| YfiN_multidomain_consensus |
| ID: | 1424716331 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 406 (396) | ||
| Sequences: | 6330 (5683.9) | ||
| Seq/Len: | 15.985 | ||
| Nf(neff/√len): | 285.6 |
Jackhmmer Results: (2015_01_07)
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: 15.985).
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 |
| 316_G | 319_H | 4.464 | 1.00 |
| 245_R | 249_H | 4.038 | 1.00 |
| 287_N | 401_A | 3.912 | 1.00 |
| 281_L | 371_I | 3.747 | 1.00 |
| 261_F | 330_A | 3.506 | 1.00 |
| 377_I | 380_A | 3.226 | 1.00 |
| 279_A | 375_M | 3.224 | 1.00 |
| 281_L | 346_C | 3.071 | 1.00 |
| 256_A | 260_A | 2.727 | 1.00 |
| 302_R | 305_I | 2.719 | 1.00 |
| 381_S | 384_K | 2.599 | 1.00 |
| 265_I | 382_A | 2.593 | 1.00 |
| 213_A | 216_H | 2.575 | 1.00 |
| 268_L | 271_N | 2.301 | 1.00 |
| 380_A | 388_L | 2.240 | 1.00 |
| 315_G | 321_A | 2.235 | 1.00 |
| 236_L | 240_N | 2.183 | 1.00 |
| 298_A | 387_E | 2.142 | 1.00 |
| 353_F | 369_L | 2.129 | 1.00 |
| 255_L | 308_A | 2.123 | 1.00 |
| 347_S | 350_T | 2.088 | 1.00 |
| 232_W | 236_L | 2.074 | 1.00 |
| 354_N | 402_E | 2.045 | 1.00 |
| 303_V | 367_M | 1.991 | 1.00 |
| 279_A | 342_V | 1.985 | 1.00 |
| 311_L | 321_A | 1.979 | 1.00 |
| 282_F | 393_M | 1.979 | 1.00 |
| 342_V | 346_C | 1.955 | 1.00 |
| 333_L | 345_I | 1.928 | 1.00 |
| 261_F | 322_Y | 1.923 | 1.00 |
| 346_C | 373_Y | 1.881 | 1.00 |
| 264_G | 267_T | 1.874 | 1.00 |
| 306_E | 309_K | 1.857 | 1.00 |
| 256_A | 320_K | 1.843 | 1.00 |
| 399_Q | 403_K | 1.834 | 1.00 |
| 240_N | 244_L | 1.825 | 1.00 |
| 94_D | 98_N | 1.814 | 1.00 |
| 347_S | 351_Q | 1.802 | 1.00 |
| 368_T | 402_E | 1.792 | 1.00 |
| 233_Q | 236_L | 1.778 | 1.00 |
| 260_A | 264_G | 1.775 | 1.00 |
| 337_Q | 341_E | 1.715 | 1.00 |
| 283_L | 369_L | 1.709 | 1.00 |
| 237_Q | 240_N | 1.708 | 1.00 |
| 387_E | 391_H | 1.671 | 1.00 |
| 255_L | 321_A | 1.654 | 1.00 |
| 248_L | 263_S | 1.646 | 1.00 |
| 186_A | 214_E | 1.645 | 1.00 |
| 289_K | 293_D | 1.644 | 1.00 |
| 307_I | 353_F | 1.643 | 1.00 |
| 242_Q | 246_T | 1.641 | 1.00 |
| 240_N | 243_L | 1.620 | 1.00 |
| 324_L | 330_A | 1.618 | 1.00 |
| 297_H | 394_Y | 1.613 | 1.00 |
| 395_Q | 399_Q | 1.612 | 1.00 |
| 310_R | 356_P | 1.602 | 1.00 |
| 345_I | 348_A | 1.599 | 1.00 |
| 315_G | 331_M | 1.599 | 1.00 |
| 292_N | 300_G | 1.588 | 1.00 |
| 390_D | 394_Y | 1.576 | 1.00 |
