| T0772 60-265 |
| ID: | 1399654118 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 206 (191) | ||
| Sequences: | 906 (724.4) | ||
| Seq/Len: | 4.743 | ||
| Nf(neff/√len): | 52.4 |
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: 4.743).
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 |
| 15_D | 18_D | 5.572 | 1.00 |
| 62_E | 199_R | 4.386 | 1.00 |
| 62_E | 200_N | 3.670 | 1.00 |
| 52_Q | 205_E | 3.235 | 1.00 |
| 60_H | 129_D | 3.127 | 1.00 |
| 83_L | 151_V | 3.017 | 1.00 |
| 64_Q | 197_S | 2.936 | 1.00 |
| 53_K | 181_A | 2.832 | 1.00 |
| 21_A | 51_K | 2.754 | 1.00 |
| 148_T | 160_N | 2.750 | 1.00 |
| 62_E | 127_V | 2.637 | 1.00 |
| 58_Q | 129_D | 2.608 | 1.00 |
| 152_I | 157_V | 2.557 | 1.00 |
| 55_N | 181_A | 2.456 | 1.00 |
| 23_E | 51_K | 2.362 | 1.00 |
| 61_I | 81_I | 2.340 | 1.00 |
| 131_I | 152_I | 2.219 | 1.00 |
| 19_L | 34_V | 2.178 | 1.00 |
| 60_H | 127_V | 2.078 | 1.00 |
| 58_Q | 204_R | 2.034 | 1.00 |
| 61_I | 128_Y | 1.892 | 1.00 |
| 81_I | 130_I | 1.867 | 1.00 |
| 109_Y | 189_H | 1.864 | 1.00 |
| 35_H | 40_T | 1.821 | 1.00 |
| 40_T | 197_S | 1.791 | 1.00 |
| 38_V | 197_S | 1.774 | 1.00 |
| 126_N | 154_N | 1.763 | 1.00 |
| 19_L | 39_F | 1.749 | 1.00 |
| 58_Q | 131_I | 1.698 | 0.99 |
| 15_D | 20_S | 1.681 | 0.99 |
| 157_V | 160_N | 1.636 | 0.99 |
| 60_H | 202_W | 1.623 | 0.99 |
| 91_V | 198_F | 1.619 | 0.99 |
| 61_I | 201_I | 1.610 | 0.99 |
| 54_F | 203_I | 1.598 | 0.99 |
| 34_V | 37_G | 1.530 | 0.99 |
| 14_F | 34_V | 1.525 | 0.99 |
| 89_V | 151_V | 1.519 | 0.98 |
| 89_V | 130_I | 1.503 | 0.98 |
| 10_A | 204_R | 1.502 | 0.98 |
| 129_D | 152_I | 1.487 | 0.98 |
| 79_S | 187_Q | 1.483 | 0.98 |
| 134_A | 146_H | 1.473 | 0.98 |
| 89_V | 128_Y | 1.465 | 0.98 |
| 59_M | 81_I | 1.459 | 0.98 |
| 81_I | 128_Y | 1.451 | 0.98 |
| 11_I | 54_F | 1.446 | 0.98 |
| 56_D | 133_T | 1.419 | 0.97 |
| 17_K | 34_V | 1.401 | 0.97 |
| 59_M | 184_I | 1.393 | 0.97 |
| 50_T | 54_F | 1.385 | 0.97 |
| 35_H | 197_S | 1.381 | 0.97 |
| 12_V | 202_W | 1.365 | 0.96 |
| 83_L | 89_V | 1.362 | 0.96 |
| 64_Q | 124_E | 1.356 | 0.96 |
| 10_A | 202_W | 1.290 | 0.95 |
| 9_D | 204_R | 1.263 | 0.94 |
| 78_N | 88_E | 1.239 | 0.93 |
| 50_T | 184_I | 1.218 | 0.92 |
| 17_K | 21_A | 1.210 | 0.92 |
| 83_L | 149_V | 1.194 | 0.91 |
| 65_V | 77_G | 1.191 | 0.91 |
| 151_V | 158_L | 1.171 | 0.90 |
| 18_D | 34_V | 1.135 | 0.88 |
| 150_T | 157_V | 1.135 | 0.88 |
| 106_G | 158_L | 1.112 | 0.87 |
| 63_W | 105_T | 1.104 | 0.86 |
| 131_I | 150_T | 1.102 | 0.86 |
| 15_D | 34_V | 1.094 | 0.86 |
| 150_T | 160_N | 1.080 | 0.85 |
| 59_M | 203_I | 1.074 | 0.84 |
| 199_R | 202_W | 1.069 | 0.84 |
| 32_W | 188_S | 1.059 | 0.83 |
| 57_F | 203_I | 1.059 | 0.83 |
| 11_I | 52_Q | 1.046 | 0.82 |
| 32_W | 77_G | 1.045 | 0.82 |
| 79_S | 196_I | 1.044 | 0.82 |
| 39_F | 48_I | 1.043 | 0.82 |
| 21_A | 34_V | 1.038 | 0.81 |
| 79_S | 198_F | 1.037 | 0.81 |
| 56_D | 134_A | 1.025 | 0.80 |
| 71_G | 75_S | 1.012 | 0.79 |
| 61_I | 91_V | 1.009 | 0.79 |
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 | |
| 4jqtA | 2 | 0.8835 | 100 | 0.234 | Contact Map |
| 3hbkA | 1 | 0.8883 | 100 | 0.235 | Contact Map |
| 3u1xA | 2 | 0.8835 | 100 | 0.238 | Contact Map |
| 3osdA | 1 | 0.8883 | 100 | 0.241 | Contact Map |
| 3h3lA | 3 | 0.8689 | 100 | 0.247 | Contact Map |
| 3s5qA | 1 | 0.8641 | 100 | 0.284 | Contact Map |
| 3immA | 3 | 0.8301 | 100 | 0.292 | Contact Map |
| 4b1mA | 3 | 0.767 | 100 | 0.488 | Contact Map |
| 1oq1A | 4 | 0.8738 | 99.9 | 0.589 | Contact Map |
| 4ccdA | 1 | 0.8107 | 99.6 | 0.728 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)