| T0835 -force run |
| ID: | 1403893222 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (370) | ||
| Sequences: | 285 (250.3) | ||
| Seq/Len: | 0.770 | ||
| Nf(neff/√len): | 13.0 |
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: 0.770).
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 |
| 144_T | 208_A | 2.980 | 1.00 |
| 373_I | 388_S | 2.501 | 0.99 |
| 68_I | 101_I | 2.217 | 0.96 |
| 330_V | 399_T | 2.099 | 0.95 |
| 286_L | 336_A | 2.034 | 0.94 |
| 287_D | 345_Y | 1.996 | 0.93 |
| 282_A | 345_Y | 1.958 | 0.92 |
| 270_G | 282_A | 1.944 | 0.91 |
| 28_L | 397_L | 1.934 | 0.91 |
| 142_A | 230_A | 1.877 | 0.89 |
| 71_V | 74_A | 1.826 | 0.88 |
| 379_D | 383_T | 1.811 | 0.87 |
| 177_N | 198_A | 1.733 | 0.84 |
| 35_V | 119_H | 1.641 | 0.79 |
| 270_G | 273_L | 1.609 | 0.77 |
| 354_L | 359_N | 1.609 | 0.77 |
| 366_M | 374_A | 1.599 | 0.76 |
| 177_N | 304_V | 1.581 | 0.75 |
| 237_V | 277_D | 1.580 | 0.75 |
| 63_E | 67_A | 1.553 | 0.73 |
| 111_F | 119_H | 1.520 | 0.71 |
| 221_I | 225_M | 1.512 | 0.70 |
| 27_H | 393_T | 1.502 | 0.70 |
| 308_G | 317_K | 1.498 | 0.69 |
| 267_L | 282_A | 1.482 | 0.68 |
| 34_K | 119_H | 1.476 | 0.68 |
| 100_F | 320_S | 1.448 | 0.65 |
| 375_F | 386_K | 1.447 | 0.65 |
| 334_I | 349_A | 1.432 | 0.64 |
| 270_G | 279_I | 1.426 | 0.64 |
| 303_T | 325_I | 1.412 | 0.63 |
| 74_A | 97_L | 1.407 | 0.62 |
| 259_G | 324_Y | 1.381 | 0.60 |
| 263_A | 282_A | 1.379 | 0.60 |
| 267_L | 339_I | 1.369 | 0.59 |
| 141_W | 144_T | 1.366 | 0.59 |
| 200_D | 253_N | 1.351 | 0.57 |
| 303_T | 320_S | 1.350 | 0.57 |
| 113_N | 260_N | 1.343 | 0.57 |
| 264_Y | 352_L | 1.332 | 0.56 |
| 201_Q | 207_M | 1.332 | 0.56 |
| 65_V | 322_I | 1.326 | 0.55 |
| 27_H | 397_L | 1.321 | 0.55 |
| 121_I | 288_H | 1.320 | 0.55 |
| 328_P | 395_E | 1.314 | 0.54 |
| 257_G | 308_G | 1.309 | 0.54 |
| 357_F | 363_Q | 1.308 | 0.54 |
| 313_L | 373_I | 1.288 | 0.52 |
| 230_A | 278_M | 1.285 | 0.52 |
| 32_Y | 97_L | 1.279 | 0.51 |
| 30_A | 388_S | 1.278 | 0.51 |
| 132_P | 263_A | 1.277 | 0.51 |
| 60_D | 63_E | 1.275 | 0.51 |
| 40_K | 63_E | 1.266 | 0.50 |
| 98_V | 160_R | 1.266 | 0.50 |
| 40_K | 325_I | 1.260 | 0.50 |
| 165_I | 378_I | 1.259 | 0.50 |
| 59_K | 253_N | 1.255 | 0.49 |
| 40_K | 119_H | 1.254 | 0.49 |
| 137_W | 249_L | 1.253 | 0.49 |
| 123_K | 130_A | 1.253 | 0.49 |
| 119_H | 293_L | 1.251 | 0.49 |
| 201_Q | 204_V | 1.247 | 0.49 |
| 40_K | 130_A | 1.247 | 0.49 |
