| TMEM163_wild type -force run |
| ID: | 1471677613 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 289 (235) | ||
| Sequences: | 79 (42.6) | ||
| Seq/Len: | 0.336 | ||
| Nf(neff/√len): | 2.8 |
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: 0.336).
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 |
| 198_I | 238_L | 2.080 | 0.80 |
| 233_G | 236_I | 2.074 | 0.80 |
| 117_S | 221_T | 1.851 | 0.68 |
| 121_F | 124_D | 1.804 | 0.65 |
| 124_D | 225_N | 1.705 | 0.59 |
| 132_S | 222_D | 1.600 | 0.52 |
| 146_H | 279_V | 1.552 | 0.48 |
| 197_G | 231_V | 1.527 | 0.47 |
| 172_K | 261_G | 1.514 | 0.46 |
| 192_V | 242_V | 1.509 | 0.45 |
| 151_E | 253_D | 1.483 | 0.43 |
| 114_Y | 246_D | 1.478 | 0.43 |
| 146_H | 149_H | 1.419 | 0.39 |
| 123_F | 230_G | 1.410 | 0.39 |
| 194_I | 237_L | 1.403 | 0.38 |
| 70_L | 203_L | 1.394 | 0.38 |
| 128_D | 253_D | 1.390 | 0.37 |
| 124_D | 138_R | 1.386 | 0.37 |
| 116_A | 196_S | 1.386 | 0.37 |
| 200_C | 226_S | 1.375 | 0.36 |
| 91_V | 175_H | 1.358 | 0.35 |
| 167_I | 260_I | 1.353 | 0.35 |
| 225_N | 229_G | 1.346 | 0.34 |
| 192_V | 216_S | 1.319 | 0.33 |
| 229_G | 279_V | 1.311 | 0.32 |
| 89_L | 194_I | 1.308 | 0.32 |
| 173_A | 206_L | 1.300 | 0.32 |
| 231_V | 234_F | 1.298 | 0.32 |
| 110_S | 121_F | 1.290 | 0.31 |
| 101_A | 238_L | 1.270 | 0.30 |
| 102_L | 226_S | 1.257 | 0.29 |
| 82_Q | 252_L | 1.255 | 0.29 |
| 102_L | 225_N | 1.253 | 0.29 |
| 218_A | 222_D | 1.251 | 0.29 |
| 110_S | 268_G | 1.251 | 0.29 |
| 229_G | 254_G | 1.243 | 0.28 |
| 129_V | 196_S | 1.238 | 0.28 |
| 97_I | 259_L | 1.238 | 0.28 |
| 197_G | 261_G | 1.229 | 0.28 |
| 257_G | 281_Q | 1.227 | 0.27 |
| 97_I | 258_V | 1.219 | 0.27 |
| 271_L | 281_Q | 1.216 | 0.27 |
| 121_F | 229_G | 1.212 | 0.27 |
| 117_S | 219_L | 1.210 | 0.27 |
| 207_K | 226_S | 1.210 | 0.27 |
| 102_L | 125_A | 1.206 | 0.26 |
| 134_I | 198_I | 1.196 | 0.26 |
| 71_E | 114_Y | 1.185 | 0.25 |
| 99_T | 200_C | 1.180 | 0.25 |
| 118_A | 239_S | 1.175 | 0.25 |
| 99_T | 125_A | 1.156 | 0.24 |
| 180_R | 255_S | 1.155 | 0.24 |
| 117_S | 124_D | 1.153 | 0.24 |
| 211_G | 259_L | 1.151 | 0.23 |
| 132_S | 207_K | 1.150 | 0.23 |
| 137_W | 216_S | 1.148 | 0.23 |
| 96_I | 198_I | 1.145 | 0.23 |
| 107_F | 177_L | 1.143 | 0.23 |
| 63_G | 101_A | 1.142 | 0.23 |
| 146_H | 229_G | 1.137 | 0.23 |
| 123_F | 158_L | 1.136 | 0.23 |
| 180_R | 235_S | 1.133 | 0.23 |
| 177_L | 196_S | 1.130 | 0.22 |
| 101_A | 143_A | 1.121 | 0.22 |
| 121_F | 233_G | 1.119 | 0.22 |
| 125_A | 200_C | 1.116 | 0.22 |
| 159_G | 268_G | 1.104 | 0.21 |
| 158_L | 162_F | 1.098 | 0.21 |
| 72_S | 262_L | 1.094 | 0.21 |
