| NRPL12 -force run |
| ID: | 1445773798 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (389) | ||
| Sequences: | 168 (127.8) | ||
| Seq/Len: | 0.432 | ||
| Nf(neff/√len): | 6.5 |
HHblits Results: (2015_06)
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: 0.432).
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 |
| 297_D | 343_R | 2.065 | 0.85 |
| 153_L | 253_R | 1.918 | 0.79 |
| 229_K | 233_D | 1.858 | 0.76 |
| 220_G | 294_D | 1.791 | 0.72 |
| 221_I | 376_K | 1.761 | 0.70 |
| 77_F | 89_G | 1.735 | 0.68 |
| 13_L | 20_L | 1.721 | 0.67 |
| 70_W | 77_F | 1.713 | 0.67 |
| 233_D | 297_D | 1.652 | 0.63 |
| 20_L | 29_K | 1.649 | 0.63 |
| 229_K | 346_A | 1.633 | 0.61 |
| 365_F | 373_Y | 1.587 | 0.58 |
| 29_K | 81_N | 1.578 | 0.58 |
| 86_W | 89_G | 1.572 | 0.57 |
| 276_S | 371_K | 1.569 | 0.57 |
| 253_R | 298_E | 1.567 | 0.57 |
| 374_F | 391_V | 1.554 | 0.56 |
| 277_A | 289_L | 1.549 | 0.55 |
| 6_G | 10_L | 1.524 | 0.54 |
| 367_E | 370_R | 1.521 | 0.53 |
| 26_K | 55_E | 1.507 | 0.52 |
| 81_N | 394_N | 1.490 | 0.51 |
| 340_I | 346_A | 1.485 | 0.51 |
| 59_L | 286_P | 1.473 | 0.50 |
| 380_N | 384_A | 1.449 | 0.48 |
| 154_S | 345_T | 1.433 | 0.47 |
| 227_A | 288_R | 1.421 | 0.46 |
| 13_L | 17_L | 1.416 | 0.46 |
| 117_S | 121_P | 1.415 | 0.46 |
| 44_P | 51_A | 1.414 | 0.45 |
| 25_L | 336_L | 1.398 | 0.44 |
| 374_F | 401_C | 1.396 | 0.44 |
| 180_G | 183_H | 1.394 | 0.44 |
| 223_K | 295_G | 1.381 | 0.43 |
| 176_L | 183_H | 1.379 | 0.43 |
| 331_K | 378_F | 1.374 | 0.43 |
| 220_G | 295_G | 1.364 | 0.42 |
| 232_L | 253_R | 1.344 | 0.40 |
| 199_L | 290_L | 1.342 | 0.40 |
| 214_V | 268_I | 1.335 | 0.40 |
| 17_L | 20_L | 1.333 | 0.40 |
| 219_A | 346_A | 1.333 | 0.40 |
| 25_L | 337_S | 1.331 | 0.39 |
| 229_K | 333_L | 1.326 | 0.39 |
| 237_G | 267_L | 1.317 | 0.38 |
| 295_G | 298_E | 1.307 | 0.38 |
| 167_S | 172_V | 1.292 | 0.37 |
| 230_V | 377_Y | 1.289 | 0.37 |
| 227_A | 331_K | 1.288 | 0.36 |
| 378_F | 384_A | 1.284 | 0.36 |
| 215_M | 328_I | 1.284 | 0.36 |
| 133_V | 362_I | 1.281 | 0.36 |
| 220_G | 364_G | 1.278 | 0.36 |
| 68_E | 268_I | 1.269 | 0.35 |
| 294_D | 364_G | 1.260 | 0.35 |
| 142_D | 303_F | 1.255 | 0.34 |
| 291_F | 311_C | 1.254 | 0.34 |
| 178_D | 181_R | 1.252 | 0.34 |
| 89_G | 314_W | 1.251 | 0.34 |
| 217_G | 220_G | 1.248 | 0.34 |
| 232_L | 235_A | 1.242 | 0.33 |
| 239_L | 299_L | 1.238 | 0.33 |
| 332_L | 341_T | 1.232 | 0.33 |
| 214_V | 299_L | 1.229 | 0.33 |
| 361_E | 372_E | 1.223 | 0.32 |
| 248_F | 364_G | 1.220 | 0.32 |
| 192_S | 402_F | 1.218 | 0.32 |
| 217_G | 294_D | 1.216 | 0.32 |
