| MSJ_TMEM86A |
| ID: | 1490818369 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 240 (217) | ||
| Sequences: | 1023 (706.1) | ||
| Seq/Len: | 4.714 | ||
| Nf(neff/√len): | 47.9 |
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: 4.714).
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 |
| 78_S | 103_T | 5.623 | 1.00 |
| 107_Y | 217_Q | 4.205 | 1.00 |
| 101_A | 153_L | 2.722 | 1.00 |
| 158_G | 187_I | 2.577 | 1.00 |
| 71_I | 110_A | 2.364 | 1.00 |
| 105_M | 109_S | 2.319 | 1.00 |
| 77_F | 102_V | 2.074 | 1.00 |
| 179_A | 223_S | 2.053 | 1.00 |
| 192_T | 208_L | 2.033 | 1.00 |
| 97_L | 101_A | 1.999 | 1.00 |
| 44_C | 86_I | 1.951 | 1.00 |
| 84_F | 99_M | 1.884 | 1.00 |
| 212_T | 216_A | 1.843 | 1.00 |
| 44_C | 83_A | 1.796 | 1.00 |
| 193_I | 209_I | 1.776 | 1.00 |
| 46_P | 214_Y | 1.749 | 1.00 |
| 185_F | 215_V | 1.745 | 1.00 |
| 85_L | 96_G | 1.741 | 1.00 |
| 154_I | 183_A | 1.713 | 0.99 |
| 150_Y | 190_D | 1.674 | 0.99 |
| 102_V | 106_F | 1.668 | 0.99 |
| 100_F | 150_Y | 1.661 | 0.99 |
| 43_K | 85_L | 1.628 | 0.99 |
| 80_V | 99_M | 1.624 | 0.99 |
| 104_H | 193_I | 1.623 | 0.99 |
| 96_G | 190_D | 1.612 | 0.99 |
| 25_Y | 42_I | 1.565 | 0.99 |
| 150_Y | 186_F | 1.554 | 0.99 |
| 128_S | 155_G | 1.540 | 0.99 |
| 73_V | 106_F | 1.531 | 0.99 |
| 131_C | 191_L | 1.509 | 0.98 |
| 188_I | 212_T | 1.503 | 0.98 |
| 81_G | 100_F | 1.500 | 0.98 |
| 67_S | 223_S | 1.498 | 0.98 |
| 77_F | 81_G | 1.476 | 0.98 |
| 186_F | 217_Q | 1.475 | 0.98 |
| 186_F | 190_D | 1.461 | 0.98 |
| 40_T | 86_I | 1.457 | 0.98 |
| 67_S | 110_A | 1.448 | 0.98 |
| 151_V | 154_I | 1.435 | 0.98 |
| 74_G | 223_S | 1.419 | 0.97 |
| 97_L | 198_F | 1.412 | 0.97 |
| 100_F | 213_Y | 1.411 | 0.97 |
| 112_G | 160_R | 1.385 | 0.97 |
| 50_L | 209_I | 1.383 | 0.97 |
| 70_R | 109_S | 1.348 | 0.96 |
| 47_I | 50_L | 1.329 | 0.96 |
| 108_A | 153_L | 1.326 | 0.96 |
| 154_I | 157_M | 1.321 | 0.95 |
| 47_I | 214_Y | 1.303 | 0.95 |
| 82_D | 213_Y | 1.299 | 0.95 |
| 85_L | 104_H | 1.292 | 0.95 |
| 96_G | 150_Y | 1.286 | 0.95 |
| 82_D | 100_F | 1.250 | 0.93 |
| 96_G | 189_S | 1.248 | 0.93 |
| 100_F | 186_F | 1.246 | 0.93 |
| 100_F | 190_D | 1.245 | 0.93 |
| 82_D | 150_Y | 1.243 | 0.93 |
| 93_F | 97_L | 1.238 | 0.93 |
| 43_K | 96_G | 1.229 | 0.93 |
| 209_I | 212_T | 1.228 | 0.93 |
| 81_G | 85_L | 1.223 | 0.92 |
| 43_K | 100_F | 1.214 | 0.92 |
| 157_M | 183_A | 1.209 | 0.92 |
| 13_P | 19_F | 1.209 | 0.92 |
| 150_Y | 213_Y | 1.201 | 0.91 |
| 189_S | 212_T | 1.197 | 0.91 |
| 85_L | 150_Y | 1.191 | 0.91 |
| 85_L | 93_F | 1.189 | 0.91 |
| 104_H | 108_A | 1.189 | 0.91 |
| 213_Y | 217_Q | 1.186 | 0.91 |
| 84_F | 95_H | 1.177 | 0.90 |
| 78_S | 104_H | 1.167 | 0.90 |
| 46_P | 210_M | 1.162 | 0.90 |
| 97_L | 154_I | 1.160 | 0.89 |
| 104_H | 190_D | 1.132 | 0.88 |
| 100_F | 189_S | 1.127 | 0.88 |
| 74_G | 110_A | 1.126 | 0.88 |
| 70_R | 110_A | 1.120 | 0.87 |
| 67_S | 74_G | 1.119 | 0.87 |
| 43_K | 82_D | 1.116 | 0.87 |
| 50_L | 221_A | 1.108 | 0.86 |
| 158_G | 183_A | 1.105 | 0.86 |
| 46_P | 79_A | 1.103 | 0.86 |
| 161_A | 183_A | 1.097 | 0.86 |
| 85_L | 190_D | 1.093 | 0.85 |
| 93_F | 197_K | 1.092 | 0.85 |
| 51_W | 72_F | 1.088 | 0.85 |
| 190_D | 217_Q | 1.072 | 0.84 |
| 189_S | 213_Y | 1.067 | 0.83 |
| 182_G | 219_L | 1.064 | 0.83 |
| 195_L | 209_I | 1.064 | 0.83 |
| 74_G | 220_V | 1.060 | 0.83 |
| 108_A | 156_F | 1.054 | 0.82 |
| 85_L | 100_F | 1.051 | 0.82 |
| 100_F | 104_H | 1.050 | 0.82 |
| 16_V | 19_F | 1.049 | 0.82 |
| 155_G | 158_G | 1.049 | 0.82 |
| 207_A | 211_S | 1.042 | 0.81 |
| 48_F | 214_Y | 1.036 | 0.81 |
| 40_T | 44_C | 1.032 | 0.81 |
| 47_I | 217_Q | 1.032 | 0.81 |
| 94_V | 143_F | 1.029 | 0.80 |
| 16_V | 20_K | 1.014 | 0.79 |
| 54_L | 71_I | 1.008 | 0.78 |
| 218_M | 222_L | 1.005 | 0.78 |
| 43_K | 150_Y | 1.001 | 0.78 |
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 | |
| 2n2jA | 2 | 0 | 3 | 0.957 | Contact Map |
| 3qrxB | 1 | 0.0833 | 0.7 | 0.97 | Contact Map |
| 1tnsA | 1 | 0.1292 | 0.7 | 0.971 | Contact Map |
| 1g4dA | 1 | 0.1292 | 0.6 | 0.972 | Contact Map |
| 2i68A | 2 | 0.0333 | 0.6 | 0.972 | Contact Map |
| 2ksfA | 1 | 0.4125 | 0.6 | 0.973 | Contact Map |
| 4ogqB | 1 | 0.3583 | 0.5 | 0.973 | Contact Map |
| 4p6kA | 1 | 0.0958 | 0.5 | 0.973 | Contact Map |
| 3b5dA | 2 | 0.0208 | 0.5 | 0.973 | Contact Map |
| 4i7zE | 1 | 0.1167 | 0.5 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)