| 1a5c |
| ID: | 1428507084 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 342 (336) | ||
| Sequences: | 442 (259.8) | ||
| Seq/Len: | 1.315 | ||
| Nf(neff/√len): | 14.2 |
HHblits Results: (2013_03)
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: 1.315).
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 |
| 54_D | 81_E | 3.278 | 1.00 |
| 84_V | 92_N | 3.257 | 1.00 |
| 62_L | 321_L | 2.982 | 1.00 |
| 131_Y | 136_R | 2.870 | 1.00 |
| 208_F | 221_A | 2.801 | 1.00 |
| 263_V | 292_T | 2.644 | 1.00 |
| 122_G | 125_E | 2.504 | 1.00 |
| 80_N | 84_V | 2.414 | 0.99 |
| 271_E | 302_S | 2.374 | 0.99 |
| 88_N | 92_N | 2.257 | 0.99 |
| 73_E | 77_F | 2.252 | 0.99 |
| 63_G | 93_E | 2.083 | 0.98 |
| 209_K | 213_E | 2.047 | 0.98 |
| 77_F | 133_A | 2.025 | 0.98 |
| 73_E | 76_L | 2.025 | 0.98 |
| 77_F | 129_E | 2.018 | 0.98 |
| 138_A | 172_C | 1.965 | 0.97 |
| 12_T | 136_R | 1.953 | 0.97 |
| 162_A | 207_V | 1.932 | 0.97 |
| 15_K | 96_I | 1.913 | 0.96 |
| 16_L | 222_L | 1.847 | 0.95 |
| 73_E | 129_E | 1.824 | 0.95 |
| 193_I | 246_L | 1.797 | 0.94 |
| 219_E | 253_R | 1.793 | 0.94 |
| 142_T | 164_G | 1.769 | 0.94 |
| 90_L | 95_I | 1.758 | 0.93 |
| 315_A | 319_E | 1.756 | 0.93 |
| 323_Q | 327_A | 1.735 | 0.93 |
| 219_E | 258_A | 1.729 | 0.93 |
| 253_R | 258_A | 1.724 | 0.92 |
| 57_F | 90_L | 1.721 | 0.92 |
| 259_L | 262_V | 1.691 | 0.92 |
| 73_E | 133_A | 1.682 | 0.91 |
| 26_A | 57_F | 1.653 | 0.90 |
| 324_R | 336_Y | 1.649 | 0.90 |
| 65_F | 329_S | 1.649 | 0.90 |
| 158_I | 206_C | 1.647 | 0.90 |
| 62_L | 95_I | 1.625 | 0.89 |
| 10_A | 217_L | 1.622 | 0.89 |
| 303_V | 321_L | 1.618 | 0.89 |
| 34_K | 44_N | 1.599 | 0.88 |
| 124_A | 174_Q | 1.595 | 0.88 |
| 26_A | 69_A | 1.593 | 0.88 |
| 88_N | 91_H | 1.583 | 0.88 |
| 129_E | 133_A | 1.564 | 0.87 |
| 201_Q | 253_R | 1.558 | 0.86 |
| 18_Q | 21_K | 1.549 | 0.86 |
| 200_T | 226_N | 1.544 | 0.86 |
| 240_T | 277_N | 1.520 | 0.84 |
| 240_T | 243_V | 1.517 | 0.84 |
| 58_G | 86_M | 1.512 | 0.84 |
| 85_P | 88_N | 1.482 | 0.82 |
| 269_Q | 277_N | 1.473 | 0.82 |
| 192_S | 195_V | 1.466 | 0.81 |
| 241_Q | 279_N | 1.461 | 0.81 |
| 143_V | 184_E | 1.449 | 0.80 |
| 230_A | 238_T | 1.428 | 0.79 |
| 30_T | 33_I | 1.391 | 0.77 |
| 313_N | 317_A | 1.370 | 0.75 |
| 50_A | 86_M | 1.369 | 0.75 |
| 32_T | 36_R | 1.359 | 0.74 |
| 279_N | 283_A | 1.355 | 0.74 |
| 239_T | 242_D | 1.348 | 0.73 |
| 54_D | 86_M | 1.337 | 0.72 |
| 205_S | 209_K | 1.333 | 0.72 |
| 43_E | 48_N | 1.332 | 0.72 |
| 34_K | 38_D | 1.327 | 0.72 |
| 33_I | 37_F | 1.322 | 0.71 |
| 106_V | 118_Q | 1.322 | 0.71 |
| 158_I | 202_K | 1.316 | 0.71 |
| 296_G | 299_L | 1.306 | 0.70 |
| 76_L | 135_A | 1.296 | 0.69 |
| 55_L | 322_L | 1.289 | 0.68 |
| 51_S | 311_K | 1.278 | 0.67 |
| 44_N | 48_N | 1.274 | 0.67 |
| 147_D | 152_K | 1.271 | 0.67 |
| 58_G | 80_N | 1.259 | 0.66 |
| 109_P | 174_Q | 1.256 | 0.66 |
| 42_L | 306_T | 1.253 | 0.65 |
| 163_W | 214_N | 1.244 | 0.64 |
