| Bsub_YheD _BSU09770 80-445 |
| ID: | 1385674903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 366 (363) | ||
| Sequences: | 479 (323) | ||
| Seq/Len: | 1.320 | ||
| Nf(neff/√len): | 17.0 |
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: 1.320).
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 |
| 237_N | 352_R | 3.286 | 1.00 |
| 173_T | 221_D | 2.563 | 1.00 |
| 8_G | 46_F | 2.218 | 0.99 |
| 58_I | 75_L | 2.122 | 0.98 |
| 140_T | 146_I | 1.887 | 0.96 |
| 313_F | 328_A | 1.838 | 0.95 |
| 238_K | 301_H | 1.785 | 0.94 |
| 310_E | 332_P | 1.756 | 0.93 |
| 318_D | 324_W | 1.754 | 0.93 |
| 238_K | 244_W | 1.711 | 0.92 |
| 201_F | 205_F | 1.705 | 0.92 |
| 168_G | 214_F | 1.695 | 0.92 |
| 254_S | 261_T | 1.686 | 0.91 |
| 157_Y | 219_G | 1.683 | 0.91 |
| 118_W | 121_H | 1.673 | 0.91 |
| 146_I | 216_I | 1.638 | 0.90 |
| 52_N | 55_E | 1.629 | 0.89 |
| 218_Q | 324_W | 1.620 | 0.89 |
| 100_R | 103_D | 1.604 | 0.88 |
| 235_H | 252_K | 1.567 | 0.87 |
| 100_R | 105_Y | 1.563 | 0.87 |
| 144_E | 176_D | 1.542 | 0.86 |
| 247_T | 352_R | 1.540 | 0.86 |
| 118_W | 214_F | 1.516 | 0.84 |
| 158_I | 214_F | 1.509 | 0.84 |
| 40_G | 220_V | 1.490 | 0.83 |
| 223_I | 230_A | 1.487 | 0.83 |
| 284_E | 288_K | 1.470 | 0.82 |
| 134_L | 271_T | 1.451 | 0.81 |
| 142_S | 145_L | 1.442 | 0.80 |
| 136_R | 218_Q | 1.440 | 0.80 |
| 222_L | 316_G | 1.424 | 0.79 |
| 275_V | 282_R | 1.423 | 0.79 |
| 252_K | 329_N | 1.407 | 0.78 |
| 285_V | 288_K | 1.383 | 0.76 |
| 166_G | 262_H | 1.376 | 0.75 |
| 52_N | 318_D | 1.352 | 0.74 |
| 237_N | 247_T | 1.344 | 0.73 |
| 316_G | 326_F | 1.344 | 0.73 |
| 84_P | 326_F | 1.340 | 0.73 |
| 260_T | 337_F | 1.337 | 0.72 |
| 242_G | 359_Y | 1.326 | 0.72 |
| 122_Q | 150_C | 1.323 | 0.71 |
| 76_P | 105_Y | 1.322 | 0.71 |
| 148_E | 152_A | 1.322 | 0.71 |
| 166_G | 231_D | 1.306 | 0.70 |
| 67_G | 216_I | 1.305 | 0.70 |
| 179_L | 199_A | 1.296 | 0.69 |
| 76_P | 100_R | 1.293 | 0.69 |
| 166_G | 266_G | 1.290 | 0.69 |
| 6_L | 44_F | 1.282 | 0.68 |
| 155_K | 219_G | 1.273 | 0.67 |
| 176_D | 317_I | 1.273 | 0.67 |
| 231_D | 312_G | 1.268 | 0.67 |
| 118_W | 139_L | 1.261 | 0.66 |
| 283_V | 287_K | 1.261 | 0.66 |
| 316_G | 333_G | 1.258 | 0.66 |
| 60_G | 73_V | 1.254 | 0.65 |
| 76_P | 214_F | 1.250 | 0.65 |
| 271_T | 336_I | 1.243 | 0.64 |
| 134_L | 308_I | 1.239 | 0.64 |
| 215_L | 292_A | 1.235 | 0.64 |
