| bho-c |
| ID: | 1483024552 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (71) | ||
| Sequences: | 134 (94.4) | ||
| Seq/Len: | 1.887 | ||
| Nf(neff/√len): | 11.2 |
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: 1.887).
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_Y | 23_D | 3.245 | 1.00 |
| 34_I | 46_M | 2.531 | 1.00 |
| 16_D | 19_K | 2.165 | 0.99 |
| 16_D | 20_K | 1.854 | 0.98 |
| 34_I | 42_A | 1.838 | 0.98 |
| 11_Y | 19_K | 1.775 | 0.97 |
| 28_P | 32_A | 1.728 | 0.96 |
| 45_Y | 48_R | 1.720 | 0.96 |
| 58_G | 61_D | 1.528 | 0.91 |
| 29_M | 33_T | 1.451 | 0.88 |
| 25_Q | 39_Q | 1.435 | 0.87 |
| 44_Y | 48_R | 1.422 | 0.87 |
| 18_L | 33_T | 1.397 | 0.85 |
| 7_P | 52_S | 1.266 | 0.77 |
| 1_G | 42_A | 1.253 | 0.76 |
| 47_N | 50_I | 1.232 | 0.74 |
| 10_V | 14_L | 1.214 | 0.72 |
| 1_G | 41_E | 1.195 | 0.71 |
| 32_A | 36_K | 1.190 | 0.70 |
| 20_K | 24_A | 1.190 | 0.70 |
| 17_E | 36_K | 1.189 | 0.70 |
| 4_G | 14_L | 1.149 | 0.66 |
| 4_G | 15_P | 1.145 | 0.66 |
| 39_Q | 43_I | 1.144 | 0.66 |
| 59_K | 62_E | 1.142 | 0.66 |
| 18_L | 21_C | 1.142 | 0.66 |
| 21_C | 29_M | 1.131 | 0.65 |
| 20_K | 31_Q | 1.130 | 0.64 |
| 31_Q | 57_P | 1.107 | 0.62 |
| 6_D | 9_E | 1.077 | 0.59 |
| 34_I | 37_I | 1.068 | 0.58 |
| 64_P | 69_S | 1.056 | 0.57 |
| 6_D | 15_P | 1.055 | 0.57 |
| 1_G | 46_M | 1.033 | 0.54 |
| 25_Q | 28_P | 1.011 | 0.52 |
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 | |
| 1us7B | 1 | 0.6163 | 100 | 0.212 | Contact Map |
| 2kwvA | 1 | 0.3488 | 57.8 | 0.89 | Contact Map |
| 2mbbA | 1 | 0.3837 | 46 | 0.897 | Contact Map |
| 3ai4A | 1 | 0.3023 | 26.8 | 0.909 | Contact Map |
| 2khuA | 1 | 0.3372 | 26.1 | 0.91 | Contact Map |
| 4umkA | 4 | 0 | 18.5 | 0.916 | Contact Map |
| 4mdaA | 1 | 0.6047 | 13.7 | 0.921 | Contact Map |
| 2bw2A | 1 | 0.4884 | 11.6 | 0.923 | Contact Map |
| 3gvpA | 4 | 0.6279 | 11.5 | 0.924 | Contact Map |
| 1vz0A | 8 | 0.7791 | 10.8 | 0.924 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)