| ChiAtFragments |
| ID: | 1476387493 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 308 (265) | ||
| Sequences: | 379 (181.4) | ||
| Seq/Len: | 1.430 | ||
| Nf(neff/√len): | 11.1 |
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: 1.430).
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 |
| 290_D | 296_Y | 3.290 | 1.00 |
| 128_A | 257_F | 2.926 | 1.00 |
| 74_S | 98_D | 2.439 | 1.00 |
| 164_V | 187_Y | 2.439 | 1.00 |
| 83_H | 88_A | 2.321 | 0.99 |
| 186_S | 230_P | 2.248 | 0.99 |
| 236_D | 241_Q | 2.204 | 0.99 |
| 163_C | 171_C | 1.883 | 0.96 |
| 123_I | 221_L | 1.865 | 0.96 |
| 169_W | 193_P | 1.837 | 0.96 |
| 130_T | 150_Y | 1.761 | 0.94 |
| 27_Y | 35_C | 1.744 | 0.94 |
| 14_A | 35_C | 1.739 | 0.94 |
| 286_K | 296_Y | 1.699 | 0.93 |
| 268_V | 277_R | 1.698 | 0.93 |
| 272_H | 277_R | 1.674 | 0.92 |
| 202_L | 208_L | 1.650 | 0.91 |
| 194_C | 219_T | 1.617 | 0.90 |
| 27_Y | 34_Y | 1.577 | 0.89 |
| 73_S | 250_A | 1.571 | 0.89 |
| 91_A | 153_L | 1.554 | 0.88 |
| 121_R | 296_Y | 1.554 | 0.88 |
| 144_G | 148_W | 1.539 | 0.87 |
| 141_A | 144_G | 1.523 | 0.86 |
| 14_A | 27_Y | 1.520 | 0.86 |
| 123_I | 250_A | 1.506 | 0.86 |
| 80_I | 291_I | 1.489 | 0.85 |
| 74_S | 78_D | 1.483 | 0.84 |
| 81_L | 150_Y | 1.472 | 0.84 |
| 48_S | 60_G | 1.461 | 0.83 |
| 269_E | 281_R | 1.445 | 0.82 |
| 13_G | 35_C | 1.443 | 0.82 |
| 228_Q | 231_K | 1.431 | 0.81 |
| 286_K | 290_D | 1.414 | 0.80 |
| 102_A | 214_T | 1.410 | 0.80 |
| 202_L | 255_P | 1.408 | 0.80 |
| 259_V | 308_F | 1.402 | 0.79 |
| 133_E | 269_E | 1.402 | 0.79 |
| 82_L | 91_A | 1.392 | 0.79 |
| 192_G | 285_Y | 1.381 | 0.78 |
| 270_C | 302_C | 1.379 | 0.78 |
| 175_K | 207_D | 1.378 | 0.78 |
| 4_A | 7_C | 1.367 | 0.77 |
| 201_D | 204_N | 1.363 | 0.77 |
| 217_F | 224_W | 1.361 | 0.77 |
| 186_S | 203_L | 1.348 | 0.76 |
| 48_S | 61_G | 1.342 | 0.75 |
| 127_L | 243_T | 1.341 | 0.75 |
| 14_A | 34_Y | 1.323 | 0.74 |
| 109_G | 112_T | 1.304 | 0.72 |
| 262_N | 305_Q | 1.304 | 0.72 |
| 13_G | 27_Y | 1.303 | 0.72 |
| 110_F | 235_H | 1.300 | 0.72 |
| 169_W | 187_Y | 1.295 | 0.71 |
| 169_W | 192_G | 1.294 | 0.71 |
| 137_G | 141_A | 1.288 | 0.71 |
| 104_A | 201_D | 1.286 | 0.71 |
| 123_I | 215_V | 1.283 | 0.70 |
| 122_E | 235_H | 1.268 | 0.69 |
| 113_T | 189_Y | 1.264 | 0.69 |
| 186_S | 193_P | 1.263 | 0.69 |
| 68_V | 194_C | 1.243 | 0.67 |
| 5_Q | 27_Y | 1.241 | 0.67 |
| 211_S | 295_S | 1.240 | 0.67 |
| 199_G | 210_A | 1.237 | 0.66 |
| 137_G | 144_G | 1.235 | 0.66 |
| 187_Y | 230_P | 1.227 | 0.65 |
| 138_W | 142_P | 1.217 | 0.64 |
| 129_Q | 135_T | 1.203 | 0.63 |
| 261_T | 267_G | 1.200 | 0.63 |
| 131_S | 288_Y | 1.195 | 0.62 |
| 5_Q | 11_A | 1.195 | 0.62 |
