| ryancaster |
| ID: | 1487381064 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 449 (439) | ||
| Sequences: | 9409 (5716) | ||
| Seq/Len: | 21.433 | ||
| Nf(neff/√len): | 272.8 |
Jackhmmer Results: (2016_04)
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: 21.433).
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 |
| 369_N | 432_Q | 3.985 | 1.00 |
| 35_G | 102_Q | 3.982 | 1.00 |
| 112_D | 163_K | 3.591 | 1.00 |
| 108_E | 163_K | 3.145 | 1.00 |
| 384_L | 394_V | 3.117 | 1.00 |
| 108_E | 159_Y | 3.069 | 1.00 |
| 69_Q | 113_E | 3.063 | 1.00 |
| 76_Q | 117_R | 3.052 | 1.00 |
| 63_D | 66_H | 3.025 | 1.00 |
| 430_L | 434_A | 2.922 | 1.00 |
| 125_L | 156_V | 2.837 | 1.00 |
| 101_Q | 105_E | 2.811 | 1.00 |
| 105_E | 109_R | 2.748 | 1.00 |
| 113_E | 116_A | 2.732 | 1.00 |
| 297_F | 380_H | 2.660 | 1.00 |
| 93_L | 155_V | 2.655 | 1.00 |
| 383_A | 386_E | 2.608 | 1.00 |
| 101_Q | 159_Y | 2.589 | 1.00 |
| 236_S | 239_D | 2.562 | 1.00 |
| 154_E | 158_G | 2.457 | 1.00 |
| 34_L | 66_H | 2.445 | 1.00 |
| 21_V | 80_V | 2.441 | 1.00 |
| 132_Q | 136_D | 2.409 | 1.00 |
| 377_F | 399_A | 2.400 | 1.00 |
| 73_E | 117_R | 2.386 | 1.00 |
| 375_R | 379_S | 2.355 | 1.00 |
| 47_N | 59_D | 2.292 | 1.00 |
| 338_L | 390_A | 2.229 | 1.00 |
| 334_T | 390_A | 2.205 | 1.00 |
| 64_H | 106_F | 2.204 | 1.00 |
| 147_Y | 209_L | 2.195 | 1.00 |
| 420_H | 429_T | 2.186 | 1.00 |
| 212_P | 216_K | 2.176 | 1.00 |
| 69_Q | 109_R | 2.161 | 1.00 |
| 214_M | 223_H | 2.158 | 1.00 |
| 82_A | 398_F | 2.109 | 1.00 |
| 371_E | 432_Q | 2.099 | 1.00 |
| 143_R | 282_D | 2.060 | 1.00 |
| 120_K | 165_D | 2.054 | 1.00 |
| 111_I | 160_F | 2.045 | 1.00 |
| 64_H | 83_Y | 2.012 | 1.00 |
| 150_A | 213_I | 1.998 | 1.00 |
| 72_I | 117_R | 1.997 | 1.00 |
| 115_H | 163_K | 1.974 | 1.00 |
| 438_R | 442_L | 1.959 | 1.00 |
| 40_S | 90_P | 1.956 | 1.00 |
| 39_P | 44_T | 1.950 | 1.00 |
| 334_T | 386_E | 1.922 | 1.00 |
| 154_E | 217_N | 1.913 | 1.00 |
| 85_L | 111_I | 1.883 | 1.00 |
| 87_M | 123_V | 1.883 | 1.00 |
| 154_E | 213_I | 1.868 | 1.00 |
| 102_Q | 105_E | 1.860 | 1.00 |
| 265_Q | 269_E | 1.837 | 1.00 |
| 439_N | 447_E | 1.827 | 1.00 |
| 201_H | 263_Y | 1.822 | 1.00 |
| 72_I | 110_I | 1.809 | 1.00 |
| 32_A | 39_P | 1.809 | 1.00 |
| 281_G | 284_D | 1.788 | 1.00 |
| 44_T | 132_Q | 1.779 | 1.00 |
| 233_Y | 335_D | 1.770 | 1.00 |
| 31_G | 34_L | 1.769 | 1.00 |
| 44_T | 136_D | 1.763 | 1.00 |
| 23_T | 28_I | 1.755 | 1.00 |
| 113_E | 117_R | 1.734 | 1.00 |
| 120_K | 166_S | 1.722 | 1.00 |
| 218_A | 221_S | 1.718 | 1.00 |
| 108_E | 112_D | 1.717 | 1.00 |
| 108_E | 160_F | 1.715 | 1.00 |
| 72_I | 113_E | 1.706 | 1.00 |
| 150_A | 209_L | 1.685 | 1.00 |
| 19_F | 444_R | 1.675 | 1.00 |
| 363_C | 429_T | 1.671 | 1.00 |
| 114_C | 119_L | 1.661 | 1.00 |
| 209_L | 285_I | 1.661 | 1.00 |
