| ebi_allpots_4ikv_alligned |
| ID: | 1437403193 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 507 (502) | ||
| Sequences: | 1856 (951.7) | ||
| Seq/Len: | 3.697 | ||
| Nf(neff/√len): | 42.5 |
HHblits Results: (2013_03)
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: 3.697).
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 |
| 63_E | 322_K | 3.990 | 1.00 |
| 179_A | 191_L | 3.938 | 1.00 |
| 107_A | 127_L | 3.679 | 1.00 |
| 48_Y | 317_A | 3.205 | 1.00 |
| 320_A | 402_L | 3.050 | 1.00 |
| 111_A | 127_L | 3.011 | 1.00 |
| 87_L | 91_V | 2.898 | 1.00 |
| 70_M | 313_S | 2.573 | 1.00 |
| 472_G | 476_V | 2.518 | 1.00 |
| 326_L | 332_H | 2.364 | 1.00 |
| 158_F | 425_T | 2.285 | 1.00 |
| 38_S | 109_H | 2.279 | 1.00 |
| 376_L | 478_G | 2.272 | 1.00 |
| 110_I | 193_A | 2.245 | 1.00 |
| 105_I | 135_L | 2.215 | 1.00 |
| 32_E | 36_R | 2.165 | 1.00 |
| 422_S | 426_K | 2.134 | 1.00 |
| 177_G | 336_A | 2.113 | 1.00 |
| 345_F | 407_F | 2.094 | 1.00 |
| 290_S | 493_K | 2.074 | 1.00 |
| 106_M | 197_F | 2.056 | 1.00 |
| 177_G | 337_W | 2.030 | 1.00 |
| 291_R | 494_G | 2.021 | 1.00 |
| 52_Y | 185_F | 2.015 | 1.00 |
| 184_N | 187_L | 1.998 | 1.00 |
| 165_I | 441_F | 1.967 | 1.00 |
| 379_G | 475_L | 1.967 | 1.00 |
| 181_M | 335_P | 1.937 | 1.00 |
| 403_V | 407_F | 1.934 | 1.00 |
| 372_A | 478_G | 1.927 | 1.00 |
| 212_G | 215_G | 1.924 | 1.00 |
| 302_S | 443_S | 1.912 | 1.00 |
| 344_L | 348_I | 1.903 | 1.00 |
| 487_R | 490_R | 1.889 | 1.00 |
| 43_R | 70_M | 1.832 | 0.99 |
| 140_S | 441_F | 1.830 | 0.99 |
| 352_V | 356_M | 1.830 | 0.99 |
| 180_G | 336_A | 1.817 | 0.99 |
| 380_L | 408_I | 1.798 | 0.99 |
| 381_S | 409_V | 1.765 | 0.99 |
| 314_T | 455_V | 1.759 | 0.99 |
| 377_F | 411_L | 1.733 | 0.99 |
| 279_Y | 292_V | 1.726 | 0.99 |
| 170_F | 347_I | 1.697 | 0.99 |
| 342_N | 346_I | 1.685 | 0.99 |
| 35_E | 136_K | 1.672 | 0.99 |
| 92_F | 97_A | 1.640 | 0.99 |
| 80_S | 129_V | 1.614 | 0.98 |
| 169_A | 343_P | 1.600 | 0.98 |
| 478_G | 482_L | 1.599 | 0.98 |
| 324_T | 402_L | 1.592 | 0.98 |
| 492_M | 495_I | 1.590 | 0.98 |
| 36_R | 136_K | 1.586 | 0.98 |
| 103_L | 107_A | 1.583 | 0.98 |
| 43_R | 310_E | 1.576 | 0.98 |
| 345_F | 403_V | 1.571 | 0.98 |
| 385_I | 388_P | 1.568 | 0.98 |
| 339_Q | 343_P | 1.568 | 0.98 |
| 143_V | 146_M | 1.561 | 0.98 |
| 32_E | 35_E | 1.559 | 0.98 |
| 163_M | 350_A | 1.554 | 0.98 |
| 87_L | 92_F | 1.544 | 0.98 |
| 73_Y | 109_H | 1.542 | 0.98 |
| 181_M | 336_A | 1.537 | 0.98 |
| 111_A | 124_S | 1.532 | 0.98 |
| 105_I | 132_T | 1.525 | 0.97 |
| 320_A | 324_T | 1.514 | 0.97 |
| 132_T | 135_L | 1.509 | 0.97 |
| 161_F | 165_I | 1.503 | 0.97 |
| 487_R | 491_L | 1.499 | 0.97 |
| 107_A | 111_A | 1.489 | 0.97 |
| 47_V | 66_A | 1.487 | 0.97 |
| 109_H | 186_H | 1.485 | 0.97 |
| 309_Q | 410_V | 1.482 | 0.97 |
| 165_I | 421_L | 1.476 | 0.97 |
| 376_L | 482_L | 1.475 | 0.97 |
| 341_L | 403_V | 1.468 | 0.97 |