| 294_I | 361_P | 1.239 | 0.48 |
| 295_S | 299_L | 1.237 | 0.48 |
| 74_A | 142_A | 1.235 | 0.48 |
| 39_N | 114_F | 1.234 | 0.47 |
| 39_N | 60_D | 1.232 | 0.47 |
| 200_D | 260_N | 1.231 | 0.47 |
| 112_Y | 123_K | 1.229 | 0.47 |
| 275_D | 278_M | 1.225 | 0.47 |
| 39_N | 399_T | 1.215 | 0.46 |
| 362_A | 378_I | 1.214 | 0.46 |
| 40_K | 114_F | 1.206 | 0.45 |
| 31_L | 341_R | 1.195 | 0.44 |
| 143_L | 392_S | 1.191 | 0.44 |
| 97_L | 388_S | 1.189 | 0.44 |
| 103_Y | 119_H | 1.186 | 0.43 |
| 286_L | 332_A | 1.185 | 0.43 |
| 137_W | 208_A | 1.184 | 0.43 |
| 199_G | 235_M | 1.179 | 0.43 |
| 386_K | 395_E | 1.178 | 0.43 |
| 100_F | 372_G | 1.177 | 0.43 |
| 268_V | 335_K | 1.173 | 0.42 |
| 71_V | 374_A | 1.169 | 0.42 |
| 229_A | 278_M | 1.169 | 0.42 |
| 106_A | 123_K | 1.169 | 0.42 |
| 288_H | 293_L | 1.167 | 0.42 |
| 93_K | 289_F | 1.162 | 0.41 |
| 104_Q | 115_I | 1.162 | 0.41 |
| 114_F | 130_A | 1.161 | 0.41 |
| 28_L | 77_F | 1.160 | 0.41 |
| 25_A | 397_L | 1.160 | 0.41 |
| 137_W | 204_V | 1.159 | 0.41 |
| 258_Y | 322_I | 1.159 | 0.41 |
| 113_N | 138_R | 1.159 | 0.41 |
| 28_L | 37_V | 1.158 | 0.41 |
| 252_Q | 273_L | 1.157 | 0.41 |
| 41_T | 368_Y | 1.156 | 0.41 |
| 295_S | 298_L | 1.154 | 0.41 |
| 269_A | 377_G | 1.153 | 0.41 |
| 377_G | 392_S | 1.152 | 0.40 |
| 67_A | 121_I | 1.150 | 0.40 |
| 330_V | 395_E | 1.143 | 0.40 |
| 118_D | 347_E | 1.142 | 0.40 |
| 326_I | 366_M | 1.140 | 0.39 |
| 76_I | 319_F | 1.140 | 0.39 |
| 204_V | 345_Y | 1.139 | 0.39 |
| 329_M | 352_L | 1.138 | 0.39 |
| 298_L | 361_P | 1.130 | 0.39 |
| 320_S | 336_A | 1.129 | 0.39 |
| 141_W | 208_A | 1.127 | 0.38 |
| 368_Y | 371_T | 1.126 | 0.38 |
| 67_A | 294_I | 1.124 | 0.38 |
| 33_Q | 320_S | 1.123 | 0.38 |
| 155_N | 170_D | 1.118 | 0.38 |
| 130_A | 208_A | 1.118 | 0.38 |
| 147_Y | 396_A | 1.116 | 0.37 |
| 230_A | 233_M | 1.113 | 0.37 |
| 300_N | 321_Q | 1.111 | 0.37 |
| 67_A | 259_G | 1.109 | 0.37 |
| 249_L | 322_I | 1.107 | 0.37 |
| 335_K | 338_E | 1.106 | 0.37 |
| 32_Y | 289_F | 1.102 | 0.36 |
| 76_I | 142_A | 1.101 | 0.36 |
| 39_N | 322_I | 1.096 | 0.36 |
| 236_Q | 285_E | 1.089 | 0.35 |
| 27_H | 313_L | 1.086 | 0.35 |
| 226_R | 275_D | 1.081 | 0.35 |
| 326_I | 349_A | 1.080 | 0.35 |
| 285_E | 395_E | 1.078 | 0.34 |
| 68_I | 100_F | 1.076 | 0.34 |
| 41_T | 60_D | 1.073 | 0.34 |
| 202_A | 231_G | 1.070 | 0.34 |
| 61_P | 103_Y | 1.070 | 0.34 |
| 65_V | 133_N | 1.068 | 0.34 |
