| scEMC3 |
| ID: | 1504851071 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 253 (243) | ||
| Sequences: | 304 (182.1) | ||
| Seq/Len: | 1.251 | ||
| Nf(neff/√len): | 11.7 |
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: 1.251).
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 |
| 60_I | 228_M | 2.221 | 0.99 |
| 8_K | 11_V | 2.063 | 0.98 |
| 3_L | 11_V | 1.986 | 0.97 |
| 27_Q | 195_G | 1.872 | 0.95 |
| 55_W | 60_I | 1.785 | 0.93 |
| 163_G | 176_S | 1.689 | 0.91 |
| 18_V | 135_W | 1.560 | 0.85 |
| 162_T | 165_I | 1.552 | 0.85 |
| 194_I | 232_L | 1.549 | 0.85 |
| 248_V | 252_Y | 1.536 | 0.84 |
| 148_L | 166_C | 1.514 | 0.83 |
| 3_L | 8_K | 1.510 | 0.83 |
| 3_L | 193_L | 1.476 | 0.81 |
| 4_D | 14_P | 1.476 | 0.81 |
| 71_F | 237_H | 1.469 | 0.80 |
| 11_V | 193_L | 1.469 | 0.80 |
| 204_Q | 237_H | 1.461 | 0.80 |
| 71_F | 74_K | 1.455 | 0.80 |
| 154_A | 173_W | 1.434 | 0.78 |
| 13_L | 41_A | 1.422 | 0.77 |
| 38_A | 48_T | 1.416 | 0.77 |
| 67_S | 239_T | 1.406 | 0.76 |
| 49_E | 129_Q | 1.406 | 0.76 |
| 153_T | 179_W | 1.394 | 0.75 |
| 117_N | 121_G | 1.386 | 0.75 |
| 23_G | 27_Q | 1.384 | 0.75 |
| 118_M | 122_N | 1.371 | 0.74 |
| 155_K | 171_V | 1.354 | 0.72 |
| 12_L | 129_Q | 1.352 | 0.72 |
| 13_L | 20_V | 1.348 | 0.72 |
| 19_M | 131_I | 1.347 | 0.72 |
| 78_L | 81_D | 1.338 | 0.71 |
| 59_L | 232_L | 1.327 | 0.70 |
| 78_L | 88_L | 1.321 | 0.70 |
| 174_V | 181_F | 1.315 | 0.69 |
| 19_M | 139_F | 1.305 | 0.68 |
| 74_K | 77_F | 1.294 | 0.67 |
| 10_W | 14_P | 1.283 | 0.66 |
| 143_F | 176_S | 1.278 | 0.66 |
| 46_K | 218_Q | 1.277 | 0.66 |
| 129_Q | 139_F | 1.263 | 0.65 |
| 149_P | 152_L | 1.263 | 0.65 |
| 111_M | 114_A | 1.261 | 0.64 |
| 20_V | 122_N | 1.255 | 0.64 |
| 122_N | 188_N | 1.247 | 0.63 |
| 153_T | 175_S | 1.237 | 0.62 |
| 23_G | 128_P | 1.229 | 0.61 |
| 132_I | 183_S | 1.226 | 0.61 |
| 70_A | 137_N | 1.222 | 0.61 |
| 12_L | 148_L | 1.218 | 0.60 |
| 58_L | 66_L | 1.216 | 0.60 |
| 159_M | 232_L | 1.216 | 0.60 |
| 133_M | 231_D | 1.213 | 0.60 |
| 23_G | 26_K | 1.210 | 0.60 |
| 175_S | 179_W | 1.207 | 0.59 |
| 59_L | 63_G | 1.202 | 0.59 |
| 135_W | 153_T | 1.199 | 0.59 |
| 128_P | 183_S | 1.195 | 0.58 |
| 15_I | 135_W | 1.188 | 0.58 |
| 244_V | 248_V | 1.187 | 0.58 |
| 6_Q | 88_L | 1.172 | 0.56 |
| 34_T | 66_L | 1.169 | 0.56 |
| 157_K | 173_W | 1.167 | 0.56 |
| 164_I | 190_V | 1.165 | 0.55 |
| 28_Y | 226_H | 1.157 | 0.55 |
| 42_Q | 244_V | 1.155 | 0.54 |
| 171_V | 177_I | 1.152 | 0.54 |
| 12_L | 49_E | 1.150 | 0.54 |
| 49_E | 148_L | 1.146 | 0.54 |
| 136_V | 157_K | 1.146 | 0.54 |
| 4_D | 15_I | 1.146 | 0.54 |
