| yxw |
| ID: | 1486970891 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 278 (271) | ||
| Sequences: | 1198 (862.8) | ||
| Seq/Len: | 4.421 | ||
| Nf(neff/√len): | 52.4 |
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: 4.421).
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_G | 178_T | 3.585 | 1.00 |
| 164_A | 176_L | 3.490 | 1.00 |
| 112_C | 115_C | 3.001 | 1.00 |
| 246_I | 254_G | 2.967 | 1.00 |
| 158_A | 184_V | 2.896 | 1.00 |
| 161_T | 181_C | 2.680 | 1.00 |
| 97_W | 100_D | 2.593 | 1.00 |
| 79_N | 146_Y | 2.542 | 1.00 |
| 161_T | 189_L | 2.471 | 1.00 |
| 181_C | 224_P | 2.272 | 1.00 |
| 125_W | 166_V | 2.246 | 1.00 |
| 88_F | 163_G | 2.157 | 1.00 |
| 91_S | 97_W | 2.106 | 1.00 |
| 84_L | 140_M | 2.086 | 1.00 |
| 121_F | 182_P | 1.957 | 1.00 |
| 82_K | 145_G | 1.939 | 1.00 |
| 75_L | 86_V | 1.930 | 1.00 |
| 148_L | 174_V | 1.853 | 1.00 |
| 75_L | 135_K | 1.785 | 1.00 |
| 117_V | 162_L | 1.776 | 1.00 |
| 210_I | 262_D | 1.753 | 1.00 |
| 129_A | 166_V | 1.753 | 1.00 |
| 75_L | 136_I | 1.739 | 0.99 |
| 43_C | 48_C | 1.735 | 0.99 |
| 25_S | 151_T | 1.718 | 0.99 |
| 157_G | 181_C | 1.713 | 0.99 |
| 187_Y | 191_E | 1.701 | 0.99 |
| 89_R | 96_N | 1.699 | 0.99 |
| 194_T | 225_S | 1.682 | 0.99 |
| 28_A | 87_A | 1.680 | 0.99 |
| 185_G | 189_L | 1.661 | 0.99 |
| 106_Q | 119_T | 1.657 | 0.99 |
| 74_F | 87_A | 1.642 | 0.99 |
| 91_S | 100_D | 1.637 | 0.99 |
| 121_F | 158_A | 1.629 | 0.99 |
| 161_T | 184_V | 1.585 | 0.99 |
| 12_T | 16_D | 1.560 | 0.99 |
| 82_K | 146_Y | 1.552 | 0.99 |
| 191_E | 249_I | 1.538 | 0.98 |
| 148_L | 172_Y | 1.538 | 0.98 |
| 21_F | 83_R | 1.527 | 0.98 |
| 29_Y | 90_G | 1.522 | 0.98 |
| 161_T | 193_I | 1.516 | 0.98 |
| 125_W | 159_L | 1.505 | 0.98 |
| 102_D | 119_T | 1.465 | 0.98 |
| 184_V | 189_L | 1.448 | 0.97 |
| 37_D | 41_V | 1.426 | 0.97 |
| 25_S | 28_A | 1.423 | 0.97 |
| 150_F | 167_L | 1.420 | 0.97 |
| 111_L | 115_C | 1.418 | 0.97 |
| 129_A | 133_T | 1.410 | 0.97 |
| 97_W | 101_L | 1.406 | 0.97 |
| 15_L | 18_L | 1.402 | 0.97 |
| 107_D | 116_K | 1.395 | 0.97 |
| 105_L | 116_K | 1.393 | 0.96 |
| 147_T | 175_E | 1.387 | 0.96 |
| 178_T | 203_R | 1.382 | 0.96 |
| 83_R | 149_Y | 1.351 | 0.96 |
| 78_D | 81_N | 1.349 | 0.96 |
| 216_P | 219_F | 1.341 | 0.95 |
| 250_N | 254_G | 1.333 | 0.95 |
| 158_A | 182_P | 1.328 | 0.95 |
| 21_F | 179_Y | 1.318 | 0.95 |
| 65_T | 139_A | 1.312 | 0.95 |
| 24_W | 78_D | 1.308 | 0.95 |
| 88_F | 128_A | 1.305 | 0.94 |
| 137_K | 147_T | 1.298 | 0.94 |
| 205_T | 225_S | 1.287 | 0.94 |
| 13_S | 16_D | 1.272 | 0.93 |
| 208_N | 265_A | 1.264 | 0.93 |
| 128_A | 132_L | 1.264 | 0.93 |
| 84_L | 148_L | 1.258 | 0.93 |
