| bhlh -force run |
| ID: | 1492179206 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 560 (529) | ||
| Sequences: | 204 (136.6) | ||
| Seq/Len: | 0.386 | ||
| Nf(neff/√len): | 5.9 |
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: 0.386).
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 |
| 393_R | 396_L | 2.300 | 0.90 |
| 403_L | 408_P | 2.236 | 0.89 |
| 386_V | 389_E | 2.002 | 0.80 |
| 393_R | 397_N | 1.956 | 0.78 |
| 386_V | 392_R | 1.904 | 0.75 |
| 88_R | 133_N | 1.817 | 0.70 |
| 385_H | 407_V | 1.787 | 0.68 |
| 396_L | 400_F | 1.771 | 0.67 |
| 394_E | 397_N | 1.766 | 0.67 |
| 30_W | 36_W | 1.673 | 0.61 |
| 170_S | 173_T | 1.656 | 0.60 |
| 390_R | 393_R | 1.650 | 0.59 |
| 32_Y | 36_W | 1.638 | 0.58 |
| 216_E | 223_S | 1.625 | 0.57 |
| 196_P | 402_V | 1.607 | 0.56 |
| 166_A | 436_L | 1.591 | 0.55 |
| 386_V | 390_R | 1.591 | 0.55 |
| 389_E | 394_E | 1.577 | 0.54 |
| 404_K | 421_E | 1.568 | 0.53 |
| 117_D | 124_I | 1.558 | 0.53 |
| 389_E | 393_R | 1.553 | 0.52 |
| 390_R | 396_L | 1.543 | 0.52 |
| 390_R | 412_K | 1.527 | 0.50 |
| 392_R | 396_L | 1.526 | 0.50 |
| 114_D | 194_E | 1.522 | 0.50 |
| 403_L | 407_V | 1.521 | 0.50 |
| 389_E | 392_R | 1.503 | 0.49 |
| 392_R | 400_F | 1.484 | 0.47 |
| 173_T | 177_I | 1.482 | 0.47 |
| 491_V | 527_G | 1.468 | 0.46 |
| 121_Y | 486_M | 1.461 | 0.46 |
| 148_W | 162_R | 1.434 | 0.44 |
| 520_S | 532_L | 1.434 | 0.44 |
| 196_P | 208_E | 1.428 | 0.43 |
| 212_P | 215_L | 1.421 | 0.43 |
| 389_E | 396_L | 1.396 | 0.41 |
| 386_V | 395_K | 1.393 | 0.41 |
| 149_L | 152_A | 1.390 | 0.41 |
| 395_K | 399_M | 1.386 | 0.40 |
| 397_N | 400_F | 1.377 | 0.40 |
| 392_R | 412_K | 1.376 | 0.40 |
| 158_R | 166_A | 1.374 | 0.40 |
| 402_V | 507_V | 1.368 | 0.39 |
| 366_A | 434_D | 1.363 | 0.39 |
| 549_P | 554_E | 1.356 | 0.38 |
| 45_G | 147_V | 1.350 | 0.38 |
| 58_N | 63_T | 1.350 | 0.38 |
| 407_V | 492_L | 1.350 | 0.38 |
| 105_R | 436_L | 1.346 | 0.38 |
| 93_S | 461_K | 1.345 | 0.38 |
| 395_K | 400_F | 1.328 | 0.36 |
| 389_E | 397_N | 1.321 | 0.36 |
| 384_T | 407_V | 1.321 | 0.36 |
| 435_Q | 559_A | 1.320 | 0.36 |
| 386_V | 393_R | 1.313 | 0.36 |
| 171_I | 177_I | 1.302 | 0.35 |
| 260_P | 263_V | 1.300 | 0.35 |
| 84_S | 105_R | 1.295 | 0.34 |
| 389_E | 417_S | 1.292 | 0.34 |
| 386_V | 408_P | 1.283 | 0.34 |
| 384_T | 412_K | 1.282 | 0.33 |
| 392_R | 395_K | 1.277 | 0.33 |
| 110_L | 195_D | 1.277 | 0.33 |
| 393_R | 400_F | 1.272 | 0.33 |
| 148_W | 166_A | 1.270 | 0.33 |
| 359_V | 364_A | 1.269 | 0.33 |
| 122_Y | 440_R | 1.261 | 0.32 |
| 192_V | 559_A | 1.257 | 0.32 |
