| PDC1 |
| ID: | 1489526572 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 371 (322) | ||
| Sequences: | 4400 (2244.9) | ||
| Seq/Len: | 13.665 | ||
| Nf(neff/√len): | 125.1 |
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: 13.665).
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 |
| 35_A | 57_G | 7.081 | 1.00 |
| 329_T | 332_K | 7.011 | 1.00 |
| 145_A | 158_K | 4.724 | 1.00 |
| 157_T | 222_K | 3.681 | 1.00 |
| 157_T | 224_K | 3.167 | 1.00 |
| 330_G | 333_D | 2.861 | 1.00 |
| 46_M | 66_V | 2.853 | 1.00 |
| 39_D | 59_G | 2.765 | 1.00 |
| 19_S | 27_W | 2.755 | 1.00 |
| 190_S | 193_A | 2.702 | 1.00 |
| 326_D | 329_T | 2.674 | 1.00 |
| 88_M | 92_S | 2.643 | 1.00 |
| 39_D | 43_R | 2.637 | 1.00 |
| 191_V | 220_V | 2.606 | 1.00 |
| 281_T | 295_V | 2.534 | 1.00 |
| 97_T | 110_V | 2.509 | 1.00 |
| 100_T | 103_D | 2.477 | 1.00 |
| 130_D | 133_K | 2.376 | 1.00 |
| 285_T | 304_M | 2.358 | 1.00 |
| 280_G | 295_V | 2.296 | 1.00 |
| 44_K | 290_A | 2.272 | 1.00 |
| 149_C | 158_K | 2.269 | 1.00 |
| 93_T | 96_M | 2.178 | 1.00 |
| 69_V | 109_Y | 2.177 | 1.00 |
| 66_V | 110_V | 2.094 | 1.00 |
| 150_S | 169_S | 2.058 | 1.00 |
| 136_T | 215_R | 2.019 | 1.00 |
| 137_A | 226_T | 1.998 | 1.00 |
| 246_A | 251_M | 1.989 | 1.00 |
| 208_V | 217_A | 1.970 | 1.00 |
| 191_V | 203_Y | 1.969 | 1.00 |
| 87_R | 90_A | 1.919 | 1.00 |
| 145_A | 149_C | 1.905 | 1.00 |
| 285_T | 303_T | 1.872 | 1.00 |
| 298_G | 315_Y | 1.867 | 1.00 |
| 143_N | 187_S | 1.864 | 1.00 |
| 162_A | 173_Y | 1.863 | 1.00 |
| 129_N | 134_V | 1.844 | 1.00 |
| 54_S | 69_V | 1.831 | 1.00 |
| 68_V | 114_Y | 1.803 | 1.00 |
| 286_G | 290_A | 1.798 | 1.00 |
| 250_W | 254_G | 1.795 | 1.00 |
| 156_A | 160_D | 1.785 | 1.00 |
| 160_D | 227_A | 1.780 | 1.00 |
| 87_R | 91_N | 1.777 | 1.00 |
| 28_A | 306_W | 1.752 | 1.00 |
| 99_A | 104_R | 1.750 | 1.00 |
| 26_R | 306_W | 1.742 | 1.00 |
| 161_T | 174_G | 1.733 | 1.00 |
| 141_A | 189_D | 1.704 | 1.00 |
| 160_D | 231_K | 1.667 | 1.00 |
| 144_V | 190_S | 1.662 | 1.00 |
| 288_A | 294_R | 1.655 | 1.00 |
| 162_A | 167_K | 1.626 | 1.00 |
| 21_K | 24_G | 1.614 | 1.00 |
| 139_K | 231_K | 1.611 | 1.00 |
| 30_N | 34_A | 1.527 | 1.00 |
| 61_Y | 107_T | 1.525 | 1.00 |
| 225_T | 228_D | 1.514 | 1.00 |
| 74_A | 115_G | 1.508 | 1.00 |
| 177_Y | 186_V | 1.505 | 1.00 |
| 115_G | 118_V | 1.496 | 1.00 |
| 219_G | 223_V | 1.495 | 1.00 |
| 300_T | 327_H | 1.486 | 1.00 |
| 74_A | 117_N | 1.484 | 1.00 |
| 209_H | 213_M | 1.479 | 1.00 |
| 66_V | 108_T | 1.471 | 1.00 |
| 35_A | 67_H | 1.466 | 1.00 |
| 101_A | 105_C | 1.465 | 1.00 |
| 63_H | 106_R | 1.432 | 1.00 |
| 39_D | 64_V | 1.408 | 1.00 |
| 30_N | 37_A | 1.399 | 0.99 |
| 157_T | 227_A | 1.396 | 0.99 |
