| trial 1 |
| ID: | 1495563400 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 309 (252) | ||
| Sequences: | 3963 (3120.5) | ||
| Seq/Len: | 15.726 | ||
| Nf(neff/√len): | 196.6 |
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: 15.726).
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 |
| 249_I | 286_T | 3.792 | 1.00 |
| 261_M | 269_N | 3.372 | 1.00 |
| 238_I | 246_D | 3.298 | 1.00 |
| 252_A | 278_F | 3.178 | 1.00 |
| 202_Y | 206_H | 2.942 | 1.00 |
| 253_K | 286_T | 2.857 | 1.00 |
| 232_F | 243_W | 2.835 | 1.00 |
| 282_F | 293_F | 2.823 | 1.00 |
| 251_Q | 254_L | 2.756 | 1.00 |
| 204_S | 247_Q | 2.740 | 1.00 |
| 73_V | 80_E | 2.602 | 1.00 |
| 256_L | 263_I | 2.500 | 1.00 |
| 279_S | 289_S | 2.240 | 1.00 |
| 259_T | 294_R | 2.195 | 1.00 |
| 249_I | 285_C | 2.186 | 1.00 |
| 215_A | 219_Q | 2.165 | 1.00 |
| 261_M | 265_T | 2.147 | 1.00 |
| 215_A | 225_P | 2.087 | 1.00 |
| 203_I | 244_R | 2.087 | 1.00 |
| 71_Q | 84_R | 2.064 | 1.00 |
| 69_R | 85_P | 2.015 | 1.00 |
| 71_Q | 82_V | 2.000 | 1.00 |
| 206_H | 210_S | 1.983 | 1.00 |
| 255_L | 269_N | 1.955 | 1.00 |
| 199_A | 217_V | 1.947 | 1.00 |
| 291_S | 295_A | 1.916 | 1.00 |
| 223_L | 228_L | 1.893 | 1.00 |
| 62_Y | 93_P | 1.889 | 1.00 |
| 246_D | 285_C | 1.840 | 1.00 |
| 288_A | 296_G | 1.786 | 1.00 |
| 241_L | 245_E | 1.776 | 1.00 |
| 255_L | 261_M | 1.773 | 1.00 |
| 206_H | 209_D | 1.767 | 1.00 |
| 275_Q | 279_S | 1.755 | 1.00 |
| 253_K | 293_F | 1.730 | 1.00 |
| 217_V | 240_V | 1.724 | 1.00 |
| 240_V | 244_R | 1.722 | 1.00 |
| 73_V | 82_V | 1.715 | 1.00 |
| 203_I | 247_Q | 1.706 | 1.00 |
| 199_A | 221_V | 1.704 | 1.00 |
| 266_V | 294_R | 1.682 | 1.00 |
| 223_L | 227_R | 1.663 | 1.00 |
| 216_S | 220_H | 1.659 | 1.00 |
| 213_D | 216_S | 1.656 | 1.00 |
| 252_A | 270_V | 1.654 | 1.00 |
| 255_L | 270_V | 1.646 | 1.00 |
| 228_L | 240_V | 1.581 | 1.00 |
| 63_I | 97_H | 1.575 | 1.00 |
| 75_K | 80_E | 1.571 | 1.00 |
| 227_R | 231_L | 1.570 | 1.00 |
| 77_Q | 95_E | 1.544 | 1.00 |
| 66_L | 151_F | 1.521 | 1.00 |
| 262_P | 265_T | 1.509 | 1.00 |
| 212_F | 248_R | 1.508 | 1.00 |
| 202_Y | 220_H | 1.507 | 1.00 |
| 265_T | 268_R | 1.489 | 1.00 |
| 277_Y | 280_R | 1.477 | 1.00 |
| 276_L | 279_S | 1.476 | 1.00 |
| 251_Q | 255_L | 1.475 | 1.00 |
| 264_A | 275_Q | 1.430 | 1.00 |
| 281_V | 285_C | 1.429 | 1.00 |
| 201_Q | 205_D | 1.428 | 1.00 |
| 59_M | 63_I | 1.414 | 1.00 |
| 256_L | 294_R | 1.409 | 1.00 |
| 199_A | 240_V | 1.403 | 0.99 |
| 277_Y | 281_V | 1.364 | 0.99 |
| 202_Y | 212_F | 1.332 | 0.99 |