| 111_I | 115_H | 1.646 | 1.00 |
| 222_M | 349_P | 1.637 | 1.00 |
| 214_M | 221_S | 1.636 | 1.00 |
| 73_E | 113_E | 1.627 | 1.00 |
| 331_Q | 383_A | 1.625 | 1.00 |
| 260_K | 345_P | 1.619 | 1.00 |
| 297_F | 332_A | 1.618 | 1.00 |
| 112_D | 115_H | 1.615 | 1.00 |
| 26_Y | 58_G | 1.610 | 1.00 |
| 133_Y | 137_K | 1.596 | 1.00 |
| 68_W | 109_R | 1.596 | 1.00 |
| 351_Y | 395_Q | 1.588 | 1.00 |
| 334_T | 338_L | 1.575 | 1.00 |
| 355_N | 397_Y | 1.557 | 1.00 |
| 145_T | 148_K | 1.557 | 1.00 |
| 337_L | 392_V | 1.552 | 1.00 |
| 67_L | 70_Q | 1.551 | 1.00 |
| 157_S | 214_M | 1.540 | 1.00 |
| 253_W | 267_V | 1.540 | 1.00 |
| 85_L | 110_I | 1.534 | 1.00 |
| 248_A | 266_S | 1.533 | 1.00 |
| 339_R | 343_R | 1.529 | 1.00 |
| 213_I | 216_K | 1.522 | 1.00 |
| 104_L | 155_V | 1.512 | 1.00 |
| 23_T | 83_Y | 1.494 | 1.00 |
| 333_L | 384_L | 1.474 | 1.00 |
| 141_L | 195_E | 1.472 | 1.00 |
| 18_L | 82_A | 1.463 | 1.00 |
| 162_N | 218_A | 1.463 | 1.00 |
| 439_N | 443_A | 1.461 | 1.00 |
| 190_K | 195_E | 1.454 | 1.00 |
| 439_N | 442_L | 1.454 | 1.00 |
| 385_D | 389_R | 1.450 | 1.00 |
| 75_I | 80_V | 1.441 | 1.00 |
| 166_S | 222_M | 1.431 | 1.00 |
| 323_Y | 360_E | 1.430 | 1.00 |
| 31_G | 66_H | 1.423 | 1.00 |
| 82_A | 122_F | 1.419 | 1.00 |
| 168_A | 226_V | 1.414 | 1.00 |
| 72_I | 114_C | 1.413 | 1.00 |
| 93_L | 99_V | 1.412 | 1.00 |
| 200_A | 254_F | 1.410 | 1.00 |
| 262_E | 287_R | 1.405 | 0.99 |
| 255_I | 293_I | 1.400 | 0.99 |
| 278_I | 283_L | 1.387 | 0.99 |
| 122_F | 398_F | 1.385 | 0.99 |
| 48_Q | 51_A | 1.381 | 0.99 |
| 168_A | 292_F | 1.376 | 0.99 |
| 399_A | 418_I | 1.373 | 0.99 |
| 38_T | 96_D | 1.367 | 0.99 |
| 87_M | 156_V | 1.365 | 0.99 |
| 85_L | 123_V | 1.358 | 0.99 |
| 430_L | 435_I | 1.355 | 0.99 |
| 77_G | 434_A | 1.339 | 0.99 |
| 262_E | 268_L | 1.311 | 0.99 |
| 87_M | 92_I | 1.310 | 0.99 |
| 436_A | 440_T | 1.309 | 0.99 |
| 63_D | 67_L | 1.307 | 0.99 |
| 435_I | 438_R | 1.293 | 0.99 |
| 170_L | 206_A | 1.283 | 0.99 |
| 147_Y | 150_A | 1.279 | 0.99 |
| 144_E | 147_Y | 1.279 | 0.99 |
| 256_D | 343_R | 1.262 | 0.99 |
| 135_E | 190_K | 1.260 | 0.99 |
| 337_L | 384_L | 1.259 | 0.99 |
| 225_C | 258_V | 1.256 | 0.99 |
| 192_G | 195_E | 1.254 | 0.99 |
| 104_L | 159_Y | 1.244 | 0.98 |
| 62_C | 403_M | 1.244 | 0.98 |
| 138_G | 142_N | 1.233 | 0.98 |
| 367_E | 432_Q | 1.229 | 0.98 |
| 158_G | 217_N | 1.224 | 0.98 |
| 176_S | 203_L | 1.219 | 0.98 |
| 341_K | 346_N | 1.216 | 0.98 |
| 73_E | 77_G | 1.208 | 0.98 |
| 38_T | 133_Y | 1.205 | 0.98 |
| 170_L | 203_L | 1.201 | 0.98 |
| 378_Q | 382_L | 1.193 | 0.98 |
| 111_I | 123_V | 1.187 | 0.98 |
| 64_H | 110_I | 1.182 | 0.98 |
| 338_L | 392_V | 1.181 | 0.98 |
| 68_W | 113_E | 1.171 | 0.98 |
| 262_E | 345_P | 1.166 | 0.97 |
| 36_G | 100_N | 1.160 | 0.97 |
| 157_S | 210_A | 1.159 | 0.97 |