| 339_Q | 342_N | 1.462 | 0.97 |
| 175_V | 191_L | 1.457 | 0.96 |
| 369_Q | 482_L | 1.453 | 0.96 |
| 348_I | 352_V | 1.448 | 0.96 |
| 342_N | 410_V | 1.445 | 0.96 |
| 327_D | 332_H | 1.440 | 0.96 |
| 80_S | 83_I | 1.434 | 0.96 |
| 38_S | 73_Y | 1.432 | 0.96 |
| 72_I | 449_A | 1.431 | 0.96 |
| 140_S | 437_M | 1.431 | 0.96 |
| 39_Y | 74_G | 1.430 | 0.96 |
| 180_G | 184_N | 1.428 | 0.96 |
| 353_F | 411_L | 1.424 | 0.96 |
| 35_E | 40_Y | 1.414 | 0.96 |
| 384_V | 404_L | 1.413 | 0.96 |
| 109_H | 188_G | 1.410 | 0.95 |
| 170_F | 344_L | 1.407 | 0.95 |
| 110_I | 197_F | 1.406 | 0.95 |
| 50_M | 121_L | 1.397 | 0.95 |
| 62_D | 65_L | 1.397 | 0.95 |
| 427_L | 492_M | 1.395 | 0.95 |
| 486_P | 490_R | 1.390 | 0.95 |
| 350_A | 354_A | 1.386 | 0.95 |
| 306_W | 417_S | 1.386 | 0.95 |
| 465_A | 468_G | 1.377 | 0.95 |
| 486_P | 489_G | 1.377 | 0.95 |
| 21_H | 25_L | 1.373 | 0.95 |
| 476_V | 479_L | 1.366 | 0.94 |
| 178_T | 336_A | 1.365 | 0.94 |
| 36_R | 165_I | 1.362 | 0.94 |
| 32_E | 136_K | 1.361 | 0.94 |
| 400_I | 404_L | 1.360 | 0.94 |
| 106_M | 110_I | 1.353 | 0.94 |
| 294_A | 491_L | 1.337 | 0.93 |
| 475_L | 478_G | 1.333 | 0.93 |
| 74_G | 448_Q | 1.328 | 0.93 |
| 309_Q | 312_G | 1.320 | 0.93 |
| 420_G | 440_W | 1.315 | 0.93 |
| 45_I | 176_V | 1.313 | 0.93 |
| 476_V | 483_A | 1.312 | 0.93 |
| 21_H | 147_Y | 1.312 | 0.93 |
| 45_I | 188_G | 1.303 | 0.92 |
| 76_L | 129_V | 1.301 | 0.92 |
| 287_E | 494_G | 1.294 | 0.92 |
| 143_V | 211_L | 1.289 | 0.92 |
| 52_Y | 56_K | 1.281 | 0.91 |
| 373_L | 415_C | 1.275 | 0.91 |
| 140_S | 165_I | 1.273 | 0.91 |
| 374_G | 378_A | 1.271 | 0.91 |
| 471_G | 475_L | 1.270 | 0.91 |
| 180_G | 183_Y | 1.261 | 0.91 |
| 47_V | 318_N | 1.260 | 0.91 |
| 309_Q | 342_N | 1.258 | 0.90 |
| 373_L | 377_F | 1.257 | 0.90 |
| 304_M | 477_L | 1.245 | 0.90 |
| 187_L | 190_G | 1.245 | 0.90 |
| 67_L | 314_T | 1.243 | 0.90 |
| 312_G | 409_V | 1.242 | 0.90 |
| 157_G | 425_T | 1.240 | 0.90 |
| 407_F | 411_L | 1.232 | 0.89 |
| 379_G | 478_G | 1.230 | 0.89 |
| 70_M | 314_T | 1.229 | 0.89 |
| 36_R | 40_Y | 1.228 | 0.89 |
| 104_L | 130_L | 1.223 | 0.89 |
| 139_V | 165_I | 1.221 | 0.89 |
| 112_L | 124_S | 1.221 | 0.89 |
| 52_Y | 321_D | 1.211 | 0.88 |
| 295_Y | 424_T | 1.207 | 0.88 |
| 75_A | 449_A | 1.202 | 0.88 |
| 349_L | 411_L | 1.200 | 0.87 |
| 289_R | 486_P | 1.195 | 0.87 |
| 369_Q | 489_G | 1.193 | 0.87 |
| 173_P | 340_S | 1.191 | 0.87 |
| 106_M | 193_A | 1.191 | 0.87 |
| 87_L | 97_A | 1.186 | 0.87 |
| 478_G | 491_L | 1.180 | 0.86 |
| 81_G | 88_A | 1.179 | 0.86 |
| 140_S | 144_G | 1.177 | 0.86 |
| 48_Y | 335_P | 1.173 | 0.86 |
| 172_A | 378_A | 1.169 | 0.86 |
| 145_D | 214_A | 1.166 | 0.85 |
| 77_V | 138_N | 1.163 | 0.85 |
| 169_A | 173_P | 1.163 | 0.85 |
| 115_P | 294_A | 1.162 | 0.85 |
| 180_G | 187_L | 1.159 | 0.85 |
| 109_H | 190_G | 1.157 | 0.85 |
| 119_A | 123_V | 1.155 | 0.85 |
| 479_L | 483_A | 1.153 | 0.84 |
