| HA2 chain BA trimer designs |
| ID: | 1491594522 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (98) | ||
| Sequences: | 130 (107.5) | ||
| Seq/Len: | 1.327 | ||
| Nf(neff/√len): | 10.9 |
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: 1.327).
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 |
| 89_A | 93_A | 5.544 | 1.00 |
| 67_E | 71_K | 3.588 | 1.00 |
| 2_T | 65_R | 3.049 | 1.00 |
| 15_E | 19_Q | 2.402 | 0.99 |
| 46_A | 79_A | 2.296 | 0.99 |
| 23_K | 26_R | 2.246 | 0.99 |
| 48_F | 52_L | 2.243 | 0.99 |
| 9_V | 57_A | 1.926 | 0.97 |
| 42_Y | 46_A | 1.879 | 0.96 |
| 75_K | 79_A | 1.852 | 0.95 |
| 6_A | 57_A | 1.666 | 0.91 |
| 6_A | 9_V | 1.595 | 0.88 |
| 18_K | 21_P | 1.536 | 0.85 |
| 33_Q | 89_A | 1.457 | 0.81 |
| 42_Y | 79_A | 1.447 | 0.80 |
| 4_E | 8_R | 1.446 | 0.80 |
| 46_A | 75_K | 1.397 | 0.77 |
| 55_M | 59_Q | 1.397 | 0.77 |
| 77_R | 91_D | 1.394 | 0.77 |
| 38_V | 46_A | 1.369 | 0.75 |
| 14_V | 42_Y | 1.334 | 0.72 |
| 7_N | 79_A | 1.326 | 0.72 |
| 32_Q | 35_E | 1.325 | 0.72 |
| 51_E | 84_V | 1.298 | 0.69 |
| 46_A | 50_A | 1.291 | 0.69 |
| 26_R | 61_Q | 1.285 | 0.68 |
| 22_T | 91_D | 1.274 | 0.67 |
| 14_V | 18_K | 1.222 | 0.63 |
| 5_M | 87_E | 1.216 | 0.62 |
| 94_K | 98_G | 1.211 | 0.62 |
| 43_L | 98_G | 1.183 | 0.59 |
| 41_T | 44_R | 1.141 | 0.55 |
| 49_F | 76_T | 1.137 | 0.54 |
| 33_Q | 96_S | 1.111 | 0.52 |
| 25_K | 28_E | 1.110 | 0.52 |
| 14_V | 23_K | 1.104 | 0.51 |
| 7_N | 46_A | 1.088 | 0.50 |
| 26_R | 37_Y | 1.087 | 0.49 |
| 38_V | 98_G | 1.080 | 0.49 |
| 10_K | 16_Q | 1.078 | 0.49 |
| 7_N | 76_T | 1.067 | 0.47 |
| 70_R | 92_A | 1.059 | 0.47 |
| 55_M | 87_E | 1.040 | 0.45 |
| 2_T | 44_R | 1.021 | 0.43 |
| 5_M | 43_L | 1.013 | 0.42 |
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 | |
| 4wsrA | 6 | 1 | 100 | 0.168 | Contact Map |
| 2yp5A | 1 | 1 | 100 | 0.172 | Contact Map |
| 4mc5A | 3 | 1 | 100 | 0.173 | Contact Map |
| 2wr1A | 3 | 1 | 100 | 0.173 | Contact Map |
| 4lvhA | 4 | 0.1429 | 100 | 0.2 | Contact Map |
| 4f23A | 3 | 1 | 100 | 0.2 | Contact Map |
| 2wrgI | 3 | 1 | 100 | 0.224 | Contact Map |
| 1mqmB | 3 | 1 | 100 | 0.225 | Contact Map |
| 4m44B | 3 | 1 | 100 | 0.232 | Contact Map |
| 1jsdB | 1 | 1 | 100 | 0.237 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)