| 1IMQ |
| ID: | 1429455143 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (86) | ||
| Sequences: | 179 (143.9) | ||
| Seq/Len: | 2.081 | ||
| Nf(neff/√len): | 15.5 |
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: 2.081).
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 |
| 19_V | 68_V | 3.323 | 1.00 |
| 45_E | 80_K | 2.499 | 1.00 |
| 69_N | 73_Q | 2.319 | 1.00 |
| 39_H | 42_E | 2.190 | 1.00 |
| 77_A | 82_G | 2.077 | 0.99 |
| 73_Q | 77_A | 1.937 | 0.99 |
| 39_H | 43_M | 1.768 | 0.97 |
| 63_S | 66_G | 1.737 | 0.97 |
| 78_N | 82_G | 1.716 | 0.97 |
| 60_D | 70_T | 1.678 | 0.96 |
| 27_T | 36_L | 1.636 | 0.95 |
| 62_D | 66_G | 1.610 | 0.95 |
| 48_S | 57_K | 1.591 | 0.94 |
| 77_A | 80_K | 1.441 | 0.89 |
| 49_G | 52_L | 1.416 | 0.88 |
| 12_E | 72_K | 1.409 | 0.88 |
| 16_L | 68_V | 1.409 | 0.88 |
| 58_E | 66_G | 1.377 | 0.86 |
| 56_P | 66_G | 1.360 | 0.85 |
| 77_A | 85_Q | 1.352 | 0.85 |
| 81_S | 84_K | 1.325 | 0.83 |
| 5_H | 9_D | 1.318 | 0.83 |
| 30_E | 33_L | 1.299 | 0.82 |
| 41_E | 50_S | 1.296 | 0.81 |
| 30_E | 37_V | 1.242 | 0.77 |
| 23_C | 61_D | 1.227 | 0.76 |
| 7_I | 86_G | 1.213 | 0.75 |
| 59_G | 63_S | 1.184 | 0.73 |
| 18_L | 40_F | 1.177 | 0.72 |
| 57_K | 60_D | 1.163 | 0.71 |
| 36_L | 67_I | 1.154 | 0.70 |
| 23_C | 67_I | 1.142 | 0.69 |
| 1_M | 80_K | 1.108 | 0.65 |
| 56_P | 63_S | 1.096 | 0.64 |
| 17_Q | 67_I | 1.093 | 0.64 |
| 37_V | 54_Y | 1.081 | 0.62 |
| 11_T | 84_K | 1.072 | 0.61 |
| 66_G | 69_N | 1.066 | 0.61 |
| 66_G | 70_T | 1.050 | 0.59 |
| 56_P | 62_D | 1.036 | 0.58 |
| 44_T | 69_N | 1.012 | 0.55 |
| 4_K | 14_E | 1.011 | 0.55 |
| 76_A | 82_G | 1.001 | 0.54 |
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 | |
| 4f37A | 2 | 0.9884 | 100 | 0.102 | Contact Map |
| 1fr2A | 1 | 0.9651 | 100 | 0.107 | Contact Map |
| 1unkA | 4 | 1 | 100 | 0.108 | Contact Map |
| 3u43A | 1 | 0.9767 | 100 | 0.123 | Contact Map |
| 1gxgA | 1 | 0.9884 | 100 | 0.125 | Contact Map |
| 2k0dX | 1 | 0.9884 | 100 | 0.139 | Contact Map |
| 3pfeA | 1 | 0.7674 | 17.8 | 0.925 | Contact Map |
| 3ebhA | 1 | 0.814 | 15 | 0.928 | Contact Map |
| 2wqdA | 1 | 0.4535 | 13.7 | 0.929 | Contact Map |
| 4ghjA | 2 | 0.3023 | 12.7 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)