| 187_L | 191_Y | 1.141 | 0.53 |
| 15_I | 153_T | 1.139 | 0.53 |
| 66_L | 172_R | 1.137 | 0.53 |
| 241_L | 245_E | 1.132 | 0.52 |
| 185_L | 220_Q | 1.124 | 0.51 |
| 105_P | 132_I | 1.120 | 0.51 |
| 12_L | 15_I | 1.119 | 0.51 |
| 171_V | 174_V | 1.118 | 0.51 |
| 62_N | 71_F | 1.117 | 0.51 |
| 88_L | 213_P | 1.114 | 0.50 |
| 45_V | 126_F | 1.109 | 0.50 |
| 91_A | 113_N | 1.108 | 0.50 |
| 12_L | 16_S | 1.107 | 0.50 |
| 123_M | 176_S | 1.107 | 0.50 |
| 71_F | 118_M | 1.104 | 0.49 |
| 145_L | 225_M | 1.101 | 0.49 |
| 149_P | 161_Q | 1.101 | 0.49 |
| 12_L | 18_V | 1.100 | 0.49 |
| 55_W | 172_R | 1.098 | 0.49 |
| 71_F | 160_L | 1.097 | 0.49 |
| 248_V | 251_Q | 1.090 | 0.48 |
| 128_P | 132_I | 1.089 | 0.48 |
| 127_I | 172_R | 1.080 | 0.47 |
| 53_L | 228_M | 1.075 | 0.47 |
| 11_V | 14_P | 1.069 | 0.46 |
| 239_T | 242_D | 1.069 | 0.46 |
| 19_M | 23_G | 1.068 | 0.46 |
| 121_G | 169_L | 1.067 | 0.46 |
| 111_M | 117_N | 1.065 | 0.46 |
| 119_A | 164_I | 1.065 | 0.46 |
| 134_W | 144_I | 1.060 | 0.45 |
| 138_H | 184_V | 1.056 | 0.45 |
| 122_N | 131_I | 1.053 | 0.44 |
| 53_L | 248_V | 1.051 | 0.44 |
| 56_A | 229_A | 1.047 | 0.44 |
| 154_A | 170_D | 1.047 | 0.44 |
| 78_L | 249_L | 1.047 | 0.44 |
| 124_A | 131_I | 1.046 | 0.44 |
| 243_N | 248_V | 1.044 | 0.44 |
| 160_L | 175_S | 1.042 | 0.43 |
| 81_D | 88_L | 1.042 | 0.43 |
| 221_V | 224_A | 1.041 | 0.43 |
| 150_F | 156_F | 1.041 | 0.43 |
| 143_F | 193_L | 1.037 | 0.43 |
| 7_L | 162_T | 1.034 | 0.43 |
| 129_Q | 171_V | 1.032 | 0.42 |
| 6_Q | 155_K | 1.026 | 0.42 |
| 182_I | 234_I | 1.022 | 0.41 |
| 175_S | 181_F | 1.020 | 0.41 |
| 66_L | 102_V | 1.019 | 0.41 |
| 190_V | 194_I | 1.017 | 0.41 |
| 29_I | 232_L | 1.014 | 0.41 |
| 13_L | 197_N | 1.012 | 0.40 |
| 53_L | 157_K | 1.011 | 0.40 |
| 125_S | 128_P | 1.010 | 0.40 |
| 105_P | 115_M | 1.009 | 0.40 |
| 13_L | 181_F | 1.007 | 0.40 |
| 152_L | 156_F | 1.007 | 0.40 |
| 82_L | 86_R | 1.007 | 0.40 |
| 22_T | 207_I | 1.002 | 0.39 |
| 31_T | 47_L | 1.001 | 0.39 |
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 | |
| 4wrtB | 1 | 0.2727 | 7.5 | 0.975 | Contact Map |
| 4wsbB | 1 | 0.2767 | 6 | 0.976 | Contact Map |
| 3wcaA | 4 | 0.3281 | 3.3 | 0.979 | Contact Map |
| 4bj1A | 1 | 0.2648 | 2.6 | 0.98 | Contact Map |
| 4g9qA | 1 | 0.2727 | 2.4 | 0.981 | Contact Map |
| 2mkbA | 1 | 0.0949 | 2.3 | 0.981 | Contact Map |
| 2y9yB | 1 | 0.1937 | 2.3 | 0.981 | Contact Map |
| 1nvpB | 1 | 0.1344 | 2.2 | 0.981 | Contact Map |
| 3vfzA | 2 | 0.0988 | 2.2 | 0.981 | Contact Map |
| 2hfrA | 1 | 0.1067 | 2 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)