| 146_H | 254_G | 1.092 | 0.21 |
| 207_K | 256_I | 1.090 | 0.21 |
| 172_K | 265_F | 1.087 | 0.20 |
| 141_N | 254_G | 1.087 | 0.20 |
| 97_I | 130_L | 1.087 | 0.20 |
| 91_V | 135_V | 1.087 | 0.20 |
| 211_G | 219_L | 1.086 | 0.20 |
| 228_V | 271_L | 1.083 | 0.20 |
| 125_A | 250_W | 1.083 | 0.20 |
| 110_S | 233_G | 1.078 | 0.20 |
| 225_N | 279_V | 1.077 | 0.20 |
| 100_L | 174_I | 1.077 | 0.20 |
| 138_R | 176_D | 1.076 | 0.20 |
| 268_G | 281_Q | 1.071 | 0.20 |
| 166_S | 261_G | 1.071 | 0.20 |
| 110_S | 127_L | 1.070 | 0.20 |
| 50_R | 53_R | 1.069 | 0.20 |
| 156_V | 161_I | 1.064 | 0.19 |
| 159_G | 252_L | 1.063 | 0.19 |
| 100_L | 171_V | 1.058 | 0.19 |
| 153_I | 156_V | 1.055 | 0.19 |
| 140_S | 177_L | 1.054 | 0.19 |
| 165_S | 169_I | 1.050 | 0.19 |
| 97_I | 265_F | 1.049 | 0.19 |
| 173_A | 264_I | 1.044 | 0.19 |
| 115_S | 118_A | 1.043 | 0.19 |
| 162_F | 225_N | 1.041 | 0.18 |
| 79_H | 82_Q | 1.039 | 0.18 |
| 145_V | 241_E | 1.039 | 0.18 |
| 102_L | 200_C | 1.038 | 0.18 |
| 105_A | 161_I | 1.038 | 0.18 |
| 122_A | 142_A | 1.036 | 0.18 |
| 165_S | 230_G | 1.035 | 0.18 |
| 125_A | 221_T | 1.034 | 0.18 |
| 155_C | 218_A | 1.033 | 0.18 |
| 149_H | 229_G | 1.031 | 0.18 |
| 117_S | 153_I | 1.031 | 0.18 |
| 100_L | 283_R | 1.030 | 0.18 |
| 106_A | 200_C | 1.027 | 0.18 |
| 94_F | 100_L | 1.027 | 0.18 |
| 149_H | 279_V | 1.027 | 0.18 |
| 185_V | 196_S | 1.026 | 0.18 |
| 121_F | 151_E | 1.025 | 0.18 |
| 104_V | 194_I | 1.022 | 0.18 |
| 88_A | 134_I | 1.021 | 0.18 |
| 221_T | 250_W | 1.019 | 0.18 |
| 54_I | 170_V | 1.018 | 0.17 |
| 200_C | 225_N | 1.018 | 0.17 |
| 158_L | 226_S | 1.016 | 0.17 |
| 116_A | 129_V | 1.015 | 0.17 |
| 170_V | 193_S | 1.012 | 0.17 |
| 149_H | 245_H | 1.011 | 0.17 |
| 199_L | 277_P | 1.009 | 0.17 |
| 113_R | 135_V | 1.009 | 0.17 |
| 165_S | 260_I | 1.009 | 0.17 |
| 210_L | 213_V | 1.009 | 0.17 |
| 139_Y | 162_F | 1.006 | 0.17 |
| 121_F | 162_F | 1.005 | 0.17 |
| 233_G | 256_I | 1.005 | 0.17 |
| 58_G | 61_S | 1.003 | 0.17 |
| 93_W | 220_I | 1.002 | 0.17 |
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 | |
| 3j1zP | 2 | 0.7266 | 100 | 0.589 | Contact Map |
| 3h90A | 4 | 0.6955 | 100 | 0.596 | Contact Map |
| 2kogA | 1 | 0.3391 | 34.8 | 0.965 | Contact Map |
| 3tu5B | 1 | 0 | 23.7 | 0.968 | Contact Map |
| 2kncB | 1 | 0.1661 | 21.3 | 0.969 | Contact Map |
| 3m0cC | 1 | 0 | 17.2 | 0.97 | Contact Map |
| 3m73A | 1 | 0.4533 | 13.9 | 0.971 | Contact Map |
| 3ioxA | 1 | 0.1834 | 11.3 | 0.972 | Contact Map |
| 2ww9C | 1 | 0.0727 | 11.3 | 0.972 | Contact Map |
| 3mk7C | 4 | 0.3287 | 10.5 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)