| abeta |
| ID: | 1434116621 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 13 (4.2) | ||
| Seq/Len: | 0.325 | ||
| Nf(neff/√len): | 0.7 |
Jackhmmer Results: (2015_01_07)
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: 0.325).
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 |
| 12_H | 16_V | 2.483 | 0.92 |
| 10_Y | 17_F | 2.159 | 0.83 |
| 3_E | 19_A | 1.990 | 0.75 |
| 10_Y | 19_A | 1.932 | 0.72 |
| 3_E | 17_F | 1.700 | 0.57 |
| 2_A | 6_H | 1.619 | 0.52 |
| 9_G | 17_F | 1.559 | 0.48 |
| 3_E | 10_Y | 1.495 | 0.43 |
| 10_Y | 15_L | 1.449 | 0.40 |
| 2_A | 12_H | 1.446 | 0.40 |
| 2_A | 14_K | 1.446 | 0.40 |
| 2_A | 16_V | 1.446 | 0.40 |
| 15_L | 19_A | 1.401 | 0.37 |
| 4_F | 9_G | 1.395 | 0.37 |
| 7_D | 16_V | 1.340 | 0.33 |
| 7_D | 14_K | 1.340 | 0.33 |
| 7_D | 12_H | 1.340 | 0.33 |
| 2_A | 7_D | 1.331 | 0.33 |
| 9_G | 19_A | 1.314 | 0.32 |
| 8_S | 11_H | 1.183 | 0.25 |
| 13_Q | 16_V | 1.125 | 0.22 |
| 8_S | 21_D | 1.092 | 0.20 |
| 1_D | 6_H | 1.049 | 0.18 |
| 3_E | 9_G | 1.039 | 0.18 |
| 4_F | 19_A | 1.033 | 0.18 |
| 1_D | 18_F | 1.000 | 0.16 |
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.
Sequence Conservation (Image Generated using WebLogo v3)