| T0843 |
| ID: | 1404412385 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 369 (351) | ||
| Sequences: | 32380 (21779.6) | ||
| Seq/Len: | 92.251 | ||
| Nf(neff/√len): | 1162.5 |
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: 92.251).
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 |
| 266_F | 359_E | 4.633 | 1.00 |
| 270_E | 362_V | 4.036 | 1.00 |
| 310_A | 367_S | 3.991 | 1.00 |
| 114_E | 149_E | 3.860 | 1.00 |
| 19_A | 23_A | 3.297 | 1.00 |
| 266_F | 355_E | 3.278 | 1.00 |
| 135_D | 138_R | 3.232 | 1.00 |
| 140_A | 148_R | 3.050 | 1.00 |
| 39_A | 251_E | 2.869 | 1.00 |
| 354_T | 357_D | 2.702 | 1.00 |
| 16_D | 20_E | 2.609 | 1.00 |
| 74_E | 121_T | 2.527 | 1.00 |
| 306_K | 309_A | 2.486 | 1.00 |
| 112_D | 116_K | 2.479 | 1.00 |
| 140_A | 156_V | 2.474 | 1.00 |
| 74_E | 118_S | 2.458 | 1.00 |
| 262_E | 355_E | 2.437 | 1.00 |
| 360_H | 364_T | 2.399 | 1.00 |
| 259_L | 263_N | 2.344 | 1.00 |
| 110_L | 142_I | 2.320 | 1.00 |
| 112_D | 115_R | 2.314 | 1.00 |
| 74_E | 97_T | 2.300 | 1.00 |
| 110_L | 138_R | 2.297 | 1.00 |
| 266_F | 270_E | 2.283 | 1.00 |
| 270_E | 359_E | 2.273 | 1.00 |
| 138_R | 141_G | 2.262 | 1.00 |
| 265_A | 269_K | 2.208 | 1.00 |
| 270_E | 273_G | 2.199 | 1.00 |
| 12_P | 16_D | 2.177 | 1.00 |
| 124_I | 147_E | 2.129 | 1.00 |
| 73_D | 122_R | 2.089 | 1.00 |
| 38_S | 42_A | 2.086 | 1.00 |
| 141_G | 149_E | 2.083 | 1.00 |
| 74_E | 95_R | 2.077 | 1.00 |
| 114_E | 150_H | 2.056 | 1.00 |
| 100_D | 112_D | 2.049 | 1.00 |
| 15_L | 19_A | 2.034 | 1.00 |
| 347_L | 361_V | 2.013 | 1.00 |
| 39_A | 247_L | 2.011 | 1.00 |
| 306_K | 310_A | 2.004 | 1.00 |
| 74_E | 120_A | 1.975 | 1.00 |
| 152_F | 155_A | 1.930 | 1.00 |
| 52_V | 58_G | 1.915 | 1.00 |
| 310_A | 364_T | 1.906 | 1.00 |
| 312_I | 364_T | 1.844 | 1.00 |
| 48_R | 202_D | 1.839 | 1.00 |
| 307_M | 314_A | 1.801 | 1.00 |
| 79_P | 100_D | 1.797 | 1.00 |
| 147_E | 156_V | 1.754 | 1.00 |
| 255_E | 258_R | 1.746 | 1.00 |
| 305_R | 309_A | 1.743 | 1.00 |
| 259_L | 262_E | 1.735 | 1.00 |
| 123_A | 157_I | 1.727 | 1.00 |
| 147_E | 152_F | 1.708 | 1.00 |
| 62_A | 179_M | 1.707 | 1.00 |
| 160_C | 180_C | 1.706 | 1.00 |
| 102_D | 105_T | 1.703 | 1.00 |
| 118_S | 121_T | 1.701 | 1.00 |
| 258_R | 262_E | 1.700 | 1.00 |
| 114_E | 142_I | 1.694 | 1.00 |
| 199_L | 205_H | 1.684 | 1.00 |
| 355_E | 359_E | 1.682 | 1.00 |
| 109_D | 112_D | 1.671 | 1.00 |
| 99_V | 116_K | 1.660 | 1.00 |
| 137_D | 141_G | 1.647 | 1.00 |
| 126_V | 139_L | 1.643 | 1.00 |
| 299_D | 302_A | 1.641 | 1.00 |
| 124_I | 152_F | 1.623 | 1.00 |
| 76_L | 121_T | 1.612 | 1.00 |
| 13_T | 248_A | 1.611 | 1.00 |
| 148_R | 178_N | 1.607 | 1.00 |
| 114_E | 118_S | 1.605 | 1.00 |
| 15_L | 23_A | 1.593 | 1.00 |
| 53_H | 57_S | 1.588 | 1.00 |
| 270_E | 363_A | 1.578 | 1.00 |
| 142_I | 150_H | 1.570 | 1.00 |
| 270_E | 366_R | 1.566 | 1.00 |
| 111_D | 114_E | 1.564 | 1.00 |
| 125_I | 157_I | 1.562 | 1.00 |
| 268_D | 293_Y | 1.556 | 1.00 |
| 360_H | 363_A | 1.544 | 1.00 |
| 59_L | 84_A | 1.529 | 1.00 |
| 306_K | 368_G | 1.517 | 1.00 |
| 202_D | 206_E | 1.507 | 1.00 |
| 248_A | 251_E | 1.489 | 1.00 |
| 68_A | 94_R | 1.489 | 1.00 |
| 113_L | 139_L | 1.486 | 1.00 |
