| B peptide |
| ID: | 1463808074 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (121) | ||
| Sequences: | 485 (354.6) | ||
| Seq/Len: | 4.008 | ||
| Nf(neff/√len): | 32.2 |
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: 4.008).
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 |
| 107_S | 113_I | 4.600 | 1.00 |
| 51_L | 114_F | 2.205 | 1.00 |
| 10_N | 13_T | 1.990 | 1.00 |
| 99_I | 102_D | 1.737 | 0.99 |
| 37_F | 41_L | 1.701 | 0.99 |
| 5_V | 8_I | 1.699 | 0.99 |
| 25_M | 29_V | 1.605 | 0.99 |
| 100_A | 114_F | 1.497 | 0.98 |
| 73_F | 77_Q | 1.494 | 0.97 |
| 30_V | 34_I | 1.493 | 0.97 |
| 31_R | 35_T | 1.435 | 0.97 |
| 58_R | 116_L | 1.404 | 0.96 |
| 37_F | 63_A | 1.396 | 0.96 |
| 64_Q | 68_A | 1.343 | 0.95 |
| 75_K | 116_L | 1.342 | 0.94 |
| 55_Q | 114_F | 1.336 | 0.94 |
| 5_V | 78_N | 1.324 | 0.94 |
| 94_D | 97_E | 1.286 | 0.93 |
| 91_N | 96_I | 1.249 | 0.91 |
| 77_Q | 92_D | 1.236 | 0.91 |
| 85_E | 89_N | 1.216 | 0.90 |
| 18_K | 23_Q | 1.215 | 0.90 |
| 75_K | 81_I | 1.214 | 0.90 |
| 43_A | 70_E | 1.210 | 0.89 |
| 87_L | 91_N | 1.207 | 0.89 |
| 32_R | 59_N | 1.187 | 0.88 |
| 5_V | 12_Y | 1.184 | 0.88 |
| 2_K | 48_L | 1.176 | 0.88 |
| 32_R | 39_G | 1.173 | 0.87 |
| 74_Q | 77_Q | 1.149 | 0.86 |
| 7_H | 13_T | 1.143 | 0.85 |
| 32_R | 56_K | 1.142 | 0.85 |
| 67_K | 70_E | 1.140 | 0.85 |
| 8_I | 90_L | 1.137 | 0.85 |
| 32_R | 36_V | 1.127 | 0.84 |
| 40_V | 50_I | 1.127 | 0.84 |
| 81_I | 91_N | 1.107 | 0.83 |
| 5_V | 47_V | 1.094 | 0.82 |
| 90_L | 107_S | 1.093 | 0.82 |
| 101_R | 108_N | 1.090 | 0.82 |
| 103_D | 106_L | 1.090 | 0.82 |
| 45_I | 91_N | 1.088 | 0.81 |
| 73_F | 96_I | 1.083 | 0.81 |
| 70_E | 109_K | 1.083 | 0.81 |
| 52_L | 84_K | 1.082 | 0.81 |
| 26_K | 30_V | 1.081 | 0.81 |
| 16_E | 19_K | 1.076 | 0.80 |
| 101_R | 111_E | 1.075 | 0.80 |
| 65_E | 114_F | 1.073 | 0.80 |
| 103_D | 114_F | 1.073 | 0.80 |
| 61_I | 72_Q | 1.060 | 0.79 |
| 8_I | 15_Q | 1.044 | 0.78 |
| 8_I | 13_T | 1.044 | 0.78 |
| 10_N | 98_K | 1.043 | 0.77 |
| 30_V | 114_F | 1.041 | 0.77 |
| 6_E | 10_N | 1.037 | 0.77 |
| 105_Y | 115_R | 1.019 | 0.75 |
| 16_E | 52_L | 1.012 | 0.74 |
| 21_Q | 36_V | 1.012 | 0.74 |
| 101_R | 107_S | 1.005 | 0.74 |
| 15_Q | 18_K | 1.005 | 0.74 |
| 26_K | 69_K | 1.000 | 0.73 |
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 | |
| 4q4gX | 1 | 0 | 79.3 | 0.875 | Contact Map |
| 4cgkA | 2 | 0.4923 | 60.3 | 0.892 | Contact Map |
| 1rz2A | 1 | 0.5846 | 53.9 | 0.896 | Contact Map |
| 4dznA | 3 | 0.2385 | 37.6 | 0.905 | Contact Map |
| 2w3zA | 1 | 0.3615 | 35.9 | 0.907 | Contact Map |
| 2ap3A | 1 | 0.7231 | 35.8 | 0.907 | Contact Map |
| 2m8rA | 1 | 0.4308 | 22.9 | 0.915 | Contact Map |
| 4etpB | 1 | 0.5154 | 21 | 0.917 | Contact Map |
| 2kogA | 1 | 0.4231 | 15.9 | 0.921 | Contact Map |
| 4e61A | 2 | 0.5231 | 15.5 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)