| NadC |
| ID: | 1381261284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 462 (419) | ||
| Sequences: | 8092 (5333.4) | ||
| Seq/Len: | 19.313 | ||
| Nf(neff/√len): | 260.6 |
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: 19.313).
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 |
| 143_A | 229_L | 3.900 | 1.00 |
| 343_V | 347_N | 3.798 | 1.00 |
| 366_A | 410_A | 3.748 | 1.00 |
| 112_H | 313_E | 3.739 | 1.00 |
| 357_G | 360_V | 3.607 | 1.00 |
| 310_H | 313_E | 3.536 | 1.00 |
| 434_K | 437_E | 3.507 | 1.00 |
| 436_S | 440_R | 3.172 | 1.00 |
| 136_F | 233_I | 3.007 | 1.00 |
| 279_S | 285_L | 2.829 | 1.00 |
| 84_E | 87_A | 2.825 | 1.00 |
| 226_M | 230_P | 2.778 | 1.00 |
| 142_T | 158_M | 2.660 | 1.00 |
| 231_M | 452_L | 2.534 | 1.00 |
| 235_I | 448_A | 2.374 | 1.00 |
| 443_L | 447_I | 2.311 | 1.00 |
| 130_K | 133_V | 2.281 | 1.00 |
| 179_V | 437_E | 2.187 | 1.00 |
| 258_D | 261_K | 2.184 | 1.00 |
| 437_E | 440_R | 2.178 | 1.00 |
| 447_I | 451_G | 2.148 | 1.00 |
| 312_K | 316_K | 2.113 | 1.00 |
| 208_A | 214_F | 2.112 | 1.00 |
| 394_E | 400_P | 2.100 | 1.00 |
| 238_F | 242_P | 2.087 | 1.00 |
| 312_K | 315_Q | 2.077 | 1.00 |
| 356_M | 360_V | 2.026 | 1.00 |
| 234_A | 238_F | 2.018 | 1.00 |
| 347_N | 351_D | 1.988 | 1.00 |
| 259_K | 263_V | 1.967 | 1.00 |
| 344_F | 347_N | 1.962 | 1.00 |
| 361_V | 396_F | 1.957 | 1.00 |
| 361_V | 365_V | 1.936 | 1.00 |
| 371_F | 375_F | 1.891 | 1.00 |
| 138_L | 186_A | 1.871 | 1.00 |
| 334_N | 338_Q | 1.862 | 1.00 |
| 372_L | 381_S | 1.838 | 1.00 |
| 366_A | 457_A | 1.831 | 1.00 |
| 122_K | 126_M | 1.819 | 1.00 |
| 204_A | 405_V | 1.798 | 1.00 |
| 393_A | 403_L | 1.795 | 1.00 |
| 167_S | 179_V | 1.786 | 1.00 |
| 344_F | 348_A | 1.780 | 1.00 |
| 336_L | 341_T | 1.777 | 1.00 |
| 208_A | 217_W | 1.732 | 1.00 |
| 136_F | 237_Y | 1.723 | 1.00 |
| 251_D | 254_P | 1.708 | 1.00 |
| 87_A | 338_Q | 1.704 | 1.00 |
| 213_S | 216_D | 1.701 | 1.00 |
| 122_K | 125_A | 1.688 | 1.00 |
| 367_T | 371_F | 1.679 | 1.00 |
| 238_F | 241_K | 1.653 | 1.00 |
| 340_G | 343_V | 1.635 | 1.00 |
| 397_G | 400_P | 1.630 | 1.00 |
| 231_M | 448_A | 1.605 | 1.00 |
| 117_K | 121_D | 1.579 | 1.00 |
| 347_N | 350_S | 1.576 | 1.00 |
| 209_E | 382_A | 1.574 | 1.00 |
| 346_A | 350_S | 1.573 | 1.00 |
| 139_F | 189_A | 1.555 | 1.00 |
| 108_A | 111_H | 1.542 | 1.00 |
| 363_L | 454_T | 1.521 | 1.00 |
| 369_V | 385_L | 1.510 | 1.00 |
| 92_F | 327_G | 1.509 | 1.00 |
