| 3A72_A non default parameters |
| ID: | 1482669983 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 355 (341) | ||
| Sequences: | 484 (340.4) | ||
| Seq/Len: | 1.419 | ||
| Nf(neff/√len): | 18.4 |
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: 1.419).
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 |
| 225_G | 235_F | 2.610 | 1.00 |
| 185_D | 188_N | 2.206 | 0.99 |
| 180_H | 195_D | 2.168 | 0.99 |
| 139_E | 146_L | 2.152 | 0.99 |
| 57_S | 61_G | 2.044 | 0.98 |
| 244_D | 247_N | 1.986 | 0.98 |
| 162_I | 246_E | 1.978 | 0.98 |
| 177_T | 194_E | 1.899 | 0.97 |
| 178_M | 208_P | 1.892 | 0.97 |
| 207_M | 223_E | 1.880 | 0.96 |
| 56_R | 126_M | 1.869 | 0.96 |
| 90_E | 159_G | 1.859 | 0.96 |
| 66_E | 69_R | 1.846 | 0.96 |
| 123_D | 127_T | 1.846 | 0.96 |
| 134_I | 163_C | 1.787 | 0.95 |
| 291_T | 305_E | 1.784 | 0.95 |
| 52_F | 104_G | 1.692 | 0.93 |
| 122_Q | 129_D | 1.651 | 0.91 |
| 144_N | 175_G | 1.637 | 0.91 |
| 217_Q | 243_S | 1.636 | 0.91 |
| 327_R | 350_D | 1.589 | 0.89 |
| 95_F | 129_D | 1.582 | 0.89 |
| 35_D | 56_R | 1.568 | 0.88 |
| 142_P | 146_L | 1.555 | 0.88 |
| 118_L | 154_L | 1.553 | 0.88 |
| 182_V | 190_G | 1.551 | 0.88 |
| 121_S | 125_G | 1.546 | 0.87 |
| 29_E | 100_L | 1.533 | 0.87 |
| 162_I | 210_V | 1.515 | 0.86 |
| 271_V | 318_L | 1.505 | 0.85 |
| 91_R | 96_K | 1.499 | 0.85 |
| 151_E | 223_E | 1.486 | 0.84 |
| 128_W | 189_W | 1.473 | 0.84 |
| 211_T | 270_A | 1.470 | 0.83 |
| 174_Y | 197_T | 1.466 | 0.83 |
| 123_D | 185_D | 1.452 | 0.82 |
| 189_W | 303_W | 1.443 | 0.82 |
| 181_Q | 192_V | 1.439 | 0.82 |
| 160_K | 182_V | 1.426 | 0.81 |
| 141_R | 146_L | 1.402 | 0.79 |
| 95_F | 186_L | 1.396 | 0.79 |
| 87_S | 124_D | 1.388 | 0.78 |
| 29_E | 87_S | 1.382 | 0.78 |
| 57_S | 64_W | 1.379 | 0.78 |
| 176_Q | 204_R | 1.370 | 0.77 |
| 160_K | 184_N | 1.369 | 0.77 |
| 32_P | 87_S | 1.369 | 0.77 |
| 93_G | 99_T | 1.354 | 0.76 |
| 150_W | 268_P | 1.351 | 0.76 |
| 75_N | 106_S | 1.350 | 0.76 |
| 106_S | 117_V | 1.345 | 0.75 |
| 13_S | 17_D | 1.345 | 0.75 |
| 99_T | 120_A | 1.331 | 0.74 |
| 39_T | 169_R | 1.330 | 0.74 |
| 151_E | 204_R | 1.330 | 0.74 |
| 6_L | 9_V | 1.327 | 0.74 |
| 160_K | 246_E | 1.320 | 0.73 |
