| VC0032 |
| ID: | 1403874151 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 507 (496) | ||
| Sequences: | 1413 (1013.9) | ||
| Seq/Len: | 2.849 | ||
| Nf(neff/√len): | 45.5 |
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: 2.849).
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 |
| 191_L | 407_V | 5.026 | 1.00 |
| 205_E | 410_R | 4.044 | 1.00 |
| 478_E | 485_H | 3.657 | 1.00 |
| 23_V | 88_G | 3.632 | 1.00 |
| 116_I | 157_A | 3.600 | 1.00 |
| 202_R | 488_E | 3.523 | 1.00 |
| 402_E | 410_R | 3.405 | 1.00 |
| 246_T | 296_N | 3.403 | 1.00 |
| 322_G | 338_R | 3.194 | 1.00 |
| 32_F | 67_V | 3.193 | 1.00 |
| 441_L | 444_D | 3.182 | 1.00 |
| 205_E | 402_E | 3.112 | 1.00 |
| 206_I | 472_I | 3.000 | 1.00 |
| 402_E | 407_V | 2.967 | 1.00 |
| 205_E | 407_V | 2.964 | 1.00 |
| 157_A | 163_V | 2.926 | 1.00 |
| 226_M | 230_R | 2.829 | 1.00 |
| 268_R | 290_E | 2.823 | 1.00 |
| 126_A | 136_L | 2.688 | 1.00 |
| 348_S | 360_A | 2.665 | 1.00 |
| 135_C | 153_R | 2.595 | 1.00 |
| 407_V | 410_R | 2.584 | 1.00 |
| 304_M | 343_G | 2.547 | 1.00 |
| 106_F | 137_V | 2.520 | 1.00 |
| 140_H | 158_Q | 2.498 | 1.00 |
| 323_E | 334_R | 2.482 | 1.00 |
| 234_L | 404_T | 2.409 | 1.00 |
| 193_D | 230_R | 2.407 | 1.00 |
| 279_L | 311_V | 2.364 | 1.00 |
| 382_M | 468_V | 2.337 | 1.00 |
| 87_L | 106_F | 2.317 | 1.00 |
| 242_E | 265_R | 2.294 | 1.00 |
| 414_A | 475_L | 2.268 | 1.00 |
| 209_A | 475_L | 2.249 | 1.00 |
| 158_Q | 162_E | 2.245 | 1.00 |
| 204_L | 227_L | 2.237 | 1.00 |
| 91_A | 101_L | 2.225 | 1.00 |
| 211_N | 427_A | 2.196 | 1.00 |
| 247_A | 262_W | 2.191 | 1.00 |
| 24_H | 55_N | 2.191 | 1.00 |
| 274_S | 278_A | 2.183 | 1.00 |
| 296_N | 428_L | 2.174 | 1.00 |
| 194_I | 230_R | 2.142 | 1.00 |
| 403_S | 406_A | 2.138 | 1.00 |
| 214_L | 342_V | 2.116 | 1.00 |
| 434_I | 467_K | 2.115 | 1.00 |
| 206_I | 382_M | 2.114 | 1.00 |
| 444_D | 486_L | 2.108 | 1.00 |
| 231_L | 342_V | 2.105 | 1.00 |
| 237_E | 412_W | 2.102 | 1.00 |
| 108_G | 139_P | 2.060 | 1.00 |
| 476_Q | 485_H | 2.031 | 1.00 |
| 435_E | 463_H | 2.012 | 1.00 |
| 312_L | 376_L | 2.002 | 1.00 |
| 273_S | 314_S | 1.991 | 1.00 |
| 350_T | 360_A | 1.989 | 1.00 |
| 104_Y | 135_C | 1.981 | 1.00 |
| 204_L | 231_L | 1.962 | 0.99 |
| 126_A | 152_E | 1.940 | 0.99 |
| 438_C | 481_I | 1.908 | 0.99 |
| 209_A | 414_A | 1.898 | 0.99 |
| 355_G | 388_A | 1.887 | 0.99 |
| 361_N | 364_S | 1.869 | 0.99 |
| 286_P | 335_F | 1.859 | 0.99 |
| 478_E | 482_A | 1.808 | 0.99 |
| 451_A | 490_L | 1.808 | 0.99 |
| 422_S | 429_L | 1.805 | 0.99 |
| 9_R | 105_E | 1.801 | 0.99 |
| 274_S | 279_L | 1.789 | 0.99 |
| 7_H | 18_P | 1.784 | 0.99 |
