| carinaclean |
| ID: | 1462277394 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (454) | ||
| Sequences: | 2112 (1065.1) | ||
| Seq/Len: | 4.652 | ||
| Nf(neff/√len): | 50.0 |
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: 4.652).
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 |
| 160_A | 172_L | 3.912 | 1.00 |
| 43_D | 294_R | 3.837 | 1.00 |
| 87_L | 108_I | 3.645 | 1.00 |
| 91_V | 108_I | 3.415 | 1.00 |
| 67_L | 71_L | 3.136 | 1.00 |
| 33_L | 289_S | 2.967 | 1.00 |
| 139_F | 400_T | 2.886 | 1.00 |
| 350_L | 460_A | 2.812 | 1.00 |
| 472_L | 476_P | 2.678 | 1.00 |
| 85_M | 116_F | 2.582 | 1.00 |
| 353_A | 458_C | 2.562 | 1.00 |
| 50_F | 285_G | 2.528 | 1.00 |
| 90_V | 174_G | 2.471 | 1.00 |
| 37_H | 166_W | 2.435 | 1.00 |
| 158_G | 308_A | 2.425 | 1.00 |
| 286_S | 428_A | 2.339 | 1.00 |
| 274_G | 416_T | 2.291 | 1.00 |
| 161_A | 308_A | 2.273 | 1.00 |
| 317_A | 382_A | 2.257 | 1.00 |
| 316_I | 320_L | 2.240 | 1.00 |
| 263_A | 482_E | 2.230 | 1.00 |
| 397_A | 401_R | 2.193 | 1.00 |
| 355_G | 384_M | 2.172 | 1.00 |
| 121_S | 414_L | 2.155 | 1.00 |
| 354_C | 383_L | 2.141 | 1.00 |
| 324_V | 328_L | 2.137 | 1.00 |
| 262_R | 481_Q | 2.110 | 1.00 |
| 158_G | 309_L | 2.063 | 1.00 |
| 156_A | 172_L | 2.058 | 1.00 |
| 351_L | 386_F | 2.036 | 1.00 |
| 192_Q | 196_S | 2.029 | 1.00 |
| 23_S | 89_H | 2.008 | 1.00 |
| 292_I | 377_M | 2.003 | 1.00 |
| 165_G | 168_V | 1.998 | 1.00 |
| 162_Q | 307_T | 1.965 | 1.00 |
| 86_T | 178_F | 1.960 | 1.00 |
| 346_A | 460_A | 1.947 | 1.00 |
| 314_N | 318_V | 1.931 | 1.00 |
| 24_F | 54_A | 1.913 | 1.00 |
| 314_N | 385_G | 1.870 | 1.00 |
| 395_A | 412_Y | 1.849 | 1.00 |
| 358_L | 383_L | 1.817 | 1.00 |
| 317_A | 378_I | 1.814 | 1.00 |
| 358_L | 379_S | 1.811 | 1.00 |
| 254_M | 264_L | 1.800 | 1.00 |
| 32_I | 46_A | 1.797 | 1.00 |
| 313_V | 378_I | 1.778 | 1.00 |
| 151_I | 316_I | 1.758 | 1.00 |
| 28_R | 50_F | 1.753 | 1.00 |
| 28_R | 282_Q | 1.752 | 1.00 |
| 296_V | 377_M | 1.747 | 1.00 |
| 85_M | 113_Y | 1.746 | 1.00 |
| 155_I | 309_L | 1.711 | 0.99 |
| 298_R | 304_E | 1.681 | 0.99 |
| 460_A | 465_L | 1.681 | 0.99 |
| 72_L | 77_A | 1.671 | 0.99 |
| 162_Q | 308_A | 1.666 | 0.99 |
| 146_G | 414_L | 1.654 | 0.99 |
| 87_L | 91_V | 1.652 | 0.99 |
| 37_H | 293_D | 1.650 | 0.99 |
| 90_V | 178_F | 1.624 | 0.99 |
| 42_D | 45_H | 1.621 | 0.99 |
| 2_K | 5_S | 1.611 | 0.99 |
| 480_I | 483_S | 1.609 | 0.99 |
| 278_W | 392_D | 1.593 | 0.99 |
| 6_Q | 10_I | 1.591 | 0.99 |
| 89_H | 167_H | 1.588 | 0.99 |
| 136_D | 397_A | 1.572 | 0.99 |
