| drosophila cryptochrome namrata |
| ID: | 1487099407 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 542 (501) | ||
| Sequences: | 1978 (1264.9) | ||
| Seq/Len: | 3.948 | ||
| Nf(neff/√len): | 56.5 |
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: 3.948).
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 |
| 371_L | 403_H | 4.468 | 1.00 |
| 368_R | 460_E | 4.278 | 1.00 |
| 269_H | 274_C | 4.165 | 1.00 |
| 368_R | 458_V | 3.324 | 1.00 |
| 362_L | 383_T | 3.284 | 1.00 |
| 392_G | 501_A | 3.217 | 1.00 |
| 392_G | 498_L | 3.214 | 1.00 |
| 63_S | 274_C | 3.060 | 1.00 |
| 350_L | 399_H | 3.029 | 1.00 |
| 350_L | 354_R | 2.983 | 1.00 |
| 366_A | 380_L | 2.946 | 1.00 |
| 444_A | 470_H | 2.754 | 1.00 |
| 371_L | 407_Y | 2.713 | 1.00 |
| 360_F | 387_F | 2.704 | 1.00 |
| 444_A | 454_I | 2.648 | 1.00 |
| 352_S | 495_I | 2.561 | 1.00 |
| 60_L | 272_F | 2.509 | 1.00 |
| 351_Q | 355_L | 2.419 | 1.00 |
| 442_A | 446_R | 2.408 | 1.00 |
| 63_S | 226_G | 2.403 | 1.00 |
| 372_A | 457_Y | 2.396 | 1.00 |
| 68_D | 72_Q | 2.347 | 1.00 |
| 455_K | 466_K | 2.318 | 1.00 |
| 471_E | 474_R | 2.283 | 1.00 |
| 497_D | 500_M | 2.273 | 1.00 |
| 480_Q | 487_I | 2.254 | 1.00 |
| 450_D | 466_K | 2.252 | 1.00 |
| 360_F | 498_L | 2.235 | 1.00 |
| 332_E | 338_L | 2.192 | 1.00 |
| 464_V | 475_M | 2.100 | 1.00 |
| 345_P | 349_L | 2.072 | 1.00 |
| 20_N | 107_E | 2.071 | 1.00 |
| 403_H | 407_Y | 2.065 | 1.00 |
| 227_E | 279_R | 2.056 | 1.00 |
| 405_L | 411_A | 2.051 | 1.00 |
| 11_F | 38_P | 2.027 | 1.00 |
| 7_N | 105_C | 2.005 | 1.00 |
| 455_K | 469_V | 1.987 | 1.00 |
| 380_L | 453_Y | 1.981 | 1.00 |
| 400_G | 420_W | 1.965 | 1.00 |
| 502_V | 506_M | 1.962 | 1.00 |
| 349_L | 495_I | 1.940 | 1.00 |
| 66_D | 228_T | 1.932 | 1.00 |
| 480_Q | 485_C | 1.902 | 1.00 |
| 270_L | 280_F | 1.879 | 1.00 |
| 498_L | 501_A | 1.871 | 1.00 |
| 476_S | 479_Q | 1.855 | 1.00 |
| 388_L | 400_G | 1.829 | 1.00 |
| 343_A | 349_L | 1.808 | 1.00 |
| 105_C | 135_K | 1.798 | 0.99 |
| 401_L | 417_A | 1.788 | 0.99 |
| 11_F | 71_L | 1.785 | 0.99 |
| 441_V | 473_W | 1.761 | 0.99 |
| 106_I | 132_F | 1.748 | 0.99 |
| 58_R | 62_D | 1.745 | 0.99 |
| 21_P | 137_S | 1.743 | 0.99 |
| 9_I | 20_N | 1.705 | 0.99 |
| 343_A | 508_A | 1.669 | 0.99 |
| 68_D | 80_R | 1.648 | 0.99 |
| 70_Q | 227_E | 1.629 | 0.99 |
| 245_F | 249_F | 1.628 | 0.99 |
| 373_E | 457_Y | 1.626 | 0.99 |
| 504_R | 508_A | 1.622 | 0.99 |
| 12_R | 118_D | 1.602 | 0.99 |
| 227_E | 230_A | 1.585 | 0.98 |
| 468_F | 476_S | 1.580 | 0.98 |
| 393_L | 496_I | 1.570 | 0.98 |
| 486_L | 489_V | 1.560 | 0.98 |
| 445_K | 471_E | 1.558 | 0.98 |
| 63_S | 225_G | 1.549 | 0.98 |
| 475_M | 483_Y | 1.532 | 0.98 |
| 18_H | 279_R | 1.531 | 0.98 |
| 379_T | 443_L | 1.530 | 0.98 |
| 96_H | 101_L | 1.524 | 0.98 |
| 487_I | 490_H | 1.520 | 0.98 |
| 437_V | 506_M | 1.515 | 0.98 |