| 390_R | 397_N | 1.256 | 0.32 |
| 40_A | 490_V | 1.254 | 0.32 |
| 396_L | 412_K | 1.253 | 0.32 |
| 212_P | 484_V | 1.252 | 0.32 |
| 118_G | 365_W | 1.252 | 0.32 |
| 97_G | 432_R | 1.247 | 0.31 |
| 61_I | 68_G | 1.247 | 0.31 |
| 396_L | 410_I | 1.246 | 0.31 |
| 57_Y | 65_K | 1.246 | 0.31 |
| 294_D | 302_S | 1.245 | 0.31 |
| 157_T | 469_K | 1.245 | 0.31 |
| 55_G | 59_G | 1.242 | 0.31 |
| 38_I | 44_P | 1.240 | 0.31 |
| 208_E | 515_C | 1.235 | 0.31 |
| 390_R | 395_K | 1.232 | 0.30 |
| 32_Y | 50_L | 1.232 | 0.30 |
| 24_A | 184_L | 1.229 | 0.30 |
| 152_A | 166_A | 1.228 | 0.30 |
| 281_G | 295_E | 1.220 | 0.30 |
| 389_E | 502_L | 1.220 | 0.30 |
| 364_A | 406_L | 1.219 | 0.30 |
| 386_V | 396_L | 1.217 | 0.29 |
| 128_Y | 523_A | 1.211 | 0.29 |
| 385_H | 389_E | 1.207 | 0.29 |
| 511_I | 538_Q | 1.207 | 0.29 |
| 356_L | 530_L | 1.206 | 0.29 |
| 392_R | 408_P | 1.206 | 0.29 |
| 201_R | 248_E | 1.204 | 0.29 |
| 137_P | 166_A | 1.200 | 0.28 |
| 384_T | 397_N | 1.199 | 0.28 |
| 218_K | 553_T | 1.197 | 0.28 |
| 396_L | 408_P | 1.197 | 0.28 |
| 93_S | 202_I | 1.197 | 0.28 |
| 138_G | 148_W | 1.196 | 0.28 |
| 411_H | 421_E | 1.193 | 0.28 |
| 138_G | 162_R | 1.191 | 0.28 |
| 104_R | 530_L | 1.190 | 0.28 |
| 36_W | 55_G | 1.190 | 0.28 |
| 392_R | 403_L | 1.190 | 0.28 |
| 103_A | 404_K | 1.188 | 0.28 |
| 405_S | 408_P | 1.182 | 0.27 |
| 45_G | 198_M | 1.180 | 0.27 |
| 404_K | 408_P | 1.177 | 0.27 |
| 385_H | 396_L | 1.177 | 0.27 |
| 406_L | 536_A | 1.176 | 0.27 |
| 394_E | 400_F | 1.175 | 0.27 |
| 206_F | 395_K | 1.170 | 0.27 |
| 307_P | 410_I | 1.169 | 0.27 |
| 61_I | 125_S | 1.169 | 0.27 |
| 23_A | 416_A | 1.167 | 0.27 |
| 137_P | 187_G | 1.164 | 0.26 |
| 359_V | 477_S | 1.162 | 0.26 |
| 403_L | 412_K | 1.161 | 0.26 |
| 383_N | 422_T | 1.160 | 0.26 |
| 385_H | 392_R | 1.160 | 0.26 |
| 384_T | 402_V | 1.159 | 0.26 |
| 389_E | 400_F | 1.158 | 0.26 |
| 27_S | 201_R | 1.156 | 0.26 |
| 386_V | 394_E | 1.150 | 0.26 |
| 392_R | 397_N | 1.150 | 0.26 |
| 116_G | 386_V | 1.148 | 0.26 |
| 464_V | 518_V | 1.148 | 0.26 |
| 313_S | 533_K | 1.148 | 0.26 |
| 50_L | 57_Y | 1.145 | 0.25 |
| 408_P | 412_K | 1.145 | 0.25 |
| 549_P | 552_I | 1.144 | 0.25 |
| 34_I | 39_S | 1.143 | 0.25 |
| 383_N | 421_E | 1.143 | 0.25 |
| 190_D | 242_D | 1.139 | 0.25 |
| 389_E | 395_K | 1.139 | 0.25 |
| 362_G | 375_V | 1.139 | 0.25 |
| 135_G | 417_S | 1.137 | 0.25 |
| 89_E | 405_S | 1.137 | 0.25 |
| 43_R | 528_G | 1.133 | 0.25 |
| 30_W | 55_G | 1.133 | 0.25 |
| 30_W | 45_G | 1.132 | 0.25 |
| 204_T | 448_T | 1.128 | 0.24 |