| 221_V | 228_L | 1.329 | 0.99 |
| 227_R | 230_H | 1.319 | 0.99 |
| 279_S | 291_S | 1.312 | 0.99 |
| 288_A | 292_E | 1.307 | 0.99 |
| 249_I | 272_F | 1.289 | 0.99 |
| 229_S | 239_S | 1.286 | 0.99 |
| 252_A | 255_L | 1.268 | 0.99 |
| 196_V | 236_L | 1.266 | 0.99 |
| 84_R | 87_D | 1.240 | 0.98 |
| 248_R | 270_V | 1.240 | 0.98 |
| 171_N | 178_L | 1.239 | 0.98 |
| 202_Y | 217_V | 1.230 | 0.98 |
| 207_L | 247_Q | 1.218 | 0.98 |
| 226_S | 229_S | 1.207 | 0.98 |
| 224_S | 227_R | 1.199 | 0.98 |
| 246_D | 250_S | 1.193 | 0.98 |
| 253_K | 282_F | 1.191 | 0.98 |
| 214_I | 229_S | 1.191 | 0.98 |
| 254_L | 258_T | 1.186 | 0.98 |
| 236_L | 243_W | 1.171 | 0.98 |
| 272_F | 281_V | 1.166 | 0.97 |
| 212_F | 217_V | 1.161 | 0.97 |
| 73_V | 100_G | 1.157 | 0.97 |
| 61_G | 114_Y | 1.145 | 0.97 |
| 202_Y | 221_V | 1.142 | 0.97 |
| 225_P | 229_S | 1.140 | 0.97 |
| 247_Q | 251_Q | 1.136 | 0.97 |
| 204_S | 243_W | 1.135 | 0.97 |
| 59_M | 97_H | 1.134 | 0.97 |
| 263_I | 291_S | 1.118 | 0.96 |
| 75_K | 98_H | 1.110 | 0.96 |
| 67_T | 72_G | 1.108 | 0.96 |
| 286_T | 293_F | 1.105 | 0.96 |
| 248_R | 271_G | 1.103 | 0.96 |
| 259_T | 266_V | 1.101 | 0.96 |
| 241_L | 277_Y | 1.089 | 0.96 |
| 261_M | 266_V | 1.064 | 0.95 |
| 278_F | 290_P | 1.064 | 0.95 |
| 255_L | 266_V | 1.061 | 0.95 |
| 265_T | 269_N | 1.059 | 0.95 |
| 69_R | 107_E | 1.057 | 0.95 |
| 195_R | 223_L | 1.057 | 0.95 |
| 238_I | 242_S | 1.054 | 0.95 |
| 253_K | 257_S | 1.051 | 0.94 |
| 245_E | 272_F | 1.048 | 0.94 |
| 64_L | 90_L | 1.042 | 0.94 |
| 65_N | 112_W | 1.041 | 0.94 |
| 168_L | 171_N | 1.039 | 0.94 |
| 248_R | 281_V | 1.038 | 0.94 |
| 200_C | 204_S | 1.036 | 0.94 |
| 199_A | 202_Y | 1.035 | 0.94 |
| 172_L | 175_Q | 1.028 | 0.94 |
| 149_D | 153_Q | 1.024 | 0.93 |
| 289_S | 292_E | 1.023 | 0.93 |
| 229_S | 240_V | 1.022 | 0.93 |
| 274_D | 277_Y | 1.020 | 0.93 |
| 69_R | 106_R | 1.010 | 0.93 |
| 249_I | 281_V | 1.008 | 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 | |
| 3gbgA | 1 | 0.8058 | 100 | 0.392 | Contact Map |
| 1bl0A | 1 | 0.3754 | 100 | 0.547 | Contact Map |
| 3oouA | 1 | 0.3398 | 100 | 0.547 | Contact Map |
| 3oioA | 1 | 0.3625 | 100 | 0.547 | Contact Map |
| 2k9sA | 1 | 0.3463 | 100 | 0.548 | Contact Map |
| 3mn2A | 2 | 0.343 | 100 | 0.552 | Contact Map |
| 3lsgA | 5 | 0.3333 | 100 | 0.554 | Contact Map |
| 3mklA | 2 | 0.3592 | 100 | 0.555 | Contact Map |
| 3w6vA | 1 | 0.3592 | 99.9 | 0.558 | Contact Map |
| 1d5yA | 4 | 0.3786 | 99.9 | 0.565 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)