| C7_1E-04 |
| ID: | 1501519967 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 481 (437) | ||
| Sequences: | 1208 (832.7) | ||
| Seq/Len: | 2.764 | ||
| Nf(neff/√len): | 39.8 |
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: 2.764).
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 |
| 321_R | 337_D | 4.454 | 1.00 |
| 98_N | 101_A | 4.074 | 1.00 |
| 30_D | 33_E | 3.955 | 1.00 |
| 296_K | 299_D | 3.413 | 1.00 |
| 308_V | 318_Y | 3.388 | 1.00 |
| 204_G | 220_F | 3.180 | 1.00 |
| 258_N | 261_L | 3.044 | 1.00 |
| 89_E | 105_S | 3.035 | 1.00 |
| 178_R | 181_E | 2.915 | 1.00 |
| 55_R | 71_D | 2.893 | 1.00 |
| 330_Q | 333_E | 2.754 | 1.00 |
| 90_G | 106_F | 2.577 | 1.00 |
| 287_R | 303_D | 2.532 | 1.00 |
| 380_S | 383_E | 2.435 | 1.00 |
| 332_E | 336_R | 2.302 | 1.00 |
| 305_T | 321_R | 2.280 | 1.00 |
| 64_R | 67_E | 2.275 | 1.00 |
| 333_E | 336_R | 2.159 | 1.00 |
| 318_Y | 337_D | 2.116 | 1.00 |
| 73_Q | 89_E | 2.111 | 1.00 |
| 144_D | 147_K | 2.089 | 1.00 |
| 301_I | 328_T | 1.912 | 0.99 |
| 74_Q | 77_R | 1.885 | 0.99 |
| 332_E | 335_V | 1.882 | 0.99 |
| 35_Y | 58_T | 1.875 | 0.99 |
| 339_E | 358_Q | 1.857 | 0.99 |
| 263_Y | 290_V | 1.847 | 0.99 |
| 361_L | 364_S | 1.813 | 0.99 |
| 93_H | 98_N | 1.759 | 0.99 |
| 325_Y | 337_D | 1.736 | 0.98 |
| 59_L | 67_E | 1.673 | 0.98 |
| 54_N | 57_A | 1.668 | 0.98 |
| 391_R | 394_M | 1.666 | 0.98 |
| 76_V | 86_H | 1.642 | 0.97 |
| 439_D | 442_E | 1.639 | 0.97 |
| 33_E | 36_N | 1.630 | 0.97 |
| 103_C | 107_Q | 1.609 | 0.97 |
| 322_A | 338_Y | 1.608 | 0.97 |
| 325_Y | 330_Q | 1.585 | 0.97 |
| 86_H | 105_S | 1.552 | 0.96 |
| 260_K | 294_L | 1.547 | 0.96 |
| 270_L | 284_Y | 1.533 | 0.96 |
| 212_C | 215_K | 1.518 | 0.95 |
| 332_E | 361_L | 1.514 | 0.95 |
| 39_T | 55_R | 1.509 | 0.95 |
| 221_V | 225_R | 1.506 | 0.95 |
| 361_L | 365_K | 1.504 | 0.95 |
| 305_T | 337_D | 1.477 | 0.94 |
| 291_N | 296_K | 1.471 | 0.94 |
| 335_V | 354_L | 1.471 | 0.94 |
| 39_T | 71_D | 1.468 | 0.94 |
| 250_G | 286_N | 1.467 | 0.94 |
| 306_N | 309_K | 1.463 | 0.94 |
| 18_F | 37_Y | 1.461 | 0.94 |
| 422_F | 426_S | 1.457 | 0.94 |
| 224_L | 228_P | 1.443 | 0.93 |
| 260_K | 264_E | 1.440 | 0.93 |
| 266_Y | 286_N | 1.431 | 0.93 |
