q | 1.578 | 1.00 |
| 246_R | 254_I | 1.565 | 1.00 |
| 356_T | 360_T | 1.563 | 1.00 |
| 249_D | 253_N | 1.558 | 1.00 |
| 287_C | 364_M | 1.550 | 1.00 |
| 338_L | 341_M | 1.545 | 1.00 |
| 252_I | 257_I | 1.541 | 1.00 |
| 352_L | 364_M | 1.519 | 1.00 |
| 323_G | 359_G | 1.505 | 1.00 |
| 205_A | 223_V | 1.494 | 1.00 |
| 253_N | 257_I | 1.489 | 1.00 |
| 266_I | 269_E | 1.488 | 1.00 |
| 202_S | 227_A | 1.485 | 1.00 |
| 246_R | 249_D | 1.475 | 1.00 |
| 262_D | 265_F | 1.474 | 1.00 |
| 203_D | 228_R | 1.459 | 0.99 |
| 295_V | 301_A | 1.443 | 0.99 |
| 251_L | 255_K | 1.440 | 0.99 |
| 206_R | 220_L | 1.437 | 0.99 |
| 276_I | 280_N | 1.430 | 0.99 |
| 245_I | 253_N | 1.421 | 0.99 |
| 192_G | 196_S | 1.419 | 0.99 |
| 206_R | 217_A | 1.401 | 0.99 |
| 308_I | 317_I | 1.400 | 0.99 |
| 247_L | 252_I | 1.399 | 0.99 |
| 293_T | 297_K | 1.393 | 0.99 |
| 263_I | 267_Y | 1.392 | 0.99 |
| 190_T | 233_E | 1.384 | 0.99 |
| 261_A | 264_M | 1.376 | 0.99 |
| 243_K | 247_L | 1.368 | 0.99 |
| 316_V | 365_A | 1.361 | 0.99 |
| 251_L | 254_I | 1.358 | 0.99 |
| 199_G | 228_R | 1.340 | 0.99 |
| 250_E | 253_N | 1.333 | 0.99 |
| 249_D | 252_I | 1.329 | 0.99 |
| 201_K | 219_E | 1.323 | 0.99 |
| 279_L | 282_N | 1.317 | 0.99 |
| 173_E | 176_K | 1.315 | 0.99 |
| 306_V | 319_V | 1.311 | 0.99 |
| 246_R | 251_L | 1.311 | 0.99 |
| 277_S | 280_N | 1.311 | 0.99 |
| 342_R | 346_E | 1.304 | 0.99 |
| 307_D | 318_T | 1.300 | 0.99 |
| 264_M | 269_E | 1.293 | 0.98 |
| 243_K | 251_L | 1.292 | 0.98 |
| 247_L | 250_E | 1.287 | 0.98 |
| 224_Q | 228_R | 1.273 | 0.98 |
| 287_C | 341_M | 1.268 | 0.98 |
| 173_E | 177_L | 1.266 | 0.98 |
| 244_G | 248_K | 1.262 | 0.98 |
| 267_Y | 271_K | 1.259 | 0.98 |
| 278_L | 281_E | 1.254 | 0.98 |
| 247_L | 255_K | 1.248 | 0.98 |
| 265_F | 270_E | 1.245 | 0.98 |
| 264_M | 268_E | 1.225 | 0.98 |
| 263_I | 268_E | 1.224 | 0.98 |
| 248_K | 256_Q | 1.219 | 0.97 |
| 244_G | 247_L | 1.218 | 0.97 |
| 174_L | 178_E | 1.209 | 0.97 |
| 194_K | 230_S | 1.207 | 0.97 |
| 185_R | 343_E | 1.207 | 0.97 |
| 284_L | 364_M | 1.207 | 0.97 |
| 209_I | 216_A | 1.205 | 0.97 |
| 249_D | 260_A | 1.199 | 0.97 |
| 253_N | 260_A | 1.183 | 0.97 |
| 248_K | 255_K | 1.181 | 0.97 |
| 247_L | 253_N | 1.179 | 0.97 |
| 248_K | 251_L | 1.174 | 0.97 |
| 254_I | 258_L | 1.172 | 0.97 |
| 288_L | 306_V | 1.171 | 0.97 |
| 245_I | 251_L | 1.170 | 0.97 |
