| plant cell wall - jackhmmer |
| ID: | 1496264346 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 441 (431) | ||
| Sequences: | 4937 (3980.3) | ||
| Seq/Len: | 11.455 | ||
| Nf(neff/√len): | 191.7 |
Jackhmmer Results: (2016_04)
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: 11.455).
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 |
| 208_K | 211_V | 2.864 | 1.00 |
| 66_T | 174_T | 2.579 | 1.00 |
| 225_R | 431_E | 2.528 | 1.00 |
| 33_D | 301_N | 2.515 | 1.00 |
| 238_K | 252_R | 2.484 | 1.00 |
| 191_N | 194_L | 2.360 | 1.00 |
| 195_A | 198_V | 2.342 | 1.00 |
| 12_K | 60_V | 2.332 | 1.00 |
| 254_E | 330_R | 2.330 | 1.00 |
| 338_K | 342_E | 2.312 | 1.00 |
| 143_F | 149_A | 2.295 | 1.00 |
| 44_I | 149_A | 2.251 | 1.00 |
| 381_P | 384_E | 2.210 | 1.00 |
| 73_L | 159_A | 2.152 | 1.00 |
| 61_K | 65_E | 2.131 | 1.00 |
| 62_S | 175_T | 2.073 | 1.00 |
| 210_A | 213_P | 2.041 | 1.00 |
| 161_G | 380_M | 2.035 | 1.00 |
| 230_D | 233_A | 2.030 | 1.00 |
| 282_R | 285_T | 2.023 | 1.00 |
| 251_T | 254_E | 1.983 | 1.00 |
| 422_M | 427_M | 1.966 | 1.00 |
| 331_G | 335_N | 1.962 | 1.00 |
| 98_V | 141_S | 1.926 | 1.00 |
| 197_L | 200_A | 1.914 | 1.00 |
| 62_S | 171_W | 1.907 | 1.00 |
| 75_G | 84_V | 1.876 | 1.00 |
| 198_V | 201_R | 1.870 | 1.00 |
| 208_K | 212_M | 1.860 | 1.00 |
| 66_T | 171_W | 1.851 | 1.00 |
| 315_Q | 325_L | 1.849 | 1.00 |
| 233_A | 236_A | 1.831 | 1.00 |
| 163_T | 299_C | 1.825 | 1.00 |
| 101_P | 104_E | 1.786 | 1.00 |
| 159_A | 163_T | 1.772 | 1.00 |
| 48_N | 103_N | 1.763 | 1.00 |
| 140_M | 148_L | 1.763 | 1.00 |
| 66_T | 167_F | 1.749 | 1.00 |
| 227_F | 427_M | 1.748 | 1.00 |
| 99_N | 144_K | 1.742 | 1.00 |
| 313_G | 317_K | 1.742 | 1.00 |
| 221_K | 424_E | 1.739 | 1.00 |
| 322_L | 326_V | 1.718 | 1.00 |
| 279_L | 282_R | 1.715 | 1.00 |
| 57_E | 61_K | 1.704 | 1.00 |
| 154_L | 159_A | 1.693 | 1.00 |
| 250_P | 255_V | 1.687 | 1.00 |
| 257_T | 374_F | 1.669 | 1.00 |
| 229_F | 418_A | 1.658 | 1.00 |
| 311_R | 314_N | 1.656 | 1.00 |
| 308_T | 332_K | 1.655 | 1.00 |
| 275_L | 282_R | 1.651 | 1.00 |
| 194_L | 199_P | 1.638 | 1.00 |
| 257_T | 275_L | 1.629 | 1.00 |
| 46_F | 149_A | 1.619 | 1.00 |
| 430_F | 436_I | 1.610 | 1.00 |
| 228_L | 417_E | 1.601 | 1.00 |
| 193_E | 196_T | 1.594 | 1.00 |
| 231_E | 235_S | 1.578 | 1.00 |
| 328_L | 331_G | 1.573 | 1.00 |
| 194_L | 198_V | 1.562 | 1.00 |
| 198_V | 203_L | 1.561 | 1.00 |
| 229_F | 256_V | 1.555 | 1.00 |
| 266_N | 433_D | 1.546 | 1.00 |
| 195_A | 199_P | 1.537 | 1.00 |
| 352_E | 355_S | 1.529 | 1.00 |
| 195_A | 200_A | 1.525 | 1.00 |
| 253_V | 277_F | 1.513 | 1.00 |
| 250_P | 326_V | 1.509 | 1.00 |
| 168_T | 385_T | 1.505 | 1.00 |
| 200_A | 204_S | 1.491 | 1.00 |
| 201_R | 204_S | 1.490 | 1.00 |
| 392_P | 395_V | 1.487 | 1.00 |
| 209_P | 212_M | 1.487 | 1.00 |