| 149_L | 160_F | 1.125 | 0.24 |
| 211_L | 506_Q | 1.124 | 0.24 |
| 162_R | 166_A | 1.124 | 0.24 |
| 352_S | 448_T | 1.124 | 0.24 |
| 84_S | 114_D | 1.122 | 0.24 |
| 325_E | 328_R | 1.122 | 0.24 |
| 280_G | 427_R | 1.121 | 0.24 |
| 110_L | 332_F | 1.121 | 0.24 |
| 239_E | 435_Q | 1.120 | 0.24 |
| 495_V | 530_L | 1.120 | 0.24 |
| 517_D | 527_G | 1.119 | 0.24 |
| 389_E | 412_K | 1.118 | 0.24 |
| 54_D | 433_V | 1.116 | 0.24 |
| 140_S | 144_N | 1.115 | 0.24 |
| 280_G | 432_R | 1.115 | 0.24 |
| 30_W | 54_D | 1.114 | 0.24 |
| 112_P | 353_Q | 1.113 | 0.24 |
| 190_D | 488_D | 1.110 | 0.23 |
| 104_R | 330_S | 1.107 | 0.23 |
| 244_N | 507_V | 1.103 | 0.23 |
| 186_L | 355_L | 1.103 | 0.23 |
| 249_G | 490_V | 1.102 | 0.23 |
| 466_A | 527_G | 1.102 | 0.23 |
| 153_Q | 430_K | 1.102 | 0.23 |
| 413_V | 426_L | 1.100 | 0.23 |
| 384_T | 400_F | 1.098 | 0.23 |
| 32_Y | 55_G | 1.097 | 0.23 |
| 108_A | 350_G | 1.097 | 0.23 |
| 137_P | 148_W | 1.095 | 0.23 |
| 22_A | 26_R | 1.093 | 0.23 |
| 50_L | 55_G | 1.092 | 0.23 |
| 93_S | 330_S | 1.091 | 0.23 |
| 36_W | 59_G | 1.090 | 0.22 |
| 140_S | 153_Q | 1.087 | 0.22 |
| 393_R | 398_E | 1.086 | 0.22 |
| 184_L | 495_V | 1.086 | 0.22 |
| 434_D | 476_E | 1.085 | 0.22 |
| 95_L | 369_Y | 1.080 | 0.22 |
| 436_L | 497_C | 1.079 | 0.22 |
| 153_Q | 483_N | 1.078 | 0.22 |
| 200_K | 204_T | 1.078 | 0.22 |
| 82_H | 463_I | 1.077 | 0.22 |
| 58_N | 64_R | 1.074 | 0.22 |
| 373_T | 376_R | 1.073 | 0.22 |
| 396_L | 422_T | 1.071 | 0.22 |
| 494_E | 530_L | 1.070 | 0.21 |
| 83_R | 90_L | 1.069 | 0.21 |
| 93_S | 109_S | 1.063 | 0.21 |
| 209_L | 432_R | 1.063 | 0.21 |
| 358_K | 543_G | 1.062 | 0.21 |
| 25_V | 128_Y | 1.062 | 0.21 |
| 58_N | 62_K | 1.062 | 0.21 |
| 86_Q | 105_R | 1.061 | 0.21 |
| 295_E | 524_S | 1.059 | 0.21 |
| 161_P | 459_A | 1.057 | 0.21 |
| 384_T | 390_R | 1.057 | 0.21 |
| 165_L | 194_E | 1.054 | 0.21 |
| 432_R | 443_S | 1.054 | 0.21 |
| 66_I | 316_D | 1.054 | 0.21 |
| 61_I | 64_R | 1.052 | 0.21 |
| 202_I | 293_M | 1.052 | 0.21 |
| 148_W | 160_F | 1.050 | 0.21 |
| 183_V | 186_L | 1.050 | 0.21 |
| 384_T | 393_R | 1.050 | 0.21 |
| 154_Y | 532_L | 1.049 | 0.20 |
| 418_I | 535_R | 1.049 | 0.20 |
| 541_A | 546_M | 1.049 | 0.20 |
| 511_I | 551_A | 1.049 | 0.20 |
| 407_V | 414_D | 1.047 | 0.20 |
| 385_H | 403_L | 1.046 | 0.20 |
| 54_D | 139_K | 1.046 | 0.20 |
| 554_E | 559_A | 1.046 | 0.20 |
| 168_T | 173_T | 1.046 | 0.20 |
| 279_L | 517_D | 1.045 | 0.20 |
| 89_E | 386_V | 1.043 | 0.20 |
| 398_E | 406_L | 1.042 | 0.20 |
| 138_G | 187_G | 1.041 | 0.20 |
| 105_R | 115_L | 1.041 | 0.20 |
