| RPE65 |
| ID: | 1491296839 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 533 (509) | ||
| Sequences: | 1903 (1178.9) | ||
| Seq/Len: | 3.739 | ||
| Nf(neff/√len): | 52.3 |
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: 3.739).
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 |
| 248_N | 319_E | 5.404 | 1.00 |
| 432_T | 451_N | 5.136 | 1.00 |
| 449_K | 482_D | 4.428 | 1.00 |
| 475_H | 483_D | 4.356 | 1.00 |
| 291_I | 324_L | 4.293 | 1.00 |
| 34_I | 504_I | 4.046 | 1.00 |
| 422_N | 425_K | 4.017 | 1.00 |
| 67_L | 155_I | 3.817 | 1.00 |
| 315_I | 434_A | 3.769 | 1.00 |
| 132_A | 145_A | 3.477 | 1.00 |
| 37_W | 485_V | 3.474 | 1.00 |
| 327_D | 367_R | 3.434 | 1.00 |
| 472_F | 484_G | 3.413 | 1.00 |
| 142_D | 154_K | 3.365 | 1.00 |
| 244_G | 317_T | 3.255 | 1.00 |
| 68_H | 79_Y | 2.976 | 1.00 |
| 135_N | 529_L | 2.941 | 1.00 |
| 509_D | 512_E | 2.915 | 1.00 |
| 323_F | 369_V | 2.895 | 1.00 |
| 70_F | 77_V | 2.754 | 1.00 |
| 323_F | 371_P | 2.752 | 1.00 |
| 433_Y | 449_K | 2.697 | 1.00 |
| 327_D | 431_Y | 2.690 | 1.00 |
| 70_F | 502_L | 2.587 | 1.00 |
| 210_P | 214_A | 2.494 | 1.00 |
| 435_Y | 449_K | 2.349 | 1.00 |
| 66_L | 81_R | 2.343 | 1.00 |
| 31_T | 517_E | 2.311 | 1.00 |
| 447_L | 488_S | 2.222 | 1.00 |
| 421_I | 427_C | 2.190 | 1.00 |
| 85_R | 90_V | 2.177 | 1.00 |
| 156_N | 159_T | 2.175 | 1.00 |
| 430_P | 453_K | 2.171 | 1.00 |
| 487_L | 502_L | 2.128 | 1.00 |
| 318_Y | 325_I | 2.123 | 1.00 |
| 31_T | 515_R | 2.078 | 1.00 |
| 435_Y | 482_D | 2.049 | 1.00 |
| 483_D | 508_K | 2.047 | 1.00 |
| 130_D | 150_N | 2.041 | 1.00 |
| 188_T | 294_K | 1.993 | 1.00 |
| 178_T | 181_P | 1.983 | 1.00 |
| 315_I | 365_V | 1.951 | 1.00 |
| 72_F | 502_L | 1.936 | 1.00 |
| 318_Y | 431_Y | 1.915 | 1.00 |
| 458_W | 511_S | 1.911 | 1.00 |
| 43_L | 67_L | 1.907 | 1.00 |
| 505_L | 510_L | 1.891 | 1.00 |
| 501_Y | 517_E | 1.885 | 1.00 |
| 293_D | 296_R | 1.876 | 1.00 |
| 432_T | 453_K | 1.876 | 1.00 |
| 85_R | 89_Y | 1.870 | 1.00 |
| 422_N | 482_D | 1.837 | 1.00 |
| 506_N | 509_D | 1.829 | 0.99 |
| 95_E | 99_V | 1.825 | 0.99 |
| 501_Y | 515_R | 1.819 | 0.99 |
| 420_Q | 471_I | 1.787 | 0.99 |
| 290_H | 303_K | 1.782 | 0.99 |
| 33_R | 36_L | 1.760 | 0.99 |
| 447_L | 510_L | 1.759 | 0.99 |
| 190_Y | 245_L | 1.758 | 0.99 |
| 470_P | 486_V | 1.758 | 0.99 |
| 486_V | 510_L | 1.725 | 0.99 |
| 486_V | 507_A | 1.715 | 0.99 |
| 41_S | 69_K | 1.695 | 0.99 |
| 480_E | 508_K | 1.683 | 0.99 |
| 253_V | 326_V | 1.667 | 0.99 |
| 320_D | 430_P | 1.663 | 0.99 |
| 184_E | 294_K | 1.661 | 0.99 |
| 154_K | 163_I | 1.646 | 0.99 |
| 84_I | 155_I | 1.612 | 0.98 |
| 167_D | 170_N | 1.609 | 0.98 |
| 473_V | 487_L | 1.608 | 0.98 |
| 503_L | 515_R | 1.604 | 0.98 |
| 425_K | 474_S | 1.601 | 0.98 |
