| T0794 - roll 1-300 -force run |
| ID: | 1401228339 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 300 (297) | ||
| Sequences: | 166 (78.1) | ||
| Seq/Len: | 0.559 | ||
| Nf(neff/√len): | 4.5 |
Jackhmmer Results: (2014_04_16)
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: 0.559).
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 |
| 80_D | 156_H | 2.049 | 0.89 |
| 76_E | 156_H | 1.982 | 0.87 |
| 215_T | 226_A | 1.947 | 0.86 |
| 71_L | 159_N | 1.868 | 0.83 |
| 73_P | 119_G | 1.852 | 0.82 |
| 120_D | 156_H | 1.851 | 0.82 |
| 189_T | 214_P | 1.816 | 0.80 |
| 51_A | 227_V | 1.791 | 0.79 |
| 76_E | 120_D | 1.780 | 0.78 |
| 68_R | 134_D | 1.738 | 0.76 |
| 37_D | 102_R | 1.643 | 0.70 |
| 43_I | 114_V | 1.543 | 0.63 |
| 98_P | 139_Y | 1.531 | 0.62 |
| 230_H | 243_A | 1.508 | 0.60 |
| 60_A | 134_D | 1.498 | 0.60 |
| 134_D | 159_N | 1.489 | 0.59 |
| 39_L | 56_T | 1.458 | 0.56 |
| 177_T | 185_F | 1.440 | 0.55 |
| 59_D | 188_F | 1.428 | 0.54 |
| 294_N | 298_Y | 1.421 | 0.53 |
| 25_R | 86_I | 1.402 | 0.52 |
| 37_D | 184_S | 1.397 | 0.52 |
| 86_I | 139_Y | 1.392 | 0.51 |
| 295_W | 298_Y | 1.387 | 0.51 |
| 228_E | 283_L | 1.387 | 0.51 |
| 136_R | 145_F | 1.384 | 0.51 |
| 211_I | 234_A | 1.381 | 0.50 |
| 74_Y | 201_T | 1.366 | 0.49 |
| 273_T | 281_S | 1.366 | 0.49 |
| 76_E | 118_I | 1.361 | 0.49 |
| 134_D | 145_F | 1.361 | 0.49 |
| 24_S | 154_R | 1.356 | 0.48 |
| 199_A | 239_V | 1.353 | 0.48 |
| 168_N | 197_D | 1.346 | 0.48 |
| 161_F | 230_H | 1.345 | 0.47 |
| 238_R | 284_D | 1.334 | 0.47 |
| 179_N | 184_S | 1.332 | 0.46 |
| 75_L | 138_Q | 1.331 | 0.46 |
| 24_S | 27_E | 1.327 | 0.46 |
| 15_L | 40_E | 1.311 | 0.45 |
| 60_A | 68_R | 1.299 | 0.44 |
| 124_C | 131_C | 1.294 | 0.43 |
| 186_G | 191_F | 1.285 | 0.43 |
| 159_N | 249_P | 1.261 | 0.41 |
| 43_I | 150_K | 1.257 | 0.41 |
| 59_D | 121_K | 1.233 | 0.39 |
| 128_D | 159_N | 1.232 | 0.39 |
| 159_N | 224_L | 1.227 | 0.38 |
| 213_F | 236_G | 1.226 | 0.38 |
| 178_F | 185_F | 1.219 | 0.38 |
| 80_D | 280_L | 1.218 | 0.38 |
| 32_M | 119_G | 1.214 | 0.37 |
| 89_N | 108_K | 1.211 | 0.37 |
| 161_F | 220_V | 1.205 | 0.37 |
| 47_A | 50_G | 1.200 | 0.36 |
| 98_P | 159_N | 1.196 | 0.36 |
| 110_N | 259_Y | 1.194 | 0.36 |
| 74_Y | 282_Q | 1.192 | 0.36 |
| 219_N | 254_T | 1.189 | 0.35 |
| 4_F | 145_F | 1.186 | 0.35 |
| 152_V | 210_T | 1.181 | 0.35 |
| 69_D | 282_Q | 1.178 | 0.35 |
| 90_N | 227_V | 1.177 | 0.35 |
| 181_T | 233_W | 1.175 | 0.34 |
| 117_N | 142_D | 1.175 | 0.34 |
| 213_F | 246_I | 1.172 | 0.34 |
| 59_D | 160_L | 1.167 | 0.34 |
| 219_N | 245_N | 1.167 | 0.34 |
| 8_V | 153_A | 1.166 | 0.34 |
| 150_K | 237_M | 1.156 | 0.33 |
| 74_Y | 246_I | 1.152 | 0.33 |
| 127_S | 172_E | 1.147 | 0.33 |
| 86_I | 112_I | 1.146 | 0.32 |
| 265_R | 283_L | 1.141 | 0.32 |
| 142_D | 189_T | 1.140 | 0.32 |
| 161_F | 243_A | 1.132 | 0.31 |
| 102_R | 184_S | 1.130 | 0.31 |
| 72_Y | 121_K | 1.126 | 0.31 |
| 25_R | 42_A | 1.126 | 0.31 |
| 194_L | 218_M | 1.124 | 0.31 |
| 87_P | 143_V | 1.119 | 0.31 |
| 74_Y | 80_D | 1.119 | 0.31 |
