| vipB 15-375 |
| ID: | 1396559863 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 361 (356) | ||
| Sequences: | 372 (225.6) | ||
| Seq/Len: | 1.045 | ||
| Nf(neff/√len): | 12.0 |
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: 1.045).
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 |
| 67_D | 247_Y | 4.324 | 1.00 |
| 213_L | 222_L | 4.247 | 1.00 |
| 146_I | 268_A | 3.874 | 1.00 |
| 231_L | 261_G | 2.900 | 1.00 |
| 148_N | 265_F | 2.610 | 1.00 |
| 258_Y | 299_H | 2.591 | 1.00 |
| 172_H | 221_Y | 2.413 | 0.99 |
| 237_P | 248_A | 2.190 | 0.98 |
| 213_L | 350_I | 2.184 | 0.98 |
| 223_G | 349_S | 2.143 | 0.98 |
| 147_G | 175_F | 2.018 | 0.96 |
| 62_I | 66_M | 1.952 | 0.95 |
| 176_I | 267_F | 1.949 | 0.95 |
| 270_R | 273_D | 1.869 | 0.93 |
| 222_L | 350_I | 1.864 | 0.93 |
| 86_K | 90_D | 1.836 | 0.93 |
| 93_D | 98_N | 1.765 | 0.90 |
| 87_L | 91_R | 1.762 | 0.90 |
| 104_H | 109_E | 1.703 | 0.88 |
| 144_A | 271_L | 1.703 | 0.88 |
| 298_V | 309_S | 1.689 | 0.88 |
| 183_F | 330_F | 1.666 | 0.87 |
| 99_K | 140_E | 1.661 | 0.87 |
| 112_E | 243_K | 1.638 | 0.86 |
| 88_F | 269_T | 1.632 | 0.85 |
| 151_F | 160_L | 1.608 | 0.84 |
| 212_S | 340_D | 1.602 | 0.84 |
| 268_A | 349_S | 1.592 | 0.83 |
| 228_R | 314_E | 1.579 | 0.83 |
| 35_N | 38_G | 1.532 | 0.80 |
| 58_L | 62_I | 1.471 | 0.76 |
| 236_D | 239_E | 1.465 | 0.76 |
| 80_S | 259_L | 1.457 | 0.75 |
| 106_T | 109_E | 1.456 | 0.75 |
| 134_Y | 221_Y | 1.453 | 0.75 |
| 137_F | 172_H | 1.428 | 0.73 |
| 169_A | 218_D | 1.422 | 0.72 |
| 326_A | 349_S | 1.418 | 0.72 |
| 13_T | 35_N | 1.393 | 0.70 |
| 220_R | 351_Q | 1.377 | 0.69 |
| 164_M | 171_A | 1.366 | 0.68 |
| 229_F | 261_G | 1.361 | 0.68 |
| 29_V | 33_I | 1.354 | 0.67 |
| 88_F | 100_V | 1.352 | 0.67 |
| 60_K | 73_S | 1.335 | 0.65 |
| 57_E | 60_K | 1.334 | 0.65 |
| 64_A | 247_Y | 1.329 | 0.65 |
| 125_L | 164_M | 1.323 | 0.64 |
| 323_F | 327_E | 1.316 | 0.64 |
| 223_G | 331_I | 1.311 | 0.63 |
| 267_F | 347_A | 1.304 | 0.63 |
| 115_E | 159_K | 1.303 | 0.63 |
| 209_K | 295_D | 1.298 | 0.62 |
| 127_K | 352_K | 1.293 | 0.62 |
| 179_V | 183_F | 1.270 | 0.60 |
| 13_T | 31_A | 1.268 | 0.60 |
| 215_E | 352_K | 1.263 | 0.59 |
| 101_E | 142_V | 1.253 | 0.58 |
| 133_G | 291_G | 1.252 | 0.58 |
| 21_G | 24_I | 1.248 | 0.58 |
| 162_Q | 350_I | 1.242 | 0.57 |
| 321_K | 324_E | 1.233 | 0.56 |
| 332_A | 349_S | 1.225 | 0.56 |
| 151_F | 161_L | 1.224 | 0.56 |
| 4_S | 209_K | 1.218 | 0.55 |
| 114_F | 331_I | 1.214 | 0.55 |
| 21_G | 29_V | 1.211 | 0.54 |
| 293_V | 344_F | 1.210 | 0.54 |
| 149_Y | 173_A | 1.209 | 0.54 |
| 66_M | 69_I | 1.208 | 0.54 |
| 213_L | 236_D | 1.204 | 0.54 |
| 12_Q | 102_I | 1.201 | 0.53 |
| 135_G | 320_R | 1.200 | 0.53 |
| 131_S | 318_T | 1.197 | 0.53 |
| 170_M | 285_I | 1.196 | 0.53 |
| 160_L | 236_D | 1.188 | 0.52 |
| 177_S | 225_T | 1.185 | 0.52 |
| 223_G | 268_A | 1.180 | 0.51 |
| 130_Y | 322_E | 1.170 | 0.50 |
| 102_I | 202_F | 1.170 | 0.50 |
| 255_H | 310_K | 1.159 | 0.49 |
| 168_G | 222_L | 1.158 | 0.49 |
| 305_G | 320_R | 1.146 | 0.48 |
| 55_L | 66_M | 1.145 | 0.48 |