| 222_Q | 225_R | 1.428 | 0.93 |
| 367_K | 420_E | 1.406 | 0.92 |
| 56_A | 72_A | 1.391 | 0.92 |
| 322_A | 341_V | 1.380 | 0.91 |
| 431_K | 435_D | 1.373 | 0.91 |
| 298_D | 328_T | 1.371 | 0.91 |
| 415_F | 419_G | 1.365 | 0.91 |
| 267_T | 287_R | 1.363 | 0.91 |
| 140_F | 168_L | 1.362 | 0.91 |
| 216_A | 240_A | 1.362 | 0.91 |
| 18_F | 40_K | 1.348 | 0.90 |
| 433_R | 438_Q | 1.348 | 0.90 |
| 291_N | 299_D | 1.344 | 0.90 |
| 169_K | 173_L | 1.335 | 0.89 |
| 251_N | 266_Y | 1.330 | 0.89 |
| 106_F | 122_E | 1.325 | 0.89 |
| 267_T | 303_D | 1.323 | 0.89 |
| 325_Y | 333_E | 1.322 | 0.89 |
| 391_R | 395_H | 1.306 | 0.88 |
| 110_L | 119_A | 1.306 | 0.88 |
| 170_A | 431_K | 1.305 | 0.88 |
| 126_A | 130_M | 1.302 | 0.88 |
| 251_N | 286_N | 1.300 | 0.88 |
| 174_A | 182_A | 1.300 | 0.88 |
| 360_E | 366_R | 1.291 | 0.87 |
| 408_Q | 412_E | 1.289 | 0.87 |
| 359_L | 363_K | 1.264 | 0.86 |
| 204_G | 219_F | 1.260 | 0.85 |
| 93_H | 101_A | 1.260 | 0.85 |
| 319_L | 350_H | 1.260 | 0.85 |
| 208_Y | 273_D | 1.257 | 0.85 |
| 253_A | 265_L | 1.256 | 0.85 |
| 263_Y | 291_N | 1.250 | 0.85 |
| 340_K | 343_Q | 1.248 | 0.85 |
| 263_Y | 294_L | 1.245 | 0.84 |
| 385_K | 422_F | 1.245 | 0.84 |
| 299_D | 302_E | 1.245 | 0.84 |
| 289_T | 320_R | 1.235 | 0.84 |
| 127_N | 131_E | 1.227 | 0.83 |
| 388_Y | 396_H | 1.215 | 0.82 |
| 215_K | 218_Q | 1.212 | 0.82 |
| 360_E | 363_K | 1.211 | 0.82 |
| 103_C | 130_M | 1.210 | 0.82 |
| 247_K | 251_N | 1.209 | 0.82 |
| 35_Y | 59_L | 1.208 | 0.82 |
| 14_E | 18_F | 1.205 | 0.82 |
| 392_A | 396_H | 1.200 | 0.81 |
| 204_G | 223_A | 1.186 | 0.80 |
| 412_E | 416_K | 1.179 | 0.80 |
| 264_E | 268_E | 1.166 | 0.79 |
| 119_A | 122_E | 1.156 | 0.78 |
| 13_R | 17_T | 1.151 | 0.77 |
| 288_G | 303_D | 1.147 | 0.77 |
| 285_C | 314_Y | 1.146 | 0.77 |
| 15_A | 44_M | 1.144 | 0.77 |
| 21_Q | 25_Y | 1.143 | 0.77 |
| 89_E | 93_H | 1.143 | 0.77 |
| 336_R | 339_E | 1.142 | 0.77 |
| 90_G | 109_A | 1.139 | 0.76 |
| 152_M | 168_L | 1.139 | 0.76 |
| 395_H | 418_V | 1.126 | 0.75 |
| 21_Q | 24_A | 1.123 | 0.75 |
| 170_A | 189_I | 1.119 | 0.75 |
| 314_Y | 317_A | 1.118 | 0.74 |
| 38_Y | 41_A | 1.118 | 0.74 |
| 34_A | 38_Y | 1.112 | 0.74 |
| 289_T | 316_K | 1.110 | 0.74 |
| 372_I | 417_E | 1.110 | 0.74 |
