| twa1 |
| ID: | 1516820589 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 228 (217) | ||
| Sequences: | 683 (508.8) | ||
| Seq/Len: | 3.147 | ||
| Nf(neff/√len): | 34.5 |
HHblits Results: (2016_02)
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: 3.147).
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 |
| 86_I | 176_V | 3.919 | 1.00 |
| 78_Q | 81_E | 3.865 | 1.00 |
| 117_E | 120_A | 2.345 | 1.00 |
| 80_Q | 108_H | 2.314 | 1.00 |
| 103_H | 175_E | 2.200 | 1.00 |
| 67_R | 177_N | 2.139 | 1.00 |
| 112_L | 121_A | 1.933 | 1.00 |
| 6_K | 9_E | 1.914 | 0.99 |
| 177_N | 181_L | 1.855 | 0.99 |
| 33_I | 37_L | 1.839 | 0.99 |
| 77_G | 169_R | 1.760 | 0.99 |
| 111_E | 114_R | 1.717 | 0.99 |
| 74_I | 176_V | 1.713 | 0.99 |
| 67_R | 181_L | 1.707 | 0.99 |
| 213_Y | 216_M | 1.660 | 0.98 |
| 107_Q | 168_Q | 1.655 | 0.98 |
| 145_R | 162_D | 1.654 | 0.98 |
| 30_N | 49_F | 1.619 | 0.98 |
| 17_E | 21_N | 1.569 | 0.97 |
| 34_M | 46_A | 1.547 | 0.97 |
| 149_L | 164_L | 1.538 | 0.97 |
| 190_P | 193_A | 1.537 | 0.97 |
| 6_K | 10_I | 1.530 | 0.97 |
| 101_Y | 105_Q | 1.518 | 0.96 |
| 154_S | 157_E | 1.516 | 0.96 |
| 111_E | 169_R | 1.509 | 0.96 |
| 94_L | 100_L | 1.433 | 0.95 |
| 2_S | 5_E | 1.432 | 0.95 |
| 83_I | 124_F | 1.421 | 0.94 |
| 110_I | 114_R | 1.409 | 0.94 |
| 6_K | 11_T | 1.408 | 0.94 |
| 2_S | 6_K | 1.384 | 0.93 |
| 7_P | 10_I | 1.379 | 0.93 |
| 5_E | 11_T | 1.376 | 0.93 |
| 3_Y | 6_K | 1.325 | 0.91 |
| 212_K | 218_D | 1.313 | 0.90 |
| 4_A | 10_I | 1.308 | 0.90 |
| 8_D | 13_D | 1.306 | 0.90 |
| 151_A | 155_P | 1.293 | 0.90 |
| 74_I | 79_I | 1.277 | 0.89 |
| 5_E | 17_E | 1.265 | 0.88 |
| 43_K | 65_D | 1.265 | 0.88 |
| 108_H | 112_L | 1.259 | 0.88 |
| 198_L | 201_W | 1.248 | 0.87 |
| 149_L | 152_F | 1.247 | 0.87 |
| 67_R | 173_W | 1.239 | 0.87 |
| 77_G | 111_E | 1.234 | 0.86 |
| 50_R | 55_I | 1.233 | 0.86 |
| 107_Q | 172_V | 1.232 | 0.86 |
| 34_M | 38_V | 1.226 | 0.86 |
| 42_F | 133_G | 1.220 | 0.86 |
| 6_K | 13_D | 1.218 | 0.85 |
| 94_L | 143_M | 1.202 | 0.84 |
| 4_A | 7_P | 1.199 | 0.84 |
| 9_E | 13_D | 1.198 | 0.84 |
| 87_N | 143_M | 1.188 | 0.83 |
| 5_E | 8_D | 1.185 | 0.83 |
| 17_E | 22_L | 1.182 | 0.83 |
| 30_N | 143_M | 1.173 | 0.82 |
| 102_F | 113_I | 1.168 | 0.82 |
| 4_A | 9_E | 1.163 | 0.82 |
| 9_E | 12_K | 1.155 | 0.81 |
| 30_N | 33_I | 1.143 | 0.80 |
| 116_R | 121_A | 1.142 | 0.80 |
| 207_D | 213_Y | 1.142 | 0.80 |
| 3_Y | 8_D | 1.132 | 0.79 |
| 11_T | 17_E | 1.123 | 0.78 |
| 107_Q | 199_L | 1.111 | 0.77 |
| 2_S | 11_T | 1.109 | 0.77 |
| 3_Y | 14_E | 1.106 | 0.77 |
| 90_H | 183_Y | 1.084 | 0.75 |
| 29_M | 36_Y | 1.073 | 0.74 |
| 82_A | 104_L | 1.072 | 0.74 |
| 140_L | 144_E | 1.072 | 0.74 |
| 77_G | 177_N | 1.071 | 0.74 |
| 125_A | 148_A | 1.065 | 0.73 |
| 11_T | 212_K | 1.061 | 0.73 |
| 4_A | 11_T | 1.060 | 0.73 |
| 206_L | 214_P | 1.058 | 0.72 |
| 99_Y | 139_C | 1.055 | 0.72 |
| 12_K | 18_K | 1.047 | 0.71 |
| 82_A | 173_W | 1.043 | 0.71 |
| 8_D | 216_M | 1.041 | 0.71 |
| 109_L | 144_E | 1.039 | 0.70 |
| 72_E | 76_K | 1.032 | 0.70 |
| 73_M | 78_Q | 1.030 | 0.69 |
| 77_G | 91_P | 1.029 | 0.69 |
| 149_L | 163_L | 1.029 | 0.69 |
| 107_Q | 147_L | 1.027 | 0.69 |
| 198_L | 202_A | 1.024 | 0.69 |
| 169_R | 177_N | 1.015 | 0.68 |
| 114_R | 164_L | 1.009 | 0.67 |
| 109_L | 113_I | 1.008 | 0.67 |
| 42_F | 177_N | 1.004 | 0.67 |
| 199_L | 213_Y | 1.002 | 0.66 |
| 4_A | 8_D | 1.001 | 0.66 |
| 15_W | 19_L | 1.000 | 0.66 |
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 | |
| 4zheA | 4 | 0 | 100 | 0.514 | Contact Map |
| 2xtcA | 2 | 0.3246 | 86.3 | 0.914 | Contact Map |
| 2d68A | 2 | 0.3421 | 71.2 | 0.925 | Contact Map |
| 1uujA | 4 | 0.3421 | 41.9 | 0.938 | Contact Map |
| 2j4bA | 5 | 0.5833 | 22.3 | 0.946 | Contact Map |
| 2xpiA | 2 | 0.7193 | 21 | 0.946 | Contact Map |
| 4bzjA | 2 | 0.8202 | 18.9 | 0.948 | Contact Map |
| 4ui9F | 2 | 0 | 16 | 0.949 | Contact Map |
| 3uq3A | 1 | 0.614 | 15.5 | 0.949 | Contact Map |
| 4apoA | 2 | 0.6009 | 14.8 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)