| atl |
| ID: | 1486983788 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 276 (269) | ||
| Sequences: | 1351 (979.2) | ||
| Seq/Len: | 5.022 | ||
| Nf(neff/√len): | 59.7 |
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: 5.022).
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 |
| 157_A | 179_S | 3.848 | 1.00 |
| 164_A | 177_V | 3.590 | 1.00 |
| 245_I | 253_G | 3.363 | 1.00 |
| 112_C | 115_C | 3.060 | 1.00 |
| 161_T | 182_S | 2.912 | 1.00 |
| 158_A | 185_V | 2.819 | 1.00 |
| 161_T | 190_L | 2.683 | 1.00 |
| 97_W | 100_N | 2.650 | 1.00 |
| 79_S | 146_Y | 2.532 | 1.00 |
| 88_F | 163_G | 2.410 | 1.00 |
| 125_W | 166_E | 2.394 | 1.00 |
| 182_S | 223_P | 2.217 | 1.00 |
| 192_E | 248_V | 2.064 | 1.00 |
| 84_I | 140_R | 1.963 | 1.00 |
| 188_L | 192_E | 1.949 | 1.00 |
| 209_I | 261_D | 1.917 | 1.00 |
| 157_A | 182_S | 1.888 | 1.00 |
| 75_L | 135_E | 1.876 | 1.00 |
| 25_S | 151_T | 1.831 | 1.00 |
| 91_S | 97_W | 1.818 | 1.00 |
| 75_L | 86_L | 1.784 | 1.00 |
| 121_F | 183_P | 1.769 | 1.00 |
| 195_T | 224_S | 1.713 | 1.00 |
| 129_S | 166_E | 1.693 | 1.00 |
| 82_K | 146_Y | 1.693 | 1.00 |
| 179_S | 202_R | 1.693 | 1.00 |
| 74_Y | 87_S | 1.675 | 0.99 |
| 150_F | 167_L | 1.665 | 0.99 |
| 55_D | 78_D | 1.654 | 0.99 |
| 82_K | 145_D | 1.653 | 0.99 |
| 117_V | 162_L | 1.615 | 0.99 |
| 186_G | 190_L | 1.613 | 0.99 |
| 161_T | 194_I | 1.598 | 0.99 |
| 228_W | 256_G | 1.580 | 0.99 |
| 107_D | 116_K | 1.566 | 0.99 |
| 91_S | 100_N | 1.563 | 0.99 |
| 89_R | 96_N | 1.546 | 0.99 |
| 148_L | 175_I | 1.543 | 0.99 |
| 106_D | 119_G | 1.535 | 0.99 |
| 25_S | 28_A | 1.535 | 0.99 |
| 21_F | 83_L | 1.513 | 0.99 |
| 194_I | 200_I | 1.504 | 0.99 |
| 161_T | 185_V | 1.499 | 0.99 |
| 59_L | 139_A | 1.495 | 0.98 |
| 75_L | 136_I | 1.486 | 0.98 |
| 147_K | 176_D | 1.481 | 0.98 |
| 43_C | 48_C | 1.472 | 0.98 |
| 18_L | 203_A | 1.461 | 0.98 |
| 121_F | 158_A | 1.446 | 0.98 |
| 150_F | 163_G | 1.386 | 0.97 |
| 28_A | 87_S | 1.374 | 0.97 |
| 24_Y | 56_T | 1.372 | 0.97 |
| 148_L | 173_W | 1.371 | 0.97 |
| 207_N | 264_A | 1.369 | 0.97 |
| 262_A | 266_S | 1.350 | 0.97 |
| 62_F | 73_G | 1.349 | 0.97 |
| 105_F | 116_K | 1.340 | 0.96 |
| 125_W | 159_I | 1.339 | 0.96 |
| 135_E | 139_A | 1.334 | 0.96 |
| 97_W | 101_L | 1.333 | 0.96 |
| 129_S | 133_K | 1.332 | 0.96 |
| 102_D | 119_G | 1.327 | 0.96 |
| 21_F | 149_V | 1.324 | 0.96 |
| 128_V | 132_L | 1.321 | 0.96 |
| 204_T | 224_S | 1.309 | 0.96 |
| 29_Y | 90_G | 1.304 | 0.96 |
| 138_K | 142_A | 1.297 | 0.95 |
| 28_A | 74_Y | 1.293 | 0.95 |
| 224_S | 248_V | 1.289 | 0.95 |
| 83_L | 149_V | 1.280 | 0.95 |