| 229_K | 364_G | 1.214 | 0.32 |
| 29_K | 69_A | 1.210 | 0.31 |
| 233_D | 343_R | 1.208 | 0.31 |
| 372_E | 405_L | 1.206 | 0.31 |
| 26_K | 32_L | 1.204 | 0.31 |
| 381_A | 386_Q | 1.202 | 0.31 |
| 264_M | 380_N | 1.201 | 0.31 |
| 23_V | 27_K | 1.199 | 0.31 |
| 24_E | 73_A | 1.196 | 0.30 |
| 404_P | 407_C | 1.195 | 0.30 |
| 399_T | 402_F | 1.194 | 0.30 |
| 48_M | 272_W | 1.193 | 0.30 |
| 55_E | 61_I | 1.193 | 0.30 |
| 211_R | 330_K | 1.192 | 0.30 |
| 275_P | 390_Y | 1.192 | 0.30 |
| 159_R | 266_D | 1.173 | 0.29 |
| 58_Q | 77_F | 1.170 | 0.29 |
| 248_F | 327_L | 1.170 | 0.29 |
| 223_K | 327_L | 1.168 | 0.29 |
| 51_A | 59_L | 1.166 | 0.29 |
| 341_T | 376_K | 1.166 | 0.29 |
| 246_Y | 370_R | 1.166 | 0.29 |
| 28_F | 316_E | 1.166 | 0.29 |
| 24_E | 48_M | 1.162 | 0.28 |
| 14_S | 224_S | 1.161 | 0.28 |
| 134_R | 146_R | 1.157 | 0.28 |
| 70_W | 86_W | 1.155 | 0.28 |
| 291_F | 327_L | 1.151 | 0.28 |
| 234_W | 333_L | 1.149 | 0.28 |
| 215_M | 387_V | 1.145 | 0.27 |
| 73_A | 331_K | 1.145 | 0.27 |
| 237_G | 292_I | 1.144 | 0.27 |
| 254_E | 346_A | 1.142 | 0.27 |
| 59_L | 317_K | 1.142 | 0.27 |
| 226_L | 288_R | 1.141 | 0.27 |
| 250_I | 271_C | 1.138 | 0.27 |
| 317_K | 348_E | 1.137 | 0.27 |
| 364_G | 404_P | 1.137 | 0.27 |
| 267_L | 374_F | 1.135 | 0.27 |
| 214_V | 350_L | 1.134 | 0.27 |
| 298_E | 341_T | 1.133 | 0.27 |
| 130_R | 238_K | 1.132 | 0.27 |
| 76_T | 320_T | 1.130 | 0.26 |
| 35_A | 38_L | 1.130 | 0.26 |
| 28_F | 69_A | 1.129 | 0.26 |
| 157_Y | 333_L | 1.128 | 0.26 |
| 264_M | 302_S | 1.127 | 0.26 |
| 293_I | 372_E | 1.125 | 0.26 |
| 244_F | 337_S | 1.122 | 0.26 |
| 202_P | 264_M | 1.122 | 0.26 |
| 96_R | 99_P | 1.121 | 0.26 |
| 197_E | 244_F | 1.117 | 0.26 |
| 55_E | 384_A | 1.117 | 0.26 |
| 323_L | 332_L | 1.117 | 0.26 |
| 16_Y | 70_W | 1.116 | 0.26 |
| 214_V | 347_L | 1.115 | 0.26 |
| 303_F | 340_I | 1.112 | 0.25 |
| 109_Q | 119_V | 1.110 | 0.25 |
| 16_Y | 19_E | 1.109 | 0.25 |
| 7_R | 10_L | 1.106 | 0.25 |
| 197_E | 405_L | 1.105 | 0.25 |
| 219_A | 233_D | 1.104 | 0.25 |
| 48_M | 89_G | 1.104 | 0.25 |
| 338_L | 357_P | 1.096 | 0.25 |
| 315_E | 389_N | 1.094 | 0.24 |
| 264_M | 359_H | 1.093 | 0.24 |
| 214_V | 354_L | 1.093 | 0.24 |
| 152_N | 300_K | 1.092 | 0.24 |
| 334_P | 338_L | 1.087 | 0.24 |
| 97_D | 100_P | 1.086 | 0.24 |
| 384_A | 397_L | 1.086 | 0.24 |
| 250_I | 368_A | 1.081 | 0.24 |
| 67_E | 264_M | 1.081 | 0.24 |
| 384_A | 387_V | 1.079 | 0.24 |
| 57_A | 323_L | 1.079 | 0.24 |
| 144_N | 299_L | 1.075 | 0.23 |
| 199_L | 252_C | 1.075 | 0.23 |
| 365_F | 378_F | 1.073 | 0.23 |
| 294_D | 333_L | 1.073 | 0.23 |