| 61_I | 72_Y | 1.118 | 0.31 |
| 56_T | 212_V | 1.116 | 0.30 |
| 152_V | 208_V | 1.113 | 0.30 |
| 220_V | 228_E | 1.108 | 0.30 |
| 159_N | 165_N | 1.106 | 0.30 |
| 48_D | 206_F | 1.105 | 0.30 |
| 161_F | 244_S | 1.105 | 0.30 |
| 33_N | 37_D | 1.101 | 0.29 |
| 124_C | 134_D | 1.097 | 0.29 |
| 160_L | 164_E | 1.093 | 0.29 |
| 117_N | 208_V | 1.091 | 0.29 |
| 252_K | 263_S | 1.089 | 0.29 |
| 221_L | 276_G | 1.086 | 0.28 |
| 114_V | 148_Q | 1.085 | 0.28 |
| 220_V | 252_K | 1.085 | 0.28 |
| 124_C | 132_P | 1.080 | 0.28 |
| 16_P | 151_L | 1.079 | 0.28 |
| 40_E | 152_V | 1.079 | 0.28 |
| 101_E | 122_K | 1.077 | 0.28 |
| 194_L | 278_L | 1.076 | 0.28 |
| 213_F | 252_K | 1.074 | 0.28 |
| 43_I | 106_L | 1.073 | 0.28 |
| 34_R | 110_N | 1.073 | 0.28 |
| 191_F | 259_Y | 1.072 | 0.28 |
| 293_V | 298_Y | 1.071 | 0.27 |
| 108_K | 174_E | 1.070 | 0.27 |
| 53_I | 144_V | 1.069 | 0.27 |
| 73_P | 247_H | 1.061 | 0.27 |
| 42_A | 260_A | 1.056 | 0.27 |
| 78_I | 120_D | 1.056 | 0.27 |
| 100_Q | 209_D | 1.056 | 0.27 |
| 80_D | 120_D | 1.055 | 0.26 |
| 76_E | 279_L | 1.051 | 0.26 |
| 81_P | 154_R | 1.049 | 0.26 |
| 176_V | 281_S | 1.048 | 0.26 |
| 43_I | 54_I | 1.048 | 0.26 |
| 108_K | 113_Y | 1.043 | 0.26 |
| 241_F | 283_L | 1.043 | 0.26 |
| 178_F | 198_P | 1.042 | 0.26 |
| 15_L | 32_M | 1.042 | 0.26 |
| 177_T | 207_H | 1.040 | 0.26 |
| 204_K | 241_F | 1.038 | 0.25 |
| 37_D | 214_P | 1.037 | 0.25 |
| 209_D | 237_M | 1.037 | 0.25 |
| 84_N | 118_I | 1.035 | 0.25 |
| 112_I | 199_A | 1.033 | 0.25 |
| 213_F | 263_S | 1.032 | 0.25 |
| 27_E | 147_S | 1.031 | 0.25 |
| 150_K | 279_L | 1.031 | 0.25 |
| 32_M | 99_V | 1.030 | 0.25 |
| 74_Y | 229_F | 1.027 | 0.25 |
| 129_P | 137_Y | 1.027 | 0.25 |
| 50_G | 253_M | 1.026 | 0.25 |
| 124_C | 135_G | 1.024 | 0.25 |
| 114_V | 241_F | 1.024 | 0.25 |
| 31_L | 73_P | 1.023 | 0.25 |
| 183_G | 224_L | 1.020 | 0.24 |
| 109_N | 145_F | 1.019 | 0.24 |
| 135_G | 276_G | 1.017 | 0.24 |
| 236_G | 263_S | 1.017 | 0.24 |
| 173_P | 195_F | 1.016 | 0.24 |
| 217_W | 257_G | 1.013 | 0.24 |
| 118_I | 156_H | 1.013 | 0.24 |
| 4_F | 97_T | 1.011 | 0.24 |
| 125_D | 128_D | 1.011 | 0.24 |
| 6_A | 222_P | 1.011 | 0.24 |
| 131_C | 134_D | 1.009 | 0.24 |
| 174_E | 197_D | 1.009 | 0.24 |
| 60_A | 161_F | 1.009 | 0.24 |
| 10_E | 117_N | 1.009 | 0.24 |
| 116_A | 151_L | 1.005 | 0.23 |
| 218_M | 253_M | 1.003 | 0.23 |
| 53_I | 167_F | 1.002 | 0.23 |
| 4_F | 18_A | 1.002 | 0.23 |
| 97_T | 138_Q | 1.000 | 0.23 |
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 | |
| 2vhhA | 4 | 0.89 | 100 | 0.752 | Contact Map |
| 3ivzA | 2 | 0.82 | 100 | 0.76 | Contact Map |
| 1f89A | 2 | 0.85 | 100 | 0.762 | Contact Map |
| 3p8kA | 2 | 0.8333 | 100 | 0.763 | Contact Map |
| 4lf0A | 1 | 0.8667 | 100 | 0.764 | Contact Map |
| 2w1vA | 2 | 0.83 | 100 | 0.764 | Contact Map |
| 2dyuA | 2 | 0.8567 | 100 | 0.765 | Contact Map |
| 1emsA | 2 | 0.8467 | 100 | 0.765 | Contact Map |
| 4izuA | 1 | 0.7933 | 100 | 0.768 | Contact Map |
| 2e11A | 4 | 0.8233 | 100 | 0.771 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)