| E9Q3E3_MOUSE |
| ID: | 1408920893 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 307 (254) | ||
| Sequences: | 1057 (702) | ||
| Seq/Len: | 4.161 | ||
| Nf(neff/√len): | 44.0 |
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: 4.161).
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 |
| 62_R | 122_F | 4.008 | 1.00 |
| 228_L | 231_F | 3.531 | 1.00 |
| 95_Q | 98_T | 2.936 | 1.00 |
| 143_L | 213_F | 2.916 | 1.00 |
| 225_K | 228_L | 2.521 | 1.00 |
| 225_K | 231_F | 2.420 | 1.00 |
| 64_L | 130_V | 2.271 | 1.00 |
| 138_L | 163_L | 2.107 | 1.00 |
| 183_C | 197_C | 2.026 | 1.00 |
| 119_P | 167_R | 1.991 | 1.00 |
| 181_L | 199_M | 1.935 | 1.00 |
| 146_A | 202_E | 1.865 | 1.00 |
| 226_I | 231_F | 1.849 | 1.00 |
| 113_D | 171_V | 1.809 | 1.00 |
| 86_I | 105_I | 1.788 | 1.00 |
| 112_N | 168_D | 1.739 | 0.99 |
| 94_I | 185_L | 1.724 | 0.99 |
| 112_N | 170_D | 1.714 | 0.99 |
| 243_C | 255_C | 1.665 | 0.99 |
| 225_K | 230_Q | 1.652 | 0.99 |
| 281_V | 298_R | 1.593 | 0.99 |
| 284_S | 301_L | 1.581 | 0.99 |
| 113_D | 116_L | 1.574 | 0.98 |
| 196_R | 261_T | 1.558 | 0.98 |
| 226_I | 233_I | 1.547 | 0.98 |
| 154_H | 160_N | 1.537 | 0.98 |
| 139_W | 169_G | 1.533 | 0.98 |
| 300_P | 304_L | 1.522 | 0.98 |
| 111_W | 139_W | 1.497 | 0.98 |
| 264_R | 276_P | 1.490 | 0.98 |
| 230_Q | 233_I | 1.463 | 0.97 |
| 196_R | 259_I | 1.462 | 0.97 |
| 240_Y | 243_C | 1.447 | 0.97 |
| 113_D | 138_L | 1.442 | 0.97 |
| 183_C | 193_D | 1.413 | 0.96 |
| 269_Y | 302_G | 1.411 | 0.96 |
| 226_I | 230_Q | 1.407 | 0.96 |
| 67_Y | 113_D | 1.394 | 0.96 |
| 109_Q | 143_L | 1.390 | 0.96 |
| 111_W | 141_P | 1.369 | 0.96 |
| 203_S | 206_Y | 1.344 | 0.95 |
| 103_V | 181_L | 1.343 | 0.95 |
| 175_M | 298_R | 1.325 | 0.94 |
| 141_P | 169_G | 1.317 | 0.94 |
| 189_L | 260_F | 1.304 | 0.94 |
| 100_D | 149_K | 1.300 | 0.94 |
| 64_L | 165_I | 1.273 | 0.93 |
| 212_R | 254_T | 1.264 | 0.92 |
| 83_V | 214_I | 1.263 | 0.92 |
| 113_D | 139_W | 1.260 | 0.92 |
| 59_I | 63_L | 1.254 | 0.92 |
| 108_R | 174_S | 1.247 | 0.92 |
| 94_I | 101_Y | 1.240 | 0.91 |
| 138_L | 171_V | 1.226 | 0.91 |
| 55_S | 58_N | 1.218 | 0.90 |
| 194_T | 261_T | 1.215 | 0.90 |
| 207_T | 210_D | 1.207 | 0.90 |
| 151_A | 304_L | 1.200 | 0.90 |
