| BipA |
| ID: | 1504741287 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 196 (187) | ||
| Sequences: | 31281 (13144.8) | ||
| Seq/Len: | 167.278 | ||
| Nf(neff/√len): | 961.2 |
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: 167.278).
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 |
| 169_N | 181_E | 3.358 | 1.00 |
| 163_V | 189_A | 3.268 | 1.00 |
| 24_K | 170_G | 3.179 | 1.00 |
| 126_V | 165_A | 2.675 | 1.00 |
| 101_A | 127_I | 2.601 | 1.00 |
| 161_P | 189_A | 2.530 | 1.00 |
| 96_L | 126_V | 2.378 | 1.00 |
| 13_H | 109_T | 2.340 | 1.00 |
| 9_A | 92_V | 2.333 | 1.00 |
| 98_V | 128_N | 2.332 | 1.00 |
| 189_A | 192_D | 2.298 | 1.00 |
| 21_L | 98_V | 2.236 | 1.00 |
| 130_V | 164_Y | 2.165 | 1.00 |
| 126_V | 186_L | 2.081 | 1.00 |
| 141_V | 164_Y | 2.076 | 1.00 |
| 189_A | 193_H | 2.041 | 1.00 |
| 141_V | 145_F | 1.997 | 1.00 |
| 62_A | 69_R | 1.986 | 1.00 |
| 102_F | 132_R | 1.929 | 1.00 |
| 182_D | 185_P | 1.928 | 1.00 |
| 97_L | 113_T | 1.924 | 1.00 |
| 145_F | 149_V | 1.899 | 1.00 |
| 130_V | 181_E | 1.877 | 1.00 |
| 127_I | 164_Y | 1.816 | 1.00 |
| 24_K | 183_M | 1.810 | 1.00 |
| 128_N | 167_A | 1.799 | 1.00 |
| 7_N | 71_N | 1.770 | 1.00 |
| 110_R | 147_L | 1.715 | 1.00 |
| 20_T | 167_A | 1.711 | 1.00 |
| 10_I | 96_L | 1.678 | 1.00 |
| 60_N | 71_N | 1.663 | 1.00 |
| 10_I | 22_V | 1.659 | 1.00 |
| 94_S | 124_I | 1.655 | 1.00 |
| 64_K | 69_R | 1.649 | 1.00 |
| 21_L | 183_M | 1.589 | 1.00 |
| 101_A | 130_V | 1.563 | 1.00 |
| 96_L | 190_I | 1.546 | 1.00 |
| 165_A | 186_L | 1.523 | 1.00 |
| 144_V | 148_F | 1.507 | 1.00 |
| 86_E | 115_K | 1.505 | 1.00 |
| 124_I | 163_V | 1.500 | 1.00 |
| 21_L | 186_L | 1.474 | 1.00 |
| 99_V | 125_V | 1.466 | 1.00 |
| 124_I | 189_A | 1.455 | 1.00 |
| 5_L | 71_N | 1.423 | 1.00 |
| 74_D | 77_G | 1.419 | 1.00 |
| 188_Q | 192_D | 1.418 | 1.00 |
| 68_Y | 191_V | 1.405 | 0.99 |
| 96_L | 124_I | 1.368 | 0.99 |
| 161_P | 193_H | 1.364 | 0.99 |
| 104_G | 143_Q | 1.359 | 0.99 |
| 142_D | 146_D | 1.343 | 0.99 |
| 136_R | 139_W | 1.339 | 0.99 |
| 184_T | 188_Q | 1.333 | 0.99 |
| 99_V | 162_I | 1.324 | 0.99 |
| 6_R | 194_V | 1.324 | 0.99 |
| 62_A | 71_N | 1.308 | 0.99 |
| 185_P | 189_A | 1.276 | 0.99 |
| 183_M | 187_Y | 1.271 | 0.99 |
| 70_I | 191_V | 1.268 | 0.99 |
| 127_I | 162_I | 1.254 | 0.99 |
| 100_D | 103_D | 1.242 | 0.98 |
| 94_S | 190_I | 1.238 | 0.98 |
| 143_Q | 146_D | 1.235 | 0.98 |
| 8_I | 94_S | 1.209 | 0.98 |
| 185_P | 188_Q | 1.207 | 0.98 |
| 94_S | 194_V | 1.206 | 0.98 |
| 25_L | 187_Y | 1.176 | 0.98 |
| 13_H | 16_H | 1.175 | 0.98 |
| 95_V | 116_A | 1.167 | 0.97 |
| 103_D | 106_M | 1.162 | 0.97 |
| 24_K | 28_Q | 1.162 | 0.97 |
| 143_Q | 147_L | 1.155 | 0.97 |
| 96_L | 186_L | 1.128 | 0.97 |
| 125_V | 162_I | 1.123 | 0.97 |
| 60_N | 73_V | 1.105 | 0.96 |
| 21_L | 165_A | 1.094 | 0.96 |
| 131_D | 166_S | 1.091 | 0.96 |
| 95_V | 121_L | 1.077 | 0.95 |
| 22_V | 72_I | 1.075 | 0.95 |
| 187_Y | 190_I | 1.071 | 0.95 |
| 108_Q | 111_F | 1.065 | 0.95 |
| 117_F | 123_P | 1.064 | 0.95 |
| 161_P | 164_Y | 1.049 | 0.94 |
| 110_R | 114_K | 1.044 | 0.94 |
| 107_P | 110_R | 1.036 | 0.94 |
| 105_P | 108_Q | 1.030 | 0.94 |
| 21_L | 167_A | 1.022 | 0.93 |
| 23_D | 32_F | 1.017 | 0.93 |
| 140_V | 143_Q | 1.010 | 0.93 |
| 12_A | 17_G | 1.008 | 0.93 |
| 188_Q | 191_V | 1.006 | 0.93 |
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 | |
| 4zciA | 2 | 0 | 100 | 0.119 | Contact Map |
| 2yweA | 1 | 0.7806 | 100 | 0.179 | Contact Map |
| 3cb4D | 6 | 0.75 | 100 | 0.184 | Contact Map |
| 3vqtA | 4 | 0.8622 | 100 | 0.188 | Contact Map |
| 3j25A | 1 | 0.9337 | 100 | 0.194 | Contact Map |
| 4qjty | 1 | 0.7704 | 99.9 | 0.208 | Contact Map |
| 2h5eA | 2 | 0.8214 | 99.9 | 0.21 | Contact Map |
| 3tr5A | 4 | 0.9439 | 99.9 | 0.21 | Contact Map |
| 2c78A | 1 | 0.9796 | 99.9 | 0.214 | Contact Map |
| 4kiyV | 1 | 0.9133 | 99.9 | 0.218 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)