| 321_M | 328_Y | 1.514 | 0.98 |
| 362_L | 444_A | 1.508 | 0.98 |
| 235_D | 283_S | 1.505 | 0.98 |
| 399_H | 402_Q | 1.491 | 0.97 |
| 62_D | 225_G | 1.489 | 0.97 |
| 452_T | 455_K | 1.489 | 0.97 |
| 387_F | 495_I | 1.485 | 0.97 |
| 353_W | 367_M | 1.481 | 0.97 |
| 465_P | 468_F | 1.480 | 0.97 |
| 503_K | 507_L | 1.448 | 0.97 |
| 353_W | 356_G | 1.444 | 0.97 |
| 388_L | 395_Q | 1.437 | 0.97 |
| 241_E | 248_G | 1.427 | 0.96 |
| 475_M | 480_Q | 1.422 | 0.96 |
| 138_H | 319_Y | 1.411 | 0.96 |
| 226_G | 230_A | 1.408 | 0.96 |
| 104_I | 125_C | 1.405 | 0.96 |
| 319_Y | 412_D | 1.404 | 0.96 |
| 8_V | 101_L | 1.402 | 0.96 |
| 369_Q | 453_Y | 1.396 | 0.96 |
| 242_Q | 245_F | 1.390 | 0.96 |
| 249_F | 429_E | 1.390 | 0.96 |
| 11_F | 67_I | 1.379 | 0.95 |
| 18_H | 227_E | 1.377 | 0.95 |
| 245_F | 250_Y | 1.369 | 0.95 |
| 499_S | 503_K | 1.369 | 0.95 |
| 40_F | 60_L | 1.353 | 0.95 |
| 404_F | 408_L | 1.352 | 0.95 |
| 464_V | 480_Q | 1.346 | 0.94 |
| 234_L | 280_F | 1.346 | 0.94 |
| 318_F | 418_G | 1.344 | 0.94 |
| 241_E | 245_F | 1.343 | 0.94 |
| 45_E | 87_E | 1.337 | 0.94 |
| 19_D | 278_R | 1.334 | 0.94 |
| 360_F | 392_G | 1.332 | 0.94 |
| 394_W | 505_N | 1.331 | 0.94 |
| 106_I | 148_E | 1.313 | 0.93 |
| 394_W | 508_A | 1.312 | 0.93 |
| 162_L | 313_I | 1.309 | 0.93 |
| 369_Q | 373_E | 1.306 | 0.93 |
| 307_H | 310_G | 1.306 | 0.93 |
| 451_G | 472_P | 1.303 | 0.93 |
| 106_I | 134_E | 1.300 | 0.93 |
| 500_M | 503_K | 1.298 | 0.93 |
| 352_S | 357_Q | 1.298 | 0.93 |
| 6_A | 35_A | 1.298 | 0.93 |
| 92_F | 104_I | 1.296 | 0.93 |
| 480_Q | 488_G | 1.294 | 0.93 |
| 38_P | 79_G | 1.292 | 0.93 |
| 122_R | 134_E | 1.291 | 0.93 |
| 137_S | 278_R | 1.288 | 0.93 |
| 394_W | 504_R | 1.288 | 0.93 |
| 354_R | 403_H | 1.288 | 0.93 |
| 229_Q | 233_L | 1.276 | 0.92 |
| 311_Q | 415_V | 1.275 | 0.92 |
| 480_Q | 490_H | 1.271 | 0.92 |
| 175_T | 178_A | 1.270 | 0.92 |
| 311_Q | 382_N | 1.264 | 0.92 |
| 104_I | 134_E | 1.263 | 0.92 |
| 351_Q | 354_R | 1.263 | 0.92 |
| 313_I | 316_E | 1.256 | 0.91 |
| 461_L | 491_Y | 1.254 | 0.91 |
| 55_N | 407_Y | 1.246 | 0.91 |
| 9_I | 22_A | 1.243 | 0.91 |
| 66_D | 70_Q | 1.238 | 0.91 |
| 350_L | 395_Q | 1.237 | 0.90 |
| 6_A | 101_L | 1.227 | 0.90 |
| 108_Q | 134_E | 1.227 | 0.90 |
| 245_F | 429_E | 1.225 | 0.90 |
| 6_A | 37_I | 1.223 | 0.90 |
| 327_N | 331_M | 1.219 | 0.90 |
| 8_V | 39_V | 1.218 | 0.90 |
| 283_S | 287_L | 1.198 | 0.89 |
| 413_W | 417_A | 1.197 | 0.88 |
| 230_A | 275_L | 1.197 | 0.88 |
| 59_F | 225_G | 1.197 | 0.88 |
| 477_A | 481_E | 1.197 | 0.88 |
| 109_D | 114_W | 1.193 | 0.88 |
| 250_Y | 429_E | 1.188 | 0.88 |
| 59_F | 274_C | 1.182 | 0.88 |
| 39_V | 84_F | 1.181 | 0.88 |
| 480_Q | 483_Y | 1.179 | 0.87 |
| 104_I | 132_F | 1.178 | 0.87 |
| 59_F | 269_H | 1.178 | 0.87 |
| 284_V | 309_T | 1.175 | 0.87 |
| 344_K | 399_H | 1.173 | 0.87 |
| 480_Q | 484_E | 1.173 | 0.87 |