| 144_Y | 154_K | 1.593 | 0.98 |
| 431_Y | 452_V | 1.584 | 0.98 |
| 34_I | 516_A | 1.570 | 0.98 |
| 476_P | 479_L | 1.550 | 0.98 |
| 37_W | 475_H | 1.546 | 0.98 |
| 319_E | 324_L | 1.542 | 0.98 |
| 367_R | 431_Y | 1.527 | 0.98 |
| 288_W | 303_K | 1.525 | 0.98 |
| 433_Y | 451_N | 1.507 | 0.97 |
| 147_T | 150_N | 1.504 | 0.97 |
| 244_G | 314_H | 1.497 | 0.97 |
| 182_H | 242_S | 1.487 | 0.97 |
| 434_A | 452_V | 1.486 | 0.97 |
| 135_N | 181_P | 1.482 | 0.97 |
| 420_Q | 470_P | 1.479 | 0.97 |
| 435_Y | 507_A | 1.468 | 0.97 |
| 315_I | 418_F | 1.455 | 0.96 |
| 330_C | 366_R | 1.449 | 0.96 |
| 304_Y | 370_L | 1.449 | 0.96 |
| 304_Y | 372_L | 1.439 | 0.96 |
| 43_L | 143_Y | 1.437 | 0.96 |
| 89_Y | 93_M | 1.436 | 0.96 |
| 87_D | 90_V | 1.415 | 0.96 |
| 325_I | 369_V | 1.409 | 0.96 |
| 422_N | 426_Y | 1.400 | 0.95 |
| 34_I | 77_V | 1.396 | 0.95 |
| 420_Q | 423_Y | 1.395 | 0.95 |
| 438_G | 446_R | 1.394 | 0.95 |
| 247_P | 319_E | 1.390 | 0.95 |
| 476_P | 485_V | 1.382 | 0.95 |
| 422_N | 449_K | 1.366 | 0.94 |
| 135_N | 420_Q | 1.363 | 0.94 |
| 318_Y | 430_P | 1.348 | 0.94 |
| 485_V | 513_V | 1.346 | 0.94 |
| 421_I | 431_Y | 1.339 | 0.94 |
| 76_H | 96_K | 1.336 | 0.94 |
| 291_I | 304_Y | 1.329 | 0.93 |
| 315_I | 327_D | 1.324 | 0.93 |
| 27_T | 76_H | 1.324 | 0.93 |
| 130_D | 147_T | 1.321 | 0.93 |
| 289_L | 306_T | 1.320 | 0.93 |
| 246_T | 324_L | 1.320 | 0.93 |
| 433_Y | 481_E | 1.318 | 0.93 |
| 88_A | 92_A | 1.312 | 0.93 |
| 148_E | 193_G | 1.312 | 0.93 |
| 64_Q | 92_A | 1.309 | 0.93 |
| 137_Y | 146_C | 1.307 | 0.93 |
| 253_V | 287_V | 1.304 | 0.92 |
| 449_K | 481_E | 1.303 | 0.92 |
| 154_K | 166_V | 1.274 | 0.91 |
| 406_E | 455_K | 1.263 | 0.91 |
| 326_V | 370_L | 1.262 | 0.91 |
| 46_G | 523_P | 1.260 | 0.91 |
| 433_Y | 482_D | 1.259 | 0.91 |
| 460_W | 505_L | 1.257 | 0.91 |
| 255_T | 311_L | 1.255 | 0.90 |
| 477_D | 480_E | 1.248 | 0.90 |
| 57_F | 98_I | 1.241 | 0.90 |
| 318_Y | 327_D | 1.237 | 0.90 |
| 41_S | 71_D | 1.231 | 0.89 |
| 45_C | 132_A | 1.229 | 0.89 |
| 70_F | 489_V | 1.229 | 0.89 |
| 248_N | 295_K | 1.227 | 0.89 |
| 88_A | 129_T | 1.221 | 0.89 |
| 39_T | 74_E | 1.210 | 0.88 |
| 365_V | 434_A | 1.203 | 0.88 |
| 84_I | 162_T | 1.201 | 0.88 |
| 422_N | 474_S | 1.199 | 0.88 |
| 256_P | 281_S | 1.197 | 0.87 |
| 324_L | 372_L | 1.194 | 0.87 |
| 142_D | 163_I | 1.189 | 0.87 |
| 473_V | 504_I | 1.189 | 0.87 |
| 420_Q | 529_L | 1.188 | 0.87 |
| 137_Y | 189_V | 1.187 | 0.87 |
| 302_N | 380_G | 1.187 | 0.87 |
| 85_R | 93_M | 1.185 | 0.87 |
| 134_V | 418_F | 1.185 | 0.87 |
| 146_C | 179_A | 1.183 | 0.87 |
| 482_D | 508_K | 1.181 | 0.87 |
| 374_I | 380_G | 1.178 | 0.86 |
| 492_S | 497_Q | 1.163 | 0.85 |
| 287_V | 309_F | 1.161 | 0.85 |
| 289_L | 370_L | 1.161 | 0.85 |
| 440_N | 445_D | 1.161 | 0.85 |
