| hVDAC1 |
| ID: | 1378800354 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 283 (282) | ||
| Sequences: | 625 (417.9) | ||
| Seq/Len: | 2.216 | ||
| Nf(neff/√len): | 24.9 |
HHblits Results: (2013_03)
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: 2.216).
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 |
| 9_D | 12_K | 2.146 | 1.00 |
| 14_A | 193_S | 2.078 | 0.99 |
| 12_K | 16_D | 1.925 | 0.99 |
| 145_G | 151_A | 1.921 | 0.99 |
| 203_E | 224_K | 1.886 | 0.99 |
| 181_H | 193_S | 1.819 | 0.98 |
| 264_D | 276_G | 1.800 | 0.98 |
| 250_T | 256_K | 1.750 | 0.97 |
| 182_T | 190_F | 1.711 | 0.97 |
| 6_T | 10_L | 1.661 | 0.96 |
| 148_G | 172_G | 1.646 | 0.96 |
| 97_L | 116_T | 1.624 | 0.96 |
| 248_T | 256_K | 1.578 | 0.95 |
| 15_R | 141_A | 1.576 | 0.95 |
| 11_G | 14_A | 1.536 | 0.94 |
| 14_A | 205_A | 1.484 | 0.92 |
| 122_H | 143_V | 1.459 | 0.91 |
| 264_D | 267_N | 1.447 | 0.91 |
| 77_T | 221_I | 1.435 | 0.90 |
| 257_L | 267_N | 1.429 | 0.90 |
| 153_Y | 170_A | 1.411 | 0.89 |
| 11_G | 25_G | 1.403 | 0.89 |
| 161_K | 254_G | 1.378 | 0.88 |
| 251_L | 257_L | 1.378 | 0.88 |
| 248_T | 278_G | 1.367 | 0.87 |
| 29_L | 222_A | 1.365 | 0.87 |
| 252_K | 255_I | 1.324 | 0.85 |
| 46_S | 205_A | 1.305 | 0.83 |
| 117_G | 124_N | 1.303 | 0.83 |
| 18_F | 21_G | 1.302 | 0.83 |
| 75_W | 79_N | 1.294 | 0.83 |
| 120_R | 123_I | 1.268 | 0.81 |
| 29_L | 199_N | 1.265 | 0.81 |
| 153_Y | 251_L | 1.259 | 0.80 |
| 71_F | 85_I | 1.257 | 0.80 |
| 257_L | 261_A | 1.256 | 0.80 |
| 179_Q | 205_A | 1.253 | 0.80 |
| 212_A | 218_R | 1.250 | 0.80 |
| 85_I | 114_I | 1.247 | 0.79 |
| 18_F | 206_V | 1.246 | 0.79 |
| 10_L | 181_H | 1.246 | 0.79 |
| 146_Y | 150_L | 1.245 | 0.79 |
| 97_L | 243_I | 1.240 | 0.79 |
| 156_N | 165_T | 1.236 | 0.79 |
| 130_D | 204_T | 1.232 | 0.78 |
| 18_F | 222_A | 1.226 | 0.78 |
| 68_G | 105_P | 1.218 | 0.77 |
| 23_G | 256_K | 1.216 | 0.77 |
| 179_Q | 222_A | 1.216 | 0.77 |
| 16_D | 32_K | 1.210 | 0.77 |
| 208_L | 219_F | 1.207 | 0.76 |
| 59_E | 75_W | 1.199 | 0.76 |
| 7_Y | 170_A | 1.197 | 0.75 |
| 226_Q | 229_P | 1.188 | 0.75 |
| 106_N | 151_A | 1.184 | 0.74 |
| 249_Q | 254_G | 1.181 | 0.74 |
| 195_Y | 203_E | 1.181 | 0.74 |
| 102_S | 281_F | 1.181 | 0.74 |
| 115_K | 128_D | 1.180 | 0.74 |
| 154_Q | 185_N | 1.177 | 0.74 |
| 278_G | 281_F | 1.170 | 0.73 |
| 79_N | 212_A | 1.162 | 0.72 |
| 17_V | 179_Q | 1.159 | 0.72 |
| 146_Y | 149_W | 1.154 | 0.72 |
| 84_E | 181_H | 1.152 | 0.71 |
| 2_A | 15_R | 1.148 | 0.71 |
| 99_F | 270_A | 1.143 | 0.71 |
| 194_I | 265_G | 1.142 | 0.70 |
| 12_K | 190_F | 1.142 | 0.70 |
| 64_W | 69_L | 1.141 | 0.70 |
| 225_Y | 274_K | 1.141 | 0.70 |
| 121_E | 274_K | 1.141 | 0.70 |
| 223_A | 233_F | 1.140 | 0.70 |
| 263_L | 279_L | 1.135 | 0.70 |
| 233_F | 275_L | 1.134 | 0.70 |
| 61_K | 68_G | 1.132 | 0.69 |
| 66_E | 104_S | 1.132 | 0.69 |
| 198_V | 243_I | 1.129 | 0.69 |
| 184_V | 207_N | 1.129 | 0.69 |
| 8_A | 26_L | 1.122 | 0.68 |
| 5_P | 150_L | 1.120 | 0.68 |
| 208_L | 240_S | 1.119 | 0.68 |