| 159_K | 327_E | 1.234 | 0.64 |
| 60_G | 153_Y | 1.234 | 0.64 |
| 295_T | 298_H | 1.233 | 0.63 |
| 89_E | 110_F | 1.232 | 0.63 |
| 264_S | 312_G | 1.230 | 0.63 |
| 262_H | 312_G | 1.224 | 0.63 |
| 267_G | 316_G | 1.217 | 0.62 |
| 266_G | 312_G | 1.216 | 0.62 |
| 266_G | 316_G | 1.206 | 0.61 |
| 179_L | 318_D | 1.206 | 0.61 |
| 237_N | 353_S | 1.205 | 0.61 |
| 48_A | 80_Y | 1.203 | 0.61 |
| 262_H | 326_F | 1.199 | 0.60 |
| 123_L | 134_L | 1.192 | 0.60 |
| 274_E | 282_R | 1.189 | 0.59 |
| 149_L | 215_L | 1.186 | 0.59 |
| 231_D | 266_G | 1.186 | 0.59 |
| 123_L | 299_V | 1.185 | 0.59 |
| 117_K | 327_E | 1.182 | 0.59 |
| 121_H | 134_L | 1.182 | 0.59 |
| 238_K | 324_W | 1.178 | 0.58 |
| 235_H | 310_E | 1.175 | 0.58 |
| 287_K | 291_A | 1.172 | 0.58 |
| 117_K | 159_K | 1.170 | 0.57 |
| 312_G | 333_G | 1.169 | 0.57 |
| 110_F | 309_G | 1.161 | 0.57 |
| 244_W | 324_W | 1.161 | 0.57 |
| 60_G | 161_A | 1.155 | 0.56 |
| 263_L | 269_V | 1.154 | 0.56 |
| 261_T | 325_M | 1.140 | 0.55 |
| 329_N | 332_P | 1.139 | 0.54 |
| 99_K | 203_A | 1.138 | 0.54 |
| 113_T | 308_I | 1.138 | 0.54 |
| 147_D | 216_I | 1.137 | 0.54 |
| 171_Q | 219_G | 1.137 | 0.54 |
| 46_F | 51_I | 1.136 | 0.54 |
| 141_P | 151_G | 1.134 | 0.54 |
| 241_K | 284_E | 1.133 | 0.54 |
| 48_A | 161_A | 1.133 | 0.54 |
| 325_M | 328_A | 1.129 | 0.53 |
| 108_P | 309_G | 1.122 | 0.53 |
| 55_E | 207_K | 1.121 | 0.53 |
| 66_N | 216_I | 1.119 | 0.52 |
| 82_R | 331_R | 1.117 | 0.52 |
| 158_I | 293_A | 1.112 | 0.52 |
| 128_P | 156_V | 1.105 | 0.51 |
| 235_H | 334_R | 1.104 | 0.51 |
| 144_E | 284_E | 1.101 | 0.51 |
| 37_E | 151_G | 1.100 | 0.51 |
| 53_W | 134_L | 1.100 | 0.51 |
| 36_H | 43_C | 1.099 | 0.50 |
| 122_Q | 152_A | 1.098 | 0.50 |
| 67_G | 162_N | 1.097 | 0.50 |
| 54_E | 352_R | 1.097 | 0.50 |
| 159_K | 166_G | 1.092 | 0.50 |
| 239_N | 356_Y | 1.090 | 0.50 |
| 338_S | 342_L | 1.090 | 0.50 |
| 32_L | 238_K | 1.089 | 0.49 |
| 262_H | 333_G | 1.087 | 0.49 |
| 53_W | 95_Q | 1.085 | 0.49 |
| 271_T | 274_E | 1.080 | 0.49 |
| 146_I | 156_V | 1.079 | 0.48 |
| 198_A | 216_I | 1.078 | 0.48 |
| 250_A | 296_A | 1.078 | 0.48 |
| 53_W | 313_F | 1.076 | 0.48 |
| 161_A | 351_R | 1.075 | 0.48 |
| 153_Y | 179_L | 1.075 | 0.48 |
| 261_T | 267_G | 1.074 | 0.48 |
| 49_H | 216_I | 1.070 | 0.48 |
| 79_V | 109_W | 1.066 | 0.47 |
| 172_L | 209_H | 1.065 | 0.47 |
| 4_G | 362_E | 1.064 | 0.47 |
