| agb |
| ID: | 1490111890 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (83) | ||
| Sequences: | 131 (122.3) | ||
| Seq/Len: | 1.578 | ||
| Nf(neff/√len): | 13.4 |
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: 1.578).
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 |
| 26_L | 49_G | 1.834 | 0.96 |
| 16_K | 19_D | 1.706 | 0.94 |
| 53_D | 60_K | 1.545 | 0.89 |
| 20_G | 53_D | 1.381 | 0.80 |
| 42_V | 69_L | 1.366 | 0.79 |
| 8_T | 78_A | 1.356 | 0.79 |
| 32_V | 43_G | 1.337 | 0.77 |
| 21_T | 54_K | 1.319 | 0.76 |
| 3_D | 17_T | 1.304 | 0.75 |
| 7_L | 32_V | 1.274 | 0.72 |
| 51_F | 60_K | 1.267 | 0.72 |
| 38_D | 73_E | 1.264 | 0.72 |
| 1_D | 4_R | 1.247 | 0.70 |
| 8_T | 16_K | 1.235 | 0.69 |
| 40_G | 73_E | 1.214 | 0.67 |
| 38_D | 71_G | 1.206 | 0.66 |
| 5_K | 9_A | 1.186 | 0.65 |
| 7_L | 36_D | 1.182 | 0.64 |
| 22_T | 74_A | 1.178 | 0.64 |
| 9_A | 23_T | 1.168 | 0.63 |
| 66_G | 69_L | 1.163 | 0.62 |
| 12_D | 17_T | 1.161 | 0.62 |
| 11_A | 79_F | 1.155 | 0.61 |
| 32_V | 82_D | 1.149 | 0.61 |
| 2_I | 5_K | 1.135 | 0.59 |
| 11_A | 67_I | 1.128 | 0.59 |
| 22_T | 25_N | 1.126 | 0.59 |
| 6_L | 78_A | 1.115 | 0.57 |
| 40_G | 71_G | 1.111 | 0.57 |
| 79_F | 82_D | 1.110 | 0.57 |
| 26_L | 66_G | 1.109 | 0.57 |
| 35_V | 39_E | 1.109 | 0.57 |
| 4_R | 78_A | 1.101 | 0.56 |
| 51_F | 62_V | 1.092 | 0.55 |
| 43_G | 78_A | 1.083 | 0.54 |
| 4_R | 11_A | 1.082 | 0.54 |
| 24_A | 51_F | 1.081 | 0.54 |
| 4_R | 50_A | 1.077 | 0.54 |
| 6_L | 50_A | 1.073 | 0.53 |
| 51_F | 73_E | 1.069 | 0.53 |
| 28_N | 82_D | 1.069 | 0.53 |
| 10_N | 29_V | 1.056 | 0.51 |
| 65_S | 78_A | 1.052 | 0.51 |
| 1_D | 80_D | 1.050 | 0.51 |
| 39_E | 82_D | 1.050 | 0.51 |
| 19_D | 51_F | 1.050 | 0.51 |
| 17_T | 47_T | 1.042 | 0.50 |
| 13_V | 73_E | 1.032 | 0.49 |
| 9_A | 48_T | 1.028 | 0.48 |
| 34_I | 40_G | 1.021 | 0.48 |
| 54_K | 57_G | 1.016 | 0.47 |
| 11_A | 48_T | 1.013 | 0.47 |
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 | |
| 4ng0A | 3 | 0.8864 | 6.9 | 0.894 | Contact Map |
| 2xyyA | 7 | 0.9545 | 1.8 | 0.921 | Contact Map |
| 4p99A | 4 | 0.9205 | 1.7 | 0.922 | Contact Map |
| 1cwvA | 1 | 0.8636 | 1.3 | 0.927 | Contact Map |
| 2ccvA | 1 | 0.3182 | 1.1 | 0.931 | Contact Map |
| 2wn3A | 3 | 0.3409 | 0.9 | 0.934 | Contact Map |
| 2cujA | 1 | 0.3409 | 0.9 | 0.935 | Contact Map |
| 2aqeA | 1 | 0.3409 | 0.8 | 0.935 | Contact Map |
| 4mb4A | 1 | 0.8523 | 0.8 | 0.936 | Contact Map |
| 4kdwA | 1 | 0.9091 | 0.8 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)