| 129_N | 225_T | 1.377 | 0.99 |
| 144_V | 193_A | 1.361 | 0.99 |
| 18_N | 114_Y | 1.355 | 0.99 |
| 187_S | 237_V | 1.351 | 0.99 |
| 28_A | 289_A | 1.349 | 0.99 |
| 147_A | 165_M | 1.326 | 0.99 |
| 159_K | 170_D | 1.319 | 0.99 |
| 71_V | 111_T | 1.318 | 0.99 |
| 301_V | 304_M | 1.309 | 0.99 |
| 134_V | 225_T | 1.308 | 0.99 |
| 145_A | 162_A | 1.292 | 0.99 |
| 101_A | 104_R | 1.280 | 0.99 |
| 42_A | 286_G | 1.276 | 0.99 |
| 94_T | 106_R | 1.275 | 0.99 |
| 302_S | 325_W | 1.273 | 0.99 |
| 98_D | 111_T | 1.265 | 0.99 |
| 37_A | 304_M | 1.259 | 0.99 |
| 69_V | 86_H | 1.258 | 0.99 |
| 130_D | 216_N | 1.247 | 0.99 |
| 144_V | 163_V | 1.244 | 0.98 |
| 174_G | 185_A | 1.242 | 0.98 |
| 56_N | 279_S | 1.237 | 0.98 |
| 54_S | 86_H | 1.228 | 0.98 |
| 225_T | 229_A | 1.219 | 0.98 |
| 167_K | 273_Y | 1.218 | 0.98 |
| 86_H | 109_Y | 1.205 | 0.98 |
| 133_K | 216_N | 1.202 | 0.98 |
| 259_V | 291_D | 1.198 | 0.98 |
| 22_Y | 25_M | 1.198 | 0.98 |
| 164_T | 268_T | 1.188 | 0.98 |
| 139_K | 228_D | 1.186 | 0.98 |
| 154_V | 157_T | 1.179 | 0.98 |
| 58_A | 92_S | 1.175 | 0.98 |
| 227_A | 231_K | 1.160 | 0.97 |
| 144_V | 161_T | 1.159 | 0.97 |
| 94_T | 108_T | 1.157 | 0.97 |
| 281_T | 304_M | 1.151 | 0.97 |
| 295_V | 299_S | 1.151 | 0.97 |
| 36_Y | 39_D | 1.135 | 0.97 |
| 160_D | 224_K | 1.124 | 0.97 |
| 73_S | 76_K | 1.118 | 0.96 |
| 30_N | 33_N | 1.117 | 0.96 |
| 89_S | 96_M | 1.117 | 0.96 |
| 155_K | 159_K | 1.108 | 0.96 |
| 204_K | 207_N | 1.107 | 0.96 |
| 36_Y | 279_S | 1.101 | 0.96 |
| 139_K | 230_A | 1.094 | 0.96 |
| 219_G | 222_K | 1.092 | 0.96 |
| 13_T | 27_W | 1.088 | 0.96 |
| 285_T | 289_A | 1.074 | 0.95 |
| 13_T | 19_S | 1.069 | 0.95 |
| 224_K | 227_A | 1.067 | 0.95 |
| 40_G | 286_G | 1.066 | 0.95 |
| 149_C | 191_V | 1.054 | 0.95 |
| 149_C | 169_S | 1.051 | 0.94 |
| 256_G | 260_A | 1.050 | 0.94 |
| 300_T | 309_Y | 1.048 | 0.94 |
| 76_K | 211_D | 1.046 | 0.94 |
| 54_S | 89_S | 1.043 | 0.94 |
| 249_K | 270_N | 1.032 | 0.94 |
| 12_N | 15_G | 1.019 | 0.93 |
| 259_V | 287_A | 1.018 | 0.93 |
| 179_G | 182_K | 1.018 | 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 | |
| 2vbfA | 2 | 0.973 | 100 | 0.598 | Contact Map |
| 2panA | 6 | 0.9838 | 100 | 0.599 | Contact Map |
| 2pgnA | 2 | 0.9757 | 100 | 0.601 | Contact Map |
| 2vk8A | 4 | 0.9811 | 100 | 0.605 | Contact Map |
| 1t9bA | 2 | 0.9865 | 100 | 0.606 | Contact Map |
| 4cokA | 2 | 0.9704 | 100 | 0.607 | Contact Map |
| 2nxwA | 2 | 0.9677 | 100 | 0.608 | Contact Map |
| 1ozhA | 4 | 0.973 | 100 | 0.614 | Contact Map |
| 1v5eA | 1 | 0.9784 | 100 | 0.617 | Contact Map |
| 2wvgA | 4 | 0.9838 | 100 | 0.617 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)