| 107_F | 169_W | 1.184 | 0.61 |
| 169_W | 194_C | 1.177 | 0.61 |
| 215_V | 219_T | 1.173 | 0.60 |
| 139_P | 173_P | 1.163 | 0.59 |
| 265_N | 269_E | 1.158 | 0.59 |
| 4_A | 8_G | 1.156 | 0.59 |
| 13_G | 34_Y | 1.149 | 0.58 |
| 117_D | 121_R | 1.146 | 0.58 |
| 101_V | 111_A | 1.144 | 0.57 |
| 179_G | 269_E | 1.139 | 0.57 |
| 138_W | 141_A | 1.134 | 0.56 |
| 60_G | 63_G | 1.128 | 0.56 |
| 244_P | 248_D | 1.126 | 0.56 |
| 133_E | 179_G | 1.124 | 0.55 |
| 257_F | 303_G | 1.122 | 0.55 |
| 68_V | 215_V | 1.120 | 0.55 |
| 68_V | 104_A | 1.117 | 0.55 |
| 115_D | 118_T | 1.115 | 0.54 |
| 122_E | 126_F | 1.106 | 0.54 |
| 75_S | 78_D | 1.104 | 0.53 |
| 223_F | 264_I | 1.102 | 0.53 |
| 238_I | 260_I | 1.101 | 0.53 |
| 133_E | 281_R | 1.096 | 0.53 |
| 236_D | 298_D | 1.095 | 0.52 |
| 187_Y | 260_I | 1.087 | 0.52 |
| 224_W | 235_H | 1.085 | 0.51 |
| 181_G | 191_Y | 1.085 | 0.51 |
| 72_I | 123_I | 1.081 | 0.51 |
| 284_F | 293_G | 1.078 | 0.51 |
| 230_P | 234_C | 1.072 | 0.50 |
| 256_G | 266_G | 1.069 | 0.50 |
| 154_Q | 176_K | 1.069 | 0.50 |
| 264_I | 269_E | 1.069 | 0.50 |
| 106_A | 218_K | 1.067 | 0.50 |
| 231_K | 265_N | 1.067 | 0.50 |
| 198_I | 216_S | 1.066 | 0.49 |
| 279_E | 303_G | 1.065 | 0.49 |
| 5_Q | 8_G | 1.065 | 0.49 |
| 59_G | 63_G | 1.060 | 0.49 |
| 91_A | 123_I | 1.058 | 0.49 |
| 107_F | 164_V | 1.055 | 0.48 |
| 152_F | 276_S | 1.054 | 0.48 |
| 96_T | 261_T | 1.053 | 0.48 |
| 148_W | 151_C | 1.053 | 0.48 |
| 180_R | 191_Y | 1.049 | 0.48 |
| 92_H | 230_P | 1.040 | 0.47 |
| 5_Q | 246_A | 1.038 | 0.47 |
| 6_Q | 11_A | 1.034 | 0.46 |
| 98_D | 238_I | 1.029 | 0.46 |
| 183_I | 219_T | 1.028 | 0.46 |
| 275_D | 280_D | 1.026 | 0.45 |
| 194_C | 215_V | 1.019 | 0.45 |
| 5_Q | 10_Q | 1.014 | 0.44 |
| 126_F | 148_W | 1.011 | 0.44 |
| 302_C | 305_Q | 1.007 | 0.43 |
| 110_F | 122_E | 1.007 | 0.43 |
| 248_D | 302_C | 1.007 | 0.43 |
| 82_L | 204_N | 1.004 | 0.43 |
| 91_A | 98_D | 1.004 | 0.43 |
| 108_S | 117_D | 1.003 | 0.43 |
| 71_I | 250_A | 1.002 | 0.43 |
| 154_Q | 238_I | 1.000 | 0.43 |
| 48_S | 59_G | 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 | |
| 2dkvA | 1 | 0.9253 | 100 | 0.249 | Contact Map |
| 3cqlA | 2 | 0.7857 | 100 | 0.361 | Contact Map |
| 2z37A | 4 | 0.7857 | 100 | 0.362 | Contact Map |
| 3w3eA | 2 | 0.7825 | 100 | 0.367 | Contact Map |
| 3hbeX | 1 | 0.6623 | 100 | 0.515 | Contact Map |
| 2cjlA | 2 | 0.6494 | 100 | 0.521 | Contact Map |
| 1wvvA | 2 | 0.7597 | 100 | 0.527 | Contact Map |
| 4mckA | 1 | 0.6364 | 100 | 0.531 | Contact Map |
| 3wh1A | 1 | 0.6429 | 100 | 0.54 | Contact Map |
| 4ok7A | 3 | 0.6299 | 100 | 0.713 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)