| 1DXRM |
| ID: | 1411761257 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 323 (317) | ||
| Sequences: | 374 (115) | ||
| Seq/Len: | 1.180 | ||
| Nf(neff/√len): | 6.5 |
Jackhmmer Results: (2014_04_16)
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: 1.180).
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 |
| 153_F | 157_C | 2.978 | 1.00 |
| 37_W | 40_K | 2.637 | 1.00 |
| 105_P | 114_L | 2.344 | 0.99 |
| 36_Y | 40_K | 2.296 | 0.99 |
| 59_F | 63_S | 2.033 | 0.97 |
| 124_L | 155_V | 1.951 | 0.96 |
| 113_W | 175_F | 1.922 | 0.96 |
| 63_S | 67_L | 1.893 | 0.95 |
| 296_C | 301_A | 1.804 | 0.93 |
| 83_Q | 87_Q | 1.802 | 0.93 |
| 97_K | 109_D | 1.799 | 0.93 |
| 92_G | 179_P | 1.799 | 0.93 |
| 186_A | 190_R | 1.792 | 0.93 |
| 224_V | 229_G | 1.683 | 0.90 |
| 59_F | 62_G | 1.661 | 0.89 |
| 102_M | 105_P | 1.625 | 0.87 |
| 224_V | 246_A | 1.589 | 0.86 |
| 72_N | 112_W | 1.526 | 0.82 |
| 153_F | 195_Y | 1.508 | 0.81 |
| 24_G | 34_Y | 1.504 | 0.81 |
| 249_F | 253_T | 1.490 | 0.80 |
| 105_P | 150_A | 1.466 | 0.79 |
| 187_F | 194_F | 1.462 | 0.79 |
| 166_V | 212_L | 1.458 | 0.78 |
| 67_L | 71_F | 1.441 | 0.77 |
| 117_G | 121_T | 1.428 | 0.76 |
| 9_Q | 22_E | 1.392 | 0.74 |
| 120_M | 155_V | 1.379 | 0.73 |
| 121_T | 160_C | 1.376 | 0.72 |
| 189_I | 211_G | 1.375 | 0.72 |
| 250_W | 253_T | 1.366 | 0.72 |
| 2_D | 102_M | 1.363 | 0.71 |
| 21_G | 27_D | 1.351 | 0.70 |
| 9_Q | 16_H | 1.350 | 0.70 |
| 9_Q | 201_G | 1.346 | 0.70 |
| 40_K | 43_D | 1.346 | 0.70 |
| 227_F | 237_T | 1.343 | 0.70 |
| 185_T | 190_R | 1.327 | 0.68 |
| 150_A | 275_M | 1.319 | 0.68 |
| 117_G | 175_F | 1.315 | 0.67 |
| 165_L | 189_I | 1.309 | 0.67 |
| 124_L | 129_I | 1.307 | 0.67 |
| 154_F | 278_A | 1.307 | 0.67 |
| 296_C | 302_A | 1.287 | 0.65 |
| 297_V | 302_A | 1.261 | 0.63 |
| 171_E | 213_L | 1.260 | 0.63 |
| 13_R | 34_Y | 1.258 | 0.62 |
| 124_L | 175_F | 1.250 | 0.62 |
| 66_I | 221_I | 1.247 | 0.61 |
| 13_R | 76_E | 1.239 | 0.61 |
| 258_A | 266_W | 1.231 | 0.60 |
| 2_D | 10_I | 1.224 | 0.59 |
| 66_I | 153_F | 1.224 | 0.59 |
| 13_R | 22_E | 1.217 | 0.59 |
| 64_T | 115_M | 1.216 | 0.58 |
| 56_I | 164_T | 1.214 | 0.58 |
| 247_A | 253_T | 1.210 | 0.58 |
| 7_Y | 10_I | 1.207 | 0.58 |
| 113_W | 155_V | 1.198 | 0.57 |
| 279_S | 282_I | 1.194 | 0.56 |
| 83_Q | 186_A | 1.187 | 0.56 |
| 113_W | 121_T | 1.186 | 0.56 |
| 152_I | 156_L | 1.183 | 0.55 |
| 263_V | 266_W | 1.180 | 0.55 |
| 65_A | 117_G | 1.180 | 0.55 |
| 16_H | 124_L | 1.179 | 0.55 |
| 54_S | 129_I | 1.179 | 0.55 |
| 102_M | 114_L | 1.179 | 0.55 |
| 121_T | 175_F | 1.177 | 0.55 |
| 62_G | 123_S | 1.171 | 0.54 |
| 140_L | 195_Y | 1.170 | 0.54 |
| 158_I | 195_Y | 1.169 | 0.54 |
| 22_E | 140_L | 1.168 | 0.54 |
| 40_K | 211_G | 1.163 | 0.53 |
| 158_I | 162_H | 1.160 | 0.53 |
| 134_R | 138_L | 1.156 | 0.53 |
| 29_V | 32_P | 1.154 | 0.53 |
| 40_K | 160_C | 1.152 | 0.52 |
| 89_F | 92_G | 1.151 | 0.52 |
| 14_G | 211_G | 1.147 | 0.52 |
| 102_M | 164_T | 1.147 | 0.52 |
| 5_T | 225_A | 1.143 | 0.51 |
| 14_G | 230_D | 1.141 | 0.51 |
| 12_A | 170_S | 1.141 | 0.51 |
| 211_G | 230_D | 1.136 | 0.51 |
| 153_F | 279_S | 1.130 | 0.50 |