| 58_Q | 175_T | 1.482 | 1.00 |
| 176_N | 386_E | 1.477 | 1.00 |
| 386_E | 390_G | 1.472 | 1.00 |
| 318_Q | 324_E | 1.467 | 1.00 |
| 349_L | 352_E | 1.464 | 1.00 |
| 84_V | 158_V | 1.459 | 1.00 |
| 321_E | 325_L | 1.457 | 1.00 |
| 76_R | 89_E | 1.454 | 1.00 |
| 263_A | 266_N | 1.451 | 1.00 |
| 165_A | 382_L | 1.446 | 1.00 |
| 173_N | 186_S | 1.445 | 1.00 |
| 327_K | 331_G | 1.436 | 1.00 |
| 296_F | 302_F | 1.410 | 1.00 |
| 70_F | 170_E | 1.405 | 0.99 |
| 185_V | 188_S | 1.400 | 0.99 |
| 199_P | 202_D | 1.396 | 0.99 |
| 279_L | 306_V | 1.387 | 0.99 |
| 135_I | 158_V | 1.365 | 0.99 |
| 59_L | 171_W | 1.363 | 0.99 |
| 199_P | 204_S | 1.363 | 0.99 |
| 423_D | 426_D | 1.355 | 0.99 |
| 405_V | 408_L | 1.352 | 0.99 |
| 63_L | 171_W | 1.351 | 0.99 |
| 136_V | 167_F | 1.349 | 0.99 |
| 350_F | 353_A | 1.342 | 0.99 |
| 429_Q | 432_L | 1.332 | 0.99 |
| 77_F | 135_I | 1.326 | 0.99 |
| 262_K | 266_N | 1.324 | 0.99 |
| 428_L | 432_L | 1.323 | 0.99 |
| 43_I | 377_L | 1.322 | 0.99 |
| 353_A | 357_F | 1.322 | 0.99 |
| 194_L | 197_L | 1.317 | 0.99 |
| 86_C | 90_G | 1.314 | 0.99 |
| 48_N | 393_E | 1.312 | 0.99 |
| 93_Y | 140_M | 1.310 | 0.99 |
| 337_L | 340_C | 1.305 | 0.99 |
| 55_I | 148_L | 1.303 | 0.99 |
| 280_N | 283_G | 1.281 | 0.99 |
| 225_R | 427_M | 1.275 | 0.99 |
| 56_R | 93_Y | 1.272 | 0.99 |
| 43_I | 164_A | 1.268 | 0.99 |
| 238_K | 255_V | 1.267 | 0.99 |
| 281_F | 341_S | 1.267 | 0.99 |
| 424_E | 428_L | 1.264 | 0.99 |
| 201_R | 205_T | 1.263 | 0.99 |
| 18_V | 65_E | 1.262 | 0.99 |
| 184_L | 189_P | 1.252 | 0.99 |
| 138_L | 171_W | 1.250 | 0.99 |
| 186_S | 189_P | 1.248 | 0.99 |
| 253_V | 376_T | 1.247 | 0.99 |
| 350_F | 354_A | 1.246 | 0.98 |
| 101_P | 144_K | 1.245 | 0.98 |
| 152_M | 164_A | 1.242 | 0.98 |
| 258_S | 325_L | 1.241 | 0.98 |
| 384_E | 391_K | 1.235 | 0.98 |
| 65_E | 174_T | 1.232 | 0.98 |
| 264_L | 372_R | 1.232 | 0.98 |
| 318_Q | 321_E | 1.222 | 0.98 |
| 269_K | 429_Q | 1.217 | 0.98 |
| 162_Y | 280_N | 1.213 | 0.98 |
| 70_F | 166_A | 1.212 | 0.98 |
| 260_L | 418_A | 1.210 | 0.98 |
| 45_Y | 168_T | 1.206 | 0.98 |
| 279_L | 336_T | 1.205 | 0.98 |
| 16_P | 88_D | 1.204 | 0.98 |
| 343_I | 346_A | 1.199 | 0.98 |
| 201_R | 206_V | 1.199 | 0.98 |
| 192_F | 196_T | 1.199 | 0.98 |
| 59_L | 140_M | 1.190 | 0.98 |
| 196_T | 199_P | 1.190 | 0.98 |
| 356_N | 359_I | 1.190 | 0.98 |
| 336_T | 341_S | 1.187 | 0.98 |
| 372_R | 405_V | 1.187 | 0.98 |
| 234_I | 256_V | 1.177 | 0.98 |
| 195_A | 201_R | 1.174 | 0.98 |
| 241_V | 322_L | 1.173 | 0.98 |
| 191_N | 195_A | 1.170 | 0.97 |
| 353_A | 356_N | 1.169 | 0.97 |
| 96_A | 141_S | 1.164 | 0.97 |
| 78_V | 83_Y | 1.156 | 0.97 |
| 347_D | 350_F | 1.154 | 0.97 |
| 404_I | 407_L | 1.148 | 0.97 |
| 340_C | 343_I | 1.141 | 0.97 |
| 386_E | 389_W | 1.140 | 0.97 |
| 73_L | 158_V | 1.138 | 0.97 |
