| amyb_bacce686 |
| ID: | 1433420170 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 97 (88) | ||
| Sequences: | 619 (481.2) | ||
| Seq/Len: | 7.034 | ||
| Nf(neff/√len): | 51.3 |
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: 7.034).
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 |
| 78_Q | 83_S | 3.803 | 1.00 |
| 32_D | 35_Q | 2.896 | 1.00 |
| 43_D | 46_S | 2.763 | 1.00 |
| 62_E | 82_Q | 2.685 | 1.00 |
| 20_Y | 68_K | 2.554 | 1.00 |
| 5_T | 52_N | 2.521 | 1.00 |
| 24_N | 61_I | 1.997 | 1.00 |
| 19_V | 67_I | 1.977 | 1.00 |
| 25_R | 61_I | 1.945 | 1.00 |
| 69_S | 73_T | 1.823 | 1.00 |
| 38_I | 51_G | 1.795 | 1.00 |
| 22_T | 66_F | 1.675 | 1.00 |
| 21_I | 51_G | 1.651 | 1.00 |
| 64_K | 82_Q | 1.547 | 1.00 |
| 24_N | 30_S | 1.547 | 1.00 |
| 58_E | 87_V | 1.531 | 0.99 |
| 8_V | 11_V | 1.502 | 0.99 |
| 24_N | 62_E | 1.494 | 0.99 |
| 36_Y | 66_F | 1.417 | 0.99 |
| 77_W | 82_Q | 1.407 | 0.99 |
| 55_L | 87_V | 1.402 | 0.99 |
| 42_Y | 46_S | 1.343 | 0.98 |
| 11_V | 67_I | 1.337 | 0.98 |
| 13_T | 19_V | 1.336 | 0.98 |
| 62_E | 77_W | 1.252 | 0.97 |
| 11_V | 46_S | 1.243 | 0.97 |
| 3_M | 54_V | 1.226 | 0.96 |
| 20_Y | 66_F | 1.226 | 0.96 |
| 56_P | 59_R | 1.144 | 0.94 |
| 17_D | 69_S | 1.141 | 0.94 |
| 7_V | 50_R | 1.130 | 0.94 |
| 88_P | 91_T | 1.121 | 0.93 |
| 22_T | 33_T | 1.119 | 0.93 |
| 26_A | 30_S | 1.107 | 0.93 |
| 43_D | 47_N | 1.101 | 0.92 |
| 61_I | 85_N | 1.098 | 0.92 |
| 3_M | 52_N | 1.095 | 0.92 |
| 33_T | 66_F | 1.094 | 0.92 |
| 44_S | 50_R | 1.065 | 0.91 |
| 13_T | 46_S | 1.057 | 0.90 |
| 31_W | 64_K | 1.040 | 0.89 |
| 31_W | 78_Q | 1.040 | 0.89 |
| 13_T | 47_N | 1.036 | 0.89 |
| 22_T | 77_W | 1.023 | 0.88 |
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 | |
| 2vn4A | 1 | 0.9485 | 99.9 | 0.152 | Contact Map |
| 4jcmA | 1 | 0.9897 | 99.9 | 0.174 | Contact Map |
| 1cygA | 1 | 0.9897 | 99.9 | 0.186 | Contact Map |
| 1vemA | 1 | 0.9897 | 99.9 | 0.191 | Contact Map |
| 1gcyA | 1 | 0 | 99.9 | 0.202 | Contact Map |
| 3bmvA | 1 | 0.9794 | 99.9 | 0.204 | Contact Map |
| 1d3cA | 1 | 0.9794 | 99.9 | 0.205 | Contact Map |
| 4jclA | 1 | 0.9794 | 99.9 | 0.208 | Contact Map |
| 1qhoA | 1 | 0.9588 | 99.9 | 0.211 | Contact Map |
| 1ac0A | 1 | 0.9485 | 99.9 | 0.226 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)