| 198_V | 225_A | 1.500 | 1.00 |
| 377_S | 380_A | 1.486 | 1.00 |
| 147_M | 154_T | 1.485 | 1.00 |
| 271_T | 299_A | 1.482 | 1.00 |
| 230_P | 234_A | 1.480 | 1.00 |
| 139_F | 236_L | 1.476 | 1.00 |
| 390_A | 394_E | 1.464 | 1.00 |
| 257_W | 261_K | 1.464 | 1.00 |
| 216_D | 401_V | 1.446 | 1.00 |
| 259_K | 262_V | 1.443 | 1.00 |
| 180_F | 437_E | 1.427 | 1.00 |
| 172_D | 178_Y | 1.425 | 1.00 |
| 212_L | 401_V | 1.415 | 1.00 |
| 144_L | 148_W | 1.392 | 0.99 |
| 258_D | 262_V | 1.389 | 0.99 |
| 363_L | 367_T | 1.364 | 0.99 |
| 216_D | 219_K | 1.360 | 0.99 |
| 239_L | 243_T | 1.358 | 0.99 |
| 451_G | 455_A | 1.348 | 0.99 |
| 108_A | 112_H | 1.348 | 0.99 |
| 46_V | 50_S | 1.340 | 0.99 |
| 235_I | 239_L | 1.327 | 0.99 |
| 142_T | 189_A | 1.326 | 0.99 |
| 192_G | 424_N | 1.320 | 0.99 |
| 228_M | 449_C | 1.306 | 0.99 |
| 55_I | 73_V | 1.304 | 0.99 |
| 151_N | 424_N | 1.296 | 0.99 |
| 51_M | 55_I | 1.289 | 0.99 |
| 129_G | 257_W | 1.286 | 0.99 |
| 150_S | 153_A | 1.283 | 0.99 |
| 43_H | 47_L | 1.278 | 0.99 |
| 57_V | 61_T | 1.277 | 0.99 |
| 87_A | 90_N | 1.269 | 0.99 |
| 361_V | 393_A | 1.266 | 0.99 |
| 172_D | 180_F | 1.263 | 0.99 |
| 54_F | 58_L | 1.251 | 0.99 |
| 406_L | 457_A | 1.239 | 0.98 |
| 112_H | 316_K | 1.237 | 0.98 |
| 215_T | 219_K | 1.228 | 0.98 |
| 102_G | 293_T | 1.226 | 0.98 |
| 57_V | 62_E | 1.224 | 0.98 |
| 193_G | 415_F | 1.220 | 0.98 |
| 183_L | 433_I | 1.219 | 0.98 |
| 410_A | 453_L | 1.216 | 0.98 |
| 117_K | 308_V | 1.214 | 0.98 |
| 197_L | 207_A | 1.213 | 0.98 |
| 183_L | 187_Y | 1.210 | 0.98 |
| 319_D | 323_L | 1.208 | 0.98 |
| 155_A | 428_F | 1.205 | 0.98 |
| 126_M | 262_V | 1.205 | 0.98 |
| 41_F | 45_V | 1.202 | 0.98 |
| 128_Q | 133_V | 1.198 | 0.98 |
| 340_G | 344_F | 1.197 | 0.98 |
| 381_S | 411_A | 1.189 | 0.98 |
| 127_A | 137_M | 1.187 | 0.98 |
| 374_E | 446_N | 1.184 | 0.98 |
| 257_W | 262_V | 1.180 | 0.98 |
| 65_H | 69_T | 1.171 | 0.98 |
| 348_A | 351_D | 1.169 | 0.97 |
| 124_L | 169_V | 1.167 | 0.97 |
| 334_N | 337_K | 1.164 | 0.97 |
| 207_A | 404_S | 1.162 | 0.97 |
| 183_L | 438_M | 1.158 | 0.97 |
| 151_N | 412_S | 1.158 | 0.97 |
| 223_P | 227_M | 1.155 | 0.97 |
| 359_F | 366_A | 1.152 | 0.97 |
| 353_V | 356_M | 1.151 | 0.97 |
| 129_G | 262_V | 1.145 | 0.97 |
| 410_A | 457_A | 1.145 | 0.97 |
| 150_S | 154_T | 1.142 | 0.97 |
| 109_A | 303_L | 1.141 | 0.97 |
| 109_A | 301_L | 1.140 | 0.97 |
| 234_A | 237_Y | 1.139 | 0.97 |
| 188_S | 416_M | 1.138 | 0.97 |
