| ClassA |
| ID: | 1412078274 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 310 (287) | ||
| Sequences: | 25688 (12545.3) | ||
| Seq/Len: | 89.505 | ||
| Nf(neff/√len): | 740.5 |
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: 89.505).
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 |
| 46_T | 82_A | 5.102 | 1.00 |
| 73_S | 156_W | 4.579 | 1.00 |
| 203_L | 207_R | 2.958 | 1.00 |
| 105_C | 177_C | 2.929 | 1.00 |
| 73_S | 122_H | 2.649 | 1.00 |
| 103_V | 107_I | 2.636 | 1.00 |
| 125_A | 155_V | 2.576 | 1.00 |
| 131_Y | 136_Q | 2.467 | 1.00 |
| 146_K | 150_C | 2.424 | 1.00 |
| 63_L | 68_N | 2.331 | 1.00 |
| 125_A | 151_I | 2.257 | 1.00 |
| 98_W | 101_G | 2.242 | 1.00 |
| 19_A | 180_N | 2.195 | 1.00 |
| 57_V | 72_V | 2.160 | 1.00 |
| 207_R | 210_Q | 2.051 | 1.00 |
| 110_A | 114_L | 2.022 | 1.00 |
| 131_Y | 135_T | 1.995 | 1.00 |
| 33_A | 37_A | 1.992 | 1.00 |
| 102_K | 106_G | 1.969 | 1.00 |
| 114_L | 160_A | 1.955 | 1.00 |
| 54_V | 72_V | 1.939 | 1.00 |
| 129_D | 133_S | 1.880 | 1.00 |
| 283_N | 287_Y | 1.854 | 1.00 |
| 69_L | 152_I | 1.835 | 1.00 |
| 252_F | 256_L | 1.818 | 1.00 |
| 164_S | 168_L | 1.812 | 1.00 |
| 235_V | 290_F | 1.794 | 1.00 |
| 200_I | 204_V | 1.770 | 1.00 |
| 46_T | 281_S | 1.724 | 1.00 |
| 206_I | 210_Q | 1.712 | 1.00 |
| 118_S | 159_S | 1.709 | 1.00 |
| 60_S | 297_A | 1.698 | 1.00 |
| 150_C | 154_I | 1.697 | 1.00 |
| 77_A | 118_S | 1.697 | 1.00 |
| 80_L | 115_F | 1.678 | 1.00 |
| 149_K | 153_V | 1.667 | 1.00 |
| 72_V | 76_T | 1.665 | 1.00 |
| 106_G | 171_D | 1.663 | 1.00 |
| 260_C | 263_Y | 1.662 | 1.00 |
| 151_I | 155_V | 1.660 | 1.00 |
| 242_V | 286_I | 1.647 | 1.00 |
| 78_D | 283_N | 1.621 | 1.00 |
| 247_W | 276_G | 1.616 | 1.00 |
| 131_Y | 207_R | 1.582 | 1.00 |
| 133_S | 137_A | 1.581 | 1.00 |
| 144_T | 147_R | 1.572 | 1.00 |
| 129_D | 143_R | 1.531 | 1.00 |
| 74_L | 78_D | 1.525 | 1.00 |
| 122_H | 152_I | 1.511 | 1.00 |
| 51_I | 55_I | 1.498 | 1.00 |
| 88_F | 92_N | 1.471 | 1.00 |
| 51_I | 79_I | 1.463 | 1.00 |
| 122_H | 156_W | 1.449 | 1.00 |
| 132_W | 142_K | 1.440 | 1.00 |
| 77_A | 119_S | 1.422 | 1.00 |
| 73_S | 152_I | 1.402 | 0.99 |
| 131_Y | 204_V | 1.402 | 0.99 |
| 237_A | 241_G | 1.399 | 0.99 |
| 205_Y | 208_I | 1.379 | 0.99 |
| 207_R | 211_V | 1.377 | 0.99 |
| 70_F | 148_V | 1.376 | 0.99 |
| 65_A | 68_N | 1.370 | 0.99 |
| 101_G | 104_W | 1.369 | 0.99 |
| 110_A | 167_L | 1.368 | 0.99 |
| 215_R | 219_I | 1.351 | 0.99 |
| 47_V | 82_A | 1.338 | 0.99 |
| 84_L | 87_P | 1.318 | 0.99 |
| 120_I | 124_C | 1.313 | 0.99 |
| 58_L | 72_V | 1.309 | 0.99 |
| 123_L | 201_M | 1.303 | 0.99 |
| 297_A | 300_K | 1.297 | 0.99 |
| 166_P | 169_S | 1.279 | 0.99 |
| 49_G | 281_S | 1.279 | 0.99 |
| 87_P | 90_L | 1.276 | 0.99 |
| 75_A | 78_D | 1.273 | 0.99 |
