| vif |
| ID: | 1509037146 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 192 (187) | ||
| Sequences: | 1735 (48.4) | ||
| Seq/Len: | 9.278 | ||
| 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: 9.278).
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 | 2.158 | 1.00 |
| 66_I | 102_L | 1.895 | 1.00 |
| 120_I | 127_R | 1.842 | 1.00 |
| 77_R | 80_H | 1.836 | 1.00 |
| 117_E | 158_Q | 1.802 | 1.00 |
| 170_T | 181_K | 1.780 | 1.00 |
| 50_K | 67_T | 1.728 | 1.00 |
| 22_K | 83_Q | 1.698 | 1.00 |
| 93_R | 144_S | 1.637 | 1.00 |
| 101_D | 116_S | 1.578 | 1.00 |
| 91_K | 98_V | 1.556 | 1.00 |
| 77_R | 116_S | 1.539 | 1.00 |
| 98_V | 127_R | 1.526 | 1.00 |
| 161_P | 165_S | 1.495 | 1.00 |
| 163_L | 171_E | 1.465 | 1.00 |
| 59_L | 136_Q | 1.455 | 1.00 |
| 67_T | 73_H | 1.403 | 0.99 |
| 117_E | 157_K | 1.402 | 0.99 |
| 66_I | 105_Q | 1.383 | 0.99 |
| 51_I | 98_V | 1.382 | 0.99 |
| 98_V | 122_N | 1.354 | 0.99 |
| 83_Q | 91_K | 1.349 | 0.99 |
| 161_P | 166_V | 1.337 | 0.99 |
| 50_K | 73_H | 1.331 | 0.99 |
| 47_T | 122_N | 1.320 | 0.99 |
| 34_K | 134_E | 1.305 | 0.99 |
| 160_K | 166_V | 1.291 | 0.99 |
| 18_I | 73_H | 1.284 | 0.99 |
| 162_P | 166_V | 1.275 | 0.99 |
| 102_L | 105_Q | 1.270 | 0.98 |
| 110_H | 127_R | 1.264 | 0.98 |
| 163_L | 173_R | 1.251 | 0.98 |
| 57_I | 164_P | 1.246 | 0.98 |
| 27_H | 31_I | 1.239 | 0.98 |
| 98_V | 183_H | 1.238 | 0.98 |
| 160_K | 163_L | 1.230 | 0.98 |
| 151_A | 185_G | 1.229 | 0.98 |
| 64_L | 183_H | 1.218 | 0.98 |
| 84_G | 94_Y | 1.216 | 0.98 |
| 110_H | 117_E | 1.209 | 0.98 |
| 67_T | 98_V | 1.206 | 0.98 |
| 66_I | 151_A | 1.183 | 0.97 |
| 43_H | 100_P | 1.181 | 0.97 |
| 116_S | 130_S | 1.180 | 0.97 |
| 27_H | 66_I | 1.179 | 0.97 |
| 176_K | 183_H | 1.174 | 0.97 |
| 127_R | 154_I | 1.168 | 0.97 |
| 29_M | 106_L | 1.163 | 0.97 |
| 8_M | 97_Q | 1.155 | 0.97 |
| 135_Y | 152_A | 1.151 | 0.97 |
| 161_P | 164_P | 1.149 | 0.97 |
| 73_H | 105_Q | 1.145 | 0.97 |
| 46_S | 122_N | 1.145 | 0.97 |
| 109_L | 186_S | 1.132 | 0.96 |
| 91_K | 127_R | 1.130 | 0.96 |
| 77_R | 151_A | 1.128 | 0.96 |
| 169_L | 183_H | 1.128 | 0.96 |
| 92_K | 155_K | 1.126 | 0.96 |
| 64_L | 102_L | 1.124 | 0.96 |
| 101_D | 109_L | 1.121 | 0.96 |
| 29_M | 113_D | 1.114 | 0.96 |
| 171_E | 175_N | 1.103 | 0.95 |
| 128_I | 155_K | 1.097 | 0.95 |
| 31_I | 184_R | 1.082 | 0.95 |
| 101_D | 130_S | 1.078 | 0.95 |
| 36_K | 99_D | 1.077 | 0.95 |
| 78_D | 92_K | 1.077 | 0.95 |
| 39_F | 155_K | 1.073 | 0.95 |
| 33_R | 101_D | 1.066 | 0.94 |
| 19_N | 27_H | 1.065 | 0.94 |
| 73_H | 157_K | 1.062 | 0.94 |
| 58_P | 144_S | 1.061 | 0.94 |
| 92_K | 185_G | 1.053 | 0.94 |
| 120_I | 141_K | 1.051 | 0.94 |
| 60_G | 118_S | 1.050 | 0.94 |
| 18_I | 56_H | 1.050 | 0.94 |
| 127_R | 130_S | 1.049 | 0.94 |
| 144_S | 182_G | 1.047 | 0.94 |
| 166_V | 172_D | 1.046 | 0.93 |
| 164_P | 173_R | 1.046 | 0.93 |
| 27_H | 50_K | 1.043 | 0.93 |
| 70_W | 103_A | 1.040 | 0.93 |
| 37_D | 66_I | 1.034 | 0.93 |
| 106_L | 144_S | 1.031 | 0.93 |
| 103_A | 108_H | 1.030 | 0.93 |
| 73_H | 102_L | 1.030 | 0.93 |
| 120_I | 131_P | 1.028 | 0.93 |
| 151_A | 154_I | 1.026 | 0.93 |
| 182_G | 187_H | 1.026 | 0.93 |
| 161_P | 169_L | 1.024 | 0.93 |
| 127_R | 151_A | 1.021 | 0.92 |
| 162_P | 173_R | 1.018 | 0.92 |
| 124_I | 180_T | 1.003 | 0.92 |
| 169_L | 172_D | 1.002 | 0.91 |
| 150_L | 153_L | 1.000 | 0.91 |
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 | 0.123 | Contact Map |
| 3dcgE | 2 | 0.0885 | 99.8 | 0.82 | Contact Map |
| 3v9rB | 2 | 0.3021 | 9.7 | 0.976 | Contact Map |
| 4rknA | 4 | 0.1562 | 3.9 | 0.98 | Contact Map |
| 4ne3B | 1 | 0.2917 | 3.4 | 0.981 | Contact Map |
| 4dpvZ | 1 | 0.3073 | 2.5 | 0.982 | Contact Map |
| 1vptA | 1 | 0.6927 | 2.4 | 0.982 | Contact Map |
| 1by6A | 1 | 0.1875 | 2 | 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)