| dbpa |
| ID: | 1502207942 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 457 (378) | ||
| Sequences: | 19236 (10453) | ||
| Seq/Len: | 50.889 | ||
| Nf(neff/√len): | 537.6 |
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: 50.889).
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 |
| 58_G | 91_L | 4.714 | 1.00 |
| 61_L | 74_A | 4.124 | 1.00 |
| 11_P | 63_Q | 3.869 | 1.00 |
| 37_I | 181_L | 3.697 | 1.00 |
| 78_C | 87_V | 3.629 | 1.00 |
| 128_A | 133_L | 3.388 | 1.00 |
| 41_K | 203_L | 3.072 | 1.00 |
| 29_V | 45_V | 3.030 | 1.00 |
| 285_V | 289_N | 3.004 | 1.00 |
| 286_R | 291_S | 2.804 | 1.00 |
| 20_E | 97_F | 2.730 | 1.00 |
| 88_A | 92_R | 2.525 | 1.00 |
| 269_L | 292_A | 2.519 | 1.00 |
| 248_C | 254_C | 2.472 | 1.00 |
| 136_H | 141_T | 2.459 | 1.00 |
| 88_A | 103_I | 2.447 | 1.00 |
| 312_L | 342_I | 2.388 | 1.00 |
| 329_I | 341_A | 2.384 | 1.00 |
| 138_Q | 169_D | 2.347 | 1.00 |
| 12_P | 16_T | 2.327 | 1.00 |
| 90_E | 93_R | 2.321 | 1.00 |
| 23_Y | 55_A | 2.234 | 1.00 |
| 251_K | 274_D | 2.226 | 1.00 |
| 318_L | 343_S | 2.212 | 1.00 |
| 88_A | 105_T | 2.145 | 1.00 |
| 5_S | 19_N | 2.126 | 1.00 |
| 309_S | 337_N | 2.124 | 1.00 |
| 104_L | 123_P | 2.076 | 1.00 |
| 61_L | 151_V | 2.076 | 1.00 |
| 217_E | 340_L | 2.067 | 1.00 |
| 282_Q | 286_R | 2.030 | 1.00 |
| 73_Q | 148_N | 2.023 | 1.00 |
| 258_C | 270_S | 2.018 | 1.00 |
| 168_D | 197_R | 1.993 | 1.00 |
| 218_Q | 325_H | 1.990 | 1.00 |
| 61_L | 149_T | 1.987 | 1.00 |
| 248_C | 257_V | 1.982 | 1.00 |
| 3_A | 6_T | 1.971 | 1.00 |
| 64_Q | 149_T | 1.960 | 1.00 |
| 164_S | 168_D | 1.957 | 1.00 |
| 233_Q | 264_V | 1.952 | 1.00 |
| 113_G | 117_D | 1.951 | 1.00 |
| 157_R | 160_D | 1.947 | 1.00 |
| 21_L | 93_R | 1.944 | 1.00 |
| 150_L | 171_I | 1.937 | 1.00 |
| 17_N | 97_F | 1.925 | 1.00 |
| 134_L | 169_D | 1.921 | 1.00 |
| 192_A | 204_A | 1.908 | 1.00 |
| 20_E | 96_R | 1.888 | 1.00 |
| 258_C | 268_A | 1.877 | 1.00 |
| 255_Q | 270_S | 1.874 | 1.00 |
| 315_N | 343_S | 1.825 | 1.00 |
| 218_Q | 329_I | 1.817 | 1.00 |
| 269_L | 286_R | 1.803 | 1.00 |
| 267_S | 293_R | 1.796 | 1.00 |
| 71_Q | 146_A | 1.792 | 1.00 |
| 216_I | 333_A | 1.786 | 1.00 |
| 73_Q | 124_H | 1.774 | 1.00 |
| 219_Q | 340_L | 1.766 | 1.00 |
| 248_C | 296_V | 1.764 | 1.00 |