| 150_S | 315_A | 1.568 | 0.99 |
| 311_Q | 315_A | 1.557 | 0.99 |
| 17_Q | 21_Y | 1.548 | 0.99 |
| 321_A | 386_F | 1.547 | 0.99 |
| 151_I | 319_M | 1.541 | 0.99 |
| 84_L | 111_C | 1.535 | 0.99 |
| 144_A | 322_G | 1.521 | 0.98 |
| 472_L | 477_T | 1.516 | 0.98 |
| 35_L | 102_L | 1.515 | 0.98 |
| 350_L | 465_L | 1.512 | 0.98 |
| 121_S | 409_T | 1.500 | 0.98 |
| 320_L | 324_V | 1.499 | 0.98 |
| 306_P | 309_L | 1.476 | 0.98 |
| 146_G | 396_I | 1.458 | 0.98 |
| 83_L | 87_L | 1.456 | 0.98 |
| 67_L | 72_L | 1.450 | 0.98 |
| 52_A | 422_W | 1.443 | 0.98 |
| 324_V | 327_W | 1.416 | 0.97 |
| 14_V | 145_A | 1.411 | 0.97 |
| 343_L | 465_L | 1.407 | 0.97 |
| 325_L | 386_F | 1.406 | 0.97 |
| 359_L | 362_D | 1.403 | 0.97 |
| 56_L | 110_I | 1.398 | 0.97 |
| 259_E | 262_R | 1.396 | 0.97 |
| 281_A | 385_G | 1.394 | 0.97 |
| 55_S | 422_W | 1.382 | 0.97 |
| 33_L | 307_T | 1.368 | 0.96 |
| 2_K | 8_R | 1.363 | 0.96 |
| 193_S | 198_D | 1.351 | 0.96 |
| 32_I | 290_L | 1.350 | 0.96 |
| 330_S | 334_R | 1.350 | 0.96 |
| 113_Y | 116_F | 1.344 | 0.96 |
| 23_S | 53_Y | 1.338 | 0.96 |
| 6_Q | 128_Y | 1.332 | 0.96 |
| 124_L | 127_L | 1.322 | 0.95 |
| 30_L | 169_G | 1.321 | 0.95 |
| 461_I | 466_A | 1.318 | 0.95 |
| 322_G | 326_A | 1.318 | 0.95 |
| 53_Y | 89_H | 1.317 | 0.95 |
| 353_A | 460_A | 1.313 | 0.95 |
| 21_Y | 117_K | 1.305 | 0.95 |
| 48_S | 429_Q | 1.302 | 0.95 |
| 347_F | 351_L | 1.300 | 0.95 |
| 346_A | 465_L | 1.293 | 0.95 |
| 91_V | 105_A | 1.270 | 0.94 |
| 266_Q | 477_T | 1.266 | 0.94 |
| 276_L | 459_V | 1.264 | 0.94 |
| 26_G | 157_C | 1.256 | 0.93 |
| 178_F | 182_L | 1.252 | 0.93 |
| 331_P | 335_G | 1.244 | 0.93 |
| 299_Q | 304_E | 1.236 | 0.93 |
| 291_F | 372_A | 1.235 | 0.93 |
| 161_A | 165_G | 1.234 | 0.93 |
| 19_W | 176_G | 1.233 | 0.93 |
| 47_I | 290_L | 1.230 | 0.92 |
| 279_V | 420_A | 1.230 | 0.92 |
| 284_G | 384_M | 1.229 | 0.92 |
| 347_F | 390_F | 1.227 | 0.92 |
| 378_I | 382_A | 1.226 | 0.92 |
| 298_R | 307_T | 1.222 | 0.92 |
| 467_F | 472_L | 1.222 | 0.92 |
| 20_E | 117_K | 1.218 | 0.92 |
| 136_D | 401_R | 1.217 | 0.92 |
| 171_A | 175_G | 1.216 | 0.92 |
| 375_G | 379_S | 1.212 | 0.92 |
| 321_A | 382_A | 1.208 | 0.92 |
| 348_G | 352_M | 1.204 | 0.91 |
| 89_H | 169_G | 1.204 | 0.91 |
| 49_L | 103_Y | 1.202 | 0.91 |
| 67_L | 77_A | 1.193 | 0.91 |
| 18_I | 145_A | 1.192 | 0.91 |
| 92_L | 105_A | 1.191 | 0.91 |
| 37_H | 162_Q | 1.189 | 0.91 |
| 274_G | 412_Y | 1.183 | 0.90 |
| 7_P | 10_I | 1.180 | 0.90 |
| 179_I | 183_I | 1.178 | 0.90 |
| 281_A | 284_G | 1.175 | 0.90 |