| 31_L | 277_G | 1.317 | 0.73 |
| 245_P | 248_I | 1.312 | 0.73 |
| 116_I | 134_I | 1.306 | 0.72 |
| 87_S | 227_F | 1.305 | 0.72 |
| 157_N | 246_E | 1.289 | 0.71 |
| 115_D | 133_H | 1.288 | 0.71 |
| 209_V | 221_V | 1.285 | 0.70 |
| 175_G | 201_Y | 1.281 | 0.70 |
| 25_Y | 207_M | 1.277 | 0.70 |
| 242_S | 247_N | 1.248 | 0.67 |
| 9_V | 13_S | 1.244 | 0.67 |
| 35_D | 58_K | 1.240 | 0.66 |
| 210_V | 220_Y | 1.229 | 0.65 |
| 57_S | 63_T | 1.224 | 0.65 |
| 41_E | 82_Q | 1.221 | 0.65 |
| 26_P | 332_N | 1.219 | 0.64 |
| 105_S | 117_V | 1.212 | 0.64 |
| 100_L | 247_N | 1.212 | 0.64 |
| 129_D | 323_E | 1.212 | 0.64 |
| 90_E | 156_A | 1.205 | 0.63 |
| 178_M | 196_V | 1.202 | 0.63 |
| 310_E | 313_G | 1.199 | 0.63 |
| 105_S | 114_T | 1.196 | 0.62 |
| 241_L | 248_I | 1.178 | 0.60 |
| 274_P | 323_E | 1.177 | 0.60 |
| 7_T | 12_F | 1.176 | 0.60 |
| 67_I | 126_M | 1.175 | 0.60 |
| 119_Y | 181_Q | 1.175 | 0.60 |
| 24_L | 41_E | 1.173 | 0.60 |
| 59_D | 63_T | 1.171 | 0.60 |
| 92_V | 156_A | 1.160 | 0.59 |
| 10_T | 13_S | 1.156 | 0.58 |
| 18_Y | 102_L | 1.155 | 0.58 |
| 143_N | 174_Y | 1.145 | 0.57 |
| 208_P | 220_Y | 1.145 | 0.57 |
| 123_D | 303_W | 1.142 | 0.57 |
| 166_S | 208_P | 1.140 | 0.57 |
| 93_G | 156_A | 1.137 | 0.56 |
| 213_L | 219_F | 1.133 | 0.56 |
| 242_S | 245_P | 1.126 | 0.55 |
| 96_K | 257_V | 1.122 | 0.55 |
| 20_V | 338_L | 1.119 | 0.55 |
| 223_E | 314_Y | 1.113 | 0.54 |
| 46_E | 50_V | 1.108 | 0.54 |
| 101_L | 118_L | 1.106 | 0.53 |
| 334_A | 344_V | 1.102 | 0.53 |
| 343_R | 350_D | 1.102 | 0.53 |
| 27_R | 151_E | 1.098 | 0.53 |
| 168_Q | 201_Y | 1.098 | 0.53 |
| 120_A | 248_I | 1.097 | 0.52 |
| 34_G | 159_G | 1.096 | 0.52 |
| 64_W | 189_W | 1.094 | 0.52 |
| 39_T | 52_F | 1.090 | 0.52 |
| 330_V | 334_A | 1.090 | 0.52 |
| 239_Y | 248_I | 1.087 | 0.51 |
| 41_E | 81_Y | 1.086 | 0.51 |
| 10_T | 254_Q | 1.085 | 0.51 |
| 207_M | 314_Y | 1.085 | 0.51 |
| 120_A | 131_V | 1.084 | 0.51 |
| 142_P | 337_L | 1.081 | 0.51 |
| 54_I | 85_L | 1.080 | 0.51 |
| 31_L | 34_G | 1.079 | 0.51 |
| 206_G | 223_E | 1.079 | 0.51 |
| 38_A | 303_W | 1.078 | 0.50 |
| 8_N | 254_Q | 1.072 | 0.50 |
| 13_S | 16_S | 1.062 | 0.49 |
| 151_E | 207_M | 1.058 | 0.48 |