| 47_P | 202_D | 1.472 | 1.00 |
| 114_E | 138_R | 1.453 | 1.00 |
| 274_V | 366_R | 1.452 | 1.00 |
| 16_D | 19_A | 1.437 | 1.00 |
| 18_V | 22_F | 1.433 | 1.00 |
| 266_F | 358_R | 1.431 | 1.00 |
| 58_G | 181_V | 1.417 | 1.00 |
| 261_R | 265_A | 1.405 | 0.99 |
| 102_D | 109_D | 1.376 | 0.99 |
| 302_A | 306_K | 1.362 | 0.99 |
| 263_N | 358_R | 1.357 | 0.99 |
| 111_D | 115_R | 1.349 | 0.99 |
| 268_D | 272_T | 1.348 | 0.99 |
| 59_L | 181_V | 1.347 | 0.99 |
| 73_D | 120_A | 1.346 | 0.99 |
| 303_F | 365_I | 1.334 | 0.99 |
| 359_E | 363_A | 1.333 | 0.99 |
| 312_I | 361_V | 1.330 | 0.99 |
| 13_T | 252_T | 1.322 | 0.99 |
| 20_E | 24_S | 1.311 | 0.99 |
| 97_T | 116_K | 1.302 | 0.99 |
| 296_K | 343_R | 1.293 | 0.99 |
| 273_G | 366_R | 1.282 | 0.99 |
| 263_N | 355_E | 1.272 | 0.99 |
| 117_I | 142_I | 1.260 | 0.99 |
| 157_I | 181_V | 1.254 | 0.99 |
| 363_A | 367_S | 1.252 | 0.99 |
| 278_E | 296_K | 1.242 | 0.98 |
| 39_A | 42_A | 1.238 | 0.98 |
| 267_Y | 349_V | 1.233 | 0.98 |
| 269_K | 273_G | 1.233 | 0.98 |
| 59_L | 157_I | 1.232 | 0.98 |
| 76_L | 116_K | 1.214 | 0.98 |
| 40_L | 196_L | 1.212 | 0.98 |
| 357_D | 360_H | 1.204 | 0.98 |
| 66_L | 155_A | 1.193 | 0.98 |
| 362_V | 366_R | 1.191 | 0.98 |
| 307_M | 364_T | 1.190 | 0.98 |
| 15_L | 22_F | 1.185 | 0.98 |
| 182_F | 196_L | 1.183 | 0.98 |
| 117_I | 121_T | 1.180 | 0.98 |
| 267_Y | 270_E | 1.174 | 0.98 |
| 305_R | 308_E | 1.173 | 0.98 |
| 111_D | 138_R | 1.166 | 0.97 |
| 35_E | 39_A | 1.163 | 0.97 |
| 31_P | 35_E | 1.150 | 0.97 |
| 266_F | 362_V | 1.146 | 0.97 |
| 118_S | 150_H | 1.133 | 0.97 |
| 259_L | 355_E | 1.132 | 0.97 |
| 69_P | 73_D | 1.125 | 0.97 |
| 269_K | 272_T | 1.120 | 0.96 |
| 55_G | 181_V | 1.120 | 0.96 |
| 262_E | 266_F | 1.116 | 0.96 |
| 361_V | 365_I | 1.115 | 0.96 |
| 117_I | 152_F | 1.114 | 0.96 |
| 263_N | 266_F | 1.109 | 0.96 |
| 34_A | 38_S | 1.097 | 0.96 |
| 60_C | 64_R | 1.077 | 0.95 |
| 62_A | 157_I | 1.077 | 0.95 |
| 137_D | 172_P | 1.075 | 0.95 |
| 99_V | 112_D | 1.075 | 0.95 |
| 356_Q | 359_E | 1.069 | 0.95 |
| 20_E | 32_R | 1.064 | 0.95 |
| 36_F | 246_G | 1.055 | 0.95 |
| 79_P | 98_W | 1.053 | 0.95 |
| 179_M | 199_L | 1.052 | 0.95 |
| 35_E | 247_L | 1.045 | 0.94 |
| 20_E | 23_A | 1.044 | 0.94 |
| 12_P | 23_A | 1.033 | 0.94 |
| 304_H | 314_A | 1.029 | 0.94 |
| 274_V | 362_V | 1.023 | 0.93 |
| 303_F | 345_V | 1.019 | 0.93 |
| 75_V | 89_I | 1.017 | 0.93 |
| 248_A | 252_T | 1.016 | 0.93 |
| 303_F | 368_G | 1.014 | 0.93 |
| 169_R | 172_P | 1.010 | 0.93 |
| 307_M | 312_I | 1.009 | 0.93 |
| 239_T | 242_N | 1.005 | 0.93 |
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 | |
| 3dr4A | 4 | 0.9648 | 100 | 0.267 | Contact Map |
| 3frkA | 2 | 0.9566 | 100 | 0.268 | Contact Map |
| 4lc3A | 2 | 0.9702 | 100 | 0.273 | Contact Map |
| 3b8xA | 2 | 0.9648 | 100 | 0.277 | Contact Map |
| 2fnuA | 2 | 0.9702 | 100 | 0.283 | Contact Map |
| 1mdoA | 1 | 0.9621 | 100 | 0.285 | Contact Map |
| 2c81A | 1 | 0.9648 | 100 | 0.286 | Contact Map |
| 4qgrA | 2 | 0.9566 | 100 | 0.292 | Contact Map |
| 1b9hA | 1 | 0.9621 | 100 | 0.294 | Contact Map |
| 3bb8A | 2 | 0.9756 | 100 | 0.294 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)