| d3u35d_ |
| ID: | 1449072564 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (130) | ||
| Sequences: | 8623 (5864.3) | ||
| Seq/Len: | 66.331 | ||
| Nf(neff/√len): | 514.3 |
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: 66.331).
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 |
| 21_G | 30_A | 3.191 | 1.00 |
| 85_R | 120_D | 3.101 | 1.00 |
| 44_P | 118_R | 3.052 | 1.00 |
| 19_M | 30_A | 2.927 | 1.00 |
| 83_S | 122_D | 2.591 | 1.00 |
| 22_L | 58_M | 2.582 | 1.00 |
| 85_R | 118_R | 2.530 | 1.00 |
| 82_G | 119_L | 2.371 | 1.00 |
| 65_V | 119_L | 2.333 | 1.00 |
| 18_V | 67_G | 2.138 | 1.00 |
| 81_S | 123_H | 2.018 | 1.00 |
| 65_V | 84_L | 1.912 | 1.00 |
| 23_D | 62_G | 1.857 | 1.00 |
| 19_M | 32_P | 1.839 | 1.00 |
| 64_R | 83_S | 1.838 | 1.00 |
| 84_L | 117_L | 1.833 | 1.00 |
| 19_M | 68_A | 1.759 | 1.00 |
| 30_A | 68_A | 1.756 | 1.00 |
| 20_L | 65_V | 1.717 | 1.00 |
| 29_H | 58_M | 1.665 | 1.00 |
| 94_D | 110_T | 1.656 | 1.00 |
| 19_M | 70_S | 1.634 | 1.00 |
| 51_K | 115_A | 1.610 | 1.00 |
| 23_D | 28_G | 1.578 | 1.00 |
| 56_I | 117_L | 1.554 | 1.00 |
| 35_A | 69_F | 1.526 | 1.00 |
| 25_V | 61_Q | 1.516 | 1.00 |
| 44_P | 120_D | 1.508 | 1.00 |
| 10_K | 14_S | 1.477 | 1.00 |
| 46_W | 118_R | 1.472 | 1.00 |
| 31_R | 58_M | 1.426 | 1.00 |
| 86_E | 115_A | 1.411 | 1.00 |
| 54_A | 58_M | 1.406 | 0.99 |
| 59_L | 65_V | 1.400 | 0.99 |
| 83_S | 120_D | 1.387 | 0.99 |
| 86_E | 117_L | 1.374 | 0.99 |
| 30_A | 66_I | 1.364 | 0.99 |
| 47_F | 117_L | 1.339 | 0.99 |
| 84_L | 119_L | 1.335 | 0.99 |
| 47_F | 119_L | 1.323 | 0.99 |
| 54_A | 81_S | 1.300 | 0.99 |
| 80_I | 121_A | 1.276 | 0.99 |
| 12_L | 69_F | 1.257 | 0.99 |
| 94_D | 98_N | 1.254 | 0.99 |
| 29_H | 81_S | 1.243 | 0.98 |
| 71_S | 76_L | 1.242 | 0.98 |
| 67_G | 119_L | 1.232 | 0.98 |
| 33_M | 47_F | 1.213 | 0.98 |
| 52_D | 113_N | 1.191 | 0.98 |
| 66_I | 79_S | 1.187 | 0.98 |
| 67_G | 80_I | 1.186 | 0.98 |
| 66_I | 81_S | 1.176 | 0.98 |
| 60_G | 86_E | 1.174 | 0.98 |
| 47_F | 82_G | 1.167 | 0.97 |
| 49_T | 56_I | 1.165 | 0.97 |
| 38_E | 42_G | 1.152 | 0.97 |
| 15_D | 69_F | 1.127 | 0.97 |
| 80_I | 124_A | 1.125 | 0.97 |
| 7_K | 10_K | 1.115 | 0.96 |
| 59_L | 84_L | 1.104 | 0.96 |
| 38_E | 95_R | 1.095 | 0.96 |
| 29_H | 54_A | 1.088 | 0.96 |
| 56_I | 60_G | 1.076 | 0.95 |
| 50_S | 113_N | 1.069 | 0.95 |
| 40_D | 43_G | 1.064 | 0.95 |
| 45_I | 67_G | 1.044 | 0.94 |
| 57_A | 60_G | 1.033 | 0.94 |
| 87_D | 118_R | 1.011 | 0.93 |
| 15_D | 35_A | 1.010 | 0.93 |
| 9_W | 37_I | 1.006 | 0.93 |
| 5_Q | 9_W | 1.002 | 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 | |
| 3u35A | 4 | 1 | 99.9 | 0.168 | Contact Map |
| 3dmbA | 3 | 1 | 99.9 | 0.186 | Contact Map |
| 2i02A | 2 | 0.9787 | 99.9 | 0.232 | Contact Map |
| 2qeaA | 3 | 0.9787 | 99.9 | 0.232 | Contact Map |
| 2re7A | 1 | 0.922 | 99.9 | 0.244 | Contact Map |
| 2fhqA | 2 | 0.9504 | 99.8 | 0.25 | Contact Map |
| 2hq7A | 2 | 0.9929 | 99.8 | 0.256 | Contact Map |
| 1dnlA | 1 | 0.9716 | 99.8 | 0.269 | Contact Map |
| 3db0A | 2 | 0.8865 | 99.8 | 0.279 | Contact Map |
| 2iabA | 2 | 0.9645 | 99.8 | 0.281 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)