| 306_E | 310_R | 1.557 | 1.00 |
| 264_G | 322_Y | 1.514 | 1.00 |
| 395_Q | 398_H | 1.506 | 1.00 |
| 211_R | 216_H | 1.505 | 1.00 |
| 286_D | 370_S | 1.496 | 1.00 |
| 302_R | 306_E | 1.488 | 1.00 |
| 260_A | 320_K | 1.483 | 1.00 |
| 284_D | 394_Y | 1.468 | 1.00 |
| 288_F | 304_L | 1.467 | 1.00 |
| 292_N | 326_G | 1.467 | 1.00 |
| 343_Q | 347_S | 1.467 | 1.00 |
| 276_K | 335_D | 1.460 | 1.00 |
| 328_E | 390_D | 1.459 | 1.00 |
| 212_I | 216_H | 1.457 | 1.00 |
| 309_K | 312_A | 1.445 | 1.00 |
| 194_V | 222_F | 1.441 | 1.00 |
| 183_L | 186_A | 1.439 | 1.00 |
| 233_Q | 237_Q | 1.434 | 1.00 |
| 297_H | 390_D | 1.431 | 1.00 |
| 278_S | 376_T | 1.420 | 1.00 |
| 350_T | 354_N | 1.419 | 1.00 |
| 350_T | 404_L | 1.413 | 1.00 |
| 244_L | 248_L | 1.410 | 1.00 |
| 114_F | 117_F | 1.409 | 1.00 |
| 285_G | 307_I | 1.408 | 1.00 |
| 196_D | 202_N | 1.399 | 0.99 |
| 350_T | 371_I | 1.393 | 0.99 |
| 130_P | 134_N | 1.390 | 0.99 |
| 248_L | 260_A | 1.384 | 0.99 |
| 303_V | 327_D | 1.382 | 0.99 |
| 125_A | 130_P | 1.371 | 0.99 |
| 223_N | 226_L | 1.368 | 0.99 |
| 264_G | 320_K | 1.354 | 0.99 |
| 206_R | 223_N | 1.346 | 0.99 |
| 291_I | 303_V | 1.338 | 0.99 |
| 376_T | 385_L | 1.337 | 0.99 |
| 289_K | 394_Y | 1.336 | 0.99 |
| 51_L | 55_A | 1.301 | 0.99 |
| 299_T | 359_L | 1.289 | 0.99 |
| 303_V | 357_F | 1.287 | 0.99 |
| 396_A | 403_K | 1.284 | 0.99 |
| 287_N | 290_Y | 1.272 | 0.99 |
| 253_T | 304_L | 1.272 | 0.99 |
| 40_V | 44_K | 1.272 | 0.99 |
| 249_H | 256_A | 1.252 | 0.99 |
| 248_L | 256_A | 1.238 | 0.98 |
| 225_L | 229_M | 1.236 | 0.98 |
| 324_L | 386_Q | 1.232 | 0.98 |
| 327_D | 368_T | 1.231 | 0.98 |
| 289_K | 297_H | 1.227 | 0.98 |
| 268_L | 334_Y | 1.226 | 0.98 |
| 261_F | 332_V | 1.225 | 0.98 |
| 241_A | 244_L | 1.216 | 0.98 |
| 319_H | 348_A | 1.214 | 0.98 |
| 316_G | 348_A | 1.211 | 0.98 |
| 293_D | 297_H | 1.208 | 0.98 |
| 222_F | 225_L | 1.199 | 0.98 |
| 396_A | 400_R | 1.194 | 0.98 |
| 283_L | 371_I | 1.192 | 0.98 |
| 350_T | 402_E | 1.189 | 0.98 |
| 293_D | 394_Y | 1.189 | 0.98 |
| 236_L | 239_K | 1.188 | 0.98 |
| 139_G | 143_L | 1.184 | 0.98 |
| 43_L | 47_A | 1.179 | 0.98 |
| 292_N | 301_D | 1.176 | 0.98 |
| 314_F | 352_I | 1.175 | 0.98 |
| 284_D | 397_K | 1.170 | 0.97 |
| 293_D | 390_D | 1.169 | 0.97 |
| 374_A | 385_L | 1.159 | 0.97 |
| 180_H | 184_V | 1.159 | 0.97 |
| 269_M | 376_T | 1.157 | 0.97 |
