| cwet |
| ID: | 1513356916 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (109) | ||
| Sequences: | 332 (191) | ||
| Seq/Len: | 3.046 | ||
| Nf(neff/√len): | 18.3 |
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: 3.046).
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_E | 7_G | 2.468 | 1.00 |
| 53_T | 60_V | 2.414 | 1.00 |
| 1_C | 7_G | 2.035 | 1.00 |
| 2_W | 17_D | 1.865 | 0.99 |
| 63_Q | 67_W | 1.686 | 0.98 |
| 17_D | 83_K | 1.667 | 0.98 |
| 66_V | 80_A | 1.651 | 0.98 |
| 2_W | 8_E | 1.643 | 0.98 |
| 32_I | 46_D | 1.568 | 0.97 |
| 2_W | 7_G | 1.567 | 0.97 |
| 69_G | 76_M | 1.544 | 0.97 |
| 57_L | 67_W | 1.540 | 0.97 |
| 4_N | 8_E | 1.536 | 0.96 |
| 88_F | 91_R | 1.533 | 0.96 |
| 57_L | 63_Q | 1.533 | 0.96 |
| 82_V | 85_F | 1.480 | 0.95 |
| 70_L | 85_F | 1.463 | 0.95 |
| 50_F | 67_W | 1.399 | 0.93 |
| 59_L | 84_L | 1.374 | 0.92 |
| 10_I | 16_V | 1.313 | 0.90 |
| 16_V | 104_K | 1.301 | 0.89 |
| 71_Y | 109_S | 1.243 | 0.86 |
| 56_V | 77_A | 1.242 | 0.86 |
| 60_V | 106_F | 1.234 | 0.86 |
| 6_V | 78_L | 1.228 | 0.85 |
| 43_C | 72_F | 1.206 | 0.84 |
| 10_I | 104_K | 1.206 | 0.84 |
| 79_V | 87_V | 1.198 | 0.83 |
| 4_N | 7_G | 1.187 | 0.83 |
| 1_C | 9_E | 1.185 | 0.82 |
| 71_Y | 108_A | 1.179 | 0.82 |
| 29_D | 98_A | 1.165 | 0.81 |
| 33_A | 37_R | 1.162 | 0.81 |
| 50_F | 63_Q | 1.153 | 0.80 |
| 13_L | 17_D | 1.152 | 0.80 |
| 1_C | 8_E | 1.147 | 0.80 |
| 53_T | 106_F | 1.138 | 0.79 |
| 69_G | 74_P | 1.133 | 0.78 |
| 9_E | 12_K | 1.097 | 0.75 |
| 52_V | 84_L | 1.090 | 0.75 |
| 73_S | 92_Y | 1.090 | 0.75 |
| 73_S | 85_F | 1.069 | 0.72 |
| 29_D | 55_N | 1.064 | 0.72 |
| 9_E | 106_F | 1.060 | 0.72 |
| 20_V | 86_I | 1.057 | 0.71 |
| 70_L | 84_L | 1.054 | 0.71 |
| 103_K | 107_R | 1.053 | 0.71 |
| 22_I | 90_F | 1.045 | 0.70 |
| 2_W | 9_E | 1.036 | 0.69 |
| 25_G | 94_V | 1.030 | 0.68 |
| 1_C | 4_N | 1.028 | 0.68 |
| 38_T | 85_F | 1.021 | 0.67 |
| 54_S | 58_D | 1.016 | 0.67 |
| 57_L | 77_A | 1.013 | 0.67 |
| 12_K | 48_S | 1.013 | 0.67 |
| 50_F | 57_L | 1.009 | 0.66 |
| 18_L | 92_Y | 1.005 | 0.66 |
| 57_L | 60_V | 1.002 | 0.65 |
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 | |
| 2mzzA | 1 | 0 | 14.2 | 0.931 | Contact Map |
| 4xxoA | 2 | 0 | 8 | 0.939 | Contact Map |
| 4wisA | 2 | 0.9358 | 4.6 | 0.945 | Contact Map |
| 4bkfC | 2 | 0.0917 | 2.4 | 0.952 | Contact Map |
| 4k5yA | 3 | 0.9633 | 2.3 | 0.952 | Contact Map |
| 3og6A | 1 | 0.2385 | 1.7 | 0.956 | Contact Map |
| 1osnA | 4 | 0.3119 | 1.7 | 0.956 | Contact Map |
| 1jb0M | 1 | 0.1101 | 1.4 | 0.958 | Contact Map |
| 4b19A | 1 | 0.2752 | 1.2 | 0.96 | Contact Map |
| 2vq5A | 2 | 0.3578 | 1.2 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)