| AfQ2 |
| ID: | 1488359386 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 272 (253) | ||
| Sequences: | 10648 (5149.9) | ||
| Seq/Len: | 42.087 | ||
| Nf(neff/√len): | 323.8 |
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: 42.087).
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 |
| 96_P | 133_L | 3.201 | 1.00 |
| 152_I | 173_F | 2.862 | 1.00 |
| 71_N | 121_V | 2.858 | 1.00 |
| 108_Y | 153_S | 2.826 | 1.00 |
| 30_F | 53_F | 2.680 | 1.00 |
| 187_A | 202_A | 2.665 | 1.00 |
| 83_W | 92_W | 2.649 | 1.00 |
| 159_Q | 164_D | 2.530 | 1.00 |
| 83_W | 140_E | 2.268 | 1.00 |
| 156_P | 159_Q | 2.262 | 1.00 |
| 98_T | 134_P | 2.090 | 1.00 |
| 136_D | 139_G | 2.073 | 1.00 |
| 45_P | 184_E | 2.053 | 1.00 |
| 113_V | 154_Y | 1.988 | 1.00 |
| 97_L | 107_C | 1.963 | 1.00 |
| 51_S | 125_P | 1.947 | 1.00 |
| 133_L | 143_R | 1.943 | 1.00 |
| 114_E | 156_P | 1.918 | 1.00 |
| 183_A | 209_A | 1.836 | 1.00 |
| 128_D | 229_V | 1.823 | 1.00 |
| 131_R | 143_R | 1.796 | 1.00 |
| 182_N | 185_L | 1.792 | 1.00 |
| 56_F | 60_R | 1.729 | 1.00 |
| 55_E | 67_T | 1.719 | 1.00 |
| 104_G | 147_D | 1.700 | 1.00 |
| 111_E | 155_N | 1.700 | 1.00 |
| 58_A | 65_L | 1.696 | 1.00 |
| 41_M | 152_I | 1.678 | 1.00 |
| 94_D | 102_R | 1.651 | 1.00 |
| 250_V | 264_E | 1.645 | 1.00 |
| 97_L | 126_L | 1.631 | 1.00 |
| 54_V | 151_V | 1.601 | 1.00 |
| 183_A | 206_T | 1.592 | 1.00 |
| 76_A | 122_V | 1.577 | 1.00 |
| 38_L | 233_M | 1.577 | 1.00 |
| 188_G | 191_V | 1.559 | 1.00 |
| 211_A | 215_K | 1.559 | 1.00 |
| 132_T | 146_P | 1.538 | 1.00 |
| 191_V | 201_A | 1.532 | 1.00 |
| 96_P | 99_V | 1.524 | 1.00 |
| 246_R | 264_E | 1.524 | 1.00 |
| 131_R | 145_H | 1.522 | 1.00 |
| 191_V | 198_P | 1.516 | 1.00 |
| 94_D | 98_T | 1.505 | 1.00 |
| 66_V | 105_A | 1.494 | 1.00 |
| 188_G | 192_Q | 1.461 | 1.00 |
| 28_A | 31_E | 1.458 | 1.00 |
| 84_L | 91_R | 1.448 | 1.00 |
| 107_C | 150_L | 1.447 | 1.00 |
| 43_K | 179_D | 1.444 | 1.00 |
| 221_E | 231_A | 1.443 | 1.00 |
| 262_T | 266_A | 1.443 | 1.00 |
| 127_T | 150_L | 1.437 | 1.00 |
| 103_Y | 147_D | 1.431 | 1.00 |
| 208_A | 211_A | 1.426 | 1.00 |
| 45_P | 48_C | 1.415 | 1.00 |
| 26_E | 53_F | 1.409 | 1.00 |
| 38_L | 200_I | 1.397 | 0.99 |
| 159_Q | 162_M | 1.392 | 0.99 |
| 232_A | 235_M | 1.384 | 0.99 |
| 27_V | 53_F | 1.378 | 0.99 |
| 84_L | 90_T | 1.363 | 0.99 |
| 257_A | 261_A | 1.362 | 0.99 |
| 197_A | 203_Q | 1.352 | 0.99 |
| 209_A | 213_R | 1.348 | 0.99 |
| 31_E | 60_R | 1.340 | 0.99 |
| 48_C | 180_Y | 1.332 | 0.99 |
| 183_A | 187_A | 1.329 | 0.99 |
| 64_P | 99_V | 1.315 | 0.99 |