| 216_H | 219_A | 1.156 | 0.97 |
| 282_F | 330_A | 1.153 | 0.97 |
| 373_Y | 404_L | 1.153 | 0.97 |
| 281_L | 333_L | 1.152 | 0.97 |
| 284_D | 327_D | 1.151 | 0.97 |
| 285_G | 369_L | 1.148 | 0.97 |
| 346_C | 371_I | 1.142 | 0.97 |
| 264_G | 268_L | 1.141 | 0.97 |
| 299_T | 302_R | 1.137 | 0.97 |
| 326_G | 394_Y | 1.136 | 0.97 |
| 250_D | 323_R | 1.135 | 0.97 |
| 374_A | 389_A | 1.131 | 0.97 |
| 330_A | 386_Q | 1.114 | 0.96 |
| 342_V | 373_Y | 1.109 | 0.96 |
| 126_P | 130_P | 1.108 | 0.96 |
| 358_D | 362_G | 1.108 | 0.96 |
| 235_R | 238_A | 1.107 | 0.96 |
| 282_F | 386_Q | 1.103 | 0.96 |
| 263_S | 267_T | 1.100 | 0.96 |
| 278_S | 332_V | 1.096 | 0.96 |
| 291_I | 365_T | 1.096 | 0.96 |
| 260_A | 322_Y | 1.092 | 0.96 |
| 308_A | 321_A | 1.091 | 0.96 |
| 70_D | 73_A | 1.086 | 0.96 |
| 285_G | 304_L | 1.084 | 0.96 |
| 310_R | 357_F | 1.083 | 0.96 |
| 139_G | 146_R | 1.082 | 0.96 |
| 176_T | 180_H | 1.071 | 0.95 |
| 124_P | 130_P | 1.070 | 0.95 |
| 279_A | 373_Y | 1.068 | 0.95 |
| 113_T | 117_F | 1.061 | 0.95 |
| 190_I | 194_V | 1.061 | 0.95 |
| 311_L | 349_L | 1.060 | 0.95 |
| 219_A | 223_N | 1.053 | 0.95 |
| 393_M | 401_A | 1.050 | 0.94 |
| 314_F | 349_L | 1.045 | 0.94 |
| 44_K | 48_Q | 1.043 | 0.94 |
| 358_D | 364_Q | 1.043 | 0.94 |
| 300_G | 326_G | 1.038 | 0.94 |
| 187_L | 214_E | 1.038 | 0.94 |
| 281_L | 331_M | 1.036 | 0.94 |
| 248_L | 259_A | 1.034 | 0.94 |
| 302_R | 361_N | 1.033 | 0.94 |
| 272_S | 278_S | 1.029 | 0.94 |
| 111_G | 114_F | 1.025 | 0.93 |
| 314_F | 348_A | 1.024 | 0.93 |
| 282_F | 324_L | 1.023 | 0.93 |
| 289_K | 328_E | 1.022 | 0.93 |
| 345_I | 349_L | 1.014 | 0.93 |
| 394_Y | 397_K | 1.007 | 0.93 |
| 284_D | 328_E | 1.003 | 0.93 |
| 262_R | 266_N | 1.002 | 0.92 |
| 284_D | 289_K | 1.002 | 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 | |
| 3breA | 2 | 0.7266 | 100 | 0.497 | Contact Map |
| 3pjxA | 1 | 0.431 | 100 | 0.508 | Contact Map |
| 4j40A | 2 | 0 | 100 | 0.513 | Contact Map |
| 1w25A | 2 | 0.835 | 100 | 0.516 | Contact Map |
| 3ezuA | 1 | 0.7931 | 100 | 0.519 | Contact Map |
| 4h54A | 2 | 0.6552 | 100 | 0.521 | Contact Map |
| 4rnhA | 1 | 0.3793 | 100 | 0.522 | Contact Map |
| 3ignA | 1 | 0.3966 | 100 | 0.537 | Contact Map |
| 3mtkA | 2 | 0.3867 | 100 | 0.544 | Contact Map |
| 3i5cA | 2 | 0.4606 | 100 | 0.544 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)