| 4rng |
| ID: | 1500382174 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (82) | ||
| Sequences: | 572 (460.3) | ||
| Seq/Len: | 6.976 | ||
| Nf(neff/√len): | 50.8 |
HHblits Results: (2016_02)
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: 6.976).
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 |
| 30_S | 33_D | 3.767 | 1.00 |
| 4_N | 58_E | 2.231 | 1.00 |
| 11_G | 64_A | 2.042 | 1.00 |
| 29_K | 82_Y | 2.026 | 1.00 |
| 43_A | 72_I | 2.026 | 1.00 |
| 14_T | 45_G | 1.922 | 1.00 |
| 25_I | 31_A | 1.640 | 1.00 |
| 18_L | 38_M | 1.617 | 1.00 |
| 47_T | 69_L | 1.547 | 0.99 |
| 8_I | 59_I | 1.432 | 0.99 |
| 18_L | 42_M | 1.375 | 0.99 |
| 78_M | 82_Y | 1.359 | 0.98 |
| 22_A | 75_I | 1.355 | 0.98 |
| 10_A | 48_L | 1.353 | 0.98 |
| 26_Y | 78_M | 1.342 | 0.98 |
| 15_T | 68_S | 1.334 | 0.98 |
| 59_I | 63_L | 1.325 | 0.98 |
| 43_A | 69_L | 1.295 | 0.98 |
| 50_F | 54_V | 1.253 | 0.97 |
| 18_L | 39_F | 1.250 | 0.97 |
| 56_I | 61_V | 1.249 | 0.97 |
| 31_A | 82_Y | 1.194 | 0.96 |
| 39_F | 72_I | 1.186 | 0.95 |
| 46_I | 68_S | 1.182 | 0.95 |
| 36_L | 79_K | 1.181 | 0.95 |
| 14_T | 68_S | 1.170 | 0.95 |
| 42_M | 68_S | 1.163 | 0.95 |
| 4_N | 8_I | 1.146 | 0.94 |
| 6_I | 11_G | 1.130 | 0.94 |
| 14_T | 42_M | 1.126 | 0.93 |
| 70_I | 74_L | 1.113 | 0.93 |
| 31_A | 34_V | 1.108 | 0.93 |
| 42_M | 46_I | 1.101 | 0.92 |
| 39_F | 75_I | 1.100 | 0.92 |
| 9_I | 48_L | 1.070 | 0.91 |
| 2_L | 5_L | 1.066 | 0.91 |
| 34_V | 75_I | 1.055 | 0.90 |
| 18_L | 68_S | 1.044 | 0.89 |
| 19_I | 71_L | 1.037 | 0.89 |
| 3_N | 62_I | 1.017 | 0.88 |
| 34_V | 39_F | 1.016 | 0.88 |
| 50_F | 61_V | 1.009 | 0.87 |
| 51_F | 70_I | 1.005 | 0.87 |
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 | |
| 4rngA | 6 | 1 | 99.7 | 0.314 | Contact Map |
| 4x5mA | 3 | 1 | 99.7 | 0.326 | Contact Map |
| 4qncA | 2 | 0.9878 | 99.7 | 0.33 | Contact Map |
| 4qndA | 1 | 1 | 99.7 | 0.353 | Contact Map |
| 3ne5A | 1 | 0.378 | 4.8 | 0.915 | Contact Map |
| 3dh4A | 4 | 0.9512 | 2.3 | 0.928 | Contact Map |
| 3l1lA | 1 | 0.9634 | 2 | 0.93 | Contact Map |
| 3j27A | 3 | 0.6829 | 1.9 | 0.931 | Contact Map |
| 4cbfA | 3 | 0.6829 | 1.9 | 0.931 | Contact Map |
| 4cctA | 3 | 0.6829 | 1.8 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)