| 4n6t |
| ID: | 1512668099 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 79 (78) | ||
| Sequences: | 1314 (968.6) | ||
| Seq/Len: | 16.846 | ||
| Nf(neff/√len): | 109.7 |
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: 16.846).
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 |
| 29_R | 48_E | 3.265 | 1.00 |
| 34_K | 44_Y | 2.410 | 1.00 |
| 10_A | 27_F | 2.399 | 1.00 |
| 16_E | 19_K | 2.202 | 1.00 |
| 65_K | 70_F | 2.118 | 1.00 |
| 35_E | 41_T | 2.024 | 1.00 |
| 42_M | 61_K | 1.914 | 1.00 |
| 65_K | 68_E | 1.905 | 1.00 |
| 58_Y | 78_P | 1.854 | 1.00 |
| 33_A | 45_L | 1.806 | 1.00 |
| 5_E | 64_V | 1.758 | 1.00 |
| 32_K | 46_T | 1.637 | 1.00 |
| 63_W | 70_F | 1.622 | 1.00 |
| 42_M | 74_Q | 1.555 | 1.00 |
| 27_F | 47_L | 1.506 | 1.00 |
| 28_V | 50_K | 1.489 | 1.00 |
| 16_E | 73_L | 1.404 | 0.99 |
| 12_F | 73_L | 1.398 | 0.99 |
| 61_K | 75_E | 1.396 | 0.99 |
| 17_H | 21_E | 1.351 | 0.99 |
| 42_M | 63_W | 1.326 | 0.99 |
| 6_I | 33_A | 1.305 | 0.99 |
| 47_L | 60_A | 1.285 | 0.99 |
| 46_T | 59_E | 1.285 | 0.99 |
| 10_A | 45_L | 1.275 | 0.99 |
| 64_V | 71_K | 1.271 | 0.99 |
| 9_L | 64_V | 1.246 | 0.98 |
| 36_Q | 42_M | 1.175 | 0.98 |
| 3_S | 7_E | 1.139 | 0.97 |
| 44_Y | 59_E | 1.137 | 0.97 |
| 37_V | 41_T | 1.136 | 0.97 |
| 10_A | 47_L | 1.116 | 0.96 |
| 14_V | 18_N | 1.109 | 0.96 |
| 23_A | 51_D | 1.101 | 0.96 |
| 31_V | 48_E | 1.081 | 0.95 |
| 17_H | 60_A | 1.077 | 0.95 |
| 31_V | 57_L | 1.049 | 0.94 |
| 38_V | 42_M | 1.046 | 0.94 |
| 25_L | 49_A | 1.027 | 0.94 |
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 | |
| 2l4vA | 1 | 1 | 99.7 | 0.01 | Contact Map |
| 3ul5A | 4 | 1 | 99.7 | 0.02 | Contact Map |
| 1eqkA | 1 | 1 | 99.7 | 0.037 | Contact Map |
| 3imaB | 2 | 0.9747 | 99.7 | 0.05 | Contact Map |
| 4lziA | 1 | 1 | 99.7 | 0.054 | Contact Map |
| 4n6tA | 1 | 1 | 99.7 | 0.058 | Contact Map |
| 5a0oB | 2 | 0 | 99.6 | 0.083 | Contact Map |
| 2kxgA | 1 | 0.9747 | 99.6 | 0.116 | Contact Map |
| 4n6oB | 1 | 1 | 99.6 | 0.118 | Contact Map |
| 3gaxA | 2 | 1 | 99.6 | 0.121 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)