| all adjustment |
| ID: | 1387793805 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 312 (312) | ||
| Sequences: | 10002 (7834.8) | ||
| Seq/Len: | 32.058 | ||
| Nf(neff/√len): | 443.6 |
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: 32.058).
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 |
| 155_K | 214_T | 3.339 | 1.00 |
| 193_K | 197_E | 3.076 | 1.00 |
| 224_H | 237_D | 2.976 | 1.00 |
| 156_D | 160_G | 2.904 | 1.00 |
| 264_R | 283_D | 2.835 | 1.00 |
| 24_T | 45_V | 2.700 | 1.00 |
| 227_I | 255_A | 2.667 | 1.00 |
| 133_T | 157_T | 2.643 | 1.00 |
| 192_C | 203_I | 2.566 | 1.00 |
| 233_R | 240_E | 2.519 | 1.00 |
| 121_V | 195_I | 2.440 | 1.00 |
| 121_V | 196_I | 2.427 | 1.00 |
| 166_L | 207_S | 2.414 | 1.00 |
| 21_Q | 50_K | 2.368 | 1.00 |
| 252_I | 256_K | 2.357 | 1.00 |
| 170_F | 203_I | 2.326 | 1.00 |
| 113_Y | 118_M | 2.313 | 1.00 |
| 253_Y | 267_L | 2.302 | 1.00 |
| 205_V | 215_F | 2.266 | 1.00 |
| 77_Q | 113_Y | 2.242 | 1.00 |
| 149_E | 218_K | 2.144 | 1.00 |
| 113_Y | 199_H | 2.111 | 1.00 |
| 208_E | 211_K | 2.070 | 1.00 |
| 280_R | 283_D | 2.069 | 1.00 |
| 138_E | 157_T | 2.057 | 1.00 |
| 153_Y | 214_T | 2.033 | 1.00 |
| 226_E | 235_L | 2.016 | 1.00 |
| 196_I | 201_G | 2.012 | 1.00 |
| 204_D | 216_I | 1.995 | 1.00 |
| 196_I | 217_I | 1.988 | 1.00 |
| 168_Q | 171_D | 1.941 | 1.00 |
| 206_K | 216_I | 1.910 | 1.00 |
| 207_S | 213_T | 1.902 | 1.00 |
| 142_T | 153_Y | 1.888 | 1.00 |
| 140_A | 155_K | 1.882 | 1.00 |
| 162_A | 165_H | 1.862 | 1.00 |
| 153_Y | 216_I | 1.862 | 1.00 |
| 142_T | 155_K | 1.859 | 1.00 |
| 133_T | 137_D | 1.855 | 1.00 |
| 76_V | 110_V | 1.850 | 1.00 |
| 102_T | 140_A | 1.848 | 1.00 |
| 303_Q | 311_K | 1.835 | 1.00 |
| 228_D | 231_A | 1.832 | 1.00 |
| 232_H | 249_E | 1.825 | 1.00 |
| 206_K | 214_T | 1.813 | 1.00 |
| 257_T | 260_K | 1.810 | 1.00 |
| 76_V | 112_S | 1.761 | 1.00 |
| 100_N | 138_E | 1.737 | 1.00 |
| 28_V | 43_A | 1.730 | 1.00 |
| 151_I | 218_K | 1.718 | 1.00 |
| 161_I | 169_V | 1.710 | 1.00 |
| 137_D | 157_T | 1.706 | 1.00 |
| 104_N | 142_T | 1.701 | 1.00 |
| 166_L | 205_V | 1.691 | 1.00 |
| 4_D | 8_N | 1.690 | 1.00 |
| 146_N | 151_I | 1.687 | 1.00 |
| 258_P | 262_F | 1.679 | 1.00 |
| 195_I | 199_H | 1.678 | 1.00 |
| 285_H | 288_R | 1.674 | 1.00 |
| 28_V | 46_L | 1.651 | 1.00 |
| 21_Q | 53_N | 1.643 | 1.00 |
| 140_A | 157_T | 1.632 | 1.00 |
| 201_G | 219_L | 1.629 | 1.00 |
| 169_V | 205_V | 1.615 | 1.00 |
| 75_E | 115_M | 1.609 | 1.00 |
| 221_E | 226_E | 1.596 | 1.00 |
| 246_K | 249_E | 1.594 | 1.00 |
| 144_D | 151_I | 1.591 | 1.00 |
| 165_H | 174_Y | 1.591 | 1.00 |
| 296_S | 299_A | 1.562 | 1.00 |
| 165_H | 176_V | 1.558 | 1.00 |
| 127_D | 131_R | 1.532 | 1.00 |
| 144_D | 153_Y | 1.530 | 1.00 |
| 202_S | 218_K | 1.505 | 1.00 |
| 297_E | 300_H | 1.504 | 1.00 |
| 20_L | 45_V | 1.490 | 1.00 |
| 235_L | 240_E | 1.471 | 1.00 |
| 34_E | 37_E | 1.452 | 1.00 |
| 85_K | 119_D | 1.452 | 1.00 |
| 102_T | 138_E | 1.446 | 1.00 |
| 227_I | 248_Y | 1.442 | 1.00 |
| 94_A | 130_S | 1.433 | 1.00 |
| 122_L | 152_L | 1.426 | 1.00 |
| 253_Y | 270_E | 1.406 | 0.99 |
| 53_N | 57_N | 1.402 | 0.99 |
| 177_D | 180_R | 1.397 | 0.99 |
| 227_I | 234_V | 1.396 | 0.99 |
| 151_I | 216_I | 1.391 | 0.99 |
| 234_V | 241_V | 1.382 | 0.99 |
