| 4rngA |
| ID: | 1491921542 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (82) | ||
| Sequences: | 683 (558.6) | ||
| Seq/Len: | 8.329 | ||
| Nf(neff/√len): | 61.7 |
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: 8.329).
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 | 3.678 | 1.00 |
| 11_G | 64_A | 1.998 | 1.00 |
| 25_I | 31_A | 1.867 | 1.00 |
| 29_K | 82_Y | 1.863 | 1.00 |
| 43_A | 72_I | 1.845 | 1.00 |
| 14_T | 45_G | 1.783 | 1.00 |
| 4_N | 58_E | 1.758 | 1.00 |
| 18_L | 38_M | 1.587 | 1.00 |
| 39_F | 75_I | 1.570 | 1.00 |
| 50_F | 54_V | 1.557 | 1.00 |
| 8_I | 59_I | 1.519 | 1.00 |
| 14_T | 49_W | 1.406 | 0.99 |
| 47_T | 69_L | 1.392 | 0.99 |
| 78_M | 82_Y | 1.385 | 0.99 |
| 53_G | 61_V | 1.346 | 0.99 |
| 15_T | 68_S | 1.339 | 0.99 |
| 26_Y | 78_M | 1.329 | 0.99 |
| 36_L | 79_K | 1.293 | 0.98 |
| 59_I | 63_L | 1.293 | 0.98 |
| 50_F | 62_I | 1.257 | 0.98 |
| 43_A | 69_L | 1.246 | 0.98 |
| 3_N | 62_I | 1.235 | 0.98 |
| 46_I | 68_S | 1.232 | 0.98 |
| 10_A | 48_L | 1.218 | 0.97 |
| 31_A | 82_Y | 1.215 | 0.97 |
| 24_K | 33_D | 1.199 | 0.97 |
| 10_A | 49_W | 1.185 | 0.97 |
| 42_M | 68_S | 1.176 | 0.96 |
| 47_T | 51_F | 1.175 | 0.96 |
| 22_A | 75_I | 1.171 | 0.96 |
| 56_I | 61_V | 1.167 | 0.96 |
| 24_K | 28_T | 1.161 | 0.96 |
| 51_F | 70_I | 1.148 | 0.96 |
| 18_L | 72_I | 1.143 | 0.96 |
| 2_L | 5_L | 1.135 | 0.95 |
| 43_A | 73_F | 1.124 | 0.95 |
| 25_I | 75_I | 1.117 | 0.95 |
| 19_I | 23_L | 1.113 | 0.95 |
| 31_A | 34_V | 1.104 | 0.95 |
| 15_T | 67_I | 1.104 | 0.95 |
| 31_A | 79_K | 1.085 | 0.94 |
| 4_N | 8_I | 1.069 | 0.93 |
| 36_L | 76_I | 1.052 | 0.92 |
| 18_L | 42_M | 1.046 | 0.92 |
| 9_I | 48_L | 1.024 | 0.91 |
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 | 99.6 | 0.251 | Contact Map |
| 4x5mA | 3 | 1 | 99.6 | 0.261 | Contact Map |
| 4qncA | 2 | 0.9878 | 99.6 | 0.267 | Contact Map |
| 4qndA | 1 | 1 | 99.6 | 0.289 | Contact Map |
| 3ne5A | 1 | 0.378 | 3.3 | 0.908 | Contact Map |
| 2y69M | 2 | 0.3537 | 3 | 0.91 | Contact Map |
| 1v54M | 2 | 0.3537 | 2.7 | 0.911 | Contact Map |
| 3dh4A | 4 | 0.9512 | 1.8 | 0.92 | Contact Map |
| 3j27A | 3 | 0.6829 | 1.7 | 0.921 | Contact Map |
| 4cbfA | 3 | 0.6829 | 1.7 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)