| 1129 Unsolved De-novo Freestyle 56 |
| ID: | 1440628746 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 171 (150) | ||
| Sequences: | 5585 (4035.9) | ||
| Seq/Len: | 37.233 | ||
| Nf(neff/√len): | 329.5 |
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: 37.233).
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 |
| 36_E | 60_R | 3.961 | 1.00 |
| 26_R | 142_G | 3.165 | 1.00 |
| 21_R | 108_Q | 3.163 | 1.00 |
| 86_I | 103_G | 3.061 | 1.00 |
| 115_C | 137_Y | 2.776 | 1.00 |
| 16_L | 114_R | 2.699 | 1.00 |
| 121_R | 138_E | 2.576 | 1.00 |
| 66_V | 86_I | 2.418 | 1.00 |
| 116_E | 119_A | 2.418 | 1.00 |
| 35_V | 90_E | 2.369 | 1.00 |
| 62_V | 101_W | 2.336 | 1.00 |
| 70_C | 107_E | 2.275 | 1.00 |
| 54_A | 68_D | 2.230 | 1.00 |
| 17_F | 28_A | 2.187 | 1.00 |
| 120_F | 135_P | 2.184 | 1.00 |
| 58_S | 61_G | 2.075 | 1.00 |
| 54_A | 105_I | 2.059 | 1.00 |
| 54_A | 71_A | 1.925 | 1.00 |
| 33_E | 150_E | 1.923 | 1.00 |
| 21_R | 110_T | 1.841 | 1.00 |
| 134_G | 148_R | 1.788 | 1.00 |
| 15_K | 30_D | 1.708 | 1.00 |
| 35_V | 101_W | 1.678 | 1.00 |
| 71_A | 77_A | 1.649 | 1.00 |
| 64_V | 88_L | 1.631 | 1.00 |
| 58_S | 63_L | 1.599 | 1.00 |
| 13_T | 117_P | 1.551 | 1.00 |
| 40_L | 43_L | 1.497 | 1.00 |
| 39_P | 85_R | 1.494 | 1.00 |
| 51_E | 71_A | 1.454 | 1.00 |
| 21_R | 24_G | 1.445 | 1.00 |
| 19_L | 144_V | 1.413 | 1.00 |
| 23_E | 70_C | 1.408 | 1.00 |
| 68_D | 77_A | 1.408 | 1.00 |
| 131_R | 151_A | 1.401 | 0.99 |
| 55_G | 68_D | 1.377 | 0.99 |
| 148_R | 151_A | 1.351 | 0.99 |
| 28_A | 144_V | 1.337 | 0.99 |
| 17_F | 146_W | 1.333 | 0.99 |
| 18_L | 37_V | 1.332 | 0.99 |
| 43_L | 66_V | 1.329 | 0.99 |
| 19_L | 26_R | 1.312 | 0.99 |
| 66_V | 103_G | 1.306 | 0.99 |
| 84_T | 105_I | 1.281 | 0.99 |
| 69_L | 152_L | 1.275 | 0.99 |
| 30_D | 33_E | 1.274 | 0.99 |
| 68_D | 71_A | 1.271 | 0.99 |
| 157_V | 161_L | 1.249 | 0.99 |
| 29_L | 89_V | 1.244 | 0.98 |
| 30_D | 134_G | 1.230 | 0.98 |
| 87_V | 106_L | 1.204 | 0.98 |
| 89_V | 104_L | 1.201 | 0.98 |
| 19_L | 111_D | 1.196 | 0.98 |
| 120_F | 146_W | 1.168 | 0.97 |
| 35_V | 62_V | 1.166 | 0.97 |
| 133_L | 145_Q | 1.148 | 0.97 |
| 34_V | 87_V | 1.145 | 0.97 |
| 89_V | 149_V | 1.144 | 0.97 |
| 21_R | 26_R | 1.143 | 0.97 |
| 57_F | 66_V | 1.135 | 0.97 |
| 64_V | 103_G | 1.128 | 0.97 |
| 40_L | 86_I | 1.127 | 0.97 |
| 12_R | 118_S | 1.121 | 0.97 |
| 17_F | 115_C | 1.104 | 0.96 |
| 22_M | 69_L | 1.102 | 0.96 |
| 44_K | 58_S | 1.101 | 0.96 |
| 137_Y | 146_W | 1.100 | 0.96 |
| 40_L | 105_I | 1.087 | 0.96 |
| 57_F | 86_I | 1.076 | 0.95 |
| 28_A | 146_W | 1.073 | 0.95 |
| 20_F | 87_V | 1.071 | 0.95 |
| 15_K | 117_P | 1.062 | 0.95 |
| 26_R | 110_T | 1.051 | 0.94 |
| 33_E | 149_V | 1.051 | 0.94 |
| 14_S | 114_R | 1.044 | 0.94 |
| 19_L | 113_L | 1.036 | 0.94 |
| 9_D | 12_R | 1.028 | 0.94 |
| 19_L | 28_A | 1.022 | 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 | |
| 2ho9A | 1 | 0.9532 | 99.9 | 0.271 | Contact Map |
| 2qdlA | 2 | 0.8947 | 99.9 | 0.278 | Contact Map |
| 4jpbW | 1 | 0.8187 | 99.9 | 0.28 | Contact Map |
| 1b3qA | 2 | 0.8129 | 99.5 | 0.539 | Contact Map |
| 1sva1 | 6 | 0.3918 | 2.9 | 0.94 | Contact Map |
| 1oewA | 1 | 0.4971 | 2.9 | 0.94 | Contact Map |
| 2xvcA | 1 | 0.2982 | 1.7 | 0.947 | Contact Map |
| 3lapA | 6 | 0.6491 | 1.7 | 0.947 | Contact Map |
| 4o0aA | 1 | 0.6784 | 1.5 | 0.948 | Contact Map |
| 4yx7A | 2 | 0 | 1.4 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)