| hVDAC1 |
| ID: | 1378803386 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 283 (282) | ||
| Sequences: | 526 (339.4) | ||
| Seq/Len: | 1.865 | ||
| Nf(neff/√len): | 20.2 |
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: 1.865).
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 | 2.382 | 1.00 |
| 14_A | 193_S | 2.000 | 0.99 |
| 12_K | 16_D | 1.905 | 0.98 |
| 148_G | 172_G | 1.717 | 0.96 |
| 146_Y | 150_L | 1.674 | 0.95 |
| 11_G | 14_A | 1.635 | 0.94 |
| 6_T | 10_L | 1.627 | 0.94 |
| 203_E | 224_K | 1.584 | 0.93 |
| 136_P | 145_G | 1.515 | 0.91 |
| 10_L | 181_H | 1.508 | 0.90 |
| 181_H | 193_S | 1.497 | 0.90 |
| 182_T | 190_F | 1.491 | 0.90 |
| 75_W | 274_K | 1.481 | 0.89 |
| 101_S | 133_I | 1.464 | 0.89 |
| 56_G | 155_M | 1.449 | 0.88 |
| 248_T | 256_K | 1.435 | 0.87 |
| 146_Y | 149_W | 1.419 | 0.86 |
| 97_L | 116_T | 1.412 | 0.86 |
| 117_G | 124_N | 1.394 | 0.85 |
| 18_F | 21_G | 1.377 | 0.84 |
| 198_V | 243_I | 1.356 | 0.83 |
| 7_Y | 42_T | 1.351 | 0.82 |
| 250_T | 256_K | 1.351 | 0.82 |
| 260_S | 278_G | 1.349 | 0.82 |
| 248_T | 278_G | 1.346 | 0.82 |
| 195_Y | 203_E | 1.334 | 0.81 |
| 179_Q | 222_A | 1.329 | 0.81 |
| 264_D | 276_G | 1.321 | 0.80 |
| 99_F | 114_I | 1.307 | 0.80 |
| 252_K | 255_I | 1.293 | 0.78 |
| 181_H | 263_L | 1.291 | 0.78 |
| 233_F | 275_L | 1.284 | 0.78 |
| 251_L | 257_L | 1.278 | 0.77 |
| 34_K | 40_E | 1.274 | 0.77 |
| 11_G | 25_G | 1.242 | 0.74 |
| 13_S | 142_L | 1.234 | 0.74 |
| 173_Y | 237_V | 1.228 | 0.73 |
| 121_E | 148_G | 1.226 | 0.73 |
| 141_A | 164_V | 1.222 | 0.73 |
| 16_D | 143_V | 1.222 | 0.73 |
| 223_A | 233_F | 1.215 | 0.72 |
| 91_L | 179_Q | 1.208 | 0.72 |
| 129_M | 138_I | 1.202 | 0.71 |
| 122_H | 144_L | 1.198 | 0.71 |
| 195_Y | 224_K | 1.197 | 0.71 |
| 37_N | 111_N | 1.197 | 0.71 |
| 61_K | 236_K | 1.193 | 0.70 |
| 76_N | 101_S | 1.190 | 0.70 |
| 120_R | 248_T | 1.182 | 0.69 |
| 42_T | 57_S | 1.177 | 0.69 |
| 104_S | 114_I | 1.173 | 0.68 |
| 167_S | 237_V | 1.172 | 0.68 |
| 187_G | 206_V | 1.170 | 0.68 |
| 156_N | 165_T | 1.169 | 0.68 |
| 56_G | 163_R | 1.168 | 0.68 |
| 10_L | 18_F | 1.166 | 0.68 |
| 29_L | 165_T | 1.158 | 0.67 |
| 75_W | 94_G | 1.155 | 0.67 |
| 71_F | 206_V | 1.149 | 0.66 |
| 51_T | 55_T | 1.148 | 0.66 |
| 257_L | 267_N | 1.144 | 0.65 |
| 18_F | 222_A | 1.141 | 0.65 |
| 212_A | 218_R | 1.141 | 0.65 |
| 50_E | 206_V | 1.136 | 0.65 |
| 77_T | 221_I | 1.136 | 0.65 |
| 29_L | 222_A | 1.135 | 0.65 |
| 234_S | 242_L | 1.135 | 0.65 |
| 39_L | 205_A | 1.134 | 0.64 |
| 237_V | 243_I | 1.133 | 0.64 |
| 152_G | 205_A | 1.128 | 0.64 |
| 37_N | 281_F | 1.123 | 0.63 |
| 65_T | 68_G | 1.120 | 0.63 |
| 87_V | 114_I | 1.119 | 0.63 |
| 185_N | 191_G | 1.117 | 0.63 |
| 57_S | 256_K | 1.111 | 0.62 |
| 131_F | 196_Q | 1.108 | 0.62 |
| 35_S | 38_G | 1.108 | 0.62 |
| 203_E | 221_I | 1.107 | 0.62 |
| 15_R | 141_A | 1.104 | 0.61 |
| 29_L | 39_L | 1.102 | 0.61 |
| 2_A | 133_I | 1.102 | 0.61 |
| 223_A | 235_A | 1.102 | 0.61 |
| 7_Y | 170_A | 1.102 | 0.61 |