| 68_I | 112_W | 1.127 | 0.50 |
| 115_M | 205_G | 1.124 | 0.50 |
| 16_H | 225_A | 1.122 | 0.49 |
| 24_G | 31_K | 1.121 | 0.49 |
| 16_H | 43_D | 1.120 | 0.49 |
| 114_L | 149_A | 1.119 | 0.49 |
| 273_M | 280_V | 1.115 | 0.49 |
| 37_W | 140_L | 1.115 | 0.49 |
| 74_A | 195_Y | 1.114 | 0.49 |
| 9_Q | 97_K | 1.113 | 0.49 |
| 19_V | 24_G | 1.113 | 0.49 |
| 20_S | 29_V | 1.110 | 0.48 |
| 22_E | 27_D | 1.108 | 0.48 |
| 57_A | 61_F | 1.107 | 0.48 |
| 21_G | 25_D | 1.106 | 0.48 |
| 2_D | 7_Y | 1.102 | 0.48 |
| 292_W | 295_W | 1.100 | 0.47 |
| 116_A | 145_A | 1.099 | 0.47 |
| 120_M | 123_S | 1.097 | 0.47 |
| 62_G | 152_I | 1.095 | 0.47 |
| 250_W | 254_I | 1.094 | 0.47 |
| 265_R | 271_S | 1.093 | 0.47 |
| 2_D | 116_A | 1.093 | 0.47 |
| 187_F | 219_A | 1.093 | 0.47 |
| 203_S | 281_G | 1.088 | 0.46 |
| 248_L | 252_W | 1.088 | 0.46 |
| 57_A | 126_S | 1.087 | 0.46 |
| 87_Q | 179_P | 1.081 | 0.45 |
| 102_M | 166_V | 1.081 | 0.45 |
| 17_I | 24_G | 1.077 | 0.45 |
| 89_F | 201_G | 1.074 | 0.45 |
| 17_I | 23_W | 1.074 | 0.45 |
| 100_Y | 103_G | 1.064 | 0.44 |
| 73_M | 189_I | 1.062 | 0.44 |
| 92_G | 186_A | 1.061 | 0.44 |
| 250_W | 256_F | 1.061 | 0.44 |
| 9_Q | 17_I | 1.058 | 0.43 |
| 29_V | 46_I | 1.054 | 0.43 |
| 100_Y | 170_S | 1.053 | 0.43 |
| 54_S | 133_S | 1.050 | 0.43 |
| 122_L | 126_S | 1.047 | 0.42 |
| 73_M | 190_R | 1.043 | 0.42 |
| 182_D | 186_A | 1.042 | 0.42 |
| 37_W | 43_D | 1.041 | 0.42 |
| 61_F | 164_T | 1.041 | 0.42 |
| 277_S | 280_V | 1.039 | 0.41 |
| 61_F | 64_T | 1.038 | 0.41 |
| 13_R | 26_N | 1.038 | 0.41 |
| 121_T | 156_L | 1.037 | 0.41 |
| 14_G | 201_G | 1.034 | 0.41 |
| 24_G | 27_D | 1.034 | 0.41 |
| 38_L | 43_D | 1.031 | 0.41 |
| 309_L | 312_T | 1.030 | 0.41 |
| 12_A | 102_M | 1.030 | 0.41 |
| 16_H | 19_V | 1.027 | 0.40 |
| 97_K | 102_M | 1.027 | 0.40 |
| 290_D | 295_W | 1.025 | 0.40 |
| 134_R | 230_D | 1.025 | 0.40 |
| 229_G | 242_A | 1.021 | 0.40 |
| 73_M | 76_E | 1.019 | 0.40 |
| 24_G | 29_V | 1.019 | 0.40 |
| 21_G | 40_K | 1.018 | 0.40 |
| 78_H | 195_Y | 1.017 | 0.39 |
| 64_T | 67_L | 1.017 | 0.39 |
| 67_L | 76_E | 1.016 | 0.39 |
| 125_G | 156_L | 1.015 | 0.39 |
| 88_F | 195_Y | 1.014 | 0.39 |
| 208_Y | 228_G | 1.014 | 0.39 |
| 65_A | 175_F | 1.013 | 0.39 |
| 16_H | 144_I | 1.011 | 0.39 |
| 155_V | 211_G | 1.010 | 0.39 |
| 34_Y | 237_T | 1.008 | 0.39 |
| 161_I | 244_E | 1.004 | 0.38 |
| 76_E | 185_T | 1.004 | 0.38 |
| 56_I | 133_S | 1.004 | 0.38 |
| 277_S | 281_G | 1.003 | 0.38 |
| 2_D | 94_Y | 1.001 | 0.38 |
| 229_G | 246_A | 1.000 | 0.38 |
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 | |
| 2wjnM | 1 | 1 | 100 | 0.089 | Contact Map |
| 1eysM | 1 | 0.9814 | 100 | 0.128 | Contact Map |
| 1rzhM | 1 | 0.9257 | 100 | 0.134 | Contact Map |
| 1eysL | 1 | 0.839 | 100 | 0.294 | Contact Map |
| 1rzhL | 1 | 0.8669 | 100 | 0.296 | Contact Map |
| 2wjnL | 1 | 0.839 | 100 | 0.301 | Contact Map |
| 3arcA | 2 | 0.8978 | 100 | 0.319 | Contact Map |
| 3arcD | 2 | 0.8947 | 100 | 0.361 | Contact Map |
| 2lcoA | 1 | 0.0588 | 5.6 | 0.983 | Contact Map |
| 2kegA | 1 | 0.0991 | 5.1 | 0.984 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)