| 4rng |
| ID: | 1500381792 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (81) | ||
| Sequences: | 4863 (3016.5) | ||
| Seq/Len: | 60.037 | ||
| Nf(neff/√len): | 335.2 |
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: 60.037).
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 |
| 23_L | 27_K | 3.272 | 1.00 |
| 77_F | 81_R | 2.089 | 1.00 |
| 78_M | 82_Y | 1.885 | 1.00 |
| 22_A | 74_L | 1.864 | 1.00 |
| 24_K | 28_T | 1.862 | 1.00 |
| 43_A | 69_L | 1.806 | 1.00 |
| 25_I | 31_A | 1.710 | 1.00 |
| 31_A | 79_K | 1.698 | 1.00 |
| 26_Y | 78_M | 1.696 | 1.00 |
| 8_I | 12_A | 1.643 | 1.00 |
| 30_S | 33_D | 1.614 | 1.00 |
| 59_I | 63_L | 1.592 | 1.00 |
| 25_I | 78_M | 1.582 | 1.00 |
| 53_G | 61_V | 1.570 | 1.00 |
| 23_L | 26_Y | 1.437 | 1.00 |
| 47_T | 69_L | 1.422 | 1.00 |
| 54_V | 62_I | 1.395 | 0.99 |
| 4_N | 8_I | 1.376 | 0.99 |
| 74_L | 78_M | 1.350 | 0.99 |
| 39_F | 75_I | 1.341 | 0.99 |
| 19_I | 23_L | 1.338 | 0.99 |
| 29_K | 82_Y | 1.331 | 0.99 |
| 53_G | 62_I | 1.311 | 0.99 |
| 50_F | 62_I | 1.308 | 0.99 |
| 14_T | 18_L | 1.299 | 0.99 |
| 26_Y | 82_Y | 1.282 | 0.99 |
| 46_I | 68_S | 1.266 | 0.99 |
| 15_T | 68_S | 1.265 | 0.99 |
| 43_A | 73_F | 1.244 | 0.98 |
| 14_T | 17_A | 1.229 | 0.98 |
| 42_M | 46_I | 1.223 | 0.98 |
| 43_A | 72_I | 1.215 | 0.98 |
| 49_W | 53_G | 1.179 | 0.98 |
| 15_T | 18_L | 1.177 | 0.98 |
| 50_F | 66_L | 1.171 | 0.98 |
| 5_L | 9_I | 1.128 | 0.97 |
| 49_W | 52_Y | 1.125 | 0.97 |
| 15_T | 67_I | 1.124 | 0.97 |
| 71_L | 75_I | 1.101 | 0.96 |
| 40_I | 76_I | 1.096 | 0.96 |
| 66_L | 70_I | 1.084 | 0.96 |
| 36_L | 40_I | 1.060 | 0.95 |
| 36_L | 79_K | 1.057 | 0.95 |
| 34_V | 39_F | 1.054 | 0.95 |
| 20_P | 23_L | 1.017 | 0.93 |
| 36_L | 76_I | 1.010 | 0.93 |
| 4_N | 58_E | 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 | |
| 4x5mA | 3 | 1 | 99.4 | -0.014 | Contact Map |
| 4rngA | 6 | 1 | 99.4 | -0.008 | Contact Map |
| 4qncA | 2 | 0.9878 | 99.4 | -0.007 | Contact Map |
| 4qndA | 1 | 1 | 99.4 | 0.003 | Contact Map |
| 3pjzA | 2 | 0.2927 | 1.4 | 0.881 | Contact Map |
| 3s8fA | 1 | 0.4634 | 1.4 | 0.882 | Contact Map |
| 3qrxB | 1 | 0.2439 | 1.4 | 0.882 | Contact Map |
| 4qinA | 1 | 0.9756 | 1.2 | 0.886 | Contact Map |
| 4jkvA | 2 | 0.9756 | 1 | 0.89 | Contact Map |
| 4p79A | 1 | 0.3293 | 1 | 0.892 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)