| d3vpdb1 |
| ID: | 1448766129 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (88) | ||
| Sequences: | 257 (201.5) | ||
| Seq/Len: | 2.920 | ||
| Nf(neff/√len): | 21.5 |
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: 2.920).
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 |
| 10_R | 13_E | 2.623 | 1.00 |
| 8_R | 86_C | 1.884 | 0.99 |
| 1_M | 28_K | 1.819 | 0.99 |
| 2_L | 51_V | 1.638 | 0.98 |
| 9_I | 14_R | 1.546 | 0.96 |
| 57_V | 87_G | 1.497 | 0.95 |
| 76_V | 86_C | 1.489 | 0.95 |
| 70_T | 80_P | 1.486 | 0.95 |
| 11_P | 15_M | 1.444 | 0.94 |
| 28_K | 49_V | 1.364 | 0.91 |
| 52_A | 69_L | 1.353 | 0.91 |
| 32_V | 56_C | 1.325 | 0.90 |
| 1_M | 88_D | 1.313 | 0.89 |
| 64_A | 88_D | 1.309 | 0.89 |
| 58_S | 83_I | 1.285 | 0.88 |
| 24_G | 34_A | 1.273 | 0.87 |
| 12_D | 59_Q | 1.235 | 0.85 |
| 17_F | 27_Y | 1.232 | 0.85 |
| 19_R | 65_A | 1.216 | 0.84 |
| 29_K | 56_C | 1.182 | 0.81 |
| 59_Q | 62_G | 1.177 | 0.81 |
| 7_D | 57_V | 1.171 | 0.80 |
| 17_F | 22_A | 1.170 | 0.80 |
| 6_Y | 66_A | 1.166 | 0.80 |
| 59_Q | 87_G | 1.156 | 0.79 |
| 37_M | 50_T | 1.140 | 0.78 |
| 1_M | 50_T | 1.139 | 0.78 |
| 54_E | 62_G | 1.138 | 0.78 |
| 19_R | 41_E | 1.136 | 0.78 |
| 2_L | 86_C | 1.130 | 0.77 |
| 14_R | 71_A | 1.081 | 0.72 |
| 7_D | 33_P | 1.070 | 0.71 |
| 7_D | 13_E | 1.059 | 0.70 |
| 4_I | 36_P | 1.046 | 0.69 |
| 12_D | 49_V | 1.034 | 0.68 |
| 6_Y | 13_E | 1.028 | 0.67 |
| 7_D | 58_S | 1.028 | 0.67 |
| 54_E | 57_V | 1.021 | 0.66 |
| 2_L | 79_R | 1.016 | 0.66 |
| 51_V | 82_V | 1.016 | 0.66 |
| 18_E | 21_E | 1.013 | 0.65 |
| 13_E | 58_S | 1.010 | 0.65 |
| 14_R | 48_G | 1.009 | 0.65 |
| 4_I | 17_F | 1.002 | 0.64 |
| 66_A | 83_I | 1.001 | 0.64 |
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 | |
| 3vpdA | 2 | 1 | 98.8 | 0.558 | Contact Map |
| 3vpbA | 4 | 0.9659 | 98.5 | 0.604 | Contact Map |
| 4iwxA | 1 | 1 | 97.8 | 0.668 | Contact Map |
| 1gsaA | 1 | 1 | 97.7 | 0.676 | Contact Map |
| 3r5xA | 4 | 0.9545 | 97.4 | 0.694 | Contact Map |
| 4c5cA | 2 | 0.9545 | 97 | 0.71 | Contact Map |
| 2q7dA | 2 | 0.9205 | 96.9 | 0.714 | Contact Map |
| 2p0aA | 2 | 0.9545 | 96.7 | 0.721 | Contact Map |
| 3e5nA | 1 | 0.9886 | 96.6 | 0.726 | Contact Map |
| 2i87A | 2 | 1 | 96.5 | 0.73 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)