| 24_W | 56_T | 1.250 | 0.93 |
| 18_L | 204_V | 1.234 | 0.92 |
| 263_V | 267_L | 1.216 | 0.91 |
| 28_A | 74_F | 1.215 | 0.91 |
| 11_S | 14_T | 1.212 | 0.91 |
| 138_S | 142_T | 1.212 | 0.91 |
| 225_S | 249_I | 1.210 | 0.91 |
| 62_F | 73_G | 1.199 | 0.90 |
| 77_A | 146_Y | 1.191 | 0.90 |
| 150_F | 163_G | 1.189 | 0.90 |
| 100_D | 155_L | 1.188 | 0.90 |
| 251_S | 256_A | 1.179 | 0.89 |
| 187_Y | 222_S | 1.166 | 0.89 |
| 125_W | 163_G | 1.165 | 0.89 |
| 96_N | 100_D | 1.164 | 0.89 |
| 160_A | 178_T | 1.163 | 0.89 |
| 21_F | 149_Y | 1.154 | 0.88 |
| 79_N | 143_Y | 1.149 | 0.88 |
| 194_T | 201_N | 1.144 | 0.87 |
| 203_R | 227_E | 1.141 | 0.87 |
| 252_T | 255_N | 1.135 | 0.87 |
| 165_T | 193_I | 1.130 | 0.87 |
| 30_C | 43_C | 1.125 | 0.86 |
| 202_F | 228_Y | 1.124 | 0.86 |
| 14_T | 17_E | 1.110 | 0.85 |
| 176_L | 201_N | 1.110 | 0.85 |
| 19_Q | 270_F | 1.107 | 0.85 |
| 266_H | 276_C | 1.103 | 0.85 |
| 117_V | 122_W | 1.095 | 0.84 |
| 29_Y | 158_A | 1.095 | 0.84 |
| 10_V | 14_T | 1.094 | 0.84 |
| 76_A | 275_E | 1.093 | 0.84 |
| 193_I | 201_N | 1.086 | 0.83 |
| 254_G | 257_G | 1.085 | 0.83 |
| 134_S | 138_S | 1.083 | 0.83 |
| 118_H | 121_F | 1.081 | 0.83 |
| 75_L | 84_L | 1.079 | 0.83 |
| 152_G | 156_G | 1.078 | 0.83 |
| 83_R | 147_T | 1.078 | 0.83 |
| 213_R | 255_N | 1.066 | 0.82 |
| 174_V | 201_N | 1.065 | 0.82 |
| 180_G | 185_G | 1.061 | 0.82 |
| 201_N | 224_P | 1.049 | 0.80 |
| 91_S | 182_P | 1.048 | 0.80 |
| 91_S | 155_L | 1.046 | 0.80 |
| 84_L | 136_I | 1.046 | 0.80 |
| 180_G | 183_R | 1.040 | 0.80 |
| 115_C | 192_H | 1.038 | 0.80 |
| 164_A | 174_V | 1.036 | 0.79 |
| 140_M | 172_Y | 1.032 | 0.79 |
| 273_I | 276_C | 1.032 | 0.79 |
| 251_S | 254_G | 1.029 | 0.79 |
| 98_I | 102_D | 1.020 | 0.78 |
| 70_G | 93_T | 1.016 | 0.77 |
| 191_E | 195_S | 1.015 | 0.77 |
| 130_D | 134_S | 1.015 | 0.77 |
| 209_D | 215_P | 1.013 | 0.77 |
| 153_H | 156_G | 1.008 | 0.77 |
| 183_R | 215_P | 1.003 | 0.76 |
| 58_M | 61_E | 1.002 | 0.76 |
| 244_E | 253_A | 1.002 | 0.76 |
| 84_L | 139_A | 1.000 | 0.76 |
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 | |
| 1tiaA | 1 | 0.9568 | 100 | 0.215 | Contact Map |
| 1tibA | 1 | 0.964 | 100 | 0.22 | Contact Map |
| 3o0dA | 7 | 0.982 | 100 | 0.221 | Contact Map |
| 3ngmA | 4 | 0.9568 | 100 | 0.227 | Contact Map |
| 4l3wA | 1 | 0.9245 | 100 | 0.262 | Contact Map |
| 1uwcA | 2 | 0.8993 | 100 | 0.263 | Contact Map |
| 3g7nA | 2 | 0.8813 | 100 | 0.281 | Contact Map |
| 3uueA | 1 | 0.9173 | 100 | 0.308 | Contact Map |
| 1tglA | 1 | 0.9245 | 100 | 0.335 | Contact Map |
| 2yijA | 2 | 0.8885 | 100 | 0.416 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)