| 352_V | 355_W | 1.152 | 0.84 |
| 41_G | 176_V | 1.150 | 0.84 |
| 53_E | 56_K | 1.149 | 0.84 |
| 316_L | 406_Y | 1.147 | 0.84 |
| 190_G | 194_V | 1.140 | 0.84 |
| 316_L | 320_A | 1.139 | 0.83 |
| 265_I | 475_L | 1.133 | 0.83 |
| 286_A | 290_S | 1.132 | 0.83 |
| 349_L | 407_F | 1.123 | 0.82 |
| 303_A | 447_A | 1.121 | 0.82 |
| 109_H | 196_M | 1.118 | 0.82 |
| 98_V | 434_A | 1.117 | 0.82 |
| 32_E | 161_F | 1.115 | 0.82 |
| 316_L | 405_S | 1.115 | 0.82 |
| 334_S | 337_W | 1.115 | 0.82 |
| 63_E | 318_N | 1.114 | 0.82 |
| 351_P | 420_G | 1.114 | 0.82 |
| 287_E | 493_K | 1.112 | 0.81 |
| 29_F | 164_G | 1.106 | 0.81 |
| 44_A | 173_P | 1.105 | 0.81 |
| 326_L | 334_S | 1.092 | 0.80 |
| 162_Y | 413_E | 1.091 | 0.80 |
| 51_Y | 318_N | 1.091 | 0.80 |
| 36_R | 161_F | 1.091 | 0.80 |
| 449_A | 488_I | 1.090 | 0.80 |
| 22_P | 25_L | 1.087 | 0.79 |
| 178_T | 337_W | 1.081 | 0.79 |
| 33_F | 164_G | 1.080 | 0.79 |
| 52_Y | 181_M | 1.078 | 0.79 |
| 302_S | 440_W | 1.078 | 0.79 |
| 324_T | 397_V | 1.077 | 0.78 |
| 367_I | 423_A | 1.069 | 0.78 |
| 424_T | 436_T | 1.069 | 0.78 |
| 385_I | 405_S | 1.064 | 0.77 |
| 34_W | 195_G | 1.060 | 0.77 |
| 47_V | 317_A | 1.060 | 0.77 |
| 99_F | 102_G | 1.059 | 0.77 |
| 50_M | 122_F | 1.054 | 0.76 |
| 19_F | 26_F | 1.049 | 0.76 |
| 368_P | 492_M | 1.048 | 0.76 |
| 472_G | 479_L | 1.048 | 0.76 |
| 269_I | 483_A | 1.048 | 0.76 |
| 333_L | 337_W | 1.041 | 0.75 |
| 307_A | 447_A | 1.039 | 0.75 |
| 155_D | 422_S | 1.039 | 0.75 |
| 67_L | 318_N | 1.038 | 0.75 |
| 69_I | 122_F | 1.032 | 0.74 |
| 29_F | 49_Y | 1.030 | 0.74 |
| 154_R | 157_G | 1.030 | 0.74 |
| 232_A | 235_A | 1.030 | 0.74 |
| 68_A | 456_R | 1.028 | 0.74 |
| 371_F | 440_W | 1.027 | 0.74 |
| 157_G | 318_N | 1.024 | 0.73 |
| 160_I | 163_M | 1.023 | 0.73 |
| 360_L | 363_R | 1.023 | 0.73 |
| 71_S | 75_A | 1.020 | 0.73 |
| 139_V | 161_F | 1.020 | 0.73 |
| 404_L | 407_F | 1.018 | 0.73 |
| 53_E | 185_F | 1.017 | 0.73 |
| 154_R | 425_T | 1.016 | 0.73 |
| 346_I | 413_E | 1.014 | 0.72 |
| 370_K | 422_S | 1.011 | 0.72 |
| 16_R | 23_K | 1.009 | 0.72 |
| 111_A | 114_I | 1.009 | 0.72 |
| 172_A | 343_P | 1.008 | 0.72 |
| 62_D | 92_F | 1.008 | 0.72 |
| 100_Y | 205_A | 1.006 | 0.72 |
| 384_V | 408_I | 1.006 | 0.72 |
| 170_F | 341_L | 1.005 | 0.71 |
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 | |
| 4d2bA | 1 | 0.8718 | 100 | 0.479 | Contact Map |
| 2xutA | 3 | 0.8343 | 100 | 0.481 | Contact Map |
| 4tphA | 2 | 0.8422 | 100 | 0.52 | Contact Map |
| 4ikvA | 1 | 0.9704 | 100 | 0.686 | Contact Map |
| 4q65A | 1 | 0.8442 | 100 | 0.69 | Contact Map |
| 4oh3A | 2 | 0.8915 | 100 | 0.693 | Contact Map |
| 3wdoA | 1 | 0.8028 | 99.9 | 0.838 | Contact Map |
| 2cfqA | 1 | 0.8028 | 99.9 | 0.842 | Contact Map |
| 1pw4A | 1 | 0.8264 | 99.9 | 0.849 | Contact Map |
| 2gfpA | 2 | 0.7377 | 99.9 | 0.85 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)