| 356_G | 368_R | 1.173 | 0.87 |
| 41_I | 91_I | 1.166 | 0.87 |
| 322_S | 414_S | 1.165 | 0.87 |
| 236_E | 240_V | 1.162 | 0.86 |
| 43_D | 46_S | 1.161 | 0.86 |
| 229_Q | 232_L | 1.148 | 0.86 |
| 257_P | 369_Q | 1.147 | 0.85 |
| 8_V | 96_H | 1.143 | 0.85 |
| 428_F | 431_L | 1.137 | 0.85 |
| 436_L | 443_L | 1.135 | 0.85 |
| 283_S | 286_D | 1.134 | 0.85 |
| 109_D | 117_R | 1.128 | 0.84 |
| 361_P | 491_Y | 1.128 | 0.84 |
| 263_P | 375_W | 1.117 | 0.83 |
| 241_E | 429_E | 1.115 | 0.83 |
| 109_D | 271_R | 1.114 | 0.83 |
| 39_V | 95_L | 1.111 | 0.83 |
| 279_R | 283_S | 1.108 | 0.83 |
| 104_I | 130_I | 1.107 | 0.83 |
| 378_H | 438_T | 1.103 | 0.82 |
| 266_M | 275_L | 1.102 | 0.82 |
| 70_Q | 228_T | 1.098 | 0.82 |
| 422_W | 436_L | 1.093 | 0.81 |
| 387_F | 393_L | 1.090 | 0.81 |
| 385_A | 420_W | 1.081 | 0.80 |
| 408_L | 416_C | 1.081 | 0.80 |
| 485_C | 488_G | 1.078 | 0.80 |
| 408_L | 420_W | 1.068 | 0.79 |
| 379_T | 436_L | 1.066 | 0.79 |
| 140_L | 165_V | 1.065 | 0.79 |
| 161_F | 320_T | 1.065 | 0.79 |
| 360_F | 495_I | 1.064 | 0.79 |
| 438_T | 443_L | 1.064 | 0.79 |
| 245_F | 248_G | 1.064 | 0.79 |
| 103_R | 133_V | 1.058 | 0.78 |
| 454_I | 469_V | 1.057 | 0.78 |
| 311_Q | 378_H | 1.050 | 0.78 |
| 369_Q | 377_H | 1.050 | 0.78 |
| 383_T | 442_A | 1.049 | 0.78 |
| 390_R | 429_E | 1.048 | 0.78 |
| 61_L | 65_Q | 1.042 | 0.77 |
| 441_V | 451_G | 1.038 | 0.77 |
| 15_L | 81_L | 1.033 | 0.76 |
| 354_R | 406_K | 1.031 | 0.76 |
| 254_Q | 262_S | 1.028 | 0.76 |
| 451_G | 455_K | 1.026 | 0.75 |
| 491_Y | 494_R | 1.024 | 0.75 |
| 415_V | 419_N | 1.024 | 0.75 |
| 66_D | 274_C | 1.021 | 0.75 |
| 378_H | 390_R | 1.018 | 0.75 |
| 40_F | 64_L | 1.017 | 0.75 |
| 51_N | 402_Q | 1.017 | 0.75 |
| 454_I | 470_H | 1.014 | 0.74 |
| 71_L | 79_G | 1.014 | 0.74 |
| 264_K | 308_I | 1.014 | 0.74 |
| 507_L | 511_S | 1.012 | 0.74 |
| 18_H | 231_L | 1.012 | 0.74 |
| 25_A | 135_K | 1.012 | 0.74 |
| 310_G | 314_W | 1.011 | 0.74 |
| 268_A | 409_L | 1.007 | 0.73 |
| 318_F | 419_N | 1.006 | 0.73 |
| 487_I | 493_E | 1.005 | 0.73 |
| 13_H | 109_D | 1.005 | 0.73 |
| 337_C | 509_M | 1.004 | 0.73 |
| 395_Q | 399_H | 1.003 | 0.73 |
| 356_G | 458_V | 1.001 | 0.73 |
| 485_C | 490_H | 1.001 | 0.73 |
| 165_V | 313_I | 1.000 | 0.73 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4gu5A | 2 | 0.9742 | 100 | 0.132 | Contact Map |
| 4k0rA | 1 | 0.8506 | 100 | 0.186 | Contact Map |
| 3fy4A | 3 | 0.9262 | 100 | 0.191 | Contact Map |
| 4u63A | 1 | 0.8764 | 100 | 0.196 | Contact Map |
| 1u3dA | 1 | 0.8856 | 100 | 0.196 | Contact Map |
| 1np7A | 2 | 0.8708 | 100 | 0.2 | Contact Map |
| 4mlpC | 4 | 0.9041 | 100 | 0.202 | Contact Map |
| 1owlA | 1 | 0.8727 | 100 | 0.216 | Contact Map |
| 2wq7A | 1 | 0.9207 | 100 | 0.217 | Contact Map |
| 1dnpA | 2 | 0.8524 | 100 | 0.222 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)