| znt2_gremlin |
| ID: | 1496752327 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 372 (297) | ||
| Sequences: | 4353 (2836.9) | ||
| Seq/Len: | 14.657 | ||
| Nf(neff/√len): | 164.6 |
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: 14.657).
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 |
| 249_Y | 253_I | 3.962 | 1.00 |
| 320_V | 352_I | 3.311 | 1.00 |
| 304_H | 321_H | 3.127 | 1.00 |
| 294_L | 320_V | 3.005 | 1.00 |
| 132_M | 136_W | 2.792 | 1.00 |
| 155_T | 263_L | 2.605 | 1.00 |
| 159_V | 256_F | 2.537 | 1.00 |
| 240_I | 250_V | 2.517 | 1.00 |
| 331_Q | 353_Q | 2.505 | 1.00 |
| 264_G | 268_T | 2.485 | 1.00 |
| 91_G | 181_T | 2.481 | 1.00 |
| 129_T | 136_W | 2.455 | 1.00 |
| 139_A | 278_M | 2.399 | 1.00 |
| 89_V | 104_A | 2.312 | 1.00 |
| 129_T | 132_M | 2.209 | 1.00 |
| 180_I | 184_C | 2.170 | 1.00 |
| 289_A | 344_K | 2.079 | 1.00 |
| 291_R | 295_L | 2.022 | 1.00 |
| 164_E | 168_S | 1.971 | 1.00 |
| 302_A | 323_A | 1.962 | 1.00 |
| 294_L | 337_A | 1.958 | 1.00 |
| 275_L | 280_G | 1.953 | 1.00 |
| 75_Y | 118_L | 1.899 | 1.00 |
| 152_W | 266_T | 1.876 | 1.00 |
| 288_T | 292_D | 1.863 | 1.00 |
| 321_H | 355_E | 1.786 | 1.00 |
| 95_A | 178_M | 1.746 | 1.00 |
| 106_H | 223_H | 1.708 | 1.00 |
| 148_V | 270_L | 1.705 | 1.00 |
| 115_L | 119_F | 1.683 | 1.00 |
| 292_D | 296_S | 1.668 | 1.00 |
| 75_Y | 79_A | 1.665 | 1.00 |
| 131_T | 136_W | 1.653 | 1.00 |
| 297_V | 336_T | 1.646 | 1.00 |
| 183_G | 187_A | 1.639 | 1.00 |
| 293_L | 345_F | 1.620 | 1.00 |
| 301_E | 325_A | 1.615 | 1.00 |
| 160_Y | 164_E | 1.611 | 1.00 |
| 332_A | 336_T | 1.607 | 1.00 |
| 141_I | 276_V | 1.602 | 1.00 |
| 159_V | 259_S | 1.589 | 1.00 |
| 71_Q | 125_S | 1.587 | 1.00 |
| 256_F | 260_I | 1.578 | 1.00 |
| 90_V | 94_L | 1.564 | 1.00 |
| 88_E | 107_L | 1.564 | 1.00 |
| 179_L | 235_L | 1.546 | 1.00 |
| 197_H | 221_F | 1.541 | 1.00 |
| 297_V | 340_R | 1.532 | 1.00 |
| 334_L | 354_I | 1.531 | 1.00 |
| 178_M | 238_A | 1.529 | 1.00 |
| 338_S | 342_Q | 1.525 | 1.00 |
| 179_L | 239_Y | 1.521 | 1.00 |
| 218_R | 272_D | 1.504 | 1.00 |
| 179_L | 242_Y | 1.499 | 1.00 |
| 322_I | 337_A | 1.493 | 1.00 |
| 260_I | 264_G | 1.484 | 1.00 |
| 297_V | 337_A | 1.482 | 1.00 |
| 294_L | 300_V | 1.473 | 1.00 |
| 289_A | 345_F | 1.471 | 1.00 |
| 237_A | 254_C | 1.462 | 1.00 |
| 271_R | 275_L | 1.455 | 1.00 |
| 304_H | 355_E | 1.449 | 1.00 |
| 293_L | 344_K | 1.446 | 1.00 |
| 220_A | 223_H | 1.441 | 1.00 |
| 166_L | 256_F | 1.440 | 1.00 |
| 162_A | 255_T | 1.437 | 1.00 |
| 307_H | 349_T | 1.437 | 1.00 |
| 324_I | 333_V | 1.434 | 1.00 |
| 71_Q | 122_W | 1.430 | 1.00 |
| 134_F | 319_S | 1.413 | 1.00 |
| 92_G | 101_M | 1.407 | 0.99 |
| 163_V | 167_I | 1.407 | 0.99 |
| 103_D | 231_S | 1.405 | 0.99 |
| 279_E | 317_V | 1.402 | 0.99 |
| 329_D | 332_A | 1.389 | 0.99 |
| 166_L | 252_P | 1.376 | 0.99 |
| 145_L | 149_L | 1.341 | 0.99 |
| 239_Y | 243_F | 1.337 | 0.99 |