| 65_E | 69_K | 1.138 | 0.97 |
| 354_A | 357_F | 1.136 | 0.97 |
| 403_E | 409_D | 1.136 | 0.97 |
| 191_N | 196_T | 1.133 | 0.97 |
| 192_F | 195_A | 1.132 | 0.97 |
| 102_L | 143_F | 1.131 | 0.97 |
| 310_F | 328_L | 1.128 | 0.97 |
| 162_Y | 380_M | 1.125 | 0.97 |
| 78_V | 85_D | 1.125 | 0.97 |
| 223_V | 424_E | 1.118 | 0.96 |
| 169_K | 381_P | 1.117 | 0.96 |
| 325_L | 328_L | 1.114 | 0.96 |
| 256_V | 407_L | 1.114 | 0.96 |
| 200_A | 205_T | 1.113 | 0.96 |
| 405_V | 420_V | 1.110 | 0.96 |
| 308_T | 329_L | 1.107 | 0.96 |
| 18_V | 21_P | 1.107 | 0.96 |
| 235_S | 239_D | 1.104 | 0.96 |
| 232_N | 236_A | 1.104 | 0.96 |
| 354_A | 358_N | 1.102 | 0.96 |
| 196_T | 200_A | 1.101 | 0.96 |
| 204_S | 207_I | 1.096 | 0.96 |
| 198_V | 202_D | 1.095 | 0.96 |
| 69_K | 174_T | 1.094 | 0.96 |
| 337_L | 341_S | 1.092 | 0.96 |
| 250_P | 254_E | 1.091 | 0.96 |
| 261_W | 275_L | 1.089 | 0.96 |
| 324_E | 328_L | 1.088 | 0.96 |
| 163_T | 166_A | 1.087 | 0.96 |
| 241_V | 255_V | 1.086 | 0.96 |
| 280_N | 284_K | 1.080 | 0.95 |
| 407_L | 418_A | 1.078 | 0.95 |
| 192_F | 198_V | 1.077 | 0.95 |
| 281_F | 302_F | 1.077 | 0.95 |
| 348_G | 351_L | 1.076 | 0.95 |
| 209_P | 213_P | 1.074 | 0.95 |
| 29_L | 77_F | 1.073 | 0.95 |
| 26_T | 83_Y | 1.073 | 0.95 |
| 411_K | 417_E | 1.069 | 0.95 |
| 187_S | 190_I | 1.067 | 0.95 |
| 194_L | 201_R | 1.066 | 0.95 |
| 404_I | 408_L | 1.064 | 0.95 |
| 184_L | 187_S | 1.062 | 0.95 |
| 314_N | 324_E | 1.062 | 0.95 |
| 352_E | 356_N | 1.060 | 0.95 |
| 211_V | 214_P | 1.059 | 0.95 |
| 26_T | 85_D | 1.059 | 0.95 |
| 318_Q | 325_L | 1.055 | 0.95 |
| 268_S | 426_D | 1.050 | 0.94 |
| 278_H | 282_R | 1.041 | 0.94 |
| 275_L | 374_F | 1.041 | 0.94 |
| 224_T | 421_S | 1.038 | 0.94 |
| 304_T | 341_S | 1.037 | 0.94 |
| 96_A | 139_Q | 1.034 | 0.94 |
| 268_S | 403_E | 1.030 | 0.94 |
| 160_D | 282_R | 1.023 | 0.93 |
| 264_L | 422_M | 1.022 | 0.93 |
| 73_L | 167_F | 1.016 | 0.93 |
| 200_A | 203_L | 1.014 | 0.93 |
| 349_L | 353_A | 1.012 | 0.93 |
| 152_M | 168_T | 1.010 | 0.93 |
| 64_S | 67_L | 1.009 | 0.93 |
| 346_A | 349_L | 1.003 | 0.93 |
| 238_K | 242_I | 1.001 | 0.92 |
| 254_E | 333_L | 1.000 | 0.92 |
| 90_G | 96_A | 1.000 | 0.92 |
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 | |
| 2bghA | 2 | 0.898 | 100 | 0.249 | Contact Map |
| 2xr7A | 1 | 0.9342 | 100 | 0.287 | Contact Map |
| 2e1vA | 2 | 0.9252 | 100 | 0.289 | Contact Map |
| 4ke4A | 1 | 0.9229 | 100 | 0.291 | Contact Map |
| 4g22A | 2 | 0.9184 | 100 | 0.294 | Contact Map |
| 2rkvA | 1 | 0.9002 | 100 | 0.32 | Contact Map |
| 1q9jA | 2 | 0.8186 | 99.9 | 0.758 | Contact Map |
| 2jgpA | 1 | 0.9025 | 99.9 | 0.76 | Contact Map |
| 4znmA | 2 | 0 | 99.9 | 0.761 | Contact Map |
| 4hvmA | 4 | 0.7959 | 99.9 | 0.763 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)