| HA2 chain DB trimer designs |
| ID: | 1491594656 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (123) | ||
| Sequences: | 128 (110.6) | ||
| Seq/Len: | 1.041 | ||
| Nf(neff/√len): | 10.0 |
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: 1.041).
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 |
| 11_K | 15_E | 4.550 | 1.00 |
| 57_A | 61_R | 3.586 | 1.00 |
| 51_E | 103_H | 2.708 | 1.00 |
| 2_D | 6_L | 2.428 | 0.99 |
| 36_E | 39_K | 2.360 | 0.99 |
| 53_D | 86_L | 2.334 | 0.99 |
| 18_E | 22_E | 2.334 | 0.99 |
| 61_R | 65_N | 2.276 | 0.98 |
| 46_E | 104_K | 2.194 | 0.98 |
| 112_R | 122_E | 2.166 | 0.98 |
| 107_K | 110_Q | 2.159 | 0.98 |
| 54_I | 57_A | 2.111 | 0.97 |
| 50_L | 54_I | 2.103 | 0.97 |
| 106_S | 112_R | 2.086 | 0.97 |
| 10_E | 14_N | 2.046 | 0.96 |
| 49_A | 53_D | 1.872 | 0.93 |
| 3_K | 7_K | 1.826 | 0.92 |
| 21_R | 25_E | 1.781 | 0.91 |
| 30_E | 120_I | 1.729 | 0.89 |
| 22_E | 26_R | 1.680 | 0.87 |
| 107_K | 111_E | 1.560 | 0.81 |
| 84_R | 88_K | 1.554 | 0.81 |
| 90_N | 104_K | 1.503 | 0.78 |
| 18_E | 26_R | 1.402 | 0.71 |
| 92_R | 100_K | 1.391 | 0.70 |
| 57_A | 80_F | 1.386 | 0.70 |
| 61_R | 80_F | 1.335 | 0.65 |
| 88_K | 103_H | 1.311 | 0.63 |
| 108_A | 111_E | 1.301 | 0.62 |
| 30_E | 102_V | 1.270 | 0.60 |
| 4_E | 75_V | 1.246 | 0.57 |
| 14_N | 79_L | 1.217 | 0.55 |
| 105_A | 109_D | 1.200 | 0.53 |
| 23_Q | 26_R | 1.188 | 0.52 |
| 44_Y | 48_T | 1.157 | 0.49 |
| 6_L | 10_E | 1.122 | 0.46 |
| 6_L | 44_Y | 1.110 | 0.45 |
| 8_T | 17_L | 1.088 | 0.43 |
| 12_K | 67_N | 1.074 | 0.41 |
| 16_I | 25_E | 1.068 | 0.41 |
| 56_Y | 83_T | 1.052 | 0.39 |
| 105_A | 110_Q | 1.050 | 0.39 |
| 55_F | 63_L | 1.039 | 0.38 |
| 6_L | 9_D | 1.034 | 0.38 |
| 8_T | 56_Y | 1.020 | 0.37 |
| 16_I | 64_T | 1.007 | 0.35 |
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 | 0.149 | Contact Map |
| 2yp5A | 1 | 1 | 100 | 0.151 | Contact Map |
| 4mc5A | 3 | 1 | 100 | 0.152 | Contact Map |
| 2wr1A | 3 | 1 | 100 | 0.153 | Contact Map |
| 4lvhA | 4 | 0.1138 | 100 | 0.176 | Contact Map |
| 4f23A | 3 | 1 | 100 | 0.178 | Contact Map |
| 1mqmB | 3 | 1 | 100 | 0.196 | Contact Map |
| 2wrgI | 3 | 0.9837 | 100 | 0.196 | Contact Map |
| 4m44B | 3 | 1 | 100 | 0.208 | Contact Map |
| 1jsdB | 1 | 0.9837 | 100 | 0.21 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)