| 1U6R |
| ID: | 1478860954 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 380 (376) | ||
| Sequences: | 495 (277.7) | ||
| Seq/Len: | 1.316 | ||
| Nf(neff/√len): | 14.3 |
HHblits Results: (2016_02)
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: 1.316).
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 |
| 184_Q | 188_D | 4.116 | 1.00 |
| 179_T | 182_E | 3.112 | 1.00 |
| 154_E | 172_Y | 2.921 | 1.00 |
| 40_K | 86_D | 2.850 | 1.00 |
| 240_E | 247_E | 2.773 | 1.00 |
| 244_N | 247_E | 2.476 | 1.00 |
| 93_Q | 100_K | 2.213 | 0.99 |
| 343_S | 348_Q | 2.185 | 0.99 |
| 110_N | 113_N | 2.122 | 0.98 |
| 50_F | 55_V | 2.085 | 0.98 |
| 167_E | 254_V | 1.980 | 0.97 |
| 358_L | 361_E | 1.962 | 0.97 |
| 169_K | 220_D | 1.910 | 0.96 |
| 73_C | 87_L | 1.850 | 0.95 |
| 151_R | 212_D | 1.811 | 0.95 |
| 46_T | 77_D | 1.784 | 0.94 |
| 172_Y | 215_G | 1.755 | 0.93 |
| 249_F | 253_C | 1.748 | 0.93 |
| 136_I | 153_V | 1.714 | 0.92 |
| 250_R | 254_V | 1.702 | 0.92 |
| 100_K | 103_D | 1.672 | 0.91 |
| 202_L | 207_A | 1.657 | 0.90 |
| 350_Q | 354_D | 1.657 | 0.90 |
| 32_V | 94_D | 1.615 | 0.89 |
| 302_S | 307_F | 1.606 | 0.88 |
| 323_G | 340_R | 1.596 | 0.88 |
| 150_R | 209_D | 1.558 | 0.86 |
| 41_L | 87_L | 1.550 | 0.86 |
| 73_C | 91_I | 1.539 | 0.85 |
| 185_Q | 189_D | 1.526 | 0.85 |
| 157_S | 234_L | 1.511 | 0.84 |
| 58_T | 74_V | 1.505 | 0.84 |
| 28_H | 31_K | 1.504 | 0.84 |
| 65_H | 68_I | 1.488 | 0.83 |
| 41_L | 52_L | 1.481 | 0.82 |
| 35_P | 39_K | 1.477 | 0.82 |
| 358_L | 362_M | 1.475 | 0.82 |
| 191_F | 225_L | 1.461 | 0.81 |
| 174_P | 177_S | 1.448 | 0.80 |
| 132_T | 290_L | 1.440 | 0.80 |
| 306_K | 309_E | 1.429 | 0.79 |
| 75_A | 88_F | 1.425 | 0.79 |
| 224_F | 255_G | 1.414 | 0.78 |
| 177_S | 182_E | 1.411 | 0.78 |
| 76_G | 150_R | 1.410 | 0.78 |
| 259_I | 263_F | 1.400 | 0.77 |
| 282_C | 340_R | 1.395 | 0.77 |
| 296_V | 360_V | 1.394 | 0.77 |
| 334_D | 340_R | 1.393 | 0.77 |
| 142_P | 150_R | 1.392 | 0.77 |
| 85_K | 101_P | 1.391 | 0.77 |
| 298_L | 359_M | 1.390 | 0.76 |
| 39_K | 42_R | 1.380 | 0.76 |
| 180_E | 183_Q | 1.379 | 0.76 |
| 36_D | 39_K | 1.375 | 0.75 |
| 89_D | 100_K | 1.370 | 0.75 |
| 183_Q | 187_I | 1.363 | 0.74 |
| 7_N | 10_K | 1.359 | 0.74 |
| 336_S | 340_R | 1.348 | 0.73 |
| 53_D | 57_Q | 1.343 | 0.73 |
| 196_P | 207_A | 1.334 | 0.72 |