| 85_I | 99_F | 1.101 | 0.61 |
| 6_T | 124_N | 1.098 | 0.61 |
| 81_L | 147_E | 1.097 | 0.61 |
| 275_L | 279_L | 1.096 | 0.61 |
| 131_F | 200_K | 1.096 | 0.61 |
| 196_Q | 201_K | 1.096 | 0.61 |
| 84_E | 115_K | 1.093 | 0.60 |
| 91_L | 229_P | 1.091 | 0.60 |
| 85_I | 240_S | 1.090 | 0.60 |
| 170_A | 237_V | 1.087 | 0.60 |
| 27_I | 174_K | 1.087 | 0.60 |
| 42_T | 46_S | 1.085 | 0.59 |
| 45_G | 70_T | 1.084 | 0.59 |
| 204_T | 221_I | 1.084 | 0.59 |
| 53_K | 85_I | 1.082 | 0.59 |
| 188_T | 222_A | 1.081 | 0.59 |
| 76_N | 184_V | 1.080 | 0.59 |
| 148_G | 175_T | 1.078 | 0.59 |
| 71_F | 118_Y | 1.078 | 0.59 |
| 71_F | 85_I | 1.073 | 0.58 |
| 260_S | 274_K | 1.072 | 0.58 |
| 177_E | 281_F | 1.071 | 0.58 |
| 14_A | 25_G | 1.070 | 0.58 |
| 238_N | 265_G | 1.069 | 0.58 |
| 7_Y | 274_K | 1.066 | 0.57 |
| 17_V | 234_S | 1.065 | 0.57 |
| 125_L | 155_M | 1.064 | 0.57 |
| 241_S | 262_L | 1.063 | 0.57 |
| 15_R | 234_S | 1.063 | 0.57 |
| 125_L | 142_L | 1.063 | 0.57 |
| 83_T | 165_T | 1.063 | 0.57 |
| 95_L | 105_P | 1.062 | 0.57 |
| 139_R | 147_E | 1.060 | 0.57 |
| 242_L | 262_L | 1.059 | 0.57 |
| 102_S | 171_V | 1.057 | 0.56 |
| 179_Q | 182_T | 1.053 | 0.56 |
| 138_I | 155_M | 1.049 | 0.56 |
| 154_Q | 185_N | 1.045 | 0.55 |
| 24_F | 185_N | 1.045 | 0.55 |
| 149_W | 176_D | 1.045 | 0.55 |
| 11_G | 105_P | 1.045 | 0.55 |
| 253_P | 264_D | 1.045 | 0.55 |
| 141_A | 212_A | 1.042 | 0.55 |
| 36_E | 205_A | 1.041 | 0.55 |
| 221_I | 243_I | 1.040 | 0.55 |
| 101_S | 180_L | 1.039 | 0.54 |
| 65_T | 137_S | 1.037 | 0.54 |
| 58_L | 261_A | 1.037 | 0.54 |
| 57_S | 267_N | 1.036 | 0.54 |
| 199_N | 211_T | 1.036 | 0.54 |
| 132_D | 198_V | 1.033 | 0.54 |
| 91_L | 221_I | 1.033 | 0.54 |
| 52_T | 65_T | 1.030 | 0.54 |
| 43_S | 133_I | 1.029 | 0.53 |
| 10_L | 246_G | 1.029 | 0.53 |
| 7_Y | 78_D | 1.028 | 0.53 |
| 7_Y | 237_V | 1.027 | 0.53 |
| 222_A | 239_N | 1.027 | 0.53 |
| 99_F | 170_A | 1.025 | 0.53 |
| 94_G | 105_P | 1.021 | 0.53 |
| 22_Y | 114_I | 1.020 | 0.52 |
| 17_V | 179_Q | 1.020 | 0.52 |
| 56_G | 93_R | 1.016 | 0.52 |
| 75_W | 148_G | 1.015 | 0.52 |
| 255_I | 261_A | 1.015 | 0.52 |
| 153_Y | 170_A | 1.014 | 0.52 |
| 168_N | 178_F | 1.014 | 0.52 |
| 122_H | 146_Y | 1.013 | 0.52 |
| 181_H | 265_G | 1.011 | 0.51 |
| 169_F | 265_G | 1.011 | 0.51 |
| 89_D | 269_N | 1.005 | 0.51 |
| 21_G | 241_S | 1.005 | 0.51 |
| 68_G | 175_T | 1.002 | 0.50 |
| 90_Q | 108_G | 1.000 | 0.50 |
| 88_E | 248_T | 1.000 | 0.50 |
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 | 0.083 | Contact Map |
| 2wjrA | 1 | 0.6572 | 70.8 | 0.94 | Contact Map |
| 1ormA | 1 | 0.4417 | 70.3 | 0.94 | Contact Map |
| 3qraA | 1 | 0.4735 | 57.8 | 0.944 | Contact Map |
| 4e1tA | 1 | 0.6572 | 36.8 | 0.951 | Contact Map |
| 4e1sA | 1 | 0.636 | 22.2 | 0.956 | Contact Map |
| 3pguA | 1 | 0.8516 | 15.1 | 0.959 | Contact Map |
| 2x55A | 1 | 0.8021 | 11.2 | 0.962 | Contact Map |
| 2jmmA | 1 | 0.4876 | 11 | 0.962 | Contact Map |
| 1qjpA | 1 | 0.4664 | 9.5 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)