| 3dju |
| ID: | 1453972224 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 122 (119) | ||
| Sequences: | 290 (206.6) | ||
| Seq/Len: | 2.437 | ||
| Nf(neff/√len): | 18.9 |
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: 2.437).
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 |
| 3_M | 6_E | 2.107 | 1.00 |
| 10_A | 98_V | 2.011 | 0.99 |
| 14_L | 68_M | 1.779 | 0.98 |
| 7_I | 11_V | 1.777 | 0.98 |
| 18_L | 22_G | 1.525 | 0.94 |
| 6_E | 32_F | 1.509 | 0.94 |
| 57_S | 105_Y | 1.497 | 0.94 |
| 32_F | 69_D | 1.496 | 0.94 |
| 61_C | 93_E | 1.475 | 0.93 |
| 14_L | 35_A | 1.434 | 0.92 |
| 63_R | 93_E | 1.413 | 0.91 |
| 55_K | 58_G | 1.410 | 0.91 |
| 56_G | 60_R | 1.380 | 0.89 |
| 44_Y | 80_G | 1.360 | 0.88 |
| 47_H | 56_G | 1.357 | 0.88 |
| 17_L | 32_F | 1.354 | 0.88 |
| 15_S | 33_S | 1.353 | 0.88 |
| 14_L | 71_I | 1.353 | 0.88 |
| 48_W | 99_D | 1.331 | 0.87 |
| 63_R | 102_E | 1.321 | 0.86 |
| 48_W | 100_P | 1.303 | 0.85 |
| 48_W | 60_R | 1.298 | 0.85 |
| 54_S | 78_Q | 1.295 | 0.85 |
| 99_D | 106_R | 1.276 | 0.84 |
| 72_I | 104_S | 1.210 | 0.79 |
| 53_P | 60_R | 1.209 | 0.79 |
| 99_D | 104_S | 1.207 | 0.79 |
| 85_Q | 98_V | 1.192 | 0.78 |
| 22_G | 83_Q | 1.165 | 0.75 |
| 47_H | 69_D | 1.161 | 0.75 |
| 100_P | 106_R | 1.158 | 0.75 |
| 43_H | 46_H | 1.148 | 0.74 |
| 58_G | 67_K | 1.145 | 0.73 |
| 47_H | 59_Y | 1.141 | 0.73 |
| 59_Y | 97_W | 1.130 | 0.72 |
| 81_L | 86_L | 1.127 | 0.72 |
| 76_A | 79_I | 1.125 | 0.72 |
| 53_P | 56_G | 1.123 | 0.71 |
| 48_W | 53_P | 1.122 | 0.71 |
| 48_W | 103_V | 1.119 | 0.71 |
| 3_M | 32_F | 1.117 | 0.71 |
| 6_E | 69_D | 1.114 | 0.70 |
| 97_W | 106_R | 1.095 | 0.69 |
| 114_C | 117_Y | 1.084 | 0.67 |
| 7_I | 45_K | 1.084 | 0.67 |
| 40_L | 106_R | 1.075 | 0.67 |
| 22_G | 26_E | 1.063 | 0.65 |
| 7_I | 37_Q | 1.051 | 0.64 |
| 21_R | 85_Q | 1.050 | 0.64 |
| 70_P | 107_I | 1.048 | 0.64 |
| 10_A | 94_L | 1.044 | 0.63 |
| 26_E | 29_L | 1.043 | 0.63 |
| 18_L | 68_M | 1.038 | 0.63 |
| 19_R | 29_L | 1.032 | 0.62 |
| 105_Y | 116_L | 1.030 | 0.62 |
| 111_G | 116_L | 1.023 | 0.61 |
| 56_G | 97_W | 1.021 | 0.61 |
| 3_M | 7_I | 1.019 | 0.60 |
| 78_Q | 101_Y | 1.016 | 0.60 |
| 13_F | 44_Y | 1.014 | 0.60 |
| 50_P | 104_S | 1.009 | 0.59 |
| 9_A | 76_A | 1.004 | 0.59 |
| 49_F | 109_E | 1.004 | 0.59 |
| 64_I | 81_L | 1.001 | 0.58 |
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 | |
| 3e9vA | 1 | 0.9836 | 100 | 0.013 | Contact Map |
| 2z15A | 4 | 0.9754 | 100 | 0.022 | Contact Map |
| 2kmfA | 1 | 0.3689 | 19 | 0.928 | Contact Map |
| 3a8gA | 1 | 0.8934 | 18.9 | 0.928 | Contact Map |
| 1lngA | 1 | 0.623 | 16.5 | 0.93 | Contact Map |
| 2y6xA | 1 | 0.3852 | 12 | 0.934 | Contact Map |
| 3shrA | 2 | 0.5164 | 12 | 0.934 | Contact Map |
| 3gjaA | 2 | 0.8934 | 11.1 | 0.935 | Contact Map |
| 1e5eA | 2 | 0.3525 | 10.1 | 0.937 | Contact Map |
| 1jidA | 1 | 0.7459 | 8.9 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)