| 66_W | 407_V | 1.171 | 0.90 |
| 281_A | 314_N | 1.164 | 0.89 |
| 47_I | 286_S | 1.164 | 0.89 |
| 292_I | 296_V | 1.158 | 0.89 |
| 103_Y | 153_A | 1.149 | 0.89 |
| 60_T | 110_I | 1.133 | 0.88 |
| 32_I | 36_T | 1.127 | 0.87 |
| 161_A | 168_V | 1.127 | 0.87 |
| 36_T | 290_L | 1.125 | 0.87 |
| 24_F | 28_R | 1.120 | 0.87 |
| 287_T | 428_A | 1.113 | 0.86 |
| 144_A | 148_I | 1.111 | 0.86 |
| 348_G | 391_I | 1.110 | 0.86 |
| 452_G | 458_C | 1.099 | 0.86 |
| 345_F | 348_G | 1.094 | 0.85 |
| 93_G | 171_A | 1.087 | 0.85 |
| 86_T | 174_G | 1.085 | 0.85 |
| 151_I | 312_S | 1.083 | 0.84 |
| 75_R | 198_D | 1.083 | 0.84 |
| 402_L | 480_I | 1.083 | 0.84 |
| 454_W | 476_P | 1.082 | 0.84 |
| 267_I | 399_I | 1.080 | 0.84 |
| 51_S | 55_S | 1.078 | 0.84 |
| 179_I | 182_L | 1.078 | 0.84 |
| 373_S | 376_V | 1.077 | 0.84 |
| 278_W | 393_P | 1.074 | 0.84 |
| 14_V | 392_D | 1.069 | 0.83 |
| 385_G | 389_L | 1.068 | 0.83 |
| 135_R | 400_T | 1.067 | 0.83 |
| 273_V | 464_V | 1.067 | 0.83 |
| 401_R | 483_S | 1.067 | 0.83 |
| 283_Q | 287_T | 1.064 | 0.83 |
| 288_I | 296_V | 1.063 | 0.83 |
| 351_L | 387_A | 1.057 | 0.82 |
| 382_A | 386_F | 1.055 | 0.82 |
| 100_F | 104_L | 1.053 | 0.82 |
| 80_A | 83_L | 1.045 | 0.81 |
| 392_D | 396_I | 1.044 | 0.81 |
| 284_G | 381_L | 1.043 | 0.81 |
| 41_F | 99_T | 1.042 | 0.81 |
| 120_I | 142_L | 1.042 | 0.81 |
| 379_S | 382_A | 1.040 | 0.81 |
| 357_M | 452_G | 1.039 | 0.81 |
| 30_L | 157_C | 1.034 | 0.80 |
| 144_A | 319_M | 1.034 | 0.80 |
| 321_A | 351_L | 1.033 | 0.80 |
| 313_V | 317_A | 1.032 | 0.80 |
| 275_T | 423_L | 1.028 | 0.80 |
| 32_I | 289_S | 1.026 | 0.80 |
| 124_L | 191_F | 1.020 | 0.79 |
| 73_G | 76_T | 1.017 | 0.79 |
| 89_H | 171_A | 1.014 | 0.79 |
| 86_T | 90_V | 1.011 | 0.78 |
| 8_R | 11_Y | 1.009 | 0.78 |
| 446_R | 449_S | 1.009 | 0.78 |
| 140_S | 329_A | 1.007 | 0.78 |
| 303_I | 309_L | 1.005 | 0.78 |
| 65_G | 410_G | 1.002 | 0.77 |
| 311_Q | 314_N | 1.001 | 0.77 |
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 | |
| 4uvmA | 1 | 0.9526 | 100 | 0.673 | Contact Map |
| 4q65A | 1 | 0.8887 | 100 | 0.673 | Contact Map |
| 4oh3A | 2 | 0.9134 | 100 | 0.683 | Contact Map |
| 4tphA | 2 | 0.8907 | 100 | 0.723 | Contact Map |
| 4ikvA | 1 | 0.932 | 100 | 0.725 | Contact Map |
| 4xnjA | 1 | 0 | 100 | 0.742 | Contact Map |
| 4w6vA | 1 | 0 | 100 | 0.805 | Contact Map |
| 3wdoA | 1 | 0.8021 | 99.9 | 0.833 | Contact Map |
| 2cfqA | 1 | 0.8268 | 99.9 | 0.833 | Contact Map |
| 2gfpA | 2 | 0.7691 | 99.9 | 0.844 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)