| VX |
| ID: | 1414440609 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 329 (311) | ||
| Sequences: | 640 (430.1) | ||
| Seq/Len: | 2.058 | ||
| Nf(neff/√len): | 24.4 |
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: 2.058).
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 |
| 56_A | 61_V | 2.899 | 1.00 |
| 180_A | 184_S | 2.586 | 1.00 |
| 308_P | 311_T | 2.393 | 1.00 |
| 113_T | 159_A | 2.192 | 1.00 |
| 183_E | 212_R | 2.179 | 1.00 |
| 303_R | 309_Q | 2.140 | 0.99 |
| 151_K | 185_E | 2.087 | 0.99 |
| 166_T | 178_Q | 2.056 | 0.99 |
| 207_T | 256_Q | 2.032 | 0.99 |
| 81_E | 85_A | 2.024 | 0.99 |
| 151_K | 184_S | 1.983 | 0.99 |
| 131_A | 162_V | 1.978 | 0.99 |
| 196_H | 267_D | 1.960 | 0.99 |
| 167_H | 267_D | 1.903 | 0.99 |
| 140_G | 177_Q | 1.894 | 0.98 |
| 4_N | 9_P | 1.847 | 0.98 |
| 226_I | 298_V | 1.814 | 0.98 |
| 167_H | 196_H | 1.783 | 0.97 |
| 80_A | 84_R | 1.782 | 0.97 |
| 79_L | 83_S | 1.772 | 0.97 |
| 79_L | 92_A | 1.763 | 0.97 |
| 215_L | 261_Q | 1.753 | 0.97 |
| 83_S | 92_A | 1.752 | 0.97 |
| 179_A | 212_R | 1.734 | 0.97 |
| 155_R | 185_E | 1.734 | 0.97 |
| 92_A | 115_F | 1.675 | 0.96 |
| 299_I | 303_R | 1.662 | 0.96 |
| 157_S | 187_L | 1.656 | 0.96 |
| 134_I | 153_A | 1.643 | 0.95 |
| 63_T | 89_H | 1.640 | 0.95 |
| 260_K | 314_G | 1.632 | 0.95 |
| 263_L | 319_N | 1.624 | 0.95 |
| 93_A | 123_G | 1.622 | 0.95 |
| 208_A | 211_A | 1.607 | 0.95 |
| 157_S | 164_V | 1.564 | 0.93 |
| 76_V | 92_A | 1.557 | 0.93 |
| 166_T | 194_I | 1.556 | 0.93 |
| 179_A | 214_Y | 1.543 | 0.93 |
| 154_A | 164_V | 1.505 | 0.92 |
| 309_Q | 313_A | 1.492 | 0.91 |
| 252_A | 255_D | 1.488 | 0.91 |
| 67_V | 93_A | 1.480 | 0.91 |
| 215_L | 319_N | 1.464 | 0.90 |
| 155_R | 159_A | 1.459 | 0.90 |
| 202_D | 205_Y | 1.458 | 0.90 |
| 189_P | 192_V | 1.441 | 0.89 |
| 147_E | 151_K | 1.439 | 0.89 |
| 120_I | 162_V | 1.422 | 0.88 |
| 140_G | 147_E | 1.405 | 0.88 |
| 147_E | 180_A | 1.403 | 0.87 |
| 3_I | 10_I | 1.393 | 0.87 |
| 63_T | 321_A | 1.381 | 0.86 |
| 151_K | 181_I | 1.380 | 0.86 |
| 135_K | 270_F | 1.364 | 0.85 |
| 219_D | 222_P | 1.361 | 0.85 |
| 97_W | 266_N | 1.348 | 0.84 |
| 210_A | 261_Q | 1.344 | 0.84 |
| 293_F | 298_V | 1.339 | 0.84 |
| 68_S | 76_V | 1.336 | 0.84 |
| 147_E | 181_I | 1.332 | 0.83 |
| 23_H | 196_H | 1.330 | 0.83 |
| 5_T | 8_G | 1.327 | 0.83 |
| 315_I | 319_N | 1.323 | 0.83 |
| 138_T | 166_T | 1.311 | 0.82 |
| 164_V | 274_S | 1.309 | 0.82 |
| 136_V | 153_A | 1.303 | 0.82 |
| 168_T | 175_G | 1.287 | 0.81 |
| 59_A | 296_L | 1.260 | 0.79 |
| 199_D | 220_H | 1.258 | 0.78 |
| 215_L | 322_R | 1.255 | 0.78 |
| 77_S | 111_E | 1.254 | 0.78 |
| 18_T | 320_P | 1.254 | 0.78 |
| 158_L | 187_L | 1.224 | 0.76 |
| 178_Q | 216_I | 1.223 | 0.76 |
| 69_T | 135_K | 1.222 | 0.75 |
| 17_F | 295_P | 1.219 | 0.75 |
| 216_I | 261_Q | 1.212 | 0.75 |
| 135_K | 267_D | 1.209 | 0.74 |
| 210_A | 222_P | 1.208 | 0.74 |
| 146_Q | 268_W | 1.207 | 0.74 |
| 50_V | 86_A | 1.202 | 0.74 |
| 252_A | 256_Q | 1.198 | 0.73 |