| 158_L | 255_T | 1.333 | 0.99 |
| 341_L | 347_F | 1.303 | 0.99 |
| 336_T | 340_R | 1.301 | 0.99 |
| 279_E | 309_W | 1.301 | 0.99 |
| 106_H | 151_I | 1.293 | 0.99 |
| 159_V | 163_V | 1.286 | 0.99 |
| 190_I | 225_I | 1.284 | 0.99 |
| 156_G | 160_Y | 1.277 | 0.99 |
| 119_F | 123_M | 1.256 | 0.99 |
| 331_Q | 356_D | 1.242 | 0.98 |
| 190_I | 194_L | 1.227 | 0.98 |
| 331_Q | 355_E | 1.222 | 0.98 |
| 326_Q | 358_S | 1.219 | 0.98 |
| 335_K | 339_S | 1.218 | 0.98 |
| 330_A | 354_I | 1.216 | 0.98 |
| 318_L | 347_F | 1.204 | 0.98 |
| 339_S | 343_G | 1.190 | 0.98 |
| 166_L | 249_Y | 1.186 | 0.98 |
| 247_Y | 250_V | 1.184 | 0.98 |
| 99_A | 254_C | 1.181 | 0.98 |
| 157_V | 160_Y | 1.176 | 0.98 |
| 290_V | 318_L | 1.172 | 0.98 |
| 183_G | 235_L | 1.170 | 0.97 |
| 176_G | 180_I | 1.166 | 0.97 |
| 92_G | 104_A | 1.161 | 0.97 |
| 239_Y | 242_Y | 1.157 | 0.97 |
| 342_Q | 350_V | 1.156 | 0.97 |
| 282_P | 308_I | 1.152 | 0.97 |
| 189_N | 224_V | 1.138 | 0.97 |
| 138_R | 309_W | 1.136 | 0.97 |
| 249_Y | 252_P | 1.134 | 0.97 |
| 123_M | 139_A | 1.122 | 0.97 |
| 294_L | 341_L | 1.121 | 0.97 |
| 186_V | 232_M | 1.117 | 0.96 |
| 293_L | 340_R | 1.115 | 0.96 |
| 300_V | 322_I | 1.113 | 0.96 |
| 290_V | 308_I | 1.105 | 0.96 |
| 223_H | 227_D | 1.091 | 0.96 |
| 187_A | 191_I | 1.091 | 0.96 |
| 87_G | 184_C | 1.086 | 0.96 |
| 169_G | 172_E | 1.084 | 0.96 |
| 179_L | 238_A | 1.080 | 0.95 |
| 72_R | 76_V | 1.079 | 0.95 |
| 98_L | 162_A | 1.079 | 0.95 |
| 286_D | 289_A | 1.073 | 0.95 |
| 267_L | 271_R | 1.071 | 0.95 |
| 114_M | 220_A | 1.067 | 0.95 |
| 162_A | 256_F | 1.060 | 0.95 |
| 299_G | 333_V | 1.052 | 0.95 |
| 203_H | 206_G | 1.051 | 0.94 |
| 281_T | 310_A | 1.049 | 0.94 |
| 176_G | 242_Y | 1.047 | 0.94 |
| 134_F | 309_W | 1.047 | 0.94 |
| 233_G | 254_C | 1.044 | 0.94 |
| 232_M | 236_V | 1.037 | 0.94 |
| 80_I | 188_V | 1.026 | 0.94 |
| 290_V | 341_L | 1.023 | 0.93 |
| 308_I | 318_L | 1.019 | 0.93 |
| 74_L | 117_S | 1.018 | 0.93 |
| 170_D | 173_I | 1.018 | 0.93 |
| 328_T | 332_A | 1.018 | 0.93 |
| 193_G | 225_I | 1.015 | 0.93 |
| 341_L | 350_V | 1.014 | 0.93 |
| 163_V | 256_F | 1.014 | 0.93 |
| 323_A | 357_Y | 1.013 | 0.93 |
| 177_T | 180_I | 1.010 | 0.93 |
| 287_F | 291_R | 1.009 | 0.93 |
| 244_K | 250_V | 1.008 | 0.93 |
| 140_E | 214_N | 1.006 | 0.93 |
| 142_L | 146_V | 1.005 | 0.93 |
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 | |
| 3j1zP | 2 | 0.7876 | 100 | 0.388 | Contact Map |
| 3h90A | 4 | 0.7527 | 100 | 0.396 | Contact Map |
| 2zztA | 1 | 0.207 | 99.5 | 0.836 | Contact Map |
| 3bypA | 2 | 0.207 | 99.5 | 0.841 | Contact Map |
| 3w61A | 1 | 0.2016 | 99.2 | 0.861 | Contact Map |
| 3cq1A | 1 | 0.2366 | 55.4 | 0.96 | Contact Map |
| 3lnoA | 6 | 0.2554 | 48.1 | 0.962 | Contact Map |
| 1uwdA | 1 | 0.2419 | 37.5 | 0.964 | Contact Map |
| 3b42A | 2 | 0.293 | 33 | 0.965 | Contact Map |
| 3ne5A | 1 | 0.3763 | 31.3 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)