| 295_N | 299_G | 1.057 | 0.48 |
| 20_V | 23_T | 1.056 | 0.48 |
| 70_V | 314_Y | 1.054 | 0.48 |
| 217_Q | 320_V | 1.052 | 0.48 |
| 165_Y | 203_D | 1.051 | 0.48 |
| 77_Y | 113_S | 1.048 | 0.47 |
| 343_R | 346_V | 1.048 | 0.47 |
| 41_E | 83_P | 1.045 | 0.47 |
| 44_S | 48_P | 1.045 | 0.47 |
| 10_T | 311_E | 1.040 | 0.47 |
| 335_G | 342_N | 1.039 | 0.46 |
| 52_F | 83_P | 1.033 | 0.46 |
| 10_T | 323_E | 1.030 | 0.46 |
| 21_P | 140_A | 1.028 | 0.45 |
| 128_W | 303_W | 1.027 | 0.45 |
| 138_G | 148_P | 1.026 | 0.45 |
| 32_P | 124_D | 1.026 | 0.45 |
| 341_N | 345_S | 1.026 | 0.45 |
| 31_L | 351_L | 1.026 | 0.45 |
| 17_D | 172_A | 1.023 | 0.45 |
| 167_D | 206_G | 1.023 | 0.45 |
| 214_P | 280_G | 1.023 | 0.45 |
| 286_S | 312_H | 1.023 | 0.45 |
| 41_E | 152_P | 1.023 | 0.45 |
| 242_S | 320_V | 1.023 | 0.45 |
| 215_N | 279_N | 1.022 | 0.45 |
| 14_P | 17_D | 1.022 | 0.45 |
| 170_D | 239_Y | 1.021 | 0.45 |
| 81_Y | 107_I | 1.021 | 0.45 |
| 155_L | 218_Y | 1.021 | 0.45 |
| 118_L | 280_G | 1.019 | 0.44 |
| 245_P | 316_R | 1.018 | 0.44 |
| 63_T | 247_N | 1.018 | 0.44 |
| 78_G | 104_G | 1.017 | 0.44 |
| 338_L | 341_N | 1.016 | 0.44 |
| 134_I | 280_G | 1.015 | 0.44 |
| 326_G | 331_V | 1.011 | 0.44 |
| 70_V | 162_I | 1.010 | 0.44 |
| 204_R | 222_Y | 1.009 | 0.43 |
| 156_A | 161_L | 1.007 | 0.43 |
| 24_L | 50_V | 1.006 | 0.43 |
| 108_P | 112_S | 1.005 | 0.43 |
| 91_R | 94_S | 1.003 | 0.43 |
| 13_S | 91_R | 1.003 | 0.43 |
| 25_Y | 223_E | 1.002 | 0.43 |
| 24_L | 43_Y | 1.001 | 0.43 |
| 143_N | 146_L | 1.001 | 0.43 |
| 74_V | 331_V | 1.000 | 0.43 |
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 | |
| 2ydtA | 1 | 0.9887 | 100 | 0.343 | Contact Map |
| 3a72A | 1 | 0.9915 | 100 | 0.353 | Contact Map |
| 2bf6A | 1 | 0.9014 | 100 | 0.548 | Contact Map |
| 2w20A | 2 | 0.907 | 100 | 0.555 | Contact Map |
| 4fj6A | 4 | 0.893 | 100 | 0.563 | Contact Map |
| 4q6kA | 4 | 0.8789 | 100 | 0.568 | Contact Map |
| 1w8oA | 1 | 0.8901 | 100 | 0.568 | Contact Map |
| 4x4aA | 1 | 0 | 100 | 0.57 | Contact Map |
| 2xziA | 2 | 0.8648 | 100 | 0.572 | Contact Map |
| 4j9tA | 1 | 0.8732 | 100 | 0.575 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)