| 8826_2 |
| ID: | 1433409356 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (59) | ||
| Sequences: | 66 (36.2) | ||
| Seq/Len: | 1.119 | ||
| Nf(neff/√len): | 4.7 |
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: 1.119).
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 |
| 2_L | 6_L | 1.698 | 0.89 |
| 25_A | 28_I | 1.654 | 0.88 |
| 3_Q | 9_E | 1.647 | 0.87 |
| 43_E | 56_E | 1.609 | 0.86 |
| 24_K | 33_K | 1.537 | 0.82 |
| 30_T | 50_Q | 1.432 | 0.75 |
| 22_K | 34_L | 1.430 | 0.75 |
| 5_A | 8_A | 1.426 | 0.75 |
| 12_A | 20_L | 1.422 | 0.74 |
| 6_L | 9_E | 1.387 | 0.72 |
| 42_L | 56_E | 1.377 | 0.71 |
| 16_I | 58_L | 1.325 | 0.67 |
| 34_L | 41_N | 1.322 | 0.66 |
| 34_L | 37_S | 1.257 | 0.61 |
| 1_E | 31_E | 1.255 | 0.60 |
| 3_Q | 6_L | 1.241 | 0.59 |
| 41_N | 44_L | 1.214 | 0.57 |
| 11_R | 26_S | 1.208 | 0.56 |
| 3_Q | 12_A | 1.205 | 0.56 |
| 3_Q | 20_L | 1.139 | 0.50 |
| 2_L | 9_E | 1.120 | 0.48 |
| 21_N | 32_C | 1.120 | 0.48 |
| 40_K | 45_L | 1.105 | 0.46 |
| 41_N | 47_E | 1.100 | 0.46 |
| 16_I | 39_K | 1.093 | 0.45 |
| 1_E | 5_A | 1.083 | 0.44 |
| 4_S | 13_K | 1.081 | 0.44 |
| 11_R | 16_I | 1.073 | 0.43 |
| 9_E | 20_L | 1.049 | 0.41 |
| 2_L | 8_A | 1.047 | 0.41 |
| 1_E | 14_Q | 1.044 | 0.41 |
| 33_K | 42_L | 1.041 | 0.40 |
| 31_E | 51_L | 1.033 | 0.40 |
| 23_V | 43_E | 1.031 | 0.39 |
| 30_T | 54_D | 1.025 | 0.39 |
| 29_I | 45_L | 1.011 | 0.38 |
| 28_I | 43_E | 1.007 | 0.37 |
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 | |
| 1wt6A | 3 | 0.9836 | 93.3 | 0.689 | Contact Map |
| 4q4gX | 1 | 0 | 65.3 | 0.779 | Contact Map |
| 2dfsA | 2 | 0.9508 | 60.3 | 0.786 | Contact Map |
| 1i84S | 2 | 0 | 54.1 | 0.794 | Contact Map |
| 4cgkA | 2 | 0.9016 | 53 | 0.795 | Contact Map |
| 3ojaB | 1 | 1 | 43 | 0.806 | Contact Map |
| 4ll8A | 1 | 0.5738 | 39.2 | 0.811 | Contact Map |
| 3q0xA | 2 | 0.9672 | 36.8 | 0.814 | Contact Map |
| 3hnwA | 2 | 0.9508 | 36.7 | 0.814 | Contact Map |
| 3cazA | 2 | 0.541 | 34.9 | 0.816 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)