| vipB 15-375 |
| ID: | 1396566296 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 361 (356) | ||
| Sequences: | 527 (310) | ||
| Seq/Len: | 1.480 | ||
| Nf(neff/√len): | 16.4 |
Jackhmmer Results: (2014_03_19)
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: 1.480).
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 | 4.745 | 1.00 |
| 213_L | 222_L | 4.711 | 1.00 |
| 146_I | 268_A | 3.804 | 1.00 |
| 231_L | 261_G | 3.106 | 1.00 |
| 148_N | 265_F | 2.839 | 1.00 |
| 258_Y | 299_H | 2.805 | 1.00 |
| 147_G | 175_F | 2.619 | 1.00 |
| 62_I | 66_M | 2.484 | 1.00 |
| 223_G | 349_S | 2.401 | 1.00 |
| 172_H | 221_Y | 2.351 | 1.00 |
| 176_I | 267_F | 2.287 | 0.99 |
| 86_K | 90_D | 2.121 | 0.99 |
| 144_A | 271_L | 2.017 | 0.98 |
| 237_P | 248_A | 1.996 | 0.98 |
| 228_R | 314_E | 1.991 | 0.98 |
| 222_L | 350_I | 1.916 | 0.97 |
| 101_E | 142_V | 1.867 | 0.97 |
| 298_V | 309_S | 1.853 | 0.96 |
| 215_E | 352_K | 1.790 | 0.95 |
| 236_D | 239_E | 1.780 | 0.95 |
| 183_F | 330_F | 1.771 | 0.95 |
| 213_L | 350_I | 1.755 | 0.95 |
| 106_T | 109_E | 1.735 | 0.94 |
| 323_F | 327_E | 1.732 | 0.94 |
| 99_K | 140_E | 1.728 | 0.94 |
| 134_Y | 221_Y | 1.665 | 0.92 |
| 270_R | 273_D | 1.655 | 0.92 |
| 57_E | 60_K | 1.630 | 0.91 |
| 88_F | 269_T | 1.627 | 0.91 |
| 112_E | 243_K | 1.624 | 0.91 |
| 87_L | 91_R | 1.612 | 0.91 |
| 223_G | 331_I | 1.611 | 0.91 |
| 229_F | 261_G | 1.600 | 0.90 |
| 255_H | 310_K | 1.590 | 0.90 |
| 125_L | 164_M | 1.584 | 0.90 |
| 93_D | 98_N | 1.573 | 0.89 |
| 149_Y | 173_A | 1.571 | 0.89 |
| 4_S | 7_D | 1.519 | 0.87 |
| 151_F | 160_L | 1.508 | 0.86 |
| 104_H | 109_E | 1.484 | 0.85 |
| 35_N | 38_G | 1.479 | 0.85 |
| 169_A | 218_D | 1.472 | 0.84 |
| 136_Q | 318_T | 1.459 | 0.84 |
| 80_S | 259_L | 1.448 | 0.83 |
| 326_A | 349_S | 1.442 | 0.83 |
| 231_L | 259_L | 1.415 | 0.81 |
| 137_F | 172_H | 1.408 | 0.81 |
| 131_S | 318_T | 1.402 | 0.80 |
| 101_E | 203_E | 1.390 | 0.79 |
| 155_T | 233_V | 1.381 | 0.79 |
| 254_S | 257_H | 1.375 | 0.78 |
| 135_G | 318_T | 1.352 | 0.77 |
| 212_S | 340_D | 1.349 | 0.77 |
| 64_A | 247_Y | 1.344 | 0.76 |
| 332_A | 349_S | 1.343 | 0.76 |
| 9_I | 13_T | 1.337 | 0.76 |
| 7_D | 26_K | 1.328 | 0.75 |
| 155_T | 239_E | 1.326 | 0.75 |
| 9_I | 12_Q | 1.320 | 0.74 |
| 6_L | 13_T | 1.302 | 0.73 |
| 55_L | 66_M | 1.282 | 0.71 |
| 220_R | 351_Q | 1.282 | 0.71 |
| 253_A | 257_H | 1.257 | 0.69 |
| 177_S | 225_T | 1.255 | 0.69 |
| 321_K | 324_E | 1.253 | 0.69 |
| 107_K | 213_L | 1.252 | 0.69 |
| 164_M | 175_F | 1.244 | 0.68 |
| 178_S | 262_N | 1.244 | 0.68 |
| 115_E | 159_K | 1.239 | 0.68 |
| 13_T | 31_A | 1.234 | 0.67 |
| 229_F | 266_A | 1.215 | 0.65 |
| 250_N | 257_H | 1.212 | 0.65 |
| 13_T | 35_N | 1.204 | 0.64 |
| 9_I | 26_K | 1.201 | 0.64 |
| 58_L | 62_I | 1.201 | 0.64 |
| 12_Q | 15_I | 1.197 | 0.64 |
| 287_P | 343_A | 1.195 | 0.63 |
| 146_I | 264_A | 1.193 | 0.63 |
| 184_F | 330_F | 1.183 | 0.62 |
| 165_G | 195_I | 1.170 | 0.61 |
