| 1occ-C |
| ID: | 1408346145 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 261 (260) | ||
| Sequences: | 1962 (963.1) | ||
| Seq/Len: | 7.546 | ||
| Nf(neff/√len): | 59.7 |
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: 7.546).
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 |
| 92_L | 95_T | 4.096 | 1.00 |
| 20_G | 53_T | 3.346 | 1.00 |
| 143_S | 165_I | 3.271 | 1.00 |
| 235_F | 239_A | 3.211 | 1.00 |
| 233_F | 237_A | 3.127 | 1.00 |
| 159_M | 222_Q | 3.127 | 1.00 |
| 93_F | 203_F | 2.717 | 1.00 |
| 100_A | 196_T | 2.474 | 1.00 |
| 156_R | 225_F | 2.328 | 1.00 |
| 30_G | 46_G | 2.320 | 1.00 |
| 200_A | 256_I | 2.313 | 1.00 |
| 23_S | 49_T | 2.303 | 1.00 |
| 164_F | 219_F | 2.265 | 1.00 |
| 19_T | 53_T | 2.131 | 1.00 |
| 146_W | 162_A | 2.118 | 1.00 |
| 23_S | 50_N | 2.056 | 1.00 |
| 65_S | 79_L | 2.041 | 1.00 |
| 20_G | 54_M | 1.965 | 1.00 |
| 66_T | 226_H | 1.934 | 1.00 |
| 147_A | 222_Q | 1.919 | 1.00 |
| 26_L | 46_G | 1.832 | 1.00 |
| 135_S | 139_A | 1.718 | 1.00 |
| 59_R | 63_R | 1.704 | 1.00 |
| 167_I | 219_F | 1.697 | 1.00 |
| 144_I | 215_L | 1.660 | 1.00 |
| 156_R | 160_L | 1.655 | 1.00 |
| 171_V | 209_I | 1.654 | 1.00 |
| 174_T | 209_I | 1.629 | 1.00 |
| 147_A | 235_F | 1.600 | 1.00 |
| 217_V | 220_F | 1.596 | 1.00 |
| 83_M | 87_I | 1.564 | 1.00 |
| 212_S | 216_I | 1.544 | 1.00 |
| 221_R | 226_H | 1.499 | 0.99 |
| 216_I | 220_F | 1.489 | 0.99 |
| 143_S | 166_T | 1.488 | 0.99 |
| 174_T | 212_S | 1.488 | 0.99 |
| 30_G | 42_L | 1.486 | 0.99 |
| 200_A | 203_F | 1.485 | 0.99 |
| 160_L | 223_L | 1.472 | 0.99 |
| 19_T | 49_T | 1.457 | 0.99 |
| 206_L | 210_I | 1.441 | 0.99 |
| 150_S | 162_A | 1.437 | 0.99 |
| 151_L | 159_M | 1.426 | 0.99 |
| 219_F | 223_L | 1.425 | 0.99 |
| 127_L | 253_Y | 1.408 | 0.99 |
| 214_F | 238_G | 1.408 | 0.99 |
| 25_L | 28_T | 1.398 | 0.99 |
| 124_L | 184_A | 1.396 | 0.99 |
| 241_Y | 244_F | 1.392 | 0.99 |
| 129_V | 179_S | 1.387 | 0.99 |
| 199_V | 206_L | 1.382 | 0.99 |
| 104_S | 192_V | 1.379 | 0.99 |
| 35_F | 188_I | 1.372 | 0.99 |
| 154_G | 229_S | 1.344 | 0.99 |
| 151_L | 235_F | 1.340 | 0.98 |
| 136_V | 176_L | 1.339 | 0.98 |
| 155_D | 158_H | 1.327 | 0.98 |
| 19_T | 22_L | 1.319 | 0.98 |
| 58_W | 214_F | 1.318 | 0.98 |
| 62_I | 226_H | 1.316 | 0.98 |
| 144_I | 147_A | 1.308 | 0.98 |
| 151_L | 222_Q | 1.303 | 0.98 |
| 167_I | 216_I | 1.287 | 0.98 |
| 88_I | 91_V | 1.256 | 0.97 |
| 172_Y | 176_L | 1.252 | 0.97 |
| 50_N | 54_M | 1.251 | 0.97 |
| 256_I | 260_G | 1.239 | 0.97 |
