| d2dtte_ |
| ID: | 1449072602 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (114) | ||
| Sequences: | 2412 (1557.8) | ||
| Seq/Len: | 21.158 | ||
| Nf(neff/√len): | 145.9 |
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: 21.158).
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 |
| 12_D | 30_T | 3.295 | 1.00 |
| 39_G | 46_V | 2.948 | 1.00 |
| 100_R | 114_E | 2.709 | 1.00 |
| 82_L | 86_E | 2.571 | 1.00 |
| 8_R | 32_F | 2.540 | 1.00 |
| 62_E | 87_R | 2.486 | 1.00 |
| 102_V | 112_E | 2.460 | 1.00 |
| 100_R | 112_E | 2.333 | 1.00 |
| 4_R | 38_E | 2.288 | 1.00 |
| 6_I | 36_A | 2.281 | 1.00 |
| 63_L | 83_W | 2.277 | 1.00 |
| 34_E | 102_V | 2.257 | 1.00 |
| 8_R | 34_E | 2.097 | 1.00 |
| 16_A | 67_N | 2.045 | 1.00 |
| 6_I | 110_G | 2.023 | 1.00 |
| 37_I | 52_L | 1.893 | 1.00 |
| 85_G | 113_L | 1.858 | 1.00 |
| 33_L | 103_L | 1.809 | 1.00 |
| 36_A | 100_R | 1.792 | 1.00 |
| 11_F | 33_L | 1.789 | 1.00 |
| 38_E | 99_K | 1.678 | 1.00 |
| 35_V | 88_I | 1.634 | 1.00 |
| 34_E | 104_W | 1.561 | 1.00 |
| 25_D | 66_R | 1.505 | 1.00 |
| 63_L | 84_I | 1.484 | 1.00 |
| 4_R | 36_A | 1.470 | 1.00 |
| 26_V | 67_N | 1.437 | 1.00 |
| 69_N | 75_P | 1.402 | 0.99 |
| 83_W | 87_R | 1.382 | 0.99 |
| 44_G | 79_N | 1.365 | 0.99 |
| 82_L | 113_L | 1.354 | 0.99 |
| 22_H | 50_L | 1.342 | 0.99 |
| 23_W | 65_H | 1.288 | 0.99 |
| 6_I | 102_V | 1.287 | 0.99 |
| 3_S | 82_L | 1.281 | 0.99 |
| 9_T | 53_R | 1.251 | 0.99 |
| 14_A | 67_N | 1.231 | 0.98 |
| 4_R | 112_E | 1.226 | 0.98 |
| 58_E | 91_K | 1.226 | 0.98 |
| 6_I | 34_E | 1.216 | 0.98 |
| 17_V | 20_G | 1.207 | 0.98 |
| 57_E | 61_K | 1.193 | 0.98 |
| 4_R | 99_K | 1.184 | 0.98 |
| 35_V | 56_V | 1.170 | 0.97 |
| 9_T | 56_V | 1.169 | 0.97 |
| 79_N | 82_L | 1.141 | 0.97 |
| 87_R | 90_D | 1.131 | 0.97 |
| 4_R | 114_E | 1.111 | 0.96 |
| 37_I | 47_M | 1.110 | 0.96 |
| 32_F | 107_K | 1.069 | 0.95 |
| 55_I | 58_E | 1.037 | 0.94 |
| 35_V | 101_V | 1.028 | 0.94 |
| 13_A | 31_F | 1.016 | 0.93 |
| 30_T | 107_K | 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 | |
| 2dj6A | 3 | 1 | 100 | 0.054 | Contact Map |
| 3d7jA | 6 | 1 | 100 | 0.069 | Contact Map |
| 2obaA | 6 | 0.9739 | 100 | 0.102 | Contact Map |
| 1b66A | 2 | 0.9913 | 100 | 0.111 | Contact Map |
| 2g64A | 1 | 1 | 100 | 0.112 | Contact Map |
| 4ntkA | 6 | 0.9739 | 100 | 0.119 | Contact Map |
| 3jygA | 6 | 0.9913 | 100 | 0.121 | Contact Map |
| 1y13A | 3 | 1 | 100 | 0.125 | Contact Map |
| 3lx3A | 1 | 1 | 100 | 0.129 | Contact Map |
| 3r2eA | 1 | 0.8696 | 46 | 0.897 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)