| 10seq_mg |
| ID: | 1432806378 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 306 (306) | ||
| Sequences: | 5824 (3585.2) | ||
| Seq/Len: | 19.033 | ||
| Nf(neff/√len): | 205.0 |
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: 19.033).
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 |
| 286_K | 289_E | 5.265 | 1.00 |
| 49_A | 79_G | 4.385 | 1.00 |
| 13_D | 61_K | 3.311 | 1.00 |
| 300_R | 303_D | 3.238 | 1.00 |
| 299_T | 303_D | 2.934 | 1.00 |
| 58_L | 219_F | 2.713 | 1.00 |
| 14_H | 38_R | 2.703 | 1.00 |
| 62_V | 144_Y | 2.614 | 1.00 |
| 67_G | 76_L | 2.573 | 1.00 |
| 212_G | 226_T | 2.425 | 1.00 |
| 234_A | 291_L | 2.417 | 1.00 |
| 162_E | 305_T | 2.384 | 1.00 |
| 135_V | 152_V | 2.343 | 1.00 |
| 91_V | 140_I | 2.264 | 1.00 |
| 283_D | 286_K | 2.246 | 1.00 |
| 42_V | 48_G | 2.237 | 1.00 |
| 287_V | 290_A | 2.215 | 1.00 |
| 80_L | 92_A | 2.178 | 1.00 |
| 233_F | 237_M | 2.163 | 1.00 |
| 74_T | 78_N | 2.148 | 1.00 |
| 114_P | 117_A | 2.125 | 1.00 |
| 94_L | 151_V | 2.116 | 1.00 |
| 53_A | 57_K | 2.059 | 1.00 |
| 111_N | 114_P | 2.049 | 1.00 |
| 207_N | 211_G | 2.014 | 1.00 |
| 244_V | 293_A | 1.999 | 1.00 |
| 285_G | 295_G | 1.987 | 1.00 |
| 176_D | 228_S | 1.978 | 1.00 |
| 216_Q | 249_P | 1.912 | 1.00 |
| 1_V | 29_A | 1.886 | 1.00 |
| 162_E | 165_R | 1.877 | 1.00 |
| 17_G | 39_Y | 1.846 | 1.00 |
| 165_R | 305_T | 1.842 | 1.00 |
| 62_V | 91_V | 1.834 | 1.00 |
| 219_F | 222_R | 1.816 | 1.00 |
| 243_Q | 293_A | 1.794 | 1.00 |
| 168_E | 171_A | 1.779 | 1.00 |
| 5_K | 9_A | 1.766 | 1.00 |
| 164_N | 189_D | 1.765 | 1.00 |
| 27_M | 39_Y | 1.732 | 1.00 |
| 5_K | 8_E | 1.718 | 1.00 |
| 59_T | 218_S | 1.710 | 1.00 |
| 10_W | 137_D | 1.690 | 1.00 |
| 3_M | 136_V | 1.682 | 1.00 |
| 6_V | 137_D | 1.673 | 1.00 |
| 240_I | 293_A | 1.653 | 1.00 |
| 172_I | 215_A | 1.638 | 1.00 |
| 42_V | 51_A | 1.634 | 1.00 |
| 285_G | 297_T | 1.625 | 1.00 |
| 8_E | 33_E | 1.615 | 1.00 |
| 205_M | 235_M | 1.612 | 1.00 |
| 216_Q | 223_Q | 1.607 | 1.00 |
| 40_I | 217_L | 1.599 | 1.00 |
| 289_E | 294_K | 1.589 | 1.00 |
| 128_S | 131_S | 1.576 | 1.00 |
| 237_M | 287_V | 1.575 | 1.00 |
| 1_V | 32_Q | 1.563 | 1.00 |
| 76_L | 92_A | 1.561 | 1.00 |
| 73_A | 94_L | 1.542 | 1.00 |
| 197_T | 215_A | 1.541 | 1.00 |
| 47_A | 239_D | 1.538 | 1.00 |
| 120_S | 151_V | 1.538 | 1.00 |
| 16_Y | 55_D | 1.518 | 1.00 |
| 8_E | 36_S | 1.517 | 1.00 |
| 121_I | 148_G | 1.516 | 1.00 |
| 216_Q | 248_L | 1.509 | 1.00 |
| 53_A | 82_D | 1.485 | 1.00 |
| 10_W | 140_I | 1.482 | 1.00 |
| 93_L | 154_I | 1.478 | 1.00 |
| 195_R | 222_R | 1.476 | 1.00 |
| 38_R | 246_Y | 1.472 | 1.00 |
| 176_D | 232_G | 1.471 | 1.00 |
| 213_I | 243_Q | 1.465 | 1.00 |
| 14_H | 217_L | 1.457 | 1.00 |
| 49_A | 76_L | 1.454 | 1.00 |
| 134_H | 138_E | 1.451 | 1.00 |
| 124_R | 152_V | 1.430 | 1.00 |
| 303_D | 306_P | 1.427 | 1.00 |
| 54_A | 58_L | 1.420 | 1.00 |