| 152_A | 155_K | 1.332 | 0.72 |
| 222_K | 225_L | 1.332 | 0.72 |
| 357_K | 361_E | 1.331 | 0.72 |
| 58_T | 64_G | 1.325 | 0.71 |
| 31_K | 69_M | 1.320 | 0.71 |
| 300_H | 303_K | 1.305 | 0.70 |
| 86_D | 90_P | 1.302 | 0.70 |
| 292_G | 348_Q | 1.300 | 0.69 |
| 317_Q | 320_G | 1.299 | 0.69 |
| 323_G | 334_D | 1.291 | 0.69 |
| 353_V | 357_K | 1.285 | 0.68 |
| 292_G | 352_V | 1.280 | 0.68 |
| 339_D | 351_L | 1.279 | 0.68 |
| 132_T | 150_R | 1.278 | 0.67 |
| 147_R | 151_R | 1.269 | 0.67 |
| 158_V | 213_A | 1.264 | 0.66 |
| 81_Y | 92_I | 1.258 | 0.66 |
| 375_M | 380_K | 1.241 | 0.64 |
| 167_E | 236_V | 1.237 | 0.64 |
| 265_K | 268_H | 1.227 | 0.63 |
| 41_L | 44_K | 1.223 | 0.62 |
| 324_V | 340_R | 1.219 | 0.62 |
| 59_G | 72_G | 1.215 | 0.62 |
| 283_P | 287_G | 1.208 | 0.61 |
| 29_M | 59_G | 1.206 | 0.61 |
| 182_E | 185_Q | 1.205 | 0.61 |
| 154_E | 215_G | 1.202 | 0.61 |
| 117_G | 244_N | 1.199 | 0.60 |
| 76_G | 80_S | 1.194 | 0.60 |
| 155_K | 159_E | 1.193 | 0.60 |
| 239_M | 319_R | 1.191 | 0.59 |
| 291_R | 319_R | 1.187 | 0.59 |
| 323_G | 336_S | 1.183 | 0.59 |
| 189_D | 222_K | 1.170 | 0.57 |
| 6_H | 10_K | 1.164 | 0.57 |
| 50_F | 76_G | 1.162 | 0.57 |
| 38_Y | 61_D | 1.151 | 0.56 |
| 320_G | 323_G | 1.151 | 0.56 |
| 277_G | 283_P | 1.144 | 0.55 |
| 191_F | 216_I | 1.143 | 0.55 |
| 255_G | 354_D | 1.140 | 0.54 |
| 141_L | 279_V | 1.133 | 0.54 |
| 362_M | 375_M | 1.132 | 0.54 |
| 33_L | 51_T | 1.131 | 0.54 |
| 191_F | 218_H | 1.127 | 0.53 |
| 57_Q | 61_D | 1.118 | 0.52 |
| 18_E | 42_R | 1.116 | 0.52 |
| 319_R | 340_R | 1.114 | 0.52 |
| 246_K | 250_R | 1.113 | 0.52 |
| 372_I | 377_P | 1.110 | 0.51 |
| 240_E | 360_V | 1.105 | 0.51 |
| 365_K | 374_D | 1.103 | 0.51 |
| 59_G | 71_V | 1.102 | 0.51 |
| 173_Y | 310_I | 1.100 | 0.50 |
| 304_H | 307_F | 1.100 | 0.50 |
| 75_A | 81_Y | 1.092 | 0.50 |
| 240_E | 244_N | 1.092 | 0.50 |
| 46_T | 49_G | 1.090 | 0.49 |
| 141_L | 259_I | 1.089 | 0.49 |
| 281_T | 289_G | 1.088 | 0.49 |
| 319_R | 336_S | 1.087 | 0.49 |
| 365_K | 370_Q | 1.087 | 0.49 |
| 132_T | 205_G | 1.086 | 0.49 |
| 374_D | 377_P | 1.081 | 0.49 |
| 194_D | 197_V | 1.081 | 0.49 |
| 228_V | 302_S | 1.080 | 0.48 |
| 119_D | 122_P | 1.080 | 0.48 |
| 196_P | 202_L | 1.078 | 0.48 |
| 108_D | 113_N | 1.077 | 0.48 |
| 38_Y | 53_D | 1.069 | 0.47 |
| 293_G | 324_V | 1.069 | 0.47 |