| 247_D | 339_R | 1.158 | 0.97 |
| 256_D | 260_K | 1.154 | 0.97 |
| 379_S | 382_L | 1.154 | 0.97 |
| 144_E | 148_K | 1.147 | 0.97 |
| 244_E | 248_A | 1.147 | 0.97 |
| 130_L | 145_T | 1.146 | 0.97 |
| 143_R | 202_H | 1.146 | 0.97 |
| 241_A | 245_Y | 1.143 | 0.97 |
| 381_L | 384_L | 1.141 | 0.97 |
| 104_L | 108_E | 1.141 | 0.97 |
| 140_W | 145_T | 1.137 | 0.97 |
| 95_K | 133_Y | 1.137 | 0.97 |
| 279_L | 282_D | 1.137 | 0.97 |
| 13_R | 385_D | 1.136 | 0.97 |
| 235_Y | 304_R | 1.136 | 0.97 |
| 211_M | 215_R | 1.133 | 0.97 |
| 214_M | 218_A | 1.130 | 0.97 |
| 150_A | 154_E | 1.129 | 0.97 |
| 237_E | 240_V | 1.122 | 0.97 |
| 341_K | 393_N | 1.119 | 0.96 |
| 324_I | 358_A | 1.114 | 0.96 |
| 215_R | 219_P | 1.113 | 0.96 |
| 77_G | 430_L | 1.111 | 0.96 |
| 229_A | 336_L | 1.103 | 0.96 |
| 259_L | 348_P | 1.103 | 0.96 |
| 232_A | 246_S | 1.101 | 0.96 |
| 349_P | 395_Q | 1.098 | 0.96 |
| 14_Q | 388_I | 1.097 | 0.96 |
| 108_E | 162_N | 1.094 | 0.96 |
| 150_A | 210_A | 1.094 | 0.96 |
| 122_F | 351_Y | 1.086 | 0.96 |
| 234_P | 243_A | 1.083 | 0.96 |
| 32_A | 37_R | 1.083 | 0.96 |
| 202_H | 205_L | 1.082 | 0.96 |
| 95_K | 98_Q | 1.071 | 0.95 |
| 75_I | 419_V | 1.069 | 0.95 |
| 13_R | 388_I | 1.069 | 0.95 |
| 153_A | 210_A | 1.068 | 0.95 |
| 137_K | 144_E | 1.067 | 0.95 |
| 155_V | 159_Y | 1.067 | 0.95 |
| 213_I | 217_N | 1.066 | 0.95 |
| 23_T | 85_L | 1.065 | 0.95 |
| 280_D | 283_L | 1.057 | 0.95 |
| 375_R | 378_Q | 1.055 | 0.95 |
| 67_L | 427_K | 1.055 | 0.95 |
| 262_E | 265_Q | 1.053 | 0.95 |
| 321_H | 327_E | 1.048 | 0.94 |
| 238_Q | 305_F | 1.048 | 0.94 |
| 234_P | 240_V | 1.044 | 0.94 |
| 99_V | 155_V | 1.039 | 0.94 |
| 349_P | 393_N | 1.037 | 0.94 |
| 111_I | 163_K | 1.035 | 0.94 |
| 209_L | 213_I | 1.027 | 0.94 |
| 135_E | 181_Y | 1.025 | 0.93 |
| 437_Y | 441_L | 1.024 | 0.93 |
| 331_Q | 335_D | 1.023 | 0.93 |
| 122_F | 166_S | 1.018 | 0.93 |
| 21_V | 75_I | 1.016 | 0.93 |
| 385_D | 388_I | 1.008 | 0.93 |
| 125_L | 149_F | 1.008 | 0.93 |
| 177_A | 199_S | 1.006 | 0.93 |
| 238_Q | 331_Q | 1.006 | 0.93 |
| 237_E | 241_A | 1.005 | 0.93 |
| 363_C | 367_E | 1.004 | 0.93 |
| 227_F | 255_I | 1.002 | 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
- 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 | |
| 1v02A | 5 | 0.9777 | 100 | 0.097 | Contact Map |
| 2jf7A | 2 | 0.9621 | 100 | 0.098 | Contact Map |
| 3ptmA | 2 | 0.971 | 100 | 0.098 | Contact Map |
| 2dgaA | 1 | 0.9911 | 100 | 0.099 | Contact Map |
| 1v08A | 2 | 0.9844 | 100 | 0.101 | Contact Map |
| 3w53A | 1 | 0.9822 | 100 | 0.104 | Contact Map |
| 3wq5A | 2 | 0.971 | 100 | 0.106 | Contact Map |
| 1cbgA | 1 | 0.9844 | 100 | 0.107 | Contact Map |
| 3f5lA | 2 | 0.98 | 100 | 0.111 | Contact Map |
| 3gnpA | 1 | 0.971 | 100 | 0.114 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)