| 1DUNA |
| ID: | 1411760161 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 120 (108) | ||
| Sequences: | 2123 (1249.2) | ||
| Seq/Len: | 19.657 | ||
| Nf(neff/√len): | 120.2 |
HHblits Results: (2013_03)
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: 19.657).
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 |
| 16_D | 74_G | 3.730 | 1.00 |
| 94_I | 97_Q | 2.952 | 1.00 |
| 30_P | 90_N | 2.744 | 1.00 |
| 51_G | 102_L | 2.708 | 1.00 |
| 26_D | 94_I | 2.665 | 1.00 |
| 18_G | 103_I | 2.656 | 1.00 |
| 64_L | 91_I | 2.550 | 1.00 |
| 44_Q | 76_T | 2.368 | 1.00 |
| 19_F | 112_R | 2.241 | 1.00 |
| 30_P | 33_D | 2.240 | 1.00 |
| 34_T | 63_G | 2.198 | 1.00 |
| 54_T | 70_I | 2.150 | 1.00 |
| 56_K | 98_K | 2.049 | 1.00 |
| 31_V | 90_N | 2.046 | 1.00 |
| 61_K | 82_I | 2.035 | 1.00 |
| 15_E | 73_E | 1.907 | 1.00 |
| 45_V | 104_I | 1.803 | 1.00 |
| 26_D | 95_E | 1.787 | 1.00 |
| 40_D | 78_E | 1.682 | 1.00 |
| 38_P | 80_Q | 1.679 | 1.00 |
| 28_M | 92_K | 1.672 | 1.00 |
| 52_W | 70_I | 1.671 | 1.00 |
| 33_D | 88_K | 1.658 | 1.00 |
| 52_W | 105_L | 1.574 | 1.00 |
| 36_I | 80_Q | 1.562 | 1.00 |
| 23_V | 93_L | 1.526 | 1.00 |
| 43_I | 51_G | 1.486 | 1.00 |
| 65_L | 84_T | 1.443 | 1.00 |
| 69_G | 72_D | 1.419 | 1.00 |
| 21_L | 51_G | 1.396 | 0.99 |
| 54_T | 105_L | 1.370 | 0.99 |
| 38_P | 78_E | 1.370 | 0.99 |
| 28_M | 90_N | 1.357 | 0.99 |
| 12_K | 22_C | 1.342 | 0.99 |
| 24_P | 95_E | 1.331 | 0.99 |
| 50_F | 70_I | 1.311 | 0.99 |
| 39_T | 81_V | 1.283 | 0.99 |
| 49_S | 104_I | 1.279 | 0.99 |
| 29_I | 35_K | 1.275 | 0.99 |
| 53_V | 102_L | 1.237 | 0.98 |
| 65_L | 86_I | 1.226 | 0.98 |
| 45_V | 51_G | 1.222 | 0.98 |
| 26_D | 92_K | 1.219 | 0.98 |
| 57_S | 101_Q | 1.187 | 0.98 |
| 13_R | 19_F | 1.173 | 0.98 |
| 36_I | 61_K | 1.144 | 0.97 |
| 50_F | 54_T | 1.106 | 0.96 |
| 51_G | 104_I | 1.101 | 0.96 |
| 32_S | 88_K | 1.083 | 0.96 |
| 31_V | 85_N | 1.067 | 0.95 |
| 50_F | 105_L | 1.024 | 0.93 |
| 45_V | 49_S | 1.021 | 0.93 |
| 43_I | 79_I | 1.016 | 0.93 |
| 72_D | 77_G | 1.000 | 0.92 |
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 | |
| 1dunA | 1 | 1 | 100 | 0.091 | Contact Map |
| 1f7dA | 2 | 0.9833 | 100 | 0.119 | Contact Map |
| 3f4fA | 3 | 1 | 100 | 0.135 | Contact Map |
| 3ca9A | 2 | 0.975 | 100 | 0.136 | Contact Map |
| 3lqwA | 1 | 1 | 100 | 0.137 | Contact Map |
| 3c2tA | 2 | 0.975 | 100 | 0.142 | Contact Map |
| 3p48A | 3 | 0.9917 | 100 | 0.144 | Contact Map |
| 3zf6A | 1 | 1 | 100 | 0.144 | Contact Map |
| 3so2A | 1 | 1 | 100 | 0.145 | Contact Map |
| 2ol1A | 3 | 0.9833 | 100 | 0.146 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)