| 1A53 |
| ID: | 1411070191 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 247 (243) | ||
| Sequences: | 1730 (1215.6) | ||
| Seq/Len: | 7.119 | ||
| Nf(neff/√len): | 78.0 |
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: 7.119).
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 |
| 138_E | 167_I | 4.360 | 1.00 |
| 12_V | 135_I | 3.594 | 1.00 |
| 92_Y | 124_L | 3.281 | 1.00 |
| 14_L | 87_Y | 3.023 | 1.00 |
| 162_E | 195_K | 2.839 | 1.00 |
| 207_V | 228_A | 2.580 | 1.00 |
| 194_R | 220_E | 2.541 | 1.00 |
| 137_T | 140_E | 2.529 | 1.00 |
| 99_A | 127_D | 2.435 | 1.00 |
| 64_D | 67_E | 2.427 | 1.00 |
| 193_Q | 226_V | 2.248 | 1.00 |
| 31_S | 154_E | 2.240 | 1.00 |
| 115_E | 143_S | 2.235 | 1.00 |
| 73_E | 103_S | 2.194 | 1.00 |
| 54_K | 89_N | 2.194 | 1.00 |
| 47_I | 242_I | 2.177 | 1.00 |
| 119_D | 147_Y | 2.140 | 1.00 |
| 178_I | 206_K | 2.138 | 1.00 |
| 241_K | 244_E | 2.121 | 1.00 |
| 148_A | 155_P | 2.032 | 1.00 |
| 145_L | 155_P | 2.010 | 1.00 |
| 31_S | 34_E | 1.926 | 1.00 |
| 191_E | 194_R | 1.910 | 1.00 |
| 18_R | 84_E | 1.857 | 1.00 |
| 15_S | 18_R | 1.850 | 1.00 |
| 14_L | 86_K | 1.835 | 1.00 |
| 159_I | 165_L | 1.814 | 1.00 |
| 32_L | 36_I | 1.795 | 1.00 |
| 23_A | 114_K | 1.786 | 1.00 |
| 134_K | 164_D | 1.781 | 1.00 |
| 215_R | 219_E | 1.756 | 1.00 |
| 108_M | 120_D | 1.755 | 1.00 |
| 133_V | 168_A | 1.743 | 1.00 |
| 218_I | 229_F | 1.741 | 1.00 |
| 118_I | 129_V | 1.737 | 1.00 |
| 197_I | 206_K | 1.704 | 1.00 |
| 208_A | 221_L | 1.702 | 1.00 |
| 182_D | 187_E | 1.701 | 1.00 |
| 119_D | 151_Y | 1.676 | 1.00 |
| 15_S | 84_E | 1.674 | 1.00 |
| 193_Q | 208_A | 1.663 | 1.00 |
| 191_E | 195_K | 1.644 | 1.00 |
| 93_E | 96_R | 1.642 | 1.00 |
| 131_L | 136_L | 1.619 | 1.00 |
| 149_R | 174_R | 1.604 | 1.00 |
| 92_Y | 108_M | 1.583 | 1.00 |
| 162_E | 199_M | 1.569 | 1.00 |
| 200_I | 206_K | 1.559 | 1.00 |
| 51_Y | 98_I | 1.498 | 0.99 |
| 165_L | 200_I | 1.496 | 0.99 |
| 213_S | 234_S | 1.459 | 0.99 |
| 16_L | 140_E | 1.458 | 0.99 |
| 145_L | 149_R | 1.454 | 0.99 |
| 53_R | 94_T | 1.450 | 0.99 |
| 182_D | 185_T | 1.450 | 0.99 |
| 133_V | 141_L | 1.444 | 0.99 |
| 58_G | 233_S | 1.432 | 0.99 |
| 212_I | 218_I | 1.425 | 0.99 |
| 140_E | 143_S | 1.420 | 0.99 |
| 194_R | 224_L | 1.418 | 0.99 |
| 129_V | 148_A | 1.376 | 0.99 |
| 220_E | 224_L | 1.373 | 0.99 |
| 118_I | 144_L | 1.372 | 0.99 |
| 26_Q | 116_S | 1.318 | 0.98 |
| 6_G | 9_K | 1.299 | 0.98 |
| 73_E | 104_I | 1.292 | 0.98 |
