| Tau_RDs_3_4 |
| ID: | 1492708782 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (126) | ||
| Sequences: | 149 (82.2) | ||
| Seq/Len: | 1.183 | ||
| Nf(neff/√len): | 7.3 |
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: 1.183).
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 |
| 11_K | 17_I | 2.018 | 0.97 |
| 9_D | 12_N | 1.749 | 0.92 |
| 20_T | 26_Q | 1.712 | 0.91 |
| 119_H | 123_G | 1.711 | 0.91 |
| 96_V | 107_V | 1.635 | 0.88 |
| 8_P | 17_I | 1.603 | 0.86 |
| 82_L | 86_H | 1.515 | 0.82 |
| 73_S | 79_C | 1.446 | 0.78 |
| 14_K | 17_I | 1.421 | 0.76 |
| 17_I | 20_T | 1.414 | 0.75 |
| 11_K | 14_K | 1.399 | 0.74 |
| 8_P | 11_K | 1.382 | 0.73 |
| 78_K | 89_P | 1.345 | 0.70 |
| 116_N | 119_H | 1.337 | 0.69 |
| 64_Q | 73_S | 1.333 | 0.69 |
| 64_Q | 68_K | 1.330 | 0.69 |
| 25_H | 126_K | 1.325 | 0.68 |
| 117_I | 126_K | 1.297 | 0.66 |
| 84_N | 89_P | 1.293 | 0.66 |
| 14_K | 20_T | 1.289 | 0.65 |
| 35_I | 45_Q | 1.288 | 0.65 |
| 69_P | 83_G | 1.276 | 0.64 |
| 8_P | 14_K | 1.253 | 0.62 |
| 64_Q | 79_C | 1.245 | 0.61 |
| 8_P | 20_T | 1.235 | 0.60 |
| 19_S | 30_G | 1.223 | 0.59 |
| 119_H | 122_G | 1.219 | 0.59 |
| 81_S | 87_H | 1.218 | 0.59 |
| 77_S | 87_H | 1.215 | 0.58 |
| 65_I | 89_P | 1.213 | 0.58 |
| 119_H | 124_G | 1.205 | 0.58 |
| 32_V | 37_K | 1.192 | 0.56 |
| 65_I | 84_N | 1.189 | 0.56 |
| 11_K | 26_Q | 1.184 | 0.56 |
| 78_K | 84_N | 1.176 | 0.55 |
| 97_K | 109_S | 1.171 | 0.54 |
| 72_L | 75_V | 1.169 | 0.54 |
| 15_S | 19_S | 1.134 | 0.51 |
| 64_Q | 71_D | 1.133 | 0.51 |
| 69_P | 89_P | 1.129 | 0.50 |
| 34_I | 38_K | 1.123 | 0.50 |
| 78_K | 81_S | 1.118 | 0.49 |
| 20_T | 24_K | 1.111 | 0.48 |
| 50_S | 56_H | 1.101 | 0.47 |
| 84_N | 87_H | 1.089 | 0.46 |
| 25_H | 29_G | 1.087 | 0.46 |
| 68_K | 77_S | 1.085 | 0.46 |
| 69_P | 84_N | 1.084 | 0.46 |
| 34_I | 46_S | 1.075 | 0.45 |
| 51_K | 54_I | 1.071 | 0.45 |
| 25_H | 28_G | 1.067 | 0.44 |
| 75_V | 85_I | 1.065 | 0.44 |
| 19_S | 22_N | 1.064 | 0.44 |
| 112_G | 115_D | 1.063 | 0.44 |
| 42_S | 48_C | 1.043 | 0.42 |
| 113_S | 119_H | 1.043 | 0.42 |
| 77_S | 88_K | 1.038 | 0.41 |
| 10_L | 22_N | 1.033 | 0.41 |
| 102_D | 122_G | 1.024 | 0.40 |
| 49_G | 59_G | 1.021 | 0.40 |
| 9_D | 13_V | 1.019 | 0.40 |
| 86_H | 93_Q | 1.015 | 0.39 |
| 100_K | 110_K | 1.011 | 0.39 |
| 81_S | 89_P | 1.009 | 0.39 |
| 3_A | 6_P | 1.004 | 0.38 |
| 98_S | 111_I | 1.001 | 0.38 |
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 | |
| 2mz7A | 1 | 0 | 99.8 | 0.658 | Contact Map |
| 2lmkA | 1 | 0.189 | 7.1 | 0.958 | Contact Map |
| 3qr8A | 1 | 0.5512 | 2.4 | 0.967 | Contact Map |
| 1kxpD | 1 | 0.3307 | 2 | 0.968 | Contact Map |
| 3nngA | 2 | 0.2835 | 1.8 | 0.969 | Contact Map |
| 4heiA | 2 | 0.4488 | 1.2 | 0.972 | Contact Map |
| 4r29A | 4 | 0.3543 | 1.2 | 0.972 | Contact Map |
| 1dx8A | 1 | 0.2047 | 1 | 0.973 | Contact Map |
| 2edzA | 1 | 0.3622 | 1 | 0.973 | Contact Map |
| 3tqmA | 4 | 0.4488 | 1 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)