| vif |
| ID: | 1509285971 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 192 (187) | ||
| Sequences: | 1729 (48.1) | ||
| Seq/Len: | 9.246 | ||
| Nf(neff/√len): | 3.5 |
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: 9.246).
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 |
| 64_L | 98_V | 2.098 | 1.00 |
| 170_T | 181_K | 1.872 | 1.00 |
| 66_I | 102_L | 1.862 | 1.00 |
| 77_R | 80_H | 1.814 | 1.00 |
| 120_I | 127_R | 1.798 | 1.00 |
| 22_K | 83_Q | 1.791 | 1.00 |
| 117_E | 158_Q | 1.648 | 1.00 |
| 91_K | 98_V | 1.603 | 1.00 |
| 93_R | 144_S | 1.599 | 1.00 |
| 77_R | 116_S | 1.577 | 1.00 |
| 163_L | 171_E | 1.565 | 1.00 |
| 161_P | 165_S | 1.565 | 1.00 |
| 67_T | 98_V | 1.518 | 1.00 |
| 59_L | 136_Q | 1.486 | 1.00 |
| 101_D | 116_S | 1.468 | 1.00 |
| 50_K | 67_T | 1.436 | 0.99 |
| 117_E | 157_K | 1.433 | 0.99 |
| 98_V | 127_R | 1.400 | 0.99 |
| 98_V | 122_N | 1.378 | 0.99 |
| 66_I | 105_Q | 1.370 | 0.99 |
| 161_P | 166_V | 1.355 | 0.99 |
| 83_Q | 91_K | 1.351 | 0.99 |
| 160_K | 166_V | 1.341 | 0.99 |
| 18_I | 73_H | 1.340 | 0.99 |
| 163_L | 173_R | 1.340 | 0.99 |
| 162_P | 166_V | 1.332 | 0.99 |
| 92_K | 155_K | 1.328 | 0.99 |
| 27_H | 31_I | 1.320 | 0.99 |
| 34_K | 134_E | 1.313 | 0.99 |
| 47_T | 122_N | 1.308 | 0.99 |
| 110_H | 117_E | 1.304 | 0.99 |
| 27_H | 66_I | 1.299 | 0.99 |
| 102_L | 105_Q | 1.288 | 0.99 |
| 57_I | 164_P | 1.259 | 0.98 |
| 160_K | 163_L | 1.239 | 0.98 |
| 176_K | 183_H | 1.230 | 0.98 |
| 43_H | 100_P | 1.220 | 0.98 |
| 50_K | 73_H | 1.220 | 0.98 |
| 171_E | 175_N | 1.219 | 0.98 |
| 110_H | 127_R | 1.217 | 0.98 |
| 161_P | 164_P | 1.202 | 0.98 |
| 101_D | 109_L | 1.202 | 0.98 |
| 46_S | 122_N | 1.199 | 0.98 |
| 169_L | 183_H | 1.197 | 0.98 |
| 135_Y | 152_A | 1.178 | 0.97 |
| 64_L | 183_H | 1.175 | 0.97 |
| 66_I | 151_A | 1.171 | 0.97 |
| 73_H | 105_Q | 1.159 | 0.97 |
| 39_F | 51_I | 1.153 | 0.97 |
| 166_V | 172_D | 1.143 | 0.96 |
| 29_M | 106_L | 1.137 | 0.96 |
| 51_I | 122_N | 1.137 | 0.96 |
| 98_V | 183_H | 1.133 | 0.96 |
| 116_S | 130_S | 1.109 | 0.96 |
| 92_K | 185_G | 1.107 | 0.96 |
| 161_P | 169_L | 1.105 | 0.96 |
| 84_G | 94_Y | 1.104 | 0.95 |
| 64_L | 102_L | 1.100 | 0.95 |
| 164_P | 173_R | 1.097 | 0.95 |
| 169_L | 172_D | 1.091 | 0.95 |
| 19_N | 27_H | 1.089 | 0.95 |
| 67_T | 73_H | 1.087 | 0.95 |
| 87_I | 104_D | 1.084 | 0.95 |
| 8_M | 97_Q | 1.082 | 0.95 |
| 128_I | 155_K | 1.081 | 0.95 |
| 106_L | 144_S | 1.077 | 0.95 |
| 58_P | 144_S | 1.076 | 0.95 |
| 162_P | 165_S | 1.072 | 0.94 |
| 31_I | 67_T | 1.067 | 0.94 |
| 73_H | 130_S | 1.066 | 0.94 |
| 51_I | 98_V | 1.066 | 0.94 |
| 31_I | 184_R | 1.065 | 0.94 |
| 151_A | 154_I | 1.060 | 0.94 |
| 77_R | 127_R | 1.058 | 0.94 |
| 151_A | 185_G | 1.057 | 0.94 |
| 109_L | 186_S | 1.056 | 0.94 |
| 18_I | 56_H | 1.051 | 0.94 |
| 66_I | 127_R | 1.049 | 0.94 |
| 127_R | 154_I | 1.048 | 0.94 |
| 101_D | 130_S | 1.047 | 0.93 |
| 162_P | 173_R | 1.045 | 0.93 |
| 73_H | 157_K | 1.041 | 0.93 |
| 77_R | 151_A | 1.033 | 0.93 |
| 73_H | 102_L | 1.029 | 0.93 |
| 160_K | 165_S | 1.025 | 0.93 |
| 120_I | 131_P | 1.024 | 0.92 |
| 91_K | 127_R | 1.023 | 0.92 |
| 127_R | 130_S | 1.022 | 0.92 |
| 29_M | 113_D | 1.019 | 0.92 |
| 127_R | 134_E | 1.016 | 0.92 |
| 36_K | 99_D | 1.015 | 0.92 |
| 136_Q | 185_G | 1.014 | 0.92 |
| 37_D | 66_I | 1.013 | 0.92 |
| 163_L | 166_V | 1.007 | 0.92 |
| 54_E | 65_V | 1.005 | 0.92 |
| 27_H | 50_K | 1.005 | 0.92 |
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 | |
| 4n9fb | 12 | 0.8958 | 100 | 0.122 | Contact Map |
| 3dcgE | 2 | 0.0885 | 99.8 | 0.82 | Contact Map |
| 3v9rB | 2 | 0.3021 | 9.9 | 0.976 | Contact Map |
| 4rknA | 4 | 0.1562 | 3.8 | 0.98 | Contact Map |
| 4ne3B | 1 | 0.2917 | 3.5 | 0.981 | Contact Map |
| 4dpvZ | 1 | 0.3073 | 2.4 | 0.982 | Contact Map |
| 1vptA | 1 | 0.6927 | 2.4 | 0.982 | Contact Map |
| 1by6A | 1 | 0.1875 | 2.1 | 0.983 | Contact Map |
| 4wpbC | 2 | 0.1146 | 1.9 | 0.983 | Contact Map |
| 2mdvA | 2 | 0.1927 | 1.6 | 0.984 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)