| 408_R | 412_W | 1.742 | 0.98 |
| 229_S | 321_S | 1.733 | 0.98 |
| 233_D | 404_T | 1.709 | 0.98 |
| 208_A | 231_L | 1.705 | 0.98 |
| 137_V | 163_V | 1.664 | 0.98 |
| 53_I | 60_F | 1.664 | 0.98 |
| 280_V | 291_I | 1.655 | 0.98 |
| 211_N | 425_V | 1.653 | 0.98 |
| 21_V | 84_P | 1.629 | 0.97 |
| 10_A | 81_F | 1.616 | 0.97 |
| 465_I | 490_L | 1.607 | 0.97 |
| 238_M | 265_R | 1.579 | 0.97 |
| 300_F | 344_A | 1.560 | 0.96 |
| 238_M | 246_T | 1.551 | 0.96 |
| 200_G | 227_L | 1.547 | 0.96 |
| 107_I | 125_A | 1.544 | 0.96 |
| 389_L | 393_T | 1.538 | 0.96 |
| 208_A | 235_L | 1.526 | 0.96 |
| 128_A | 131_Q | 1.512 | 0.95 |
| 189_R | 233_D | 1.482 | 0.95 |
| 308_E | 311_V | 1.474 | 0.95 |
| 440_L | 444_D | 1.471 | 0.95 |
| 40_T | 43_K | 1.467 | 0.94 |
| 304_M | 312_L | 1.463 | 0.94 |
| 392_G | 449_E | 1.453 | 0.94 |
| 305_P | 345_L | 1.448 | 0.94 |
| 143_G | 156_S | 1.446 | 0.94 |
| 405_A | 409_Q | 1.444 | 0.94 |
| 8_S | 81_F | 1.436 | 0.94 |
| 476_Q | 484_P | 1.425 | 0.93 |
| 424_K | 433_E | 1.421 | 0.93 |
| 191_L | 214_L | 1.406 | 0.93 |
| 91_A | 96_I | 1.402 | 0.92 |
| 159_S | 162_E | 1.402 | 0.92 |
| 430_Q | 433_E | 1.399 | 0.92 |
| 225_T | 321_S | 1.397 | 0.92 |
| 87_L | 163_V | 1.381 | 0.92 |
| 204_L | 214_L | 1.369 | 0.91 |
| 193_D | 226_M | 1.366 | 0.91 |
| 24_H | 54_I | 1.361 | 0.91 |
| 17_P | 74_L | 1.358 | 0.91 |
| 81_F | 292_S | 1.352 | 0.91 |
| 116_I | 163_V | 1.350 | 0.90 |
| 216_F | 382_M | 1.342 | 0.90 |
| 130_N | 151_V | 1.336 | 0.90 |
| 488_E | 492_Y | 1.335 | 0.90 |
| 447_F | 487_A | 1.323 | 0.89 |
| 406_A | 409_Q | 1.322 | 0.89 |
| 104_Y | 137_V | 1.320 | 0.89 |
| 9_R | 125_A | 1.311 | 0.89 |
| 235_L | 298_L | 1.309 | 0.89 |
| 143_G | 147_A | 1.308 | 0.89 |
| 156_S | 173_L | 1.306 | 0.88 |
| 390_P | 393_T | 1.297 | 0.88 |
| 304_M | 376_L | 1.296 | 0.88 |
| 191_L | 234_L | 1.294 | 0.88 |
| 106_F | 163_V | 1.280 | 0.87 |
| 268_R | 293_L | 1.267 | 0.86 |
| 122_V | 126_A | 1.266 | 0.86 |
| 201_K | 402_E | 1.264 | 0.86 |
| 313_D | 373_S | 1.258 | 0.86 |
| 53_I | 56_S | 1.255 | 0.86 |
| 309_R | 313_D | 1.253 | 0.86 |
| 155_K | 166_D | 1.253 | 0.86 |
| 86_A | 160_L | 1.242 | 0.85 |
| 2_G | 423_G | 1.241 | 0.85 |
| 243_A | 262_W | 1.240 | 0.85 |
| 53_I | 160_L | 1.238 | 0.85 |
| 122_V | 138_V | 1.237 | 0.85 |
| 225_T | 229_S | 1.234 | 0.84 |
| 34_L | 85_I | 1.232 | 0.84 |
| 429_L | 467_K | 1.230 | 0.84 |
| 273_S | 277_A | 1.222 | 0.84 |
| 143_G | 154_H | 1.218 | 0.83 |
| 291_I | 324_I | 1.217 | 0.83 |
| 380_F | 383_S | 1.217 | 0.83 |
| 280_V | 324_I | 1.211 | 0.83 |
| 470_R | 481_I | 1.207 | 0.83 |
| 239_S | 242_E | 1.207 | 0.83 |
