| iker2 |
| ID: | 1518192250 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 294 (270) | ||
| Sequences: | 5893 (3929.6) | ||
| Seq/Len: | 21.826 | ||
| Nf(neff/√len): | 239.1 |
Jackhmmer Results: (2016_04)
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: 21.826).
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 |
| 197_H | 202_Y | 3.346 | 1.00 |
| 159_P | 164_A | 3.331 | 1.00 |
| 92_Y | 98_D | 3.198 | 1.00 |
| 277_I | 281_W | 3.144 | 1.00 |
| 210_V | 235_G | 2.962 | 1.00 |
| 92_Y | 95_R | 2.888 | 1.00 |
| 89_D | 92_Y | 2.757 | 1.00 |
| 206_L | 239_F | 2.723 | 1.00 |
| 18_S | 23_A | 2.698 | 1.00 |
| 242_I | 246_F | 2.693 | 1.00 |
| 95_R | 98_D | 2.612 | 1.00 |
| 28_G | 32_L | 2.573 | 1.00 |
| 237_G | 272_I | 2.465 | 1.00 |
| 83_F | 87_M | 2.440 | 1.00 |
| 230_G | 278_M | 2.201 | 1.00 |
| 125_F | 129_S | 2.119 | 1.00 |
| 230_G | 275_G | 2.109 | 1.00 |
| 145_L | 204_L | 2.090 | 1.00 |
| 241_I | 245_F | 2.069 | 1.00 |
| 157_V | 194_L | 2.035 | 1.00 |
| 234_I | 275_G | 2.011 | 1.00 |
| 116_I | 120_R | 2.002 | 1.00 |
| 68_G | 113_V | 1.980 | 1.00 |
| 57_E | 121_T | 1.975 | 1.00 |
| 227_A | 283_Y | 1.952 | 1.00 |
| 72_G | 109_G | 1.924 | 1.00 |
| 234_I | 272_I | 1.919 | 1.00 |
| 47_N | 55_K | 1.898 | 1.00 |
| 85_Q | 89_D | 1.861 | 1.00 |
| 109_G | 113_V | 1.847 | 1.00 |
| 118_A | 128_V | 1.763 | 1.00 |
| 87_M | 90_P | 1.756 | 1.00 |
| 42_A | 135_L | 1.754 | 1.00 |
| 138_F | 211_L | 1.744 | 1.00 |
| 17_F | 24_L | 1.739 | 1.00 |
| 54_T | 57_E | 1.739 | 1.00 |
| 161_F | 164_A | 1.707 | 1.00 |
| 16_I | 29_L | 1.701 | 1.00 |
| 129_S | 229_S | 1.690 | 1.00 |
| 104_H | 264_G | 1.684 | 1.00 |
| 82_N | 85_Q | 1.657 | 1.00 |
| 44_R | 47_N | 1.657 | 1.00 |
| 130_D | 226_G | 1.655 | 1.00 |
| 227_A | 279_M | 1.640 | 1.00 |
| 45_R | 219_I | 1.636 | 1.00 |
| 90_P | 94_F | 1.625 | 1.00 |
| 141_G | 208_G | 1.615 | 1.00 |
| 140_L | 232_F | 1.614 | 1.00 |
| 18_S | 21_P | 1.582 | 1.00 |
| 46_A | 58_V | 1.563 | 1.00 |
| 126_F | 226_G | 1.558 | 1.00 |
| 16_I | 24_L | 1.532 | 1.00 |
| 224_P | 227_A | 1.530 | 1.00 |
| 64_A | 68_G | 1.497 | 1.00 |
| 164_A | 195_P | 1.489 | 1.00 |
| 78_V | 93_L | 1.472 | 1.00 |
| 127_Q | 225_M | 1.471 | 1.00 |
| 154_W | 196_R | 1.464 | 1.00 |
| 14_P | 25_H | 1.461 | 1.00 |
| 68_G | 109_G | 1.453 | 1.00 |
| 85_Q | 92_Y | 1.439 | 1.00 |
| 148_F | 165_M | 1.431 | 1.00 |
| 147_N | 152_E | 1.419 | 1.00 |
| 241_I | 265_Q | 1.407 | 0.99 |
| 124_S | 225_M | 1.401 | 0.99 |
| 30_M | 146_G | 1.392 | 0.99 |
| 117_F | 121_T | 1.386 | 0.99 |
| 245_F | 265_Q | 1.381 | 0.99 |
| 206_L | 243_V | 1.376 | 0.99 |
| 61_L | 128_V | 1.375 | 0.99 |