| 210_P | 328_I | 1.071 | 0.23 |
| 86_W | 225_M | 1.070 | 0.23 |
| 350_L | 370_R | 1.069 | 0.23 |
| 365_F | 404_P | 1.069 | 0.23 |
| 330_K | 388_F | 1.068 | 0.23 |
| 219_A | 298_E | 1.066 | 0.23 |
| 173_Q | 178_D | 1.065 | 0.23 |
| 213_V | 263_S | 1.064 | 0.23 |
| 237_G | 401_C | 1.061 | 0.23 |
| 32_L | 43_I | 1.060 | 0.23 |
| 219_A | 297_D | 1.057 | 0.22 |
| 368_A | 372_E | 1.056 | 0.22 |
| 255_M | 377_Y | 1.054 | 0.22 |
| 24_E | 63_H | 1.054 | 0.22 |
| 274_E | 277_A | 1.054 | 0.22 |
| 210_P | 289_L | 1.053 | 0.22 |
| 302_S | 350_L | 1.053 | 0.22 |
| 229_K | 298_E | 1.051 | 0.22 |
| 252_C | 374_F | 1.048 | 0.22 |
| 365_F | 407_C | 1.048 | 0.22 |
| 229_K | 344_P | 1.048 | 0.22 |
| 257_Q | 340_I | 1.046 | 0.22 |
| 215_M | 339_L | 1.046 | 0.22 |
| 26_K | 49_E | 1.045 | 0.22 |
| 174_Q | 227_A | 1.044 | 0.22 |
| 96_R | 122_R | 1.044 | 0.22 |
| 185_R | 259_A | 1.043 | 0.22 |
| 268_I | 398_F | 1.043 | 0.22 |
| 230_V | 236_D | 1.042 | 0.22 |
| 360_V | 377_Y | 1.042 | 0.22 |
| 232_L | 332_L | 1.038 | 0.21 |
| 245_D | 266_D | 1.037 | 0.21 |
| 70_W | 89_G | 1.037 | 0.21 |
| 141_E | 290_L | 1.036 | 0.21 |
| 252_C | 365_F | 1.036 | 0.21 |
| 105_S | 109_Q | 1.035 | 0.21 |
| 20_L | 206_R | 1.034 | 0.21 |
| 57_A | 162_L | 1.031 | 0.21 |
| 254_E | 298_E | 1.030 | 0.21 |
| 337_S | 388_F | 1.030 | 0.21 |
| 250_I | 255_M | 1.029 | 0.21 |
| 129_Y | 132_Y | 1.029 | 0.21 |
| 218_A | 400_M | 1.027 | 0.21 |
| 220_G | 333_L | 1.027 | 0.21 |
| 126_Q | 194_I | 1.025 | 0.21 |
| 263_S | 303_F | 1.020 | 0.21 |
| 331_K | 344_P | 1.019 | 0.21 |
| 258_S | 281_E | 1.018 | 0.20 |
| 251_N | 378_F | 1.012 | 0.20 |
| 330_K | 376_K | 1.012 | 0.20 |
| 64_F | 282_L | 1.011 | 0.20 |
| 72_L | 224_S | 1.011 | 0.20 |
| 73_A | 124_D | 1.009 | 0.20 |
| 234_W | 248_F | 1.009 | 0.20 |
| 249_Y | 400_M | 1.008 | 0.20 |
| 144_N | 362_I | 1.008 | 0.20 |
| 383_Q | 397_L | 1.006 | 0.20 |
| 298_E | 407_C | 1.002 | 0.20 |
| 223_K | 344_P | 1.001 | 0.20 |
| 227_A | 357_P | 1.001 | 0.20 |
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 | |
| 4kxfK | 8 | 0.6069 | 100 | 0.728 | Contact Map |
| 4ewiA | 2 | 0.2211 | 99.9 | 0.812 | Contact Map |
| 2kn6A | 1 | 0.4717 | 99.9 | 0.831 | Contact Map |
| 2do9A | 1 | 0.2629 | 99.9 | 0.833 | Contact Map |
| 2m5vA | 1 | 0.2432 | 99.9 | 0.835 | Contact Map |
| 1pn5A | 1 | 0.226 | 99.9 | 0.837 | Contact Map |
| 4n1lA | 1 | 0.2334 | 99.9 | 0.839 | Contact Map |
| 2l6aA | 1 | 0.2457 | 99.8 | 0.841 | Contact Map |
| 4o7qA | 1 | 0.231 | 99.8 | 0.844 | Contact Map |
| 2km6A | 1 | 0.2334 | 99.8 | 0.844 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)