| 1io2 |
| ID: | 1453736900 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 213 (202) | ||
| Sequences: | 3970 (2562.1) | ||
| Seq/Len: | 19.653 | ||
| Nf(neff/√len): | 180.3 |
HHblits Results: (2015_06)
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: 19.653).
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 |
| 160_K | 165_E | 5.577 | 1.00 |
| 159_L | 193_I | 2.982 | 1.00 |
| 63_Y | 147_L | 2.938 | 1.00 |
| 101_V | 129_V | 2.889 | 1.00 |
| 39_R | 136_D | 2.839 | 1.00 |
| 53_F | 57_L | 2.717 | 1.00 |
| 74_G | 197_G | 2.633 | 1.00 |
| 19_V | 67_E | 2.609 | 1.00 |
| 48_R | 51_K | 2.544 | 1.00 |
| 50_E | 154_R | 2.440 | 1.00 |
| 39_R | 43_K | 2.432 | 1.00 |
| 64_V | 94_S | 2.356 | 1.00 |
| 164_G | 178_A | 2.338 | 1.00 |
| 134_A | 141_V | 2.296 | 1.00 |
| 57_L | 63_Y | 2.249 | 1.00 |
| 20_I | 87_N | 2.233 | 1.00 |
| 199_K | 203_K | 2.200 | 1.00 |
| 46_P | 157_E | 2.039 | 1.00 |
| 67_E | 155_A | 2.000 | 1.00 |
| 53_F | 151_T | 1.973 | 1.00 |
| 181_E | 185_R | 1.972 | 1.00 |
| 53_F | 154_R | 1.971 | 1.00 |
| 46_P | 168_S | 1.865 | 1.00 |
| 81_N | 107_A | 1.863 | 1.00 |
| 53_F | 150_V | 1.857 | 1.00 |
| 103_Y | 141_V | 1.852 | 1.00 |
| 72_V | 90_K | 1.851 | 1.00 |
| 22_A | 91_A | 1.824 | 1.00 |
| 78_G | 86_E | 1.781 | 1.00 |
| 68_L | 90_K | 1.716 | 1.00 |
| 131_K | 137_I | 1.712 | 1.00 |
| 178_A | 182_N | 1.708 | 1.00 |
| 166_I | 178_A | 1.698 | 1.00 |
| 133_K | 136_D | 1.688 | 1.00 |
| 2_K | 100_D | 1.683 | 1.00 |
| 72_V | 86_E | 1.681 | 1.00 |
| 43_K | 136_D | 1.634 | 1.00 |
| 199_K | 202_K | 1.629 | 1.00 |
| 86_E | 90_K | 1.609 | 1.00 |
| 65_I | 151_T | 1.589 | 1.00 |
| 177_R | 181_E | 1.573 | 1.00 |
| 81_N | 108_D | 1.503 | 1.00 |
| 82_E | 85_V | 1.498 | 1.00 |
| 14_V | 180_L | 1.494 | 1.00 |
| 89_A | 93_N | 1.485 | 1.00 |
| 46_P | 50_E | 1.469 | 1.00 |
| 183_Y | 190_F | 1.454 | 1.00 |
| 19_V | 151_T | 1.443 | 1.00 |
| 69_P | 72_V | 1.435 | 1.00 |
| 67_E | 151_T | 1.433 | 1.00 |
| 38_V | 146_I | 1.427 | 1.00 |
| 50_E | 150_V | 1.420 | 1.00 |
| 164_G | 182_N | 1.412 | 1.00 |
| 4_A | 22_A | 1.382 | 0.99 |
| 56_I | 60_L | 1.380 | 0.99 |
| 4_A | 24_V | 1.370 | 0.99 |
| 167_G | 182_N | 1.368 | 0.99 |
| 17_P | 67_E | 1.357 | 0.99 |
| 73_I | 80_L | 1.340 | 0.99 |
| 155_A | 159_L | 1.331 | 0.99 |
| 17_P | 155_A | 1.309 | 0.99 |
| 20_I | 84_E | 1.296 | 0.99 |