| 301_F | 310_K | 1.132 | 0.47 |
| 136_Q | 336_R | 1.132 | 0.47 |
| 279_R | 285_I | 1.131 | 0.47 |
| 136_Q | 318_T | 1.130 | 0.47 |
| 143_G | 176_I | 1.129 | 0.47 |
| 92_T | 272_T | 1.127 | 0.46 |
| 137_F | 336_R | 1.126 | 0.46 |
| 113_D | 119_E | 1.120 | 0.46 |
| 262_N | 330_F | 1.116 | 0.45 |
| 204_S | 282_P | 1.116 | 0.45 |
| 151_F | 216_S | 1.116 | 0.45 |
| 134_Y | 172_H | 1.113 | 0.45 |
| 20_E | 298_V | 1.106 | 0.44 |
| 155_T | 233_V | 1.106 | 0.44 |
| 236_D | 248_A | 1.105 | 0.44 |
| 27_K | 33_I | 1.104 | 0.44 |
| 69_I | 109_E | 1.103 | 0.44 |
| 62_I | 193_P | 1.101 | 0.44 |
| 113_D | 345_F | 1.101 | 0.44 |
| 205_P | 219_A | 1.097 | 0.44 |
| 8_E | 38_G | 1.096 | 0.44 |
| 102_I | 208_T | 1.095 | 0.43 |
| 241_P | 337_K | 1.094 | 0.43 |
| 139_G | 291_G | 1.093 | 0.43 |
| 163_Y | 330_F | 1.093 | 0.43 |
| 101_E | 203_E | 1.091 | 0.43 |
| 254_S | 257_H | 1.088 | 0.43 |
| 107_K | 213_L | 1.087 | 0.43 |
| 70_L | 75_F | 1.081 | 0.42 |
| 132_A | 219_A | 1.078 | 0.42 |
| 156_P | 241_P | 1.078 | 0.42 |
| 286_G | 312_P | 1.077 | 0.42 |
| 296_L | 342_A | 1.073 | 0.41 |
| 176_I | 225_T | 1.071 | 0.41 |
| 164_M | 175_F | 1.069 | 0.41 |
| 175_F | 203_E | 1.067 | 0.41 |
| 338_G | 347_A | 1.067 | 0.41 |
| 11_A | 73_S | 1.066 | 0.41 |
| 237_P | 244_S | 1.064 | 0.41 |
| 163_Y | 166_A | 1.064 | 0.41 |
| 286_G | 322_E | 1.063 | 0.41 |
| 226_A | 264_A | 1.063 | 0.41 |
| 88_F | 192_L | 1.062 | 0.40 |
| 147_G | 207_Y | 1.062 | 0.40 |
| 84_G | 225_T | 1.059 | 0.40 |
| 122_Q | 165_G | 1.057 | 0.40 |
| 84_G | 231_L | 1.057 | 0.40 |
| 114_F | 311_I | 1.055 | 0.40 |
| 162_Q | 166_A | 1.052 | 0.40 |
| 311_I | 316_L | 1.052 | 0.40 |
| 84_G | 265_F | 1.050 | 0.39 |
| 94_F | 98_N | 1.048 | 0.39 |
| 51_V | 339_S | 1.045 | 0.39 |
| 255_H | 299_H | 1.045 | 0.39 |
| 165_G | 180_G | 1.041 | 0.39 |
| 317_I | 321_K | 1.040 | 0.38 |
| 292_A | 339_S | 1.039 | 0.38 |
| 170_M | 279_R | 1.038 | 0.38 |
| 135_G | 189_F | 1.036 | 0.38 |
| 71_H | 76_Q | 1.034 | 0.38 |
| 212_S | 310_K | 1.032 | 0.38 |
| 122_Q | 317_I | 1.030 | 0.38 |
| 147_G | 264_A | 1.026 | 0.37 |
| 81_A | 148_N | 1.026 | 0.37 |
| 18_S | 21_G | 1.025 | 0.37 |
| 104_H | 179_V | 1.022 | 0.37 |
| 282_P | 289_S | 1.018 | 0.37 |
| 217_E | 301_F | 1.016 | 0.36 |
| 101_E | 318_T | 1.013 | 0.36 |
| 136_Q | 194_N | 1.012 | 0.36 |
| 150_A | 263_T | 1.010 | 0.36 |
| 106_T | 244_S | 1.010 | 0.36 |
| 308_Q | 323_F | 1.006 | 0.36 |
| 187_D | 237_P | 1.001 | 0.35 |
| 72_N | 193_P | 1.001 | 0.35 |
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 | |
| 4egwA | 2 | 0.1607 | 19.2 | 0.978 | Contact Map |
| 3kshA | 1 | 0.4044 | 18.8 | 0.978 | Contact Map |
| 3ck6A | 5 | 0.1634 | 18 | 0.978 | Contact Map |
| 1ea0A | 2 | 0.1496 | 8.3 | 0.981 | Contact Map |
| 1t46A | 1 | 0.1662 | 7.7 | 0.981 | Contact Map |
| 4g3wA | 1 | 0.349 | 6.3 | 0.982 | Contact Map |
| 4emeA | 4 | 0.1911 | 4.9 | 0.983 | Contact Map |
| 3mmhA | 2 | 0.4488 | 4.5 | 0.983 | Contact Map |
| 1yarH | 7 | 0.1717 | 4 | 0.984 | Contact Map |
| 1csnA | 1 | 0.2022 | 3.9 | 0.984 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)