| 249_F | 346_V | 1.068 | 0.47 |
| 22_L | 135_S | 1.068 | 0.47 |
| 50_F | 281_T | 1.066 | 0.47 |
| 258_K | 261_E | 1.064 | 0.47 |
| 230_E | 235_R | 1.063 | 0.47 |
| 171_K | 220_D | 1.062 | 0.47 |
| 277_G | 287_G | 1.061 | 0.47 |
| 187_I | 194_D | 1.059 | 0.46 |
| 125_V | 296_V | 1.058 | 0.46 |
| 6_H | 11_L | 1.057 | 0.46 |
| 33_L | 52_L | 1.056 | 0.46 |
| 319_R | 334_D | 1.055 | 0.46 |
| 65_H | 74_V | 1.053 | 0.46 |
| 50_F | 80_S | 1.050 | 0.45 |
| 53_D | 147_R | 1.049 | 0.45 |
| 127_S | 131_R | 1.049 | 0.45 |
| 311_L | 321_T | 1.047 | 0.45 |
| 249_F | 259_I | 1.046 | 0.45 |
| 261_E | 265_K | 1.041 | 0.45 |
| 161_L | 164_L | 1.040 | 0.45 |
| 167_E | 185_Q | 1.034 | 0.44 |
| 49_G | 310_I | 1.033 | 0.44 |
| 130_V | 245_M | 1.033 | 0.44 |
| 328_A | 331_S | 1.033 | 0.44 |
| 124_Y | 367_E | 1.026 | 0.43 |
| 244_N | 302_S | 1.025 | 0.43 |
| 150_R | 290_L | 1.020 | 0.43 |
| 193_F | 216_I | 1.019 | 0.42 |
| 343_S | 351_L | 1.019 | 0.42 |
| 298_L | 301_L | 1.018 | 0.42 |
| 165_T | 261_E | 1.017 | 0.42 |
| 116_G | 326_T | 1.016 | 0.42 |
| 44_K | 55_V | 1.016 | 0.42 |
| 293_G | 325_D | 1.015 | 0.42 |
| 38_Y | 57_Q | 1.014 | 0.42 |
| 301_L | 366_L | 1.013 | 0.42 |
| 128_S | 293_G | 1.013 | 0.42 |
| 291_R | 294_V | 1.012 | 0.42 |
| 114_L | 353_V | 1.012 | 0.42 |
| 257_Q | 260_E | 1.011 | 0.42 |
| 218_H | 225_L | 1.011 | 0.42 |
| 152_A | 156_L | 1.007 | 0.41 |
| 139_Y | 286_L | 1.006 | 0.41 |
| 15_S | 42_R | 1.006 | 0.41 |
| 373_D | 376_I | 1.005 | 0.41 |
| 190_H | 224_F | 1.005 | 0.41 |
| 230_E | 239_M | 1.004 | 0.41 |
| 235_R | 239_M | 1.003 | 0.41 |
| 118_D | 121_D | 1.003 | 0.41 |
| 82_T | 273_N | 1.002 | 0.41 |
| 214_R | 232_D | 1.002 | 0.41 |
| 309_E | 313_R | 1.001 | 0.41 |
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 | |
| 1qh4A | 4 | 1 | 100 | 0.066 | Contact Map |
| 3l2fA | 18 | 0.9895 | 100 | 0.077 | Contact Map |
| 4z9mA | 8 | 0 | 100 | 0.081 | Contact Map |
| 3ju5A | 4 | 0.9632 | 100 | 0.089 | Contact Map |
| 3jpzA | 2 | 0.9553 | 100 | 0.095 | Contact Map |
| 4rf6A | 2 | 0.9132 | 100 | 0.148 | Contact Map |
| 4wodA | 1 | 0.8947 | 100 | 0.154 | Contact Map |
| 1m15A | 1 | 0.9237 | 100 | 0.155 | Contact Map |
| 3ghgA | 4 | 0.2842 | 32.5 | 0.977 | Contact Map |
| 2wh5A | 6 | 0.2158 | 17.3 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)