| 180_L | 184_Y | 1.295 | 0.99 |
| 6_I | 102_I | 1.274 | 0.99 |
| 38_V | 142_S | 1.264 | 0.99 |
| 85_V | 107_A | 1.252 | 0.99 |
| 190_F | 196_K | 1.235 | 0.98 |
| 68_L | 87_N | 1.218 | 0.98 |
| 164_G | 167_G | 1.217 | 0.98 |
| 6_I | 84_E | 1.212 | 0.98 |
| 38_V | 143_A | 1.209 | 0.98 |
| 4_A | 99_P | 1.202 | 0.98 |
| 44_L | 146_I | 1.174 | 0.98 |
| 55_E | 59_V | 1.173 | 0.98 |
| 158_K | 161_E | 1.166 | 0.97 |
| 180_L | 200_T | 1.155 | 0.97 |
| 15_I | 156_V | 1.150 | 0.97 |
| 54_N | 57_L | 1.149 | 0.97 |
| 131_K | 141_V | 1.147 | 0.97 |
| 162_E | 193_I | 1.144 | 0.97 |
| 109_V | 130_A | 1.142 | 0.97 |
| 78_G | 82_E | 1.133 | 0.97 |
| 107_A | 130_A | 1.131 | 0.97 |
| 66_L | 87_N | 1.128 | 0.97 |
| 66_L | 91_A | 1.128 | 0.97 |
| 21_A | 65_I | 1.126 | 0.97 |
| 15_I | 193_I | 1.126 | 0.97 |
| 54_N | 154_R | 1.118 | 0.96 |
| 92_L | 102_I | 1.117 | 0.96 |
| 68_L | 72_V | 1.113 | 0.96 |
| 44_L | 48_R | 1.108 | 0.96 |
| 44_L | 52_L | 1.106 | 0.96 |
| 157_E | 168_S | 1.102 | 0.96 |
| 101_V | 127_E | 1.097 | 0.96 |
| 178_A | 181_E | 1.095 | 0.96 |
| 138_F | 142_S | 1.095 | 0.96 |
| 131_K | 134_A | 1.093 | 0.96 |
| 14_V | 171_P | 1.089 | 0.96 |
| 133_K | 137_I | 1.088 | 0.96 |
| 70_P | 74_G | 1.088 | 0.96 |
| 72_V | 75_S | 1.088 | 0.96 |
| 57_L | 151_T | 1.083 | 0.96 |
| 151_T | 154_R | 1.080 | 0.95 |
| 131_K | 138_F | 1.073 | 0.95 |
| 26_D | 29_S | 1.073 | 0.95 |
| 72_V | 78_G | 1.067 | 0.95 |
| 79_T | 82_E | 1.064 | 0.95 |
| 51_K | 55_E | 1.064 | 0.95 |
| 9_A | 150_V | 1.056 | 0.95 |
| 11_R | 84_E | 1.049 | 0.94 |
| 109_V | 128_V | 1.047 | 0.94 |
| 57_L | 147_L | 1.046 | 0.94 |
| 37_K | 48_R | 1.023 | 0.93 |
| 45_T | 48_R | 1.018 | 0.93 |
| 4_A | 92_L | 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
- 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 | |
| 1io2A | 1 | 1 | 100 | 0.071 | Contact Map |
| 1uaxA | 2 | 0.9906 | 100 | 0.085 | Contact Map |
| 1ekeA | 2 | 0.9859 | 100 | 0.094 | Contact Map |
| 1i39A | 1 | 0.9296 | 100 | 0.131 | Contact Map |
| 3kioA | 1 | 0.9671 | 100 | 0.149 | Contact Map |
| 2d0bA | 1 | 0.9718 | 100 | 0.195 | Contact Map |
| 4py5A | 1 | 0.8779 | 100 | 0.198 | Contact Map |
| 2etjA | 1 | 0.8216 | 100 | 0.206 | Contact Map |
| 3vn5A | 1 | 0.8451 | 100 | 0.268 | Contact Map |
| 1c8bA | 2 | 0.4883 | 28.8 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)