| 218_C | 238_G | 1.237 | 0.97 |
| 14_S | 17_P | 1.230 | 0.97 |
| 171_V | 216_I | 1.229 | 0.97 |
| 51_M | 54_M | 1.219 | 0.97 |
| 20_G | 24_A | 1.216 | 0.97 |
| 51_M | 55_Y | 1.214 | 0.97 |
| 102_Y | 255_S | 1.211 | 0.97 |
| 243_H | 246_D | 1.205 | 0.96 |
| 160_L | 222_Q | 1.193 | 0.96 |
| 99_W | 103_H | 1.187 | 0.96 |
| 211_G | 242_W | 1.172 | 0.96 |
| 139_A | 142_V | 1.171 | 0.96 |
| 76_Q | 80_R | 1.170 | 0.96 |
| 209_I | 213_T | 1.169 | 0.96 |
| 208_V | 211_G | 1.167 | 0.96 |
| 88_I | 92_L | 1.165 | 0.95 |
| 249_W | 257_Y | 1.160 | 0.95 |
| 83_M | 143_S | 1.152 | 0.95 |
| 23_S | 46_G | 1.151 | 0.95 |
| 160_L | 219_F | 1.135 | 0.95 |
| 34_W | 80_R | 1.135 | 0.95 |
| 44_M | 48_T | 1.133 | 0.94 |
| 208_V | 245_V | 1.130 | 0.94 |
| 179_S | 183_E | 1.130 | 0.94 |
| 164_F | 168_T | 1.123 | 0.94 |
| 255_S | 260_G | 1.112 | 0.94 |
| 147_A | 162_A | 1.105 | 0.93 |
| 246_D | 249_W | 1.100 | 0.93 |
| 69_G | 194_G | 1.099 | 0.93 |
| 147_A | 159_M | 1.099 | 0.93 |
| 97_F | 199_V | 1.097 | 0.93 |
| 178_A | 182_Y | 1.092 | 0.93 |
| 171_V | 175_L | 1.088 | 0.93 |
| 144_I | 163_L | 1.084 | 0.93 |
| 34_W | 40_M | 1.080 | 0.92 |
| 171_V | 212_S | 1.079 | 0.92 |
| 75_V | 78_G | 1.069 | 0.92 |
| 151_L | 239_A | 1.065 | 0.92 |
| 175_L | 178_A | 1.053 | 0.91 |
| 211_G | 244_F | 1.051 | 0.91 |
| 245_V | 248_V | 1.051 | 0.91 |
| 91_V | 248_V | 1.040 | 0.90 |
| 195_S | 199_V | 1.039 | 0.90 |
| 124_L | 129_V | 1.037 | 0.90 |
| 75_V | 141_G | 1.026 | 0.90 |
| 54_M | 58_W | 1.025 | 0.90 |
| 147_A | 163_L | 1.025 | 0.90 |
| 242_W | 245_V | 1.022 | 0.89 |
| 215_L | 218_C | 1.015 | 0.89 |
| 220_F | 224_K | 1.015 | 0.89 |
| 58_W | 63_R | 1.011 | 0.89 |
| 56_Q | 59_R | 1.009 | 0.89 |
| 103_H | 107_A | 1.007 | 0.88 |
| 49_T | 53_T | 1.005 | 0.88 |
| 224_K | 254_V | 1.003 | 0.88 |
| 158_H | 162_A | 1.002 | 0.88 |
| 58_W | 61_V | 1.002 | 0.88 |
| 145_T | 148_H | 1.000 | 0.88 |
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 | |
| 1v54C | 2 | 0.9923 | 100 | 0.075 | Contact Map |
| 1m56C | 2 | 0.9923 | 100 | 0.099 | Contact Map |
| 1qleC | 1 | 0.9962 | 100 | 0.112 | Contact Map |
| 2yevA | 2 | 0.9502 | 100 | 0.185 | Contact Map |
| 1fftC | 2 | 0.6973 | 100 | 0.402 | Contact Map |
| 1fftA | 2 | 0 | 95.6 | 0.915 | Contact Map |
| 3l1lA | 1 | 0.2529 | 9.3 | 0.966 | Contact Map |
| 1p1lA | 1 | 0.1303 | 1.7 | 0.976 | Contact Map |
| 3j1zP | 2 | 0.3946 | 1.3 | 0.977 | Contact Map |
| 2wswA | 1 | 0.2452 | 1.2 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)