| 261_A | 265_H | 1.313 | 0.99 |
| 75_T | 119_T | 1.291 | 0.99 |
| 126_L | 132_T | 1.289 | 0.99 |
| 53_F | 180_Y | 1.280 | 0.99 |
| 44_G | 50_K | 1.265 | 0.99 |
| 229_V | 233_M | 1.265 | 0.99 |
| 27_V | 30_F | 1.251 | 0.99 |
| 94_D | 99_V | 1.246 | 0.98 |
| 30_F | 40_V | 1.242 | 0.98 |
| 190_L | 194_T | 1.231 | 0.98 |
| 187_A | 191_V | 1.230 | 0.98 |
| 113_V | 156_P | 1.230 | 0.98 |
| 132_T | 145_H | 1.229 | 0.98 |
| 30_F | 57_M | 1.227 | 0.98 |
| 188_G | 212_R | 1.220 | 0.98 |
| 196_V | 200_I | 1.217 | 0.98 |
| 33_A | 176_F | 1.214 | 0.98 |
| 37_R | 199_S | 1.213 | 0.98 |
| 120_T | 169_T | 1.194 | 0.98 |
| 250_V | 263_L | 1.190 | 0.98 |
| 58_A | 106_I | 1.186 | 0.98 |
| 223_I | 227_L | 1.181 | 0.98 |
| 247_M | 251_Q | 1.179 | 0.98 |
| 210_T | 213_R | 1.173 | 0.98 |
| 86_D | 91_R | 1.172 | 0.98 |
| 257_A | 260_R | 1.157 | 0.97 |
| 70_C | 109_L | 1.154 | 0.97 |
| 115_A | 119_T | 1.153 | 0.97 |
| 204_L | 231_A | 1.151 | 0.97 |
| 134_P | 144_A | 1.148 | 0.97 |
| 66_V | 99_V | 1.147 | 0.97 |
| 121_V | 124_H | 1.144 | 0.97 |
| 258_D | 261_A | 1.130 | 0.97 |
| 37_R | 104_G | 1.129 | 0.97 |
| 188_G | 217_H | 1.116 | 0.96 |
| 231_A | 235_M | 1.110 | 0.96 |
| 52_R | 55_E | 1.108 | 0.96 |
| 82_R | 92_W | 1.107 | 0.96 |
| 33_A | 40_V | 1.103 | 0.96 |
| 64_P | 105_A | 1.097 | 0.96 |
| 186_E | 212_R | 1.096 | 0.96 |
| 194_T | 229_V | 1.095 | 0.96 |
| 106_I | 149_Q | 1.094 | 0.96 |
| 112_I | 152_I | 1.089 | 0.96 |
| 207_V | 232_A | 1.084 | 0.96 |
| 117_Q | 164_D | 1.083 | 0.96 |
| 196_V | 199_S | 1.081 | 0.95 |
| 219_L | 222_G | 1.067 | 0.95 |
| 56_F | 59_W | 1.056 | 0.95 |
| 113_V | 155_N | 1.053 | 0.95 |
| 84_L | 92_W | 1.049 | 0.94 |
| 165_L | 169_T | 1.048 | 0.94 |
| 89_G | 92_W | 1.047 | 0.94 |
| 265_H | 268_D | 1.046 | 0.94 |
| 26_E | 29_L | 1.035 | 0.94 |
| 246_R | 250_V | 1.021 | 0.93 |
| 53_F | 178_F | 1.021 | 0.93 |
| 103_Y | 146_P | 1.017 | 0.93 |
| 101_A | 126_L | 1.014 | 0.93 |
| 68_V | 107_C | 1.012 | 0.93 |
| 242_R | 268_D | 1.005 | 0.93 |
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 | |
| 4rh7A | 1 | 0.9706 | 100 | 0.321 | Contact Map |
| 3vkgA | 2 | 0.9779 | 100 | 0.364 | Contact Map |
| 4akgA | 2 | 0.989 | 100 | 0.407 | Contact Map |
| 2r44A | 1 | 0.9706 | 99.9 | 0.556 | Contact Map |
| 3ja87 | 1 | 0 | 99.9 | 0.565 | Contact Map |
| 4r7yA | 2 | 0.9191 | 99.9 | 0.569 | Contact Map |
| 3ja86 | 1 | 0 | 99.9 | 0.573 | Contact Map |
| 3ja83 | 1 | 0 | 99.9 | 0.579 | Contact Map |
| 3ja84 | 1 | 0 | 99.9 | 0.589 | Contact Map |
| 3nbxX | 1 | 0.9044 | 99.8 | 0.601 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)