| 145_L | 159_L | 1.135 | 0.97 |
| 51_M | 73_V | 1.134 | 0.97 |
| 313_E | 316_K | 1.133 | 0.97 |
| 359_F | 363_L | 1.131 | 0.97 |
| 266_G | 270_L | 1.123 | 0.97 |
| 222_L | 226_M | 1.122 | 0.97 |
| 182_L | 427_V | 1.113 | 0.96 |
| 165_V | 169_V | 1.112 | 0.96 |
| 146_S | 195_A | 1.110 | 0.96 |
| 285_L | 295_V | 1.105 | 0.96 |
| 366_A | 406_L | 1.105 | 0.96 |
| 114_G | 117_K | 1.104 | 0.96 |
| 101_L | 105_A | 1.100 | 0.96 |
| 64_L | 69_T | 1.097 | 0.96 |
| 49_I | 341_T | 1.095 | 0.96 |
| 421_T | 426_I | 1.081 | 0.95 |
| 365_V | 389_F | 1.079 | 0.95 |
| 138_L | 162_V | 1.077 | 0.95 |
| 193_G | 196_T | 1.076 | 0.95 |
| 206_A | 382_A | 1.076 | 0.95 |
| 183_L | 428_F | 1.068 | 0.95 |
| 231_M | 235_I | 1.066 | 0.95 |
| 120_A | 162_V | 1.059 | 0.95 |
| 42_E | 45_V | 1.056 | 0.95 |
| 327_G | 331_C | 1.054 | 0.95 |
| 118_V | 122_K | 1.054 | 0.95 |
| 202_P | 379_T | 1.052 | 0.95 |
| 109_A | 297_L | 1.049 | 0.94 |
| 267_I | 271_T | 1.048 | 0.94 |
| 135_V | 181_V | 1.047 | 0.94 |
| 268_F | 305_F | 1.042 | 0.94 |
| 250_L | 254_P | 1.039 | 0.94 |
| 262_V | 266_G | 1.038 | 0.94 |
| 378_N | 423_P | 1.037 | 0.94 |
| 76_M | 80_F | 1.034 | 0.94 |
| 118_V | 308_V | 1.033 | 0.94 |
| 143_A | 225_A | 1.028 | 0.94 |
| 114_G | 118_V | 1.026 | 0.94 |
| 389_F | 392_V | 1.025 | 0.93 |
| 203_N | 378_N | 1.025 | 0.93 |
| 58_L | 72_L | 1.025 | 0.93 |
| 218_M | 222_L | 1.024 | 0.93 |
| 142_T | 154_T | 1.024 | 0.93 |
| 348_A | 353_V | 1.021 | 0.93 |
| 159_L | 163_L | 1.019 | 0.93 |
| 210_V | 390_A | 1.014 | 0.93 |
| 241_K | 244_L | 1.012 | 0.93 |
| 54_F | 76_M | 1.012 | 0.93 |
| 88_A | 331_C | 1.010 | 0.93 |
| 196_T | 412_S | 1.007 | 0.93 |
| 282_N | 286_G | 1.004 | 0.93 |
| 233_I | 237_Y | 1.003 | 0.93 |
| 51_M | 80_F | 1.001 | 0.92 |
| 155_A | 192_G | 1.001 | 0.92 |
| 337_K | 343_V | 1.000 | 0.92 |
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 | |
| 4f35D | 4 | 0.9437 | 100 | 0.307 | Contact Map |
| 3tdsE | 5 | 0.4957 | 49.7 | 0.959 | Contact Map |
| 3giaA | 1 | 0.461 | 14.7 | 0.969 | Contact Map |
| 3tijA | 1 | 0.4502 | 13.3 | 0.97 | Contact Map |
| 1ldfA | 1 | 0.4697 | 11.9 | 0.97 | Contact Map |
| 3zojA | 1 | 0.474 | 8.7 | 0.972 | Contact Map |
| 1j4nA | 1 | 0.4719 | 6.9 | 0.973 | Contact Map |
| 1pw4A | 1 | 0.4437 | 6.4 | 0.974 | Contact Map |
| 2kluA | 1 | 0.1472 | 5.8 | 0.974 | Contact Map |
| 3qnqA | 4 | 0.5173 | 5.4 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)