| demharters1_cox3 |
| ID: | 1496645823 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 261 (245) | ||
| Sequences: | 2309 (1131.8) | ||
| Seq/Len: | 9.424 | ||
| Nf(neff/√len): | 72.3 |
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: 9.424).
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 |
| 233_F | 237_A | 3.764 | 1.00 |
| 20_G | 53_T | 3.441 | 1.00 |
| 235_F | 239_A | 3.288 | 1.00 |
| 92_F | 95_A | 3.270 | 1.00 |
| 93_F | 203_F | 2.897 | 1.00 |
| 30_G | 46_G | 2.698 | 1.00 |
| 100_A | 196_T | 2.613 | 1.00 |
| 143_S | 165_I | 2.507 | 1.00 |
| 159_M | 222_Q | 2.472 | 1.00 |
| 23_S | 49_T | 2.327 | 1.00 |
| 164_L | 219_L | 2.036 | 1.00 |
| 104_S | 192_I | 2.010 | 1.00 |
| 102_Y | 255_S | 1.970 | 1.00 |
| 83_M | 87_I | 1.953 | 1.00 |
| 216_I | 220_L | 1.950 | 1.00 |
| 144_I | 215_L | 1.948 | 1.00 |
| 200_A | 256_I | 1.919 | 1.00 |
| 147_A | 235_F | 1.881 | 1.00 |
| 136_V | 176_L | 1.853 | 1.00 |
| 143_S | 166_T | 1.833 | 1.00 |
| 59_R | 63_R | 1.792 | 1.00 |
| 23_S | 50_N | 1.788 | 1.00 |
| 20_G | 54_M | 1.776 | 1.00 |
| 66_T | 226_H | 1.757 | 1.00 |
| 51_I | 55_Y | 1.750 | 1.00 |
| 19_T | 53_T | 1.742 | 1.00 |
| 206_L | 210_I | 1.737 | 1.00 |
| 27_L | 50_N | 1.733 | 1.00 |
| 164_L | 168_L | 1.719 | 1.00 |
| 172_Y | 176_L | 1.718 | 1.00 |
| 146_W | 162_A | 1.603 | 1.00 |
| 147_A | 159_M | 1.595 | 1.00 |
| 151_L | 159_M | 1.594 | 1.00 |
| 19_T | 49_T | 1.581 | 1.00 |
| 65_G | 79_L | 1.493 | 1.00 |
| 58_W | 61_I | 1.477 | 1.00 |
| 62_I | 226_H | 1.470 | 1.00 |
| 174_T | 209_I | 1.465 | 1.00 |
| 214_F | 238_A | 1.440 | 1.00 |
| 171_L | 216_I | 1.423 | 0.99 |
| 246_D | 249_W | 1.403 | 0.99 |
| 241_Y | 244_F | 1.399 | 0.99 |
| 75_V | 78_G | 1.399 | 0.99 |
| 19_T | 22_L | 1.396 | 0.99 |
| 26_L | 46_G | 1.395 | 0.99 |
| 20_G | 24_A | 1.362 | 0.99 |
| 255_S | 260_G | 1.358 | 0.99 |
| 18_L | 22_L | 1.344 | 0.99 |
| 178_A | 182_F | 1.328 | 0.99 |
| 127_L | 253_Y | 1.327 | 0.99 |
| 163_L | 215_L | 1.317 | 0.99 |
| 25_L | 28_T | 1.312 | 0.99 |
| 99_W | 103_H | 1.311 | 0.99 |
| 14_S | 17_P | 1.289 | 0.99 |
| 56_Q | 59_R | 1.281 | 0.99 |
| 221_R | 226_H | 1.275 | 0.99 |
| 91_V | 248_V | 1.264 | 0.98 |
| 243_H | 246_D | 1.256 | 0.98 |
| 160_N | 222_Q | 1.253 | 0.98 |
| 242_W | 245_V | 1.244 | 0.98 |
| 199_M | 206_L | 1.236 | 0.98 |
| 209_I | 213_T | 1.222 | 0.98 |