| 192_S | 234_C | 1.242 | 0.64 |
| 316_K | 320_V | 1.240 | 0.64 |
| 327_A | 330_L | 1.227 | 0.63 |
| 11_T | 15_K | 1.225 | 0.63 |
| 280_S | 283_A | 1.222 | 0.62 |
| 23_I | 229_T | 1.221 | 0.62 |
| 69_A | 90_L | 1.217 | 0.62 |
| 89_L | 203_V | 1.217 | 0.62 |
| 127_C | 172_C | 1.207 | 0.61 |
| 67_S | 97_P | 1.206 | 0.61 |
| 222_L | 263_V | 1.200 | 0.60 |
| 275_S | 328_N | 1.194 | 0.60 |
| 208_F | 255_V | 1.183 | 0.59 |
| 255_V | 262_V | 1.176 | 0.58 |
| 201_Q | 219_E | 1.174 | 0.58 |
| 291_L | 296_G | 1.174 | 0.58 |
| 221_A | 259_L | 1.166 | 0.57 |
| 80_N | 89_L | 1.164 | 0.57 |
| 48_N | 56_L | 1.164 | 0.57 |
| 17_V | 261_G | 1.160 | 0.56 |
| 118_Q | 124_A | 1.147 | 0.55 |
| 260_P | 290_A | 1.144 | 0.55 |
| 187_A | 296_G | 1.141 | 0.55 |
| 80_N | 92_N | 1.134 | 0.54 |
| 306_T | 317_A | 1.134 | 0.54 |
| 30_T | 72_F | 1.132 | 0.54 |
| 302_S | 306_T | 1.129 | 0.53 |
| 248_V | 287_H | 1.129 | 0.53 |
| 71_L | 90_L | 1.129 | 0.53 |
| 158_I | 203_V | 1.129 | 0.53 |
| 207_V | 303_V | 1.127 | 0.53 |
| 196_C | 200_T | 1.127 | 0.53 |
| 197_A | 250_T | 1.121 | 0.53 |
| 111_T | 156_L | 1.119 | 0.52 |
| 132_K | 192_S | 1.119 | 0.52 |
| 7_E | 11_T | 1.110 | 0.51 |
| 67_S | 96_I | 1.101 | 0.51 |
| 90_L | 93_E | 1.101 | 0.51 |
| 55_L | 58_G | 1.100 | 0.50 |
| 273_E | 277_N | 1.099 | 0.50 |
| 281_I | 320_V | 1.098 | 0.50 |
| 270_S | 273_E | 1.093 | 0.50 |
| 105_L | 115_K | 1.089 | 0.49 |
| 218_L | 291_L | 1.088 | 0.49 |
| 204_L | 254_T | 1.082 | 0.49 |
| 44_N | 302_S | 1.082 | 0.49 |
| 29_S | 184_E | 1.078 | 0.48 |
| 47_E | 50_A | 1.071 | 0.48 |
| 26_A | 33_I | 1.070 | 0.47 |
| 252_R | 287_H | 1.064 | 0.47 |
| 149_A | 152_K | 1.062 | 0.47 |
| 109_P | 170_S | 1.060 | 0.46 |
| 101_V | 130_Y | 1.059 | 0.46 |
| 154_T | 319_E | 1.059 | 0.46 |
| 128_K | 132_K | 1.055 | 0.46 |
| 76_L | 133_A | 1.046 | 0.45 |
| 156_L | 214_N | 1.046 | 0.45 |
| 17_V | 263_V | 1.045 | 0.45 |
| 55_L | 162_A | 1.042 | 0.45 |
| 99_I | 184_E | 1.039 | 0.44 |
| 243_V | 277_N | 1.037 | 0.44 |
| 20_G | 56_L | 1.036 | 0.44 |
| 55_L | 230_A | 1.034 | 0.44 |
| 124_A | 175_N | 1.030 | 0.44 |
| 56_L | 299_L | 1.025 | 0.43 |
| 121_D | 167_R | 1.019 | 0.42 |
| 205_S | 212_Q | 1.019 | 0.42 |
| 116_S | 127_C | 1.017 | 0.42 |
| 51_S | 314_V | 1.011 | 0.42 |
| 16_L | 23_I | 1.011 | 0.42 |
| 12_T | 96_I | 1.009 | 0.41 |
| 155_D | 202_K | 1.005 | 0.41 |
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 | |
| 2pc4A | 4 | 1 | 100 | 0.069 | Contact Map |
| 4d2jA | 1 | 0.9883 | 100 | 0.07 | Contact Map |
| 3kx6A | 4 | 0.9854 | 100 | 0.072 | Contact Map |
| 2qapA | 4 | 0.9942 | 100 | 0.086 | Contact Map |
| 3mbdA | 1 | 0.9795 | 100 | 0.088 | Contact Map |
| 3mmtA | 4 | 0.9854 | 100 | 0.091 | Contact Map |
| 3bv4A | 1 | 0.9825 | 100 | 0.093 | Contact Map |
| 2iqtA | 1 | 0.8246 | 100 | 0.351 | Contact Map |
| 3iv3A | 1 | 0.8713 | 93.7 | 0.964 | Contact Map |
| 1to3A | 1 | 0.8012 | 92.8 | 0.965 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)