| 188_S | 192_V | 1.198 | 0.73 |
| 118_R | 122_Y | 1.195 | 0.73 |
| 144_P | 147_E | 1.194 | 0.73 |
| 57_R | 62_R | 1.193 | 0.73 |
| 138_T | 178_Q | 1.189 | 0.73 |
| 19_L | 266_N | 1.188 | 0.73 |
| 180_A | 185_E | 1.188 | 0.73 |
| 138_T | 174_D | 1.183 | 0.72 |
| 113_T | 160_T | 1.175 | 0.71 |
| 135_K | 268_W | 1.163 | 0.70 |
| 261_Q | 322_R | 1.160 | 0.70 |
| 186_G | 189_P | 1.158 | 0.70 |
| 133_I | 139_T | 1.157 | 0.70 |
| 168_T | 178_Q | 1.151 | 0.69 |
| 308_P | 312_L | 1.149 | 0.69 |
| 313_A | 317_V | 1.146 | 0.69 |
| 181_I | 185_E | 1.137 | 0.68 |
| 111_E | 114_Q | 1.137 | 0.68 |
| 181_I | 184_S | 1.134 | 0.67 |
| 288_P | 313_A | 1.125 | 0.67 |
| 66_D | 205_Y | 1.124 | 0.66 |
| 116_F | 124_I | 1.118 | 0.66 |
| 166_T | 216_I | 1.117 | 0.66 |
| 158_L | 186_G | 1.114 | 0.65 |
| 259_M | 311_T | 1.111 | 0.65 |
| 50_V | 82_V | 1.104 | 0.64 |
| 179_A | 183_E | 1.103 | 0.64 |
| 264_V | 294_I | 1.098 | 0.64 |
| 166_T | 210_A | 1.090 | 0.63 |
| 113_T | 155_R | 1.086 | 0.63 |
| 117_L | 159_A | 1.079 | 0.62 |
| 135_K | 167_H | 1.079 | 0.62 |
| 7_R | 84_R | 1.077 | 0.62 |
| 228_L | 240_I | 1.070 | 0.61 |
| 54_R | 86_A | 1.056 | 0.59 |
| 17_F | 262_I | 1.056 | 0.59 |
| 307_V | 311_T | 1.054 | 0.59 |
| 19_L | 97_W | 1.053 | 0.59 |
| 114_Q | 144_P | 1.051 | 0.59 |
| 20_T | 165_T | 1.050 | 0.59 |
| 136_V | 150_L | 1.049 | 0.59 |
| 100_P | 143_T | 1.049 | 0.59 |
| 23_H | 267_D | 1.047 | 0.58 |
| 134_I | 157_S | 1.043 | 0.58 |
| 82_V | 89_H | 1.043 | 0.58 |
| 152_A | 156_A | 1.041 | 0.58 |
| 113_T | 117_L | 1.040 | 0.58 |
| 75_D | 94_T | 1.039 | 0.57 |
| 59_A | 292_A | 1.038 | 0.57 |
| 170_A | 199_D | 1.036 | 0.57 |
| 80_A | 129_I | 1.035 | 0.57 |
| 135_K | 196_H | 1.033 | 0.57 |
| 65_V | 111_E | 1.031 | 0.57 |
| 91_V | 163_P | 1.026 | 0.56 |
| 37_E | 271_G | 1.026 | 0.56 |
| 205_Y | 214_Y | 1.026 | 0.56 |
| 91_V | 132_G | 1.022 | 0.56 |
| 67_V | 135_K | 1.015 | 0.55 |
| 220_H | 227_G | 1.013 | 0.55 |
| 117_L | 160_T | 1.012 | 0.54 |
| 23_H | 167_H | 1.010 | 0.54 |
| 66_D | 162_V | 1.009 | 0.54 |
| 98_F | 169_A | 1.008 | 0.54 |
| 98_F | 220_H | 1.008 | 0.54 |
| 200_T | 206_L | 1.008 | 0.54 |
| 176_E | 180_A | 1.007 | 0.54 |
| 117_L | 156_A | 1.004 | 0.54 |
| 220_H | 228_L | 1.004 | 0.54 |
| 180_A | 212_R | 1.003 | 0.53 |
| 259_M | 305_K | 1.001 | 0.53 |
| 254_I | 311_T | 1.000 | 0.53 |
| 4_N | 130_R | 1.000 | 0.53 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3k2gA | 4 | 0.9422 | 100 | 0.376 | Contact Map |
| 3rhgA | 1 | 0.9422 | 100 | 0.4 | Contact Map |
| 3ovgA | 6 | 0.9179 | 100 | 0.514 | Contact Map |
| 3pnzA | 6 | 0.9027 | 100 | 0.525 | Contact Map |
| 4if2A | 1 | 0.9453 | 100 | 0.528 | Contact Map |
| 3tn4A | 2 | 0.9422 | 100 | 0.529 | Contact Map |
| 3gtxA | 1 | 0.9392 | 100 | 0.534 | Contact Map |
| 2ob3A | 2 | 0.9818 | 100 | 0.534 | Contact Map |
| 4kezA | 4 | 0.8997 | 100 | 0.572 | Contact Map |
| 1bf6A | 2 | 0.8632 | 100 | 0.581 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)