| 78_D | 279_N | 1.267 | 0.99 |
| 47_V | 79_I | 1.261 | 0.99 |
| 76_T | 80_L | 1.253 | 0.99 |
| 120_I | 197_P | 1.233 | 0.98 |
| 124_C | 204_V | 1.231 | 0.98 |
| 53_V | 57_V | 1.227 | 0.98 |
| 124_C | 200_I | 1.226 | 0.98 |
| 229_E | 233_T | 1.221 | 0.98 |
| 43_I | 83_T | 1.218 | 0.98 |
| 110_A | 160_A | 1.212 | 0.98 |
| 69_L | 149_K | 1.208 | 0.98 |
| 57_V | 63_L | 1.206 | 0.98 |
| 278_C | 282_L | 1.203 | 0.98 |
| 202_I | 206_I | 1.201 | 0.98 |
| 53_V | 288_T | 1.195 | 0.98 |
| 48_V | 51_I | 1.173 | 0.98 |
| 55_I | 59_T | 1.171 | 0.98 |
| 70_F | 126_I | 1.169 | 0.97 |
| 78_D | 119_S | 1.167 | 0.97 |
| 130_R | 133_S | 1.167 | 0.97 |
| 156_W | 284_P | 1.167 | 0.97 |
| 57_V | 64_K | 1.144 | 0.97 |
| 201_M | 205_Y | 1.143 | 0.97 |
| 34_S | 38_L | 1.128 | 0.97 |
| 248_F | 252_F | 1.127 | 0.97 |
| 135_T | 211_V | 1.125 | 0.97 |
| 246_C | 249_P | 1.118 | 0.96 |
| 81_V | 280_S | 1.116 | 0.96 |
| 120_I | 243_F | 1.114 | 0.96 |
| 232_F | 235_V | 1.113 | 0.96 |
| 208_I | 236_L | 1.110 | 0.96 |
| 49_G | 75_A | 1.107 | 0.96 |
| 209_Y | 213_K | 1.106 | 0.96 |
| 52_L | 56_A | 1.104 | 0.96 |
| 145_P | 149_K | 1.103 | 0.96 |
| 121_V | 155_V | 1.100 | 0.96 |
| 188_S | 192_A | 1.095 | 0.96 |
| 121_V | 197_P | 1.093 | 0.96 |
| 45_F | 281_S | 1.092 | 0.96 |
| 210_Q | 214_T | 1.092 | 0.96 |
| 209_Y | 212_A | 1.088 | 0.96 |
| 150_C | 153_V | 1.087 | 0.96 |
| 117_T | 193_S | 1.080 | 0.95 |
| 134_V | 138_V | 1.075 | 0.95 |
| 86_M | 89_S | 1.063 | 0.95 |
| 60_S | 300_K | 1.063 | 0.95 |
| 103_V | 106_G | 1.051 | 0.94 |
| 193_S | 197_P | 1.048 | 0.94 |
| 21_W | 24_D | 1.048 | 0.94 |
| 36_A | 40_S | 1.044 | 0.94 |
| 49_G | 285_A | 1.043 | 0.94 |
| 230_K | 234_F | 1.041 | 0.94 |
| 153_V | 157_L | 1.041 | 0.94 |
| 82_A | 86_M | 1.039 | 0.94 |
| 53_V | 294_F | 1.038 | 0.94 |
| 184_W | 188_S | 1.035 | 0.94 |
| 54_V | 75_A | 1.035 | 0.94 |
| 132_W | 136_Q | 1.034 | 0.94 |
| 84_L | 115_F | 1.031 | 0.94 |
| 121_V | 193_S | 1.024 | 0.93 |
| 27_Y | 31_A | 1.020 | 0.93 |
| 201_M | 240_M | 1.019 | 0.93 |
| 178_M | 181_D | 1.019 | 0.93 |
| 124_C | 201_M | 1.017 | 0.93 |
| 128_L | 204_V | 1.016 | 0.93 |
| 238_V | 290_F | 1.005 | 0.93 |
| 198_C | 244_V | 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 | |
| 4iarA | 1 | 0.9 | 100 | 0.131 | Contact Map |
| 1u19A | 2 | 0.9968 | 100 | 0.134 | Contact Map |
| 2r4rA | 1 | 0.6742 | 100 | 0.149 | Contact Map |
| 2rh1A | 1 | 0.8903 | 100 | 0.158 | Contact Map |
| 3uonA | 1 | 0.8871 | 100 | 0.16 | Contact Map |
| 4grvA | 1 | 0.8903 | 100 | 0.16 | Contact Map |
| 4pxzA | 1 | 0.8613 | 100 | 0.162 | Contact Map |
| 4phuA | 1 | 0.8226 | 100 | 0.17 | Contact Map |
| 4bvnA | 1 | 0.8742 | 100 | 0.172 | Contact Map |
| 3rzeA | 1 | 0.871 | 100 | 0.172 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)