| 165_A | 170_Q | 1.194 | 0.82 |
| 350_T | 354_E | 1.183 | 0.81 |
| 215_L | 345_L | 1.180 | 0.81 |
| 431_S | 434_I | 1.179 | 0.80 |
| 198_Q | 201_K | 1.175 | 0.80 |
| 128_A | 132_V | 1.175 | 0.80 |
| 104_Y | 166_D | 1.174 | 0.80 |
| 412_W | 416_E | 1.174 | 0.80 |
| 145_Q | 251_S | 1.172 | 0.80 |
| 211_N | 415_R | 1.159 | 0.79 |
| 472_I | 488_E | 1.158 | 0.79 |
| 301_L | 341_L | 1.158 | 0.79 |
| 296_N | 338_R | 1.140 | 0.77 |
| 354_E | 369_L | 1.137 | 0.77 |
| 413_V | 417_R | 1.133 | 0.77 |
| 216_F | 384_I | 1.131 | 0.76 |
| 217_L | 383_S | 1.126 | 0.76 |
| 434_I | 438_C | 1.120 | 0.75 |
| 157_A | 173_L | 1.120 | 0.75 |
| 110_L | 160_L | 1.115 | 0.75 |
| 348_S | 354_E | 1.113 | 0.75 |
| 129_A | 136_L | 1.106 | 0.74 |
| 441_L | 482_A | 1.102 | 0.74 |
| 482_A | 485_H | 1.100 | 0.74 |
| 138_V | 154_H | 1.097 | 0.73 |
| 161_L | 165_A | 1.093 | 0.73 |
| 349_P | 367_R | 1.084 | 0.72 |
| 200_G | 386_I | 1.083 | 0.72 |
| 157_A | 166_D | 1.081 | 0.72 |
| 58_F | 95_Q | 1.081 | 0.72 |
| 448_L | 486_L | 1.076 | 0.71 |
| 313_D | 371_R | 1.076 | 0.71 |
| 345_L | 372_L | 1.074 | 0.71 |
| 86_A | 110_L | 1.073 | 0.71 |
| 69_L | 85_I | 1.072 | 0.71 |
| 166_D | 173_L | 1.069 | 0.71 |
| 106_F | 116_I | 1.064 | 0.70 |
| 21_V | 69_L | 1.063 | 0.70 |
| 209_A | 471_T | 1.061 | 0.70 |
| 291_I | 339_F | 1.061 | 0.70 |
| 363_Q | 367_R | 1.057 | 0.69 |
| 21_V | 85_I | 1.057 | 0.69 |
| 7_H | 20_T | 1.055 | 0.69 |
| 458_S | 461_A | 1.052 | 0.69 |
| 60_F | 89_I | 1.049 | 0.68 |
| 338_R | 428_L | 1.036 | 0.67 |
| 202_R | 492_Y | 1.036 | 0.67 |
| 118_G | 142_N | 1.033 | 0.67 |
| 111_A | 117_R | 1.031 | 0.67 |
| 122_V | 146_A | 1.030 | 0.66 |
| 247_A | 317_E | 1.029 | 0.66 |
| 25_I | 93_S | 1.023 | 0.66 |
| 122_V | 147_A | 1.022 | 0.66 |
| 272_H | 317_E | 1.013 | 0.65 |
| 415_R | 419_L | 1.010 | 0.64 |
| 418_M | 426_N | 1.007 | 0.64 |
| 247_A | 261_N | 1.006 | 0.64 |
| 166_D | 172_T | 1.004 | 0.64 |
| 416_E | 419_L | 1.004 | 0.64 |
| 111_A | 163_V | 1.002 | 0.63 |
| 31_G | 64_R | 1.000 | 0.63 |
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 | |
| 1g8pA | 1 | 0.5464 | 100 | 0.794 | Contact Map |
| 1rreA | 6 | 0.3531 | 100 | 0.809 | Contact Map |
| 1xhkA | 2 | 0.3333 | 100 | 0.809 | Contact Map |
| 2x36A | 6 | 0.3393 | 100 | 0.812 | Contact Map |
| 3m6aA | 6 | 0.3294 | 100 | 0.815 | Contact Map |
| 1z0wA | 1 | 0.3669 | 100 | 0.816 | Contact Map |
| 3k1jA | 2 | 0.5838 | 100 | 0.821 | Contact Map |
| 4fwgA | 1 | 0.3708 | 100 | 0.837 | Contact Map |
| 3f8tA | 1 | 0.7968 | 100 | 0.853 | Contact Map |
| 4fdgB | 5 | 0.8264 | 100 | 0.857 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)