| 346_G | 512_K | 1.040 | 0.20 |
| 390_R | 408_P | 1.040 | 0.20 |
| 53_K | 205_S | 1.039 | 0.20 |
| 430_K | 550_G | 1.039 | 0.20 |
| 117_D | 358_K | 1.038 | 0.20 |
| 384_T | 395_K | 1.038 | 0.20 |
| 112_P | 149_L | 1.036 | 0.20 |
| 544_S | 559_A | 1.035 | 0.20 |
| 126_M | 358_K | 1.035 | 0.20 |
| 151_N | 155_A | 1.034 | 0.20 |
| 45_G | 93_S | 1.032 | 0.20 |
| 160_F | 166_A | 1.031 | 0.20 |
| 30_W | 59_G | 1.031 | 0.20 |
| 384_T | 389_E | 1.031 | 0.20 |
| 143_S | 467_G | 1.031 | 0.20 |
| 33_G | 202_I | 1.030 | 0.20 |
| 58_N | 112_P | 1.027 | 0.19 |
| 396_L | 404_K | 1.027 | 0.19 |
| 141_F | 481_V | 1.026 | 0.19 |
| 402_V | 538_Q | 1.026 | 0.19 |
| 122_Y | 404_K | 1.023 | 0.19 |
| 130_F | 206_F | 1.022 | 0.19 |
| 286_P | 396_L | 1.022 | 0.19 |
| 331_C | 391_R | 1.021 | 0.19 |
| 418_I | 492_L | 1.020 | 0.19 |
| 149_L | 158_R | 1.018 | 0.19 |
| 34_I | 117_D | 1.017 | 0.19 |
| 78_E | 397_N | 1.017 | 0.19 |
| 112_P | 335_W | 1.016 | 0.19 |
| 110_L | 335_W | 1.016 | 0.19 |
| 183_V | 187_G | 1.016 | 0.19 |
| 390_R | 417_S | 1.016 | 0.19 |
| 153_Q | 164_L | 1.015 | 0.19 |
| 396_L | 403_L | 1.015 | 0.19 |
| 332_F | 353_Q | 1.014 | 0.19 |
| 413_V | 422_T | 1.014 | 0.19 |
| 394_E | 403_L | 1.013 | 0.19 |
| 87_L | 90_L | 1.013 | 0.19 |
| 221_S | 524_S | 1.012 | 0.19 |
| 356_L | 492_L | 1.010 | 0.19 |
| 388_T | 422_T | 1.010 | 0.19 |
| 385_H | 400_F | 1.009 | 0.19 |
| 395_K | 413_V | 1.009 | 0.19 |
| 186_L | 369_Y | 1.008 | 0.19 |
| 212_P | 220_P | 1.008 | 0.19 |
| 394_E | 408_P | 1.007 | 0.19 |
| 22_A | 31_T | 1.007 | 0.19 |
| 190_D | 201_R | 1.007 | 0.19 |
| 404_K | 407_V | 1.006 | 0.19 |
| 164_L | 497_C | 1.006 | 0.19 |
| 400_F | 536_A | 1.003 | 0.18 |
| 35_F | 95_L | 1.003 | 0.18 |
| 315_D | 503_L | 1.003 | 0.18 |
| 427_R | 432_R | 1.002 | 0.18 |
| 552_I | 556_L | 1.001 | 0.18 |
| 397_N | 412_K | 1.001 | 0.18 |
| 210_H | 512_K | 1.000 | 0.18 |
| 385_H | 410_I | 1.000 | 0.18 |
| 36_W | 39_S | 1.000 | 0.18 |
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 | |
| 4ywcA | 2 | 0 | 100 | 0.753 | Contact Map |
| 4yz6A | 1 | 0 | 100 | 0.755 | Contact Map |
| 1nlwA | 2 | 0.1357 | 99.5 | 0.934 | Contact Map |
| 1am9A | 4 | 0.1446 | 99.4 | 0.935 | Contact Map |
| 1nkpB | 2 | 0.1446 | 99.4 | 0.935 | Contact Map |
| 2mh3A | 2 | 0.1107 | 99.4 | 0.935 | Contact Map |
| 1hloA | 2 | 0.1393 | 99.4 | 0.936 | Contact Map |
| 1nkpA | 2 | 0.1518 | 99.4 | 0.937 | Contact Map |
| 4atiA | 2 | 0.1143 | 99.4 | 0.937 | Contact Map |
| 4h10B | 1 | 0.1107 | 99.4 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)