| 58_S | 61_E | 1.280 | 0.95 |
| 185_V | 190_L | 1.277 | 0.95 |
| 177_V | 200_I | 1.271 | 0.95 |
| 195_T | 200_I | 1.270 | 0.95 |
| 21_F | 180_Y | 1.263 | 0.94 |
| 78_D | 81_N | 1.262 | 0.94 |
| 137_Q | 147_K | 1.261 | 0.94 |
| 212_R | 254_N | 1.259 | 0.94 |
| 30_C | 43_C | 1.259 | 0.94 |
| 96_N | 100_N | 1.246 | 0.94 |
| 140_R | 173_W | 1.233 | 0.94 |
| 117_V | 122_W | 1.223 | 0.93 |
| 188_L | 221_R | 1.221 | 0.93 |
| 11_S | 14_A | 1.218 | 0.93 |
| 265_H | 275_C | 1.215 | 0.93 |
| 24_Y | 78_D | 1.212 | 0.93 |
| 77_A | 146_Y | 1.210 | 0.93 |
| 165_A | 194_I | 1.195 | 0.92 |
| 38_G | 41_V | 1.192 | 0.92 |
| 115_C | 193_Y | 1.190 | 0.92 |
| 83_L | 147_K | 1.189 | 0.92 |
| 79_S | 143_H | 1.185 | 0.92 |
| 115_C | 187_N | 1.177 | 0.91 |
| 88_F | 128_V | 1.172 | 0.91 |
| 184_R | 214_P | 1.166 | 0.91 |
| 160_A | 179_S | 1.162 | 0.91 |
| 181_G | 186_G | 1.153 | 0.90 |
| 243_K | 252_K | 1.133 | 0.89 |
| 111_L | 115_C | 1.110 | 0.88 |
| 179_S | 182_S | 1.109 | 0.88 |
| 180_Y | 203_A | 1.102 | 0.87 |
| 212_R | 255_A | 1.100 | 0.87 |
| 164_A | 175_I | 1.100 | 0.87 |
| 251_R | 254_N | 1.095 | 0.87 |
| 93_S | 96_N | 1.094 | 0.87 |
| 84_I | 136_I | 1.084 | 0.86 |
| 70_E | 93_S | 1.080 | 0.86 |
| 128_V | 229_I | 1.075 | 0.85 |
| 185_V | 223_P | 1.074 | 0.85 |
| 137_Q | 141_T | 1.067 | 0.85 |
| 75_L | 84_I | 1.065 | 0.85 |
| 25_S | 29_Y | 1.064 | 0.85 |
| 188_L | 248_V | 1.053 | 0.84 |
| 10_V | 14_A | 1.050 | 0.84 |
| 117_V | 190_L | 1.048 | 0.83 |
| 91_S | 155_L | 1.042 | 0.83 |
| 161_T | 223_P | 1.040 | 0.83 |
| 100_N | 155_L | 1.036 | 0.82 |
| 200_I | 223_P | 1.033 | 0.82 |
| 250_S | 255_A | 1.033 | 0.82 |
| 84_I | 148_L | 1.032 | 0.82 |
| 64_A | 127_T | 1.029 | 0.82 |
| 55_D | 80_T | 1.022 | 0.81 |
| 98_I | 102_D | 1.021 | 0.81 |
| 57_T | 143_H | 1.017 | 0.81 |
| 125_W | 163_G | 1.014 | 0.81 |
| 150_F | 160_A | 1.012 | 0.80 |
| 158_A | 183_P | 1.011 | 0.80 |
| 59_L | 143_H | 1.010 | 0.80 |
| 15_L | 18_L | 1.001 | 0.79 |
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 | |
| 3o0dA | 7 | 0.9783 | 100 | 0.213 | Contact Map |
| 1tiaA | 1 | 0.9601 | 100 | 0.214 | Contact Map |
| 3ngmA | 4 | 0.9601 | 100 | 0.222 | Contact Map |
| 1tibA | 1 | 0.9638 | 100 | 0.223 | Contact Map |
| 4l3wA | 1 | 0.9312 | 100 | 0.249 | Contact Map |
| 1uwcA | 2 | 0.8949 | 100 | 0.259 | Contact Map |
| 3g7nA | 2 | 0.8841 | 100 | 0.278 | Contact Map |
| 3uueA | 1 | 0.9203 | 100 | 0.301 | Contact Map |
| 1tglA | 1 | 0.9312 | 100 | 0.324 | Contact Map |
| 2yijA | 2 | 0.913 | 100 | 0.418 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)