| 90_Y | 123_T | 1.361 | 0.99 |
| 121_V | 217_I | 1.355 | 0.99 |
| 156_D | 212_G | 1.351 | 0.99 |
| 163_P | 166_L | 1.350 | 0.99 |
| 260_K | 266_Q | 1.347 | 0.99 |
| 124_N | 192_C | 1.339 | 0.99 |
| 8_N | 172_R | 1.327 | 0.99 |
| 35_P | 38_I | 1.321 | 0.99 |
| 25_E | 46_L | 1.320 | 0.99 |
| 132_Y | 175_K | 1.308 | 0.99 |
| 118_M | 199_H | 1.308 | 0.99 |
| 229_N | 252_I | 1.306 | 0.99 |
| 207_S | 211_K | 1.305 | 0.99 |
| 253_Y | 262_F | 1.291 | 0.99 |
| 20_L | 49_S | 1.289 | 0.99 |
| 104_N | 140_A | 1.288 | 0.99 |
| 21_Q | 49_S | 1.287 | 0.99 |
| 85_K | 115_M | 1.287 | 0.99 |
| 78_P | 81_A | 1.276 | 0.99 |
| 232_H | 308_V | 1.267 | 0.99 |
| 235_L | 238_N | 1.266 | 0.99 |
| 305_V | 311_K | 1.261 | 0.99 |
| 152_L | 217_I | 1.259 | 0.99 |
| 161_I | 213_T | 1.245 | 0.98 |
| 74_K | 112_S | 1.242 | 0.98 |
| 227_I | 252_I | 1.240 | 0.98 |
| 247_E | 292_K | 1.238 | 0.98 |
| 262_F | 266_Q | 1.231 | 0.98 |
| 165_H | 168_Q | 1.225 | 0.98 |
| 197_E | 202_S | 1.221 | 0.98 |
| 222_F | 255_A | 1.213 | 0.98 |
| 296_S | 300_H | 1.210 | 0.98 |
| 205_V | 213_T | 1.208 | 0.98 |
| 24_T | 49_S | 1.195 | 0.98 |
| 244_T | 292_K | 1.194 | 0.98 |
| 24_T | 46_L | 1.192 | 0.98 |
| 89_K | 119_D | 1.186 | 0.98 |
| 12_E | 120_Q | 1.185 | 0.98 |
| 222_F | 312_F | 1.174 | 0.98 |
| 149_E | 202_S | 1.172 | 0.98 |
| 230_D | 260_K | 1.170 | 0.97 |
| 5_F | 9_V | 1.165 | 0.97 |
| 117_R | 120_Q | 1.153 | 0.97 |
| 207_S | 210_G | 1.151 | 0.97 |
| 121_V | 192_C | 1.141 | 0.97 |
| 24_T | 42_L | 1.135 | 0.97 |
| 175_K | 184_G | 1.132 | 0.97 |
| 80_A | 84_D | 1.129 | 0.97 |
| 254_L | 262_F | 1.129 | 0.97 |
| 224_H | 236_A | 1.127 | 0.97 |
| 204_D | 218_K | 1.122 | 0.97 |
| 253_Y | 257_T | 1.118 | 0.96 |
| 196_I | 203_I | 1.115 | 0.96 |
| 226_E | 238_N | 1.106 | 0.96 |
| 225_L | 234_V | 1.102 | 0.96 |
| 78_P | 108_K | 1.098 | 0.96 |
| 156_D | 213_T | 1.084 | 0.96 |
| 168_Q | 174_Y | 1.081 | 0.95 |
| 281_T | 285_H | 1.078 | 0.95 |
| 72_V | 114_D | 1.070 | 0.95 |
| 284_T | 287_K | 1.067 | 0.95 |
| 79_I | 152_L | 1.066 | 0.95 |
| 82_L | 113_Y | 1.064 | 0.95 |
| 83_L | 143_C | 1.056 | 0.95 |
| 234_V | 251_L | 1.050 | 0.94 |
| 87_K | 141_I | 1.048 | 0.94 |
| 94_A | 139_I | 1.040 | 0.94 |
| 225_L | 236_A | 1.040 | 0.94 |
| 263_D | 266_Q | 1.038 | 0.94 |
| 27_I | 42_L | 1.029 | 0.94 |
| 86_M | 126_I | 1.027 | 0.94 |
| 170_F | 215_F | 1.026 | 0.94 |
| 21_Q | 46_L | 1.024 | 0.93 |
| 232_H | 248_Y | 1.020 | 0.93 |
| 243_L | 289_L | 1.019 | 0.93 |
| 287_K | 291_E | 1.012 | 0.93 |
| 170_F | 205_V | 1.011 | 0.93 |
| 187_L | 191_I | 1.007 | 0.93 |
| 280_R | 284_T | 1.003 | 0.93 |
| 83_L | 122_L | 1.000 | 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 | |
| 4i5sA | 2 | 0.6827 | 100 | 0.505 | Contact Map |
| 2c2aA | 1 | 0.6923 | 100 | 0.508 | Contact Map |
| 4e01A | 1 | 0.6955 | 100 | 0.537 | Contact Map |
| 3jz3A | 2 | 0.516 | 100 | 0.537 | Contact Map |
| 2e0aA | 2 | 0.7596 | 100 | 0.538 | Contact Map |
| 1y8oA | 1 | 0.8077 | 100 | 0.54 | Contact Map |
| 4ew8A | 2 | 0.6987 | 100 | 0.542 | Contact Map |
| 4mpcA | 1 | 0.7692 | 100 | 0.545 | Contact Map |
| 3d36A | 2 | 0.6763 | 100 | 0.548 | Contact Map |
| 3a0rA | 1 | 0.6731 | 100 | 0.549 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)