| 40_W | 44_R | 1.371 | 0.99 |
| 206_L | 210_V | 1.368 | 0.99 |
| 234_I | 276_V | 1.358 | 0.99 |
| 134_P | 137_P | 1.353 | 0.99 |
| 45_R | 48_R | 1.327 | 0.99 |
| 57_E | 123_R | 1.314 | 0.99 |
| 115_I | 119_R | 1.305 | 0.99 |
| 230_G | 282_A | 1.300 | 0.99 |
| 37_F | 142_A | 1.300 | 0.99 |
| 91_L | 94_F | 1.295 | 0.99 |
| 230_G | 279_M | 1.292 | 0.99 |
| 231_L | 279_M | 1.291 | 0.99 |
| 208_G | 212_F | 1.276 | 0.99 |
| 166_L | 195_P | 1.270 | 0.99 |
| 160_N | 164_A | 1.269 | 0.99 |
| 205_L | 209_V | 1.268 | 0.99 |
| 38_A | 65_G | 1.267 | 0.99 |
| 44_R | 48_R | 1.237 | 0.98 |
| 148_F | 201_L | 1.230 | 0.98 |
| 137_P | 210_V | 1.229 | 0.98 |
| 199_S | 243_V | 1.229 | 0.98 |
| 234_I | 279_M | 1.222 | 0.98 |
| 43_T | 47_N | 1.215 | 0.98 |
| 211_L | 215_L | 1.214 | 0.98 |
| 115_I | 125_F | 1.210 | 0.98 |
| 91_L | 95_R | 1.203 | 0.98 |
| 124_S | 127_Q | 1.201 | 0.98 |
| 35_F | 66_F | 1.193 | 0.98 |
| 39_M | 62_L | 1.192 | 0.98 |
| 201_L | 205_L | 1.191 | 0.98 |
| 145_L | 149_I | 1.185 | 0.98 |
| 171_R | 193_V | 1.183 | 0.98 |
| 168_P | 171_R | 1.178 | 0.98 |
| 141_G | 204_L | 1.170 | 0.97 |
| 64_A | 113_V | 1.164 | 0.97 |
| 276_V | 280_V | 1.163 | 0.97 |
| 43_T | 59_E | 1.154 | 0.97 |
| 35_F | 69_V | 1.150 | 0.97 |
| 89_D | 95_R | 1.147 | 0.97 |
| 253_F | 263_M | 1.147 | 0.97 |
| 79_L | 83_F | 1.144 | 0.97 |
| 61_L | 65_G | 1.138 | 0.97 |
| 12_F | 149_I | 1.125 | 0.97 |
| 137_P | 211_L | 1.110 | 0.96 |
| 231_L | 235_G | 1.102 | 0.96 |
| 30_M | 33_V | 1.094 | 0.96 |
| 16_I | 26_W | 1.091 | 0.96 |
| 269_I | 273_V | 1.089 | 0.96 |
| 239_F | 243_V | 1.082 | 0.96 |
| 60_N | 121_T | 1.081 | 0.95 |
| 238_A | 272_I | 1.070 | 0.95 |
| 241_I | 272_I | 1.069 | 0.95 |
| 96_V | 99_G | 1.060 | 0.95 |
| 45_R | 134_P | 1.049 | 0.94 |
| 224_P | 283_Y | 1.046 | 0.94 |
| 123_R | 128_V | 1.035 | 0.94 |
| 238_A | 242_I | 1.034 | 0.94 |
| 56_N | 59_E | 1.024 | 0.93 |
| 212_F | 216_N | 1.018 | 0.93 |
| 273_V | 277_I | 1.017 | 0.93 |
| 156_R | 248_Q | 1.001 | 0.92 |
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 | |
| 2kluA | 1 | 0.1531 | 12.8 | 0.965 | Contact Map |
| 4px7A | 1 | 0.7279 | 5.4 | 0.971 | Contact Map |
| 2l9uA | 2 | 0.1361 | 4.1 | 0.972 | Contact Map |
| 2zxeA | 1 | 0.2993 | 4 | 0.973 | Contact Map |
| 2mofA | 1 | 0.1429 | 3.9 | 0.973 | Contact Map |
| 3ixzA | 1 | 0.3095 | 3.8 | 0.973 | Contact Map |
| 2ks1B | 1 | 0.1429 | 3.8 | 0.973 | Contact Map |
| 2m20A | 2 | 0.1361 | 3.6 | 0.973 | Contact Map |
| 2m59A | 2 | 0.1259 | 3.2 | 0.974 | Contact Map |
| 2ls4A | 1 | 0.0816 | 3.2 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)