| 162_Q | 295_D | 1.169 | 0.61 |
| 158_M | 259_L | 1.167 | 0.61 |
| 92_T | 272_T | 1.161 | 0.60 |
| 64_A | 68_E | 1.159 | 0.60 |
| 76_Q | 259_L | 1.152 | 0.59 |
| 9_I | 15_I | 1.142 | 0.58 |
| 163_Y | 166_A | 1.138 | 0.58 |
| 156_P | 240_N | 1.138 | 0.58 |
| 236_D | 248_A | 1.133 | 0.57 |
| 81_A | 148_N | 1.132 | 0.57 |
| 137_F | 336_R | 1.127 | 0.57 |
| 147_G | 207_Y | 1.127 | 0.57 |
| 202_F | 207_Y | 1.116 | 0.56 |
| 129_V | 145_I | 1.114 | 0.55 |
| 134_Y | 172_H | 1.110 | 0.55 |
| 106_T | 239_E | 1.108 | 0.55 |
| 122_Q | 317_I | 1.105 | 0.54 |
| 109_E | 164_M | 1.101 | 0.54 |
| 36_L | 292_A | 1.100 | 0.54 |
| 109_E | 314_E | 1.100 | 0.54 |
| 84_G | 231_L | 1.096 | 0.54 |
| 147_G | 168_G | 1.095 | 0.53 |
| 64_A | 70_L | 1.093 | 0.53 |
| 185_G | 198_L | 1.089 | 0.53 |
| 268_A | 349_S | 1.086 | 0.53 |
| 60_K | 73_S | 1.084 | 0.52 |
| 292_A | 339_S | 1.083 | 0.52 |
| 136_Q | 336_R | 1.079 | 0.52 |
| 80_S | 261_G | 1.076 | 0.52 |
| 170_M | 279_R | 1.073 | 0.51 |
| 127_K | 352_K | 1.070 | 0.51 |
| 11_A | 23_D | 1.065 | 0.50 |
| 94_F | 98_N | 1.063 | 0.50 |
| 9_I | 14_R | 1.061 | 0.50 |
| 130_Y | 322_E | 1.057 | 0.50 |
| 333_L | 344_F | 1.057 | 0.50 |
| 187_D | 237_P | 1.055 | 0.49 |
| 10_M | 18_S | 1.055 | 0.49 |
| 299_H | 310_K | 1.053 | 0.49 |
| 12_Q | 16_A | 1.053 | 0.49 |
| 146_I | 191_E | 1.053 | 0.49 |
| 143_G | 187_D | 1.050 | 0.49 |
| 113_D | 184_F | 1.048 | 0.49 |
| 66_M | 69_I | 1.046 | 0.48 |
| 135_G | 325_L | 1.045 | 0.48 |
| 102_I | 208_T | 1.043 | 0.48 |
| 213_L | 223_G | 1.040 | 0.48 |
| 143_G | 281_C | 1.038 | 0.48 |
| 150_A | 178_S | 1.037 | 0.47 |
| 10_M | 14_R | 1.037 | 0.47 |
| 57_E | 63_S | 1.036 | 0.47 |
| 117_A | 120_T | 1.034 | 0.47 |
| 20_E | 24_I | 1.031 | 0.47 |
| 60_K | 64_A | 1.030 | 0.47 |
| 12_Q | 17_P | 1.030 | 0.47 |
| 290_G | 322_E | 1.028 | 0.47 |
| 21_G | 29_V | 1.027 | 0.46 |
| 20_E | 33_I | 1.026 | 0.46 |
| 113_D | 117_A | 1.024 | 0.46 |
| 113_D | 345_F | 1.024 | 0.46 |
| 130_Y | 291_G | 1.022 | 0.46 |
| 151_F | 161_L | 1.020 | 0.46 |
| 96_E | 199_K | 1.019 | 0.46 |
| 63_S | 67_D | 1.018 | 0.46 |
| 170_M | 285_I | 1.011 | 0.45 |
| 137_F | 343_A | 1.008 | 0.45 |
| 286_G | 290_G | 1.008 | 0.45 |
| 287_P | 336_R | 1.007 | 0.44 |
| 150_A | 180_G | 1.005 | 0.44 |
| 244_S | 248_A | 1.005 | 0.44 |
| 250_N | 253_A | 1.001 | 0.44 |
| 52_D | 114_F | 1.001 | 0.44 |
| 198_L | 223_G | 1.000 | 0.44 |
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 | 11.8 | 0.979 | Contact Map |
| 4mncA | 1 | 0.2355 | 10.8 | 0.979 | Contact Map |
| 3kshA | 1 | 0.4044 | 9.6 | 0.98 | Contact Map |
| 1csnA | 1 | 0.205 | 8.9 | 0.98 | Contact Map |
| 3ck6A | 5 | 0.1634 | 8.5 | 0.98 | Contact Map |
| 1t46A | 1 | 0.1662 | 7.2 | 0.981 | Contact Map |
| 3og7A | 2 | 0.1662 | 6.6 | 0.981 | Contact Map |
| 4emeA | 4 | 0.1939 | 5.8 | 0.982 | Contact Map |
| 2xz3A | 1 | 0.3241 | 5.4 | 0.982 | Contact Map |
| 1gpjA | 1 | 0.2604 | 4.6 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)