| 14_Q | 63_Q | 1.733 | 1.00 |
| 75_L | 147_L | 1.725 | 1.00 |
| 253_D | 317_E | 1.719 | 1.00 |
| 36_A | 203_L | 1.696 | 1.00 |
| 64_Q | 148_N | 1.693 | 1.00 |
| 45_V | 183_F | 1.685 | 1.00 |
| 215_P | 338_S | 1.679 | 1.00 |
| 77_L | 133_L | 1.659 | 1.00 |
| 254_C | 270_S | 1.657 | 1.00 |
| 91_L | 103_I | 1.650 | 1.00 |
| 36_A | 39_A | 1.637 | 1.00 |
| 16_T | 97_F | 1.635 | 1.00 |
| 85_D | 281_D | 1.625 | 1.00 |
| 261_L | 296_V | 1.613 | 1.00 |
| 192_A | 196_G | 1.612 | 1.00 |
| 229_I | 260_A | 1.593 | 1.00 |
| 246_V | 294_V | 1.571 | 1.00 |
| 10_L | 59_L | 1.570 | 1.00 |
| 7_L | 10_L | 1.562 | 1.00 |
| 244_C | 314_V | 1.528 | 1.00 |
| 243_S | 309_S | 1.527 | 1.00 |
| 137_L | 173_F | 1.524 | 1.00 |
| 37_I | 43_V | 1.524 | 1.00 |
| 254_C | 272_H | 1.512 | 1.00 |
| 301_A | 305_L | 1.510 | 1.00 |
| 91_L | 125_I | 1.503 | 1.00 |
| 258_C | 262_N | 1.482 | 1.00 |
| 89_G | 93_R | 1.418 | 1.00 |
| 18_L | 23_Y | 1.415 | 1.00 |
| 63_Q | 67_A | 1.404 | 0.99 |
| 269_L | 283_T | 1.401 | 0.99 |
| 4_F | 26_M | 1.396 | 0.99 |
| 134_L | 166_A | 1.384 | 0.99 |
| 57_F | 87_V | 1.381 | 0.99 |
| 297_A | 301_A | 1.380 | 0.99 |
| 266_Q | 294_V | 1.379 | 0.99 |
| 38_L | 63_Q | 1.366 | 0.99 |
| 9_V | 15_L | 1.363 | 0.99 |
| 16_T | 19_N | 1.350 | 0.99 |
| 144_L | 147_L | 1.342 | 0.99 |
| 319_A | 325_H | 1.340 | 0.99 |
| 217_E | 338_S | 1.329 | 0.99 |
| 135_D | 139_K | 1.327 | 0.99 |
| 16_T | 20_E | 1.326 | 0.99 |
| 281_D | 285_V | 1.322 | 0.99 |
| 315_N | 329_I | 1.307 | 0.99 |
| 40_G | 179_Q | 1.306 | 0.99 |
| 78_C | 84_A | 1.306 | 0.99 |
| 84_A | 105_T | 1.296 | 0.99 |
| 28_P | 32_A | 1.292 | 0.99 |
| 235_L | 342_I | 1.291 | 0.99 |
| 111_P | 114_M | 1.289 | 0.99 |
| 219_Q | 367_Q | 1.283 | 0.99 |
| 134_L | 138_Q | 1.281 | 0.99 |
| 42_D | 200_R | 1.279 | 0.99 |
| 321_D | 324_V | 1.276 | 0.99 |
| 228_K | 317_E | 1.276 | 0.99 |
| 286_R | 292_A | 1.274 | 0.99 |
| 76_V | 91_L | 1.268 | 0.99 |
| 357_S | 363_K | 1.268 | 0.99 |
| 77_L | 128_A | 1.266 | 0.99 |
| 104_L | 118_S | 1.249 | 0.99 |
| 112_F | 139_K | 1.248 | 0.99 |
| 287_F | 295_L | 1.244 | 0.98 |
| 241_P | 244_C | 1.243 | 0.98 |
| 46_Q | 206_E | 1.237 | 0.98 |
| 242_S | 311_E | 1.219 | 0.98 |
| 74_A | 149_T | 1.205 | 0.98 |
| 116_R | 136_H | 1.202 | 0.98 |
| 3_A | 25_T | 1.199 | 0.98 |
