| spas |
| ID: | 1441489873 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 180 (152) | ||
| Sequences: | 8923 (5948.7) | ||
| Seq/Len: | 58.704 | ||
| Nf(neff/√len): | 482.5 |
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: 58.704).
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 |
| 124_T | 164_G | 4.656 | 1.00 |
| 111_R | 167_F | 3.362 | 1.00 |
| 52_T | 87_P | 3.189 | 1.00 |
| 39_V | 90_K | 2.827 | 1.00 |
| 55_P | 75_L | 2.788 | 1.00 |
| 122_N | 129_E | 2.781 | 1.00 |
| 118_D | 123_G | 2.661 | 1.00 |
| 156_N | 162_N | 2.645 | 1.00 |
| 39_V | 43_E | 2.297 | 1.00 |
| 46_D | 51_G | 2.188 | 1.00 |
| 131_K | 143_D | 2.121 | 1.00 |
| 46_D | 49_G | 1.992 | 1.00 |
| 167_F | 171_Y | 1.957 | 1.00 |
| 82_K | 86_K | 1.957 | 1.00 |
| 154_H | 169_E | 1.926 | 1.00 |
| 85_N | 92_E | 1.921 | 1.00 |
| 35_Y | 94_I | 1.894 | 1.00 |
| 127_F | 147_L | 1.877 | 1.00 |
| 142_N | 145_D | 1.862 | 1.00 |
| 154_H | 157_H | 1.790 | 1.00 |
| 89_G | 92_E | 1.769 | 1.00 |
| 154_H | 163_E | 1.730 | 1.00 |
| 82_K | 85_N | 1.710 | 1.00 |
| 115_A | 121_E | 1.658 | 1.00 |
| 107_K | 171_Y | 1.628 | 1.00 |
| 120_D | 129_E | 1.612 | 1.00 |
| 166_S | 169_E | 1.590 | 1.00 |
| 42_F | 93_F | 1.484 | 1.00 |
| 50_S | 57_E | 1.470 | 1.00 |
| 162_N | 169_E | 1.467 | 1.00 |
| 119_K | 132_A | 1.463 | 1.00 |
| 124_T | 166_S | 1.452 | 1.00 |
| 115_A | 167_F | 1.436 | 1.00 |
| 31_T | 34_D | 1.436 | 1.00 |
| 118_D | 129_E | 1.434 | 1.00 |
| 126_D | 164_G | 1.433 | 1.00 |
| 45_F | 61_V | 1.424 | 1.00 |
| 117_F | 133_I | 1.401 | 0.99 |
| 127_F | 131_K | 1.380 | 0.99 |
| 131_K | 135_K | 1.359 | 0.99 |
| 148_E | 151_H | 1.358 | 0.99 |
| 54_D | 57_E | 1.347 | 0.99 |
| 42_F | 46_D | 1.334 | 0.99 |
| 52_T | 89_G | 1.330 | 0.99 |
| 59_N | 71_N | 1.323 | 0.99 |
| 45_F | 53_I | 1.300 | 0.99 |
| 55_P | 78_I | 1.283 | 0.99 |
| 48_D | 57_E | 1.282 | 0.99 |
| 154_H | 162_N | 1.236 | 0.98 |
| 59_N | 74_I | 1.230 | 0.98 |
| 35_Y | 39_V | 1.223 | 0.98 |
| 32_A | 36_E | 1.222 | 0.98 |
| 111_R | 115_A | 1.208 | 0.98 |
| 90_K | 94_I | 1.195 | 0.98 |
| 43_E | 49_G | 1.187 | 0.98 |
| 156_N | 166_S | 1.185 | 0.98 |
| 47_E | 60_K | 1.148 | 0.97 |
| 50_S | 54_D | 1.132 | 0.97 |
| 53_I | 61_V | 1.130 | 0.97 |
| 107_K | 111_R | 1.125 | 0.97 |
| 119_K | 129_E | 1.121 | 0.97 |
| 162_N | 166_S | 1.114 | 0.96 |
| 125_V | 130_F | 1.110 | 0.96 |
| 155_V | 172_S | 1.104 | 0.96 |
| 156_N | 169_E | 1.099 | 0.96 |
| 46_D | 50_S | 1.059 | 0.95 |
| 30_L | 34_D | 1.055 | 0.95 |
| 120_D | 126_D | 1.043 | 0.94 |
| 70_R | 73_F | 1.040 | 0.94 |
| 131_K | 147_L | 1.038 | 0.94 |
| 118_D | 122_N | 1.027 | 0.94 |
| 82_K | 92_E | 1.019 | 0.93 |
| 48_D | 54_D | 1.019 | 0.93 |
| 171_Y | 175_S | 1.013 | 0.93 |
| 59_N | 63_E | 1.008 | 0.93 |
| 126_D | 129_E | 1.007 | 0.93 |
| 46_D | 57_E | 1.007 | 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 | |
| 4mvfA | 1 | 0.9444 | 99.9 | 0.297 | Contact Map |
| 3pm8A | 2 | 0.9333 | 99.9 | 0.3 | Contact Map |
| 4ociA | 1 | 0.7667 | 99.9 | 0.307 | Contact Map |
| 3u0kA | 1 | 0.9167 | 99.9 | 0.308 | Contact Map |
| 3i5gC | 1 | 0.8278 | 99.8 | 0.309 | Contact Map |
| 4i2yA | 2 | 0.9444 | 99.8 | 0.31 | Contact Map |
| 3dtpE | 2 | 0.9556 | 99.8 | 0.316 | Contact Map |
| 3qrxA | 1 | 0.8 | 99.8 | 0.319 | Contact Map |
| 3j04B | 2 | 0.7944 | 99.8 | 0.32 | Contact Map |
| 3i5gB | 1 | 0.8056 | 99.8 | 0.322 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)