| 243_F | 252_F | 1.160 | 0.85 |
| 65_A | 133_L | 1.157 | 0.85 |
| 286_G | 305_R | 1.156 | 0.85 |
| 11_G | 524_V | 1.156 | 0.85 |
| 42_L | 471_I | 1.156 | 0.85 |
| 245_L | 294_K | 1.148 | 0.84 |
| 43_L | 157_P | 1.148 | 0.84 |
| 490_V | 501_Y | 1.146 | 0.84 |
| 422_N | 433_Y | 1.145 | 0.84 |
| 139_V | 189_V | 1.145 | 0.84 |
| 92_A | 129_T | 1.144 | 0.84 |
| 467_P | 490_V | 1.143 | 0.84 |
| 481_E | 484_G | 1.143 | 0.84 |
| 416_F | 436_G | 1.140 | 0.84 |
| 451_N | 454_T | 1.136 | 0.84 |
| 470_P | 488_S | 1.134 | 0.83 |
| 77_V | 516_A | 1.131 | 0.83 |
| 210_P | 216_K | 1.130 | 0.83 |
| 87_D | 165_Q | 1.128 | 0.83 |
| 425_K | 482_D | 1.126 | 0.83 |
| 35_P | 40_G | 1.125 | 0.83 |
| 475_H | 506_N | 1.113 | 0.82 |
| 480_E | 483_D | 1.113 | 0.82 |
| 251_V | 317_T | 1.112 | 0.82 |
| 467_P | 488_S | 1.110 | 0.82 |
| 64_Q | 86_T | 1.103 | 0.81 |
| 291_I | 370_L | 1.101 | 0.81 |
| 258_K | 282_N | 1.099 | 0.81 |
| 36_L | 74_E | 1.099 | 0.81 |
| 492_S | 500_A | 1.098 | 0.81 |
| 112_C | 116_F | 1.096 | 0.80 |
| 84_I | 153_T | 1.095 | 0.80 |
| 449_K | 508_K | 1.093 | 0.80 |
| 39_T | 73_K | 1.088 | 0.80 |
| 184_E | 188_T | 1.087 | 0.80 |
| 239_Y | 242_S | 1.085 | 0.79 |
| 244_G | 326_V | 1.085 | 0.79 |
| 329_C | 332_K | 1.084 | 0.79 |
| 472_F | 481_E | 1.082 | 0.79 |
| 329_C | 363_P | 1.074 | 0.79 |
| 458_W | 509_D | 1.072 | 0.78 |
| 328_L | 368_Y | 1.069 | 0.78 |
| 15_L | 520_I | 1.068 | 0.78 |
| 311_L | 328_L | 1.065 | 0.78 |
| 281_S | 310_N | 1.064 | 0.78 |
| 87_D | 153_T | 1.061 | 0.77 |
| 32_G | 35_P | 1.051 | 0.76 |
| 247_P | 429_K | 1.050 | 0.76 |
| 193_G | 252_F | 1.044 | 0.76 |
| 481_E | 510_L | 1.037 | 0.75 |
| 418_F | 526_F | 1.034 | 0.75 |
| 137_Y | 144_Y | 1.033 | 0.75 |
| 446_R | 459_V | 1.029 | 0.74 |
| 255_T | 309_F | 1.029 | 0.74 |
| 134_V | 152_I | 1.027 | 0.74 |
| 473_V | 483_D | 1.027 | 0.74 |
| 67_L | 84_I | 1.024 | 0.74 |
| 432_T | 481_E | 1.024 | 0.74 |
| 484_G | 507_A | 1.018 | 0.73 |
| 423_Y | 427_C | 1.012 | 0.72 |
| 468_S | 525_T | 1.011 | 0.72 |
| 195_C | 205_N | 1.010 | 0.72 |
| 245_L | 427_C | 1.009 | 0.72 |
| 190_Y | 250_I | 1.008 | 0.72 |
| 426_Y | 431_Y | 1.006 | 0.72 |
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 | |
| 4rscA | 2 | 0.9456 | 100 | 0.048 | Contact Map |
| 4ou9A | 4 | 0.8649 | 100 | 0.133 | Contact Map |
| 3npeA | 1 | 0.8574 | 100 | 0.197 | Contact Map |
| 3dsmA | 1 | 0.1632 | 11.8 | 0.98 | Contact Map |
| 4aeqA | 1 | 0.1557 | 7.9 | 0.982 | Contact Map |
| 1l0qA | 4 | 0.1632 | 4.9 | 0.983 | Contact Map |
| 4c2vC | 2 | 0.0826 | 3.7 | 0.984 | Contact Map |
| 2oizA | 2 | 0.1126 | 3.6 | 0.984 | Contact Map |
| 3ziwA | 6 | 0.122 | 3.4 | 0.985 | Contact Map |
| 1gglA | 2 | 0.1332 | 2.9 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)