| 244_mafft |
| ID: | 1460310707 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 398 (164) | ||
| Sequences: | 5585 (4459.9) | ||
| Seq/Len: | 34.055 | ||
| Nf(neff/√len): | 348.3 |
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: 34.055).
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 |
| 301_F | 328_T | 3.402 | 1.00 |
| 225_E | 268_K | 3.297 | 1.00 |
| 217_P | 271_F | 2.928 | 1.00 |
| 224_L | 228_L | 2.588 | 1.00 |
| 268_K | 272_L | 2.549 | 1.00 |
| 208_G | 247_N | 2.468 | 1.00 |
| 302_L | 325_V | 2.179 | 1.00 |
| 345_L | 349_I | 2.133 | 1.00 |
| 344_T | 347_Q | 2.115 | 1.00 |
| 235_E | 238_W | 2.027 | 1.00 |
| 304_R | 307_D | 2.005 | 1.00 |
| 296_E | 304_R | 2.003 | 1.00 |
| 228_L | 238_W | 1.936 | 1.00 |
| 217_P | 221_L | 1.929 | 1.00 |
| 228_L | 233_G | 1.895 | 1.00 |
| 242_I | 267_F | 1.861 | 1.00 |
| 322_I | 348_L | 1.791 | 1.00 |
| 297_P | 300_Q | 1.768 | 1.00 |
| 305_K | 325_V | 1.674 | 1.00 |
| 302_L | 349_I | 1.634 | 1.00 |
| 325_V | 328_T | 1.631 | 1.00 |
| 210_D | 247_N | 1.612 | 1.00 |
| 221_L | 268_K | 1.611 | 1.00 |
| 239_L | 267_F | 1.583 | 1.00 |
| 292_Q | 330_Q | 1.576 | 1.00 |
| 301_F | 305_K | 1.498 | 1.00 |
| 336_F | 339_H | 1.468 | 1.00 |
| 263_S | 266_E | 1.457 | 1.00 |
| 289_D | 323_Q | 1.448 | 1.00 |
| 221_L | 272_L | 1.446 | 1.00 |
| 288_L | 324_Y | 1.438 | 1.00 |
| 342_P | 348_L | 1.420 | 1.00 |
| 224_L | 242_I | 1.397 | 0.99 |
| 347_Q | 350_Q | 1.383 | 0.99 |
| 217_P | 220_F | 1.368 | 0.99 |
| 227_Y | 241_Q | 1.357 | 0.99 |
| 243_Q | 254_W | 1.357 | 0.99 |
| 272_L | 276_E | 1.337 | 0.99 |
| 264_W | 268_K | 1.325 | 0.99 |
| 284_I | 287_E | 1.306 | 0.99 |
| 270_A | 273_Q | 1.305 | 0.99 |
| 265_V | 269_K | 1.288 | 0.99 |
| 325_V | 329_L | 1.281 | 0.99 |
| 235_E | 265_V | 1.277 | 0.99 |
| 309_Y | 321_V | 1.247 | 0.99 |
| 305_K | 309_Y | 1.235 | 0.98 |
| 355_V | 359_L | 1.227 | 0.98 |
| 293_K | 296_E | 1.194 | 0.98 |
| 298_L | 352_G | 1.186 | 0.98 |
| 289_D | 327_G | 1.182 | 0.98 |
| 299_D | 353_L | 1.172 | 0.98 |
| 325_V | 348_L | 1.168 | 0.97 |
| 283_A | 287_E | 1.160 | 0.97 |
| 344_T | 348_L | 1.145 | 0.97 |
| 250_A | 253_W | 1.143 | 0.97 |
| 217_P | 272_L | 1.128 | 0.97 |
| 287_E | 308_L | 1.127 | 0.97 |
| 292_Q | 296_E | 1.126 | 0.97 |
| 273_Q | 350_Q | 1.126 | 0.97 |
| 222_S | 255_E | 1.125 | 0.97 |
| 285_Q | 323_Q | 1.124 | 0.97 |
| 326_V | 334_K | 1.123 | 0.97 |
| 356_Q | 360_E | 1.113 | 0.96 |
| 220_F | 242_I | 1.106 | 0.96 |
| 286_R | 327_G | 1.098 | 0.96 |
| 242_I | 271_F | 1.097 | 0.96 |
| 213_I | 216_D | 1.086 | 0.96 |
| 234_S | 238_W | 1.086 | 0.96 |
| 325_V | 352_G | 1.084 | 0.96 |
| 289_D | 324_Y | 1.081 | 0.95 |
| 234_S | 237_Y | 1.077 | 0.95 |
| 269_K | 273_Q | 1.069 | 0.95 |
| 226_E | 243_Q | 1.069 | 0.95 |
| 348_L | 352_G | 1.062 | 0.95 |
| 206_S | 245_H | 1.056 | 0.95 |
| 346_E | 350_Q | 1.048 | 0.94 |
| 262_R | 266_E | 1.045 | 0.94 |
| 224_L | 264_W | 1.042 | 0.94 |
| 277_G | 280_S | 1.041 | 0.94 |
| 302_L | 306_R | 1.040 | 0.94 |
| 287_E | 304_R | 1.039 | 0.94 |
| 249_P | 252_K | 1.039 | 0.94 |
| 351_R | 354_E | 1.031 | 0.94 |
| 317_E | 320_E | 1.031 | 0.94 |
| 318_E | 321_V | 1.031 | 0.94 |
| 286_R | 290_L | 1.027 | 0.94 |
| 358_G | 362_G | 1.017 | 0.93 |
| 284_I | 311_T | 1.016 | 0.93 |
| 253_W | 264_W | 1.014 | 0.93 |
| 247_N | 250_A | 1.013 | 0.93 |
| 223_H | 251_K | 1.004 | 0.93 |
| 217_P | 253_W | 1.001 | 0.92 |
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 | |
| 4x3iA | 1 | 0 | 98.6 | 0.913 | Contact Map |
| 4x3xA | 1 | 0 | 98.3 | 0.921 | Contact Map |
| 4bhxA | 2 | 0.2111 | 89.8 | 0.957 | Contact Map |
| 4e6sA | 1 | 0.1935 | 74.9 | 0.964 | Contact Map |
| 2fi2A | 2 | 0.2186 | 73.7 | 0.965 | Contact Map |
| 3lhrA | 2 | 0.2136 | 73.3 | 0.965 | Contact Map |
| 1y7qA | 2 | 0.2286 | 69.4 | 0.966 | Contact Map |
| 3g21A | 1 | 0.1834 | 60.7 | 0.968 | Contact Map |
| 3g1gA | 2 | 0.1834 | 53.7 | 0.969 | Contact Map |
| 3ds4A | 2 | 0.1859 | 40.4 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)