| 2y64 |
| ID: | 1492603625 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (166) | ||
| Sequences: | 502 (428.8) | ||
| Seq/Len: | 3.024 | ||
| Nf(neff/√len): | 33.3 |
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: 3.024).
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 |
| 91_R | 161_G | 6.257 | 1.00 |
| 88_Y | 164_I | 4.052 | 1.00 |
| 84_V | 166_D | 3.847 | 1.00 |
| 87_T | 129_T | 3.017 | 1.00 |
| 87_T | 131_E | 2.780 | 1.00 |
| 93_R | 125_W | 2.721 | 1.00 |
| 91_R | 127_P | 2.469 | 1.00 |
| 159_I | 162_L | 2.240 | 1.00 |
| 92_A | 121_I | 2.238 | 1.00 |
| 92_A | 128_F | 2.214 | 1.00 |
| 87_T | 165_V | 2.022 | 1.00 |
| 57_L | 73_A | 1.936 | 0.99 |
| 91_R | 125_W | 1.934 | 0.99 |
| 56_V | 93_R | 1.920 | 0.99 |
| 93_R | 158_Y | 1.880 | 0.99 |
| 85_T | 133_T | 1.880 | 0.99 |
| 89_T | 127_P | 1.860 | 0.99 |
| 11_E | 160_D | 1.816 | 0.99 |
| 58_A | 158_Y | 1.751 | 0.99 |
| 67_N | 70_N | 1.550 | 0.97 |
| 61_V | 157_I | 1.548 | 0.97 |
| 56_V | 125_W | 1.529 | 0.96 |
| 110_F | 113_Y | 1.444 | 0.94 |
| 8_G | 162_L | 1.438 | 0.94 |
| 85_T | 131_E | 1.420 | 0.94 |
| 80_V | 141_I | 1.351 | 0.91 |
| 81_R | 166_D | 1.350 | 0.91 |
| 138_E | 141_I | 1.304 | 0.89 |
| 142_R | 146_H | 1.279 | 0.88 |
| 94_A | 155_N | 1.264 | 0.87 |
| 95_E | 156_T | 1.260 | 0.87 |
| 80_V | 164_I | 1.228 | 0.85 |
| 11_E | 53_G | 1.227 | 0.85 |
| 8_G | 160_D | 1.224 | 0.85 |
| 67_N | 71_I | 1.194 | 0.83 |
| 30_L | 65_G | 1.172 | 0.81 |
| 65_G | 113_Y | 1.170 | 0.81 |
| 30_L | 40_P | 1.169 | 0.81 |
| 28_W | 162_L | 1.163 | 0.81 |
| 37_T | 70_N | 1.154 | 0.80 |
| 113_Y | 134_V | 1.133 | 0.78 |
| 60_T | 156_T | 1.132 | 0.78 |
| 14_P | 23_E | 1.118 | 0.77 |
| 11_E | 55_K | 1.114 | 0.77 |
| 89_T | 163_A | 1.099 | 0.75 |
| 7_N | 75_A | 1.089 | 0.74 |
| 125_W | 160_D | 1.080 | 0.73 |
| 104_T | 142_R | 1.077 | 0.73 |
| 5_N | 8_G | 1.077 | 0.73 |
| 16_G | 19_T | 1.073 | 0.73 |
| 16_G | 20_D | 1.063 | 0.72 |
| 40_P | 71_I | 1.057 | 0.71 |
| 56_V | 160_D | 1.056 | 0.71 |
| 16_G | 21_L | 1.056 | 0.71 |
| 72_Q | 113_Y | 1.049 | 0.70 |
| 7_N | 10_F | 1.047 | 0.70 |
| 145_I | 162_L | 1.039 | 0.69 |
| 134_V | 138_E | 1.035 | 0.69 |
| 81_R | 84_V | 1.017 | 0.67 |
| 98_G | 157_I | 1.013 | 0.66 |
| 4_A | 107_N | 1.012 | 0.66 |
| 3_V | 70_N | 1.010 | 0.66 |
| 90_I | 119_Q | 1.003 | 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 | |
| 1gu3A | 1 | 0.7904 | 99.9 | 0.293 | Contact Map |
| 3k4zA | 1 | 0.9162 | 99.9 | 0.294 | Contact Map |
| 1cx1A | 1 | 0.8263 | 99.9 | 0.298 | Contact Map |
| 3p6bA | 2 | 0.9162 | 99.9 | 0.303 | Contact Map |
| 4bj0A | 1 | 0.976 | 99.9 | 0.331 | Contact Map |
| 4qpwA | 1 | 0.8443 | 99.9 | 0.357 | Contact Map |
| 4mgqA | 1 | 0.7305 | 99.9 | 0.38 | Contact Map |
| 1guiA | 1 | 0.8862 | 99.9 | 0.397 | Contact Map |
| 4d0qA | 1 | 0.9042 | 99.7 | 0.494 | Contact Map |
| 2zezA | 4 | 0.8323 | 99.6 | 0.534 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)