| 169_D | 173_F | 1.195 | 0.98 |
| 2_T | 6_T | 1.192 | 0.98 |
| 275_L | 283_T | 1.181 | 0.98 |
| 68_S | 148_N | 1.179 | 0.98 |
| 312_L | 340_L | 1.179 | 0.98 |
| 19_N | 24_L | 1.178 | 0.98 |
| 3_A | 26_M | 1.173 | 0.98 |
| 166_A | 169_D | 1.162 | 0.97 |
| 189_E | 193_A | 1.159 | 0.97 |
| 244_C | 294_V | 1.157 | 0.97 |
| 112_F | 116_R | 1.156 | 0.97 |
| 276_E | 279_D | 1.155 | 0.97 |
| 117_D | 120_Q | 1.150 | 0.97 |
| 62_L | 95_A | 1.145 | 0.97 |
| 91_L | 127_V | 1.124 | 0.97 |
| 117_D | 121_H | 1.124 | 0.97 |
| 315_N | 341_A | 1.118 | 0.96 |
| 25_T | 31_A | 1.118 | 0.96 |
| 116_R | 141_T | 1.117 | 0.96 |
| 40_G | 64_Q | 1.115 | 0.96 |
| 72_T | 126_I | 1.109 | 0.96 |
| 4_F | 7_L | 1.106 | 0.96 |
| 255_Q | 272_H | 1.099 | 0.96 |
| 65_I | 74_A | 1.097 | 0.96 |
| 102_K | 124_H | 1.096 | 0.96 |
| 250_T | 253_D | 1.096 | 0.96 |
| 123_P | 126_I | 1.095 | 0.96 |
| 283_T | 292_A | 1.092 | 0.96 |
| 224_S | 227_G | 1.086 | 0.96 |
| 89_G | 92_R | 1.083 | 0.96 |
| 128_A | 142_V | 1.080 | 0.95 |
| 5_S | 15_L | 1.070 | 0.95 |
| 115_Q | 136_H | 1.068 | 0.95 |
| 36_A | 43_V | 1.064 | 0.95 |
| 213_L | 216_I | 1.061 | 0.95 |
| 18_L | 59_L | 1.055 | 0.95 |
| 253_D | 256_A | 1.054 | 0.95 |
| 14_Q | 59_L | 1.049 | 0.94 |
| 104_L | 126_I | 1.049 | 0.94 |
| 243_S | 290_G | 1.044 | 0.94 |
| 55_A | 94_L | 1.042 | 0.94 |
| 13_A | 16_T | 1.040 | 0.94 |
| 57_F | 78_C | 1.039 | 0.94 |
| 41_K | 201_D | 1.033 | 0.94 |
| 284_L | 307_I | 1.031 | 0.94 |
| 2_T | 31_A | 1.027 | 0.94 |
| 74_A | 125_I | 1.015 | 0.93 |
| 318_L | 356_I | 1.010 | 0.93 |
| 233_Q | 237_S | 1.008 | 0.93 |
| 64_Q | 179_Q | 1.004 | 0.93 |
| 36_A | 205_I | 1.003 | 0.93 |
| 277_Q | 281_D | 1.002 | 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 | |
| 3sqwA | 1 | 0.9672 | 100 | 0.335 | Contact Map |
| 4pxaA | 1 | 0.8184 | 100 | 0.337 | Contact Map |
| 3i5xA | 1 | 0.9716 | 100 | 0.338 | Contact Map |
| 2db3A | 4 | 0.8074 | 100 | 0.345 | Contact Map |
| 3fmpB | 2 | 0.4464 | 100 | 0.35 | Contact Map |
| 4nhoA | 1 | 0.8031 | 100 | 0.361 | Contact Map |
| 4ljyA | 1 | 0.8446 | 100 | 0.361 | Contact Map |
| 4d25A | 1 | 0.8096 | 100 | 0.363 | Contact Map |
| 4w7sA | 2 | 0.8512 | 100 | 0.366 | Contact Map |
| 4c9bA | 1 | 0.8118 | 100 | 0.367 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)