| rdlB |
| ID: | 1510651752 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 154 (136) | ||
| Sequences: | 153 (74.6) | ||
| Seq/Len: | 1.125 | ||
| Nf(neff/√len): | 6.4 |
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: 1.125).
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 |
| 19_I | 23_L | 2.459 | 0.99 |
| 72_Y | 78_G | 2.283 | 0.99 |
| 98_G | 107_T | 2.279 | 0.99 |
| 24_A | 31_S | 2.269 | 0.99 |
| 62_Q | 124_E | 2.158 | 0.98 |
| 77_I | 80_I | 2.065 | 0.97 |
| 19_I | 22_T | 1.980 | 0.96 |
| 80_I | 87_P | 1.885 | 0.95 |
| 96_N | 119_N | 1.852 | 0.94 |
| 46_A | 147_G | 1.823 | 0.93 |
| 102_G | 105_P | 1.810 | 0.93 |
| 87_P | 123_T | 1.775 | 0.92 |
| 117_P | 133_E | 1.740 | 0.91 |
| 92_P | 133_E | 1.740 | 0.91 |
| 98_G | 105_P | 1.664 | 0.88 |
| 36_A | 39_A | 1.647 | 0.87 |
| 56_N | 134_A | 1.627 | 0.86 |
| 47_G | 50_H | 1.611 | 0.86 |
| 113_V | 116_S | 1.602 | 0.85 |
| 112_N | 116_S | 1.575 | 0.84 |
| 102_G | 107_T | 1.525 | 0.81 |
| 87_P | 139_L | 1.446 | 0.76 |
| 92_P | 96_N | 1.381 | 0.71 |
| 80_I | 84_L | 1.373 | 0.71 |
| 94_K | 133_E | 1.314 | 0.66 |
| 94_K | 117_P | 1.302 | 0.65 |
| 18_M | 22_T | 1.299 | 0.65 |
| 92_P | 117_P | 1.299 | 0.65 |
| 36_A | 64_F | 1.283 | 0.63 |
| 105_P | 112_N | 1.269 | 0.62 |
| 62_Q | 87_P | 1.247 | 0.60 |
| 77_I | 87_P | 1.246 | 0.60 |
| 99_S | 108_V | 1.231 | 0.58 |
| 73_M | 124_E | 1.228 | 0.58 |
| 119_N | 129_A | 1.217 | 0.57 |
| 25_T | 93_A | 1.208 | 0.56 |
| 84_L | 90_G | 1.204 | 0.56 |
| 78_G | 124_E | 1.202 | 0.56 |
| 44_M | 55_V | 1.187 | 0.54 |
| 78_G | 87_P | 1.184 | 0.54 |
| 25_T | 32_I | 1.174 | 0.53 |
| 149_G | 152_N | 1.162 | 0.52 |
| 77_I | 82_G | 1.144 | 0.50 |
| 78_G | 83_S | 1.125 | 0.48 |
| 143_P | 146_S | 1.112 | 0.47 |
| 83_S | 124_E | 1.109 | 0.47 |
| 72_Y | 77_I | 1.108 | 0.47 |
| 23_L | 33_V | 1.101 | 0.46 |
| 96_N | 117_P | 1.100 | 0.46 |
| 123_T | 139_L | 1.098 | 0.46 |
| 36_A | 141_D | 1.095 | 0.45 |
| 102_G | 119_N | 1.091 | 0.45 |
| 73_M | 153_R | 1.077 | 0.44 |
| 56_N | 116_S | 1.075 | 0.44 |
| 25_T | 113_V | 1.045 | 0.41 |
| 49_R | 91_L | 1.035 | 0.40 |
| 98_G | 102_G | 1.032 | 0.40 |
| 96_N | 133_E | 1.032 | 0.40 |
| 107_T | 143_P | 1.027 | 0.39 |
| 56_N | 90_G | 1.027 | 0.39 |
| 77_I | 84_L | 1.024 | 0.39 |
| 29_A | 35_V | 1.023 | 0.39 |
| 37_A | 124_E | 1.019 | 0.38 |
| 76_Q | 81_Q | 1.018 | 0.38 |
| 46_A | 141_D | 1.003 | 0.37 |
| 22_T | 77_I | 1.000 | 0.37 |
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 | |
| 3jywX | 1 | 0.2597 | 7.7 | 0.969 | Contact Map |
| 2vdaB | 1 | 0.1429 | 3 | 0.974 | Contact Map |
| 4ui9T | 1 | 0 | 2.8 | 0.975 | Contact Map |
| 2py5A | 2 | 0.3377 | 2.7 | 0.975 | Contact Map |
| 3kbgA | 1 | 0.2597 | 2.5 | 0.975 | Contact Map |
| 4u7tA | 2 | 0.3312 | 2.4 | 0.975 | Contact Map |
| 3p7mA | 4 | 0.7727 | 2.3 | 0.976 | Contact Map |
| 4lfuA | 1 | 0.2597 | 2.2 | 0.976 | Contact Map |
| 2qrvA | 4 | 0.3377 | 2.2 | 0.976 | Contact Map |
| 4c2mD | 2 | 0.0714 | 2.1 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)