| 284_L | 366_I | 1.169 | 0.97 |
| 192_G | 234_V | 1.166 | 0.96 |
| 243_K | 248_K | 1.159 | 0.96 |
| 339_L | 343_E | 1.156 | 0.96 |
| 201_K | 222_S | 1.155 | 0.96 |
| 301_A | 324_T | 1.151 | 0.96 |
| 241_M | 286_M | 1.144 | 0.96 |
| 253_N | 258_L | 1.140 | 0.96 |
| 245_I | 248_K | 1.139 | 0.96 |
| 305_R | 320_S | 1.136 | 0.96 |
| 290_E | 297_K | 1.128 | 0.96 |
| 300_Q | 321_D | 1.122 | 0.95 |
| 262_D | 266_I | 1.121 | 0.95 |
| 234_V | 238_V | 1.115 | 0.95 |
| 177_L | 181_Q | 1.111 | 0.95 |
| 244_G | 252_I | 1.108 | 0.95 |
| 244_G | 249_D | 1.098 | 0.95 |
| 345_L | 348_A | 1.097 | 0.95 |
| 242_K | 340_G | 1.092 | 0.94 |
| 246_R | 252_I | 1.091 | 0.94 |
| 192_G | 231_L | 1.089 | 0.94 |
| 262_D | 267_Y | 1.088 | 0.94 |
| 266_I | 270_E | 1.085 | 0.94 |
| 265_F | 269_E | 1.078 | 0.94 |
| 170_R | 174_L | 1.074 | 0.94 |
| 266_I | 271_K | 1.073 | 0.94 |
| 283_I | 348_A | 1.066 | 0.93 |
| 244_G | 250_E | 1.065 | 0.93 |
| 245_I | 258_L | 1.064 | 0.93 |
| 179_E | 182_R | 1.064 | 0.93 |
| 301_A | 321_D | 1.062 | 0.93 |
| 259_E | 262_D | 1.061 | 0.93 |
| 238_V | 336_H | 1.061 | 0.93 |
| 244_G | 253_N | 1.058 | 0.93 |
| 193_Q | 360_T | 1.055 | 0.93 |
| 260_A | 263_I | 1.050 | 0.93 |
| 253_N | 256_Q | 1.045 | 0.92 |
| 252_I | 255_K | 1.045 | 0.92 |
| 326_K | 356_T | 1.045 | 0.92 |
| 168_N | 171_I | 1.044 | 0.92 |
| 187_L | 237_I | 1.043 | 0.92 |
| 234_V | 237_I | 1.041 | 0.92 |
| 276_I | 279_L | 1.041 | 0.92 |
| 212_D | 216_A | 1.034 | 0.92 |
| 243_K | 249_D | 1.018 | 0.91 |
| 247_L | 254_I | 1.017 | 0.91 |
| 292_V | 295_V | 1.017 | 0.91 |
| 255_K | 259_E | 1.016 | 0.91 |
| 164_L | 168_N | 1.014 | 0.91 |
| 242_K | 336_H | 1.011 | 0.91 |
| 161_E | 165_E | 1.009 | 0.91 |
| 186_D | 286_M | 1.004 | 0.90 |
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 | |
| 3ehhA | 2 | 0.5283 | 100 | 0.422 | Contact Map |
| 4r39A | 4 | 0.5121 | 99.8 | 0.583 | Contact Map |
| 4bixA | 2 | 0.5499 | 99.8 | 0.597 | Contact Map |
| 4q20A | 2 | 0.5472 | 99.8 | 0.605 | Contact Map |
| 2c2aA | 1 | 0.5553 | 99.8 | 0.623 | Contact Map |
| 4ctiA | 4 | 0.6065 | 99.8 | 0.624 | Contact Map |
| 3d36A | 2 | 0.531 | 99.7 | 0.63 | Contact Map |
| 4i5sA | 2 | 0.752 | 99.7 | 0.632 | Contact Map |
| 4gczA | 2 | 0.9218 | 99.7 | 0.635 | Contact Map |
| 4fppA | 3 | 0.496 | 99.7 | 0.644 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)