| d3a0ua_ |
| ID: | 1447593067 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (115) | ||
| Sequences: | 107602 (80916) | ||
| Seq/Len: | 935.670 | ||
| Nf(neff/√len): | 7545.5 |
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: 935.670).
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 |
| 14_R | 30_T | 2.979 | 1.00 |
| 14_R | 32_E | 2.720 | 1.00 |
| 18_K | 30_T | 2.680 | 1.00 |
| 7_V | 37_A | 2.300 | 1.00 |
| 54_E | 82_Y | 2.123 | 1.00 |
| 29_D | 46_Y | 2.022 | 1.00 |
| 38_L | 66_E | 1.996 | 1.00 |
| 35_E | 57_G | 1.911 | 1.00 |
| 96_E | 110_K | 1.898 | 1.00 |
| 3_R | 29_D | 1.886 | 1.00 |
| 51_L | 63_V | 1.878 | 1.00 |
| 31_A | 40_K | 1.849 | 1.00 |
| 58_I | 66_E | 1.795 | 1.00 |
| 24_E | 108_K | 1.780 | 1.00 |
| 78_L | 94_A | 1.716 | 1.00 |
| 64_A | 76_I | 1.712 | 1.00 |
| 34_G | 58_I | 1.703 | 1.00 |
| 20_E | 104_F | 1.675 | 1.00 |
| 3_R | 27_E | 1.670 | 1.00 |
| 32_E | 36_E | 1.658 | 1.00 |
| 33_N | 57_G | 1.605 | 1.00 |
| 42_F | 70_K | 1.585 | 1.00 |
| 29_D | 40_K | 1.566 | 1.00 |
| 29_D | 44_G | 1.439 | 1.00 |
| 18_K | 22_Q | 1.430 | 1.00 |
| 68_R | 95_D | 1.419 | 1.00 |
| 53_I | 61_L | 1.419 | 1.00 |
| 5_L | 31_A | 1.413 | 1.00 |
| 49_V | 74_A | 1.383 | 0.99 |
| 66_E | 70_K | 1.370 | 0.99 |
| 33_N | 36_E | 1.367 | 0.99 |
| 3_R | 47_D | 1.350 | 0.99 |
| 65_G | 92_W | 1.344 | 0.99 |
| 34_G | 63_V | 1.316 | 0.99 |
| 59_S | 62_E | 1.269 | 0.99 |
| 40_K | 46_Y | 1.247 | 0.99 |
| 96_E | 113_K | 1.213 | 0.98 |
| 110_K | 113_K | 1.206 | 0.98 |
| 106_E | 110_K | 1.200 | 0.98 |
| 35_E | 58_I | 1.194 | 0.98 |
| 58_I | 62_E | 1.193 | 0.98 |
| 41_F | 67_I | 1.183 | 0.98 |
| 3_R | 44_G | 1.174 | 0.98 |
| 66_E | 69_K | 1.172 | 0.98 |
| 38_L | 63_V | 1.168 | 0.97 |
| 87_S | 91_S | 1.163 | 0.97 |
| 79_L | 102_F | 1.148 | 0.97 |
| 64_A | 78_L | 1.144 | 0.97 |
| 5_L | 46_Y | 1.130 | 0.97 |
| 2_K | 26_Y | 1.118 | 0.96 |
| 88_D | 92_W | 1.112 | 0.96 |
| 61_L | 89_L | 1.081 | 0.95 |
| 40_K | 44_G | 1.077 | 0.95 |
| 108_K | 112_K | 1.066 | 0.95 |
| 78_L | 89_L | 1.050 | 0.94 |
| 95_D | 114_L | 1.046 | 0.94 |
| 6_V | 17_L | 1.036 | 0.94 |
| 15_E | 18_K | 1.029 | 0.94 |
| 5_L | 37_A | 1.024 | 0.93 |
| 37_A | 63_V | 1.021 | 0.93 |
| 61_L | 88_D | 1.021 | 0.93 |
| 11_P | 32_E | 1.016 | 0.93 |
| 40_K | 43_S | 1.012 | 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 | |
| 4g97A | 1 | 0.9913 | 99.5 | -0.232 | Contact Map |
| 3n0rA | 1 | 0.9913 | 99.5 | -0.225 | Contact Map |
| 4l4uA | 1 | 1 | 99.4 | -0.195 | Contact Map |
| 3dzdA | 2 | 0.9913 | 99.4 | -0.194 | Contact Map |
| 3eq2A | 2 | 1 | 99.4 | -0.189 | Contact Map |
| 3rqiA | 1 | 0.9913 | 99.4 | -0.187 | Contact Map |
| 3r0jA | 2 | 0.9913 | 99.4 | -0.184 | Contact Map |
| 2vycA | 10 | 0.9913 | 99.4 | -0.184 | Contact Map |
| 1kgsA | 1 | 1 | 99.4 | -0.177 | Contact Map |
| 1yioA | 1 | 1 | 99.4 | -0.177 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)