| 168_E | 223_Q | 1.405 | 0.99 |
| 65_V | 76_L | 1.403 | 0.99 |
| 166_I | 305_T | 1.398 | 0.99 |
| 80_L | 90_V | 1.388 | 0.99 |
| 131_S | 134_H | 1.379 | 0.99 |
| 226_T | 252_N | 1.364 | 0.99 |
| 91_V | 143_A | 1.357 | 0.99 |
| 126_V | 132_L | 1.356 | 0.99 |
| 241_L | 245_K | 1.346 | 0.99 |
| 142_A | 150_A | 1.331 | 0.99 |
| 288_G | 295_G | 1.322 | 0.99 |
| 55_D | 218_S | 1.309 | 0.99 |
| 171_A | 223_Q | 1.305 | 0.99 |
| 243_Q | 250_I | 1.305 | 0.99 |
| 47_A | 236_Q | 1.286 | 0.99 |
| 1_V | 5_K | 1.282 | 0.99 |
| 56_A | 89_P | 1.277 | 0.99 |
| 120_S | 123_N | 1.268 | 0.99 |
| 285_G | 289_E | 1.260 | 0.99 |
| 124_R | 135_V | 1.248 | 0.99 |
| 67_G | 92_A | 1.239 | 0.98 |
| 77_I | 115_M | 1.237 | 0.98 |
| 3_M | 154_I | 1.226 | 0.98 |
| 2_A | 133_P | 1.216 | 0.98 |
| 288_G | 293_A | 1.215 | 0.98 |
| 124_R | 138_E | 1.213 | 0.98 |
| 23_F | 26_T | 1.209 | 0.98 |
| 217_L | 248_L | 1.206 | 0.98 |
| 163_I | 227_L | 1.205 | 0.98 |
| 6_V | 136_V | 1.203 | 0.98 |
| 115_M | 119_V | 1.196 | 0.98 |
| 143_A | 150_A | 1.189 | 0.98 |
| 81_Y | 202_F | 1.182 | 0.98 |
| 231_G | 260_F | 1.179 | 0.98 |
| 15_I | 30_L | 1.169 | 0.97 |
| 58_L | 215_A | 1.168 | 0.97 |
| 53_A | 88_V | 1.166 | 0.97 |
| 12_I | 64_A | 1.165 | 0.97 |
| 223_Q | 251_I | 1.163 | 0.97 |
| 237_M | 291_L | 1.159 | 0.97 |
| 49_A | 65_V | 1.156 | 0.97 |
| 84_Q | 149_V | 1.155 | 0.97 |
| 13_D | 38_R | 1.154 | 0.97 |
| 298_I | 303_D | 1.153 | 0.97 |
| 74_T | 115_M | 1.152 | 0.97 |
| 298_I | 304_L | 1.150 | 0.97 |
| 227_L | 255_F | 1.139 | 0.97 |
| 40_I | 246_Y | 1.128 | 0.97 |
| 254_V | 284_F | 1.123 | 0.97 |
| 80_L | 116_F | 1.120 | 0.96 |
| 216_Q | 221_D | 1.117 | 0.96 |
| 113_N | 123_N | 1.100 | 0.96 |
| 122_Y | 135_V | 1.100 | 0.96 |
| 136_V | 152_V | 1.097 | 0.96 |
| 253_I | 304_L | 1.096 | 0.96 |
| 172_I | 219_F | 1.084 | 0.96 |
| 286_K | 290_A | 1.079 | 0.95 |
| 62_V | 140_I | 1.078 | 0.95 |
| 8_E | 34_R | 1.078 | 0.95 |
| 208_G | 226_T | 1.075 | 0.95 |
| 6_V | 10_W | 1.065 | 0.95 |
| 167_A | 225_F | 1.061 | 0.95 |
| 216_Q | 220_P | 1.050 | 0.94 |
| 162_E | 166_I | 1.048 | 0.94 |
| 209_V | 252_N | 1.034 | 0.94 |
| 33_E | 36_S | 1.033 | 0.94 |
| 287_V | 291_L | 1.031 | 0.94 |
| 8_E | 13_D | 1.030 | 0.94 |
| 175_S | 198_T | 1.028 | 0.94 |
| 192_G | 195_R | 1.008 | 0.93 |
| 174_V | 224_V | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1ozhA | 4 | 0.9804 | 100 | 0.186 | Contact Map |
| 3eyaA | 12 | 0.9608 | 100 | 0.193 | Contact Map |
| 1ybhA | 1 | 0.9967 | 100 | 0.195 | Contact Map |
| 1v5eA | 1 | 1 | 100 | 0.196 | Contact Map |
| 4rjjA | 8 | 0.9935 | 100 | 0.196 | Contact Map |
| 1t9bA | 2 | 0.9967 | 100 | 0.198 | Contact Map |
| 2panA | 6 | 0.9967 | 100 | 0.202 | Contact Map |
| 4kgdA | 2 | 1 | 100 | 0.206 | Contact Map |
| 2ihtA | 4 | 0.9869 | 100 | 0.208 | Contact Map |
| 1q6zA | 1 | 0.9869 | 100 | 0.212 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)