| 253_N | 260_N | 1.066 | 0.34 |
| 366_M | 375_F | 1.065 | 0.33 |
| 60_D | 209_L | 1.063 | 0.33 |
| 121_I | 325_I | 1.061 | 0.33 |
| 385_N | 392_S | 1.061 | 0.33 |
| 31_L | 214_A | 1.059 | 0.33 |
| 288_H | 345_Y | 1.058 | 0.33 |
| 67_A | 77_F | 1.056 | 0.33 |
| 71_V | 139_A | 1.054 | 0.33 |
| 133_N | 258_Y | 1.054 | 0.33 |
| 246_G | 312_T | 1.053 | 0.33 |
| 65_V | 258_Y | 1.053 | 0.33 |
| 80_R | 264_Y | 1.048 | 0.32 |
| 135_W | 208_A | 1.048 | 0.32 |
| 267_L | 279_I | 1.044 | 0.32 |
| 21_K | 357_F | 1.042 | 0.32 |
| 40_K | 117_P | 1.040 | 0.32 |
| 74_A | 374_A | 1.039 | 0.31 |
| 286_L | 320_S | 1.038 | 0.31 |
| 377_G | 391_E | 1.037 | 0.31 |
| 27_H | 41_T | 1.035 | 0.31 |
| 68_I | 140_L | 1.034 | 0.31 |
| 209_L | 212_A | 1.034 | 0.31 |
| 233_M | 266_L | 1.031 | 0.31 |
| 298_L | 302_F | 1.030 | 0.31 |
| 63_E | 121_I | 1.028 | 0.31 |
| 206_L | 269_A | 1.028 | 0.31 |
| 314_I | 317_K | 1.028 | 0.31 |
| 32_Y | 139_A | 1.027 | 0.31 |
| 69_D | 73_R | 1.026 | 0.31 |
| 93_K | 303_T | 1.026 | 0.31 |
| 139_A | 160_R | 1.026 | 0.31 |
| 200_D | 322_I | 1.025 | 0.30 |
| 28_L | 32_Y | 1.022 | 0.30 |
| 142_A | 259_G | 1.020 | 0.30 |
| 229_A | 232_I | 1.019 | 0.30 |
| 233_M | 278_M | 1.018 | 0.30 |
| 116_Y | 122_N | 1.018 | 0.30 |
| 236_Q | 284_N | 1.016 | 0.30 |
| 321_Q | 361_P | 1.014 | 0.30 |
| 356_F | 397_L | 1.014 | 0.30 |
| 364_A | 384_V | 1.014 | 0.30 |
| 283_F | 345_Y | 1.013 | 0.30 |
| 362_A | 379_D | 1.012 | 0.29 |
| 68_I | 317_K | 1.010 | 0.29 |
| 31_L | 38_A | 1.007 | 0.29 |
| 59_K | 200_D | 1.005 | 0.29 |
| 140_L | 209_L | 1.005 | 0.29 |
| 340_S | 346_L | 1.005 | 0.29 |
| 115_I | 326_I | 1.003 | 0.29 |
| 23_V | 340_S | 1.002 | 0.29 |
| 69_D | 385_N | 1.001 | 0.29 |
| 63_E | 130_A | 1.000 | 0.29 |
| 258_Y | 332_A | 1.000 | 0.29 |
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 | |
| 3gt5A | 1 | 0.8538 | 100 | 0.77 | Contact Map |
| 3wkgA | 1 | 0.8868 | 100 | 0.775 | Contact Map |
| 2gz6A | 2 | 0.8349 | 100 | 0.779 | Contact Map |
| 3vw5A | 3 | 0.8679 | 100 | 0.784 | Contact Map |
| 1fp3A | 2 | 0.8868 | 100 | 0.787 | Contact Map |
| 2zblA | 6 | 0.8868 | 100 | 0.79 | Contact Map |
| 3k11A | 1 | 0.9057 | 99.6 | 0.876 | Contact Map |
| 4c1sA | 2 | 0.7193 | 99.5 | 0.88 | Contact Map |
| 3pmmA | 1 | 0.7241 | 99.5 | 0.883 | Contact Map |
| 4mu9A | 2 | 0.8066 | 99.5 | 0.886 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)