| 76_P | 285_V | 1.064 | 0.47 |
| 310_E | 331_R | 1.060 | 0.47 |
| 332_P | 349_T | 1.058 | 0.46 |
| 57_T | 72_I | 1.057 | 0.46 |
| 62_L | 76_P | 1.056 | 0.46 |
| 40_G | 142_S | 1.055 | 0.46 |
| 250_A | 339_H | 1.055 | 0.46 |
| 231_D | 261_T | 1.053 | 0.46 |
| 99_K | 151_G | 1.048 | 0.45 |
| 217_Q | 314_D | 1.047 | 0.45 |
| 81_D | 331_R | 1.046 | 0.45 |
| 76_P | 118_W | 1.046 | 0.45 |
| 10_F | 214_F | 1.046 | 0.45 |
| 158_I | 216_I | 1.046 | 0.45 |
| 157_Y | 221_D | 1.045 | 0.45 |
| 118_W | 137_S | 1.045 | 0.45 |
| 222_L | 332_P | 1.044 | 0.45 |
| 37_E | 40_G | 1.044 | 0.45 |
| 135_P | 218_Q | 1.044 | 0.45 |
| 134_L | 172_L | 1.044 | 0.45 |
| 53_W | 100_R | 1.041 | 0.45 |
| 121_H | 318_D | 1.037 | 0.44 |
| 166_G | 252_K | 1.036 | 0.44 |
| 146_I | 174_R | 1.036 | 0.44 |
| 111_N | 115_F | 1.036 | 0.44 |
| 166_G | 261_T | 1.034 | 0.44 |
| 152_A | 295_T | 1.032 | 0.44 |
| 99_K | 180_T | 1.032 | 0.44 |
| 122_Q | 126_K | 1.032 | 0.44 |
| 174_R | 177_G | 1.032 | 0.44 |
| 56_G | 75_L | 1.028 | 0.43 |
| 74_P | 153_Y | 1.027 | 0.43 |
| 266_G | 332_P | 1.019 | 0.43 |
| 246_V | 291_A | 1.019 | 0.43 |
| 169_I | 260_T | 1.019 | 0.43 |
| 144_E | 287_K | 1.017 | 0.42 |
| 121_H | 215_L | 1.016 | 0.42 |
| 301_H | 319_Q | 1.016 | 0.42 |
| 165_L | 330_S | 1.015 | 0.42 |
| 65_E | 157_Y | 1.015 | 0.42 |
| 32_L | 274_E | 1.014 | 0.42 |
| 163_G | 266_G | 1.013 | 0.42 |
| 82_R | 310_E | 1.012 | 0.42 |
| 44_F | 220_V | 1.012 | 0.42 |
| 220_V | 325_M | 1.012 | 0.42 |
| 260_T | 264_S | 1.011 | 0.42 |
| 11_T | 315_F | 1.011 | 0.42 |
| 163_G | 242_G | 1.005 | 0.41 |
| 151_G | 175_T | 1.005 | 0.41 |
| 149_L | 216_I | 1.003 | 0.41 |
| 108_P | 240_R | 1.003 | 0.41 |
| 46_F | 172_L | 1.002 | 0.41 |
| 63_Y | 77_N | 1.000 | 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 | |
| 1gsaA | 1 | 0.806 | 100 | 0.694 | Contact Map |
| 3vpbA | 4 | 0.7486 | 100 | 0.697 | Contact Map |
| 4iwxA | 1 | 0.7842 | 100 | 0.721 | Contact Map |
| 3vpdA | 2 | 0.7459 | 99.9 | 0.725 | Contact Map |
| 3n6xA | 1 | 0.6257 | 99.9 | 0.727 | Contact Map |
| 4i4tF | 1 | 0.7869 | 99.9 | 0.73 | Contact Map |
| 2q7dA | 2 | 0.7705 | 99.9 | 0.731 | Contact Map |
| 2p0aA | 2 | 0.7514 | 99.9 | 0.748 | Contact Map |
| 1iowA | 1 | 0.776 | 99.9 | 0.756 | Contact Map |
| 2i87A | 2 | 0.8169 | 99.9 | 0.757 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)