| 231_A | 249_Q | 1.116 | 0.68 |
| 239_N | 269_N | 1.116 | 0.68 |
| 81_L | 85_I | 1.114 | 0.68 |
| 263_L | 268_V | 1.110 | 0.67 |
| 61_K | 220_G | 1.109 | 0.67 |
| 27_I | 44_S | 1.109 | 0.67 |
| 255_I | 280_E | 1.107 | 0.67 |
| 127_C | 131_F | 1.106 | 0.67 |
| 143_V | 152_G | 1.104 | 0.67 |
| 145_G | 171_V | 1.102 | 0.66 |
| 260_S | 278_G | 1.102 | 0.66 |
| 160_A | 182_T | 1.098 | 0.66 |
| 31_L | 39_L | 1.095 | 0.66 |
| 101_S | 133_I | 1.094 | 0.66 |
| 29_L | 165_T | 1.092 | 0.65 |
| 169_F | 265_G | 1.091 | 0.65 |
| 197_K | 216_N | 1.090 | 0.65 |
| 255_I | 281_F | 1.090 | 0.65 |
| 93_R | 114_I | 1.089 | 0.65 |
| 223_A | 272_G | 1.089 | 0.65 |
| 235_A | 280_E | 1.086 | 0.65 |
| 174_K | 221_I | 1.084 | 0.65 |
| 135_G | 264_D | 1.084 | 0.65 |
| 124_N | 142_L | 1.083 | 0.65 |
| 141_A | 164_V | 1.082 | 0.64 |
| 71_F | 130_D | 1.079 | 0.64 |
| 206_V | 233_F | 1.077 | 0.64 |
| 6_T | 124_N | 1.077 | 0.64 |
| 36_E | 85_I | 1.075 | 0.64 |
| 260_S | 266_K | 1.069 | 0.63 |
| 170_A | 201_K | 1.069 | 0.63 |
| 149_W | 195_Y | 1.068 | 0.63 |
| 15_R | 279_L | 1.067 | 0.63 |
| 34_K | 40_E | 1.065 | 0.63 |
| 17_V | 227_I | 1.064 | 0.62 |
| 85_I | 275_L | 1.064 | 0.62 |
| 82_G | 259_L | 1.064 | 0.62 |
| 113_K | 136_P | 1.063 | 0.62 |
| 106_N | 111_N | 1.061 | 0.62 |
| 179_Q | 195_Y | 1.061 | 0.62 |
| 6_T | 117_G | 1.057 | 0.62 |
| 139_R | 143_V | 1.057 | 0.62 |
| 15_R | 234_S | 1.056 | 0.62 |
| 45_G | 49_T | 1.054 | 0.61 |
| 154_Q | 168_N | 1.047 | 0.61 |
| 225_Y | 236_K | 1.046 | 0.61 |
| 187_G | 206_V | 1.046 | 0.61 |
| 71_F | 157_F | 1.044 | 0.60 |
| 19_T | 23_G | 1.044 | 0.60 |
| 65_T | 99_F | 1.043 | 0.60 |
| 260_S | 274_K | 1.040 | 0.60 |
| 152_G | 205_A | 1.040 | 0.60 |
| 168_N | 178_F | 1.036 | 0.59 |
| 125_L | 173_Y | 1.034 | 0.59 |
| 35_S | 38_G | 1.033 | 0.59 |
| 229_P | 261_A | 1.031 | 0.59 |
| 32_K | 157_F | 1.027 | 0.58 |
| 99_F | 171_V | 1.026 | 0.58 |
| 7_Y | 237_V | 1.024 | 0.58 |
| 197_K | 222_A | 1.019 | 0.58 |
| 71_F | 244_G | 1.017 | 0.57 |
| 223_A | 235_A | 1.017 | 0.57 |
| 196_Q | 201_K | 1.016 | 0.57 |
| 41_F | 178_F | 1.015 | 0.57 |
| 241_S | 262_L | 1.015 | 0.57 |
| 10_L | 18_F | 1.015 | 0.57 |
| 92_A | 101_S | 1.014 | 0.57 |
| 64_W | 67_Y | 1.011 | 0.57 |
| 121_E | 148_G | 1.009 | 0.56 |
| 57_S | 123_I | 1.007 | 0.56 |
| 94_G | 237_V | 1.005 | 0.56 |
| 148_G | 176_D | 1.003 | 0.56 |
| 172_G | 178_F | 1.002 | 0.56 |
| 103_F | 110_K | 1.000 | 0.55 |
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 | |
| 3emnX | 1 | 1 | 100 | 0.002 | Contact Map |
| 2wjrA | 1 | 0.6537 | 39.9 | 0.933 | Contact Map |
| 1ormA | 1 | 0.4417 | 26.2 | 0.939 | Contact Map |
| 3qraA | 1 | 0.5018 | 17.1 | 0.944 | Contact Map |
| 4e1sA | 1 | 0.6466 | 10.8 | 0.949 | Contact Map |
| 4e1tA | 1 | 0.6537 | 9.8 | 0.95 | Contact Map |
| 2x9kA | 1 | 0.7032 | 3.6 | 0.959 | Contact Map |
| 4fqeA | 1 | 0.2933 | 3.5 | 0.959 | Contact Map |
| 3da0A | 3 | 0.2473 | 3.2 | 0.96 | Contact Map |
| 2jmfB | 1 | 0.0424 | 2.9 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)