| 95_L | 106_I | 1.289 | 0.98 |
| 53_R | 63_R | 1.289 | 0.98 |
| 63_R | 94_T | 1.280 | 0.97 |
| 57_S | 82_L | 1.275 | 0.97 |
| 233_S | 237_R | 1.264 | 0.97 |
| 148_A | 153_M | 1.238 | 0.97 |
| 78_G | 128_T | 1.227 | 0.97 |
| 6_G | 184_E | 1.227 | 0.97 |
| 238_N | 241_K | 1.220 | 0.96 |
| 138_E | 170_R | 1.214 | 0.96 |
| 45_T | 229_F | 1.211 | 0.96 |
| 22_R | 116_S | 1.210 | 0.96 |
| 189_N | 195_K | 1.206 | 0.96 |
| 7_W | 186_L | 1.200 | 0.96 |
| 99_A | 106_I | 1.191 | 0.96 |
| 22_R | 120_D | 1.189 | 0.96 |
| 36_I | 40_N | 1.188 | 0.96 |
| 66_I | 98_I | 1.186 | 0.96 |
| 145_L | 173_A | 1.176 | 0.95 |
| 21_F | 24_S | 1.173 | 0.95 |
| 108_M | 121_A | 1.172 | 0.95 |
| 65_P | 98_I | 1.166 | 0.95 |
| 186_L | 233_S | 1.159 | 0.95 |
| 118_I | 147_Y | 1.151 | 0.94 |
| 65_P | 69_S | 1.151 | 0.94 |
| 218_I | 231_I | 1.147 | 0.94 |
| 166_D | 199_M | 1.142 | 0.94 |
| 36_I | 39_F | 1.140 | 0.94 |
| 53_R | 89_N | 1.138 | 0.94 |
| 147_Y | 151_Y | 1.135 | 0.94 |
| 147_Y | 150_S | 1.131 | 0.94 |
| 156_L | 207_V | 1.124 | 0.94 |
| 59_L | 236_M | 1.116 | 0.93 |
| 197_I | 226_V | 1.110 | 0.93 |
| 115_E | 147_Y | 1.106 | 0.93 |
| 165_L | 199_M | 1.105 | 0.93 |
| 117_Q | 144_L | 1.092 | 0.92 |
| 15_S | 85_E | 1.090 | 0.92 |
| 180_S | 193_Q | 1.089 | 0.92 |
| 145_L | 171_I | 1.088 | 0.92 |
| 109_K | 210_S | 1.083 | 0.92 |
| 154_E | 175_F | 1.079 | 0.92 |
| 14_L | 17_R | 1.078 | 0.92 |
| 91_S | 94_T | 1.064 | 0.91 |
| 32_L | 78_G | 1.062 | 0.91 |
| 18_R | 85_E | 1.058 | 0.91 |
| 112_I | 144_L | 1.040 | 0.90 |
| 71_F | 75_Y | 1.038 | 0.89 |
| 32_L | 35_R | 1.037 | 0.89 |
| 221_L | 226_V | 1.037 | 0.89 |
| 22_R | 92_Y | 1.036 | 0.89 |
| 214_E | 217_E | 1.020 | 0.88 |
| 146_E | 150_S | 1.020 | 0.88 |
| 156_L | 177_G | 1.019 | 0.88 |
| 161_D | 184_E | 1.018 | 0.88 |
| 168_A | 173_A | 1.014 | 0.88 |
| 145_L | 172_G | 1.008 | 0.88 |
| 11_V | 15_S | 1.003 | 0.87 |
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 | |
| 1piiA | 1 | 0.9676 | 100 | 0.336 | Contact Map |
| 4a29A | 1 | 1 | 100 | 0.346 | Contact Map |
| 3tsmA | 2 | 0.9798 | 100 | 0.413 | Contact Map |
| 3qjaA | 1 | 0.9231 | 100 | 0.414 | Contact Map |
| 1vc4A | 2 | 0.9717 | 100 | 0.43 | Contact Map |
| 1i4nA | 2 | 0.9595 | 100 | 0.452 | Contact Map |
| 1hg3A | 8 | 0.8097 | 100 | 0.679 | Contact Map |
| 2h6rA | 8 | 0.7692 | 99.9 | 0.69 | Contact Map |
| 2yzrA | 3 | 0.8097 | 99.9 | 0.708 | Contact Map |
| 3o07A | 3 | 0.7652 | 99.9 | 0.717 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)