| 174_T | 212_S | 1.212 | 0.98 |
| 97_F | 200_A | 1.198 | 0.98 |
| 20_G | 23_S | 1.192 | 0.98 |
| 245_V | 249_W | 1.192 | 0.98 |
| 58_W | 214_F | 1.189 | 0.97 |
| 144_I | 163_L | 1.188 | 0.97 |
| 44_S | 48_L | 1.179 | 0.97 |
| 139_A | 142_V | 1.169 | 0.97 |
| 200_A | 252_L | 1.161 | 0.97 |
| 101_F | 105_S | 1.157 | 0.97 |
| 171_L | 209_I | 1.154 | 0.97 |
| 88_V | 92_F | 1.146 | 0.97 |
| 201_T | 208_V | 1.144 | 0.97 |
| 145_T | 148_H | 1.137 | 0.96 |
| 171_L | 175_I | 1.132 | 0.96 |
| 211_G | 242_W | 1.132 | 0.96 |
| 21_A | 26_L | 1.131 | 0.96 |
| 211_G | 244_F | 1.128 | 0.96 |
| 179_S | 183_E | 1.126 | 0.96 |
| 150_S | 162_A | 1.124 | 0.96 |
| 90_E | 207_H | 1.124 | 0.96 |
| 54_M | 58_W | 1.117 | 0.96 |
| 135_S | 139_A | 1.112 | 0.96 |
| 74_I | 77_K | 1.109 | 0.96 |
| 175_I | 178_A | 1.105 | 0.96 |
| 255_S | 261_S | 1.104 | 0.96 |
| 29_S | 32_V | 1.097 | 0.95 |
| 137_L | 249_W | 1.095 | 0.95 |
| 155_N | 158_H | 1.086 | 0.95 |
| 167_I | 212_S | 1.075 | 0.95 |
| 141_G | 243_H | 1.070 | 0.95 |
| 45_L | 48_L | 1.070 | 0.95 |
| 75_V | 82_G | 1.062 | 0.94 |
| 204_H | 207_H | 1.060 | 0.94 |
| 150_S | 158_H | 1.057 | 0.94 |
| 103_H | 107_V | 1.056 | 0.94 |
| 249_W | 257_Y | 1.055 | 0.94 |
| 201_T | 204_H | 1.047 | 0.94 |
| 211_G | 241_Y | 1.045 | 0.94 |
| 245_V | 248_V | 1.040 | 0.93 |
| 147_A | 222_Q | 1.039 | 0.93 |
| 96_G | 102_Y | 1.039 | 0.93 |
| 208_V | 245_V | 1.037 | 0.93 |
| 152_M | 225_F | 1.036 | 0.93 |
| 22_L | 44_S | 1.028 | 0.93 |
| 247_V | 252_L | 1.024 | 0.93 |
| 24_A | 28_T | 1.023 | 0.93 |
| 84_I | 88_V | 1.019 | 0.93 |
| 29_S | 213_T | 1.016 | 0.92 |
| 16_W | 60_D | 1.006 | 0.92 |
| 160_N | 219_L | 1.005 | 0.92 |
| 253_Y | 257_Y | 1.004 | 0.92 |
| 137_L | 173_F | 1.004 | 0.92 |
| 147_A | 162_A | 1.003 | 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 | |
| 1v54C | 2 | 0.9923 | 100 | 0.065 | Contact Map |
| 1m56C | 2 | 0.9923 | 100 | 0.077 | Contact Map |
| 1qleC | 1 | 0.9962 | 100 | 0.087 | Contact Map |
| 2yevA | 2 | 0.9502 | 100 | 0.151 | Contact Map |
| 1fftC | 2 | 0.6973 | 100 | 0.319 | Contact Map |
| 1fftA | 2 | 0 | 96.9 | 0.885 | Contact Map |
| 1fftB | 2 | 0.2874 | 5.9 | 0.962 | Contact Map |
| 4o6yA | 2 | 0.5939 | 2.6 | 0.968 | Contact Map |
| 3l1lA | 1 | 0.2414 | 2.1 | 0.97 | Contact Map |
| 3ktpB | 1 | 0.0613 | 0.9 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)