| 142_D | 203_S | 1.190 | 0.89 |
| 225_K | 233_I | 1.182 | 0.89 |
| 268_F | 302_G | 1.176 | 0.88 |
| 228_L | 233_I | 1.168 | 0.88 |
| 193_D | 197_C | 1.166 | 0.88 |
| 298_R | 301_L | 1.165 | 0.88 |
| 231_F | 235_K | 1.161 | 0.87 |
| 213_F | 254_T | 1.157 | 0.87 |
| 280_I | 302_G | 1.156 | 0.87 |
| 57_S | 61_N | 1.152 | 0.87 |
| 297_A | 300_P | 1.144 | 0.86 |
| 281_V | 286_L | 1.143 | 0.86 |
| 280_I | 301_L | 1.140 | 0.86 |
| 288_F | 296_A | 1.140 | 0.86 |
| 113_D | 141_P | 1.138 | 0.86 |
| 269_Y | 273_V | 1.132 | 0.86 |
| 270_M | 275_A | 1.128 | 0.85 |
| 208_T | 254_T | 1.125 | 0.85 |
| 92_G | 178_S | 1.121 | 0.85 |
| 63_L | 67_Y | 1.120 | 0.85 |
| 287_S | 302_G | 1.117 | 0.84 |
| 67_Y | 73_P | 1.116 | 0.84 |
| 235_K | 238_I | 1.101 | 0.83 |
| 106_F | 203_S | 1.085 | 0.82 |
| 147_N | 199_M | 1.085 | 0.82 |
| 165_I | 169_G | 1.078 | 0.81 |
| 58_N | 62_R | 1.078 | 0.81 |
| 113_D | 302_G | 1.078 | 0.81 |
| 60_L | 68_D | 1.061 | 0.80 |
| 93_S | 102_R | 1.059 | 0.80 |
| 93_S | 100_D | 1.055 | 0.80 |
| 81_D | 212_R | 1.053 | 0.79 |
| 71_I | 148_E | 1.052 | 0.79 |
| 88_I | 272_G | 1.052 | 0.79 |
| 173_V | 187_L | 1.047 | 0.79 |
| 67_Y | 116_L | 1.047 | 0.79 |
| 200_Q | 257_E | 1.046 | 0.79 |
| 86_I | 265_Q | 1.036 | 0.78 |
| 190_F | 269_Y | 1.032 | 0.77 |
| 268_F | 289_W | 1.029 | 0.77 |
| 113_D | 298_R | 1.027 | 0.77 |
| 64_L | 138_L | 1.026 | 0.77 |
| 183_C | 195_Q | 1.024 | 0.77 |
| 253_Y | 277_T | 1.020 | 0.76 |
| 110_K | 170_D | 1.018 | 0.76 |
| 127_A | 211_L | 1.016 | 0.76 |
| 176_R | 187_L | 1.012 | 0.75 |
| 85_N | 108_R | 1.009 | 0.75 |
| 163_L | 280_I | 1.003 | 0.75 |
| 118_L | 122_F | 1.002 | 0.74 |
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 | |
| 4aq5E | 1 | 0.8111 | 100 | 0.295 | Contact Map |
| 4aq5C | 1 | 0.7948 | 100 | 0.303 | Contact Map |
| 2bg9E | 1 | 0.8111 | 100 | 0.304 | Contact Map |
| 4aq5A | 2 | 0.8046 | 100 | 0.309 | Contact Map |
| 4aq5B | 1 | 0.7948 | 100 | 0.31 | Contact Map |
| 2bg9A | 2 | 0.8078 | 100 | 0.311 | Contact Map |
| 2bg9B | 1 | 0.798 | 100 | 0.314 | Contact Map |
| 3rhwA | 5 | 0.8078 | 100 | 0.314 | Contact Map |
| 2bg9C | 1 | 0.8013 | 100 | 0.314 | Contact Map |
| 4cofA | 5 | 0.8371 | 100 | 0.321 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)