| 384_I | 388_Y | 1.108 | 0.74 |
| 443_E | 446_N | 1.107 | 0.73 |
| 432_T | 436_S | 1.106 | 0.73 |
| 26_Y | 89_E | 1.105 | 0.73 |
| 100_M | 130_M | 1.105 | 0.73 |
| 93_H | 105_S | 1.103 | 0.73 |
| 38_Y | 266_Y | 1.102 | 0.73 |
| 162_C | 165_F | 1.100 | 0.73 |
| 301_I | 324_C | 1.096 | 0.72 |
| 422_F | 425_L | 1.094 | 0.72 |
| 305_T | 309_K | 1.093 | 0.72 |
| 216_A | 220_F | 1.091 | 0.72 |
| 262_A | 266_Y | 1.091 | 0.72 |
| 308_V | 317_A | 1.087 | 0.71 |
| 339_E | 343_Q | 1.087 | 0.71 |
| 401_S | 411_E | 1.085 | 0.71 |
| 54_N | 286_N | 1.084 | 0.71 |
| 72_A | 88_R | 1.084 | 0.71 |
| 257_G | 293_K | 1.081 | 0.71 |
| 286_N | 316_K | 1.080 | 0.71 |
| 107_Q | 111_E | 1.079 | 0.71 |
| 410_E | 414_K | 1.075 | 0.70 |
| 249_D | 265_L | 1.071 | 0.70 |
| 440_L | 443_E | 1.066 | 0.69 |
| 134_K | 138_T | 1.066 | 0.69 |
| 26_Y | 31_Y | 1.065 | 0.69 |
| 376_D | 379_A | 1.063 | 0.69 |
| 106_F | 300_A | 1.061 | 0.69 |
| 171_E | 232_K | 1.059 | 0.69 |
| 323_Q | 338_Y | 1.057 | 0.68 |
| 292_S | 324_C | 1.055 | 0.68 |
| 250_G | 262_A | 1.054 | 0.68 |
| 427_D | 430_K | 1.053 | 0.68 |
| 223_A | 233_A | 1.053 | 0.68 |
| 15_A | 18_F | 1.052 | 0.68 |
| 301_I | 305_T | 1.050 | 0.68 |
| 38_Y | 72_A | 1.047 | 0.67 |
| 194_S | 228_P | 1.046 | 0.67 |
| 396_H | 399_R | 1.045 | 0.67 |
| 342_Y | 354_L | 1.045 | 0.67 |
| 75_S | 85_G | 1.045 | 0.67 |
| 398_D | 415_F | 1.044 | 0.67 |
| 395_H | 400_H | 1.043 | 0.67 |
| 409_K | 412_E | 1.042 | 0.67 |
| 373_L | 418_V | 1.042 | 0.67 |
| 221_V | 237_C | 1.041 | 0.67 |
| 16_E | 19_K | 1.041 | 0.67 |
| 402_G | 412_E | 1.037 | 0.66 |
| 113_D | 116_N | 1.036 | 0.66 |
| 250_G | 266_Y | 1.036 | 0.66 |
| 247_K | 286_N | 1.035 | 0.66 |
| 353_L | 356_N | 1.035 | 0.66 |
| 389_R | 398_D | 1.032 | 0.66 |
| 35_Y | 62_L | 1.030 | 0.66 |
| 294_L | 348_K | 1.024 | 0.65 |
| 221_V | 249_D | 1.021 | 0.65 |
| 193_D | 196_N | 1.018 | 0.64 |
| 103_C | 127_N | 1.017 | 0.64 |
| 375_V | 379_A | 1.010 | 0.63 |
| 305_T | 325_Y | 1.008 | 0.63 |
| 385_K | 399_R | 1.008 | 0.63 |
| 332_E | 364_S | 1.008 | 0.63 |
| 182_A | 206_C | 1.007 | 0.63 |
| 396_H | 425_L | 1.005 | 0.63 |
| 25_Y | 37_Y | 1.004 | 0.63 |
| 136_A | 168_L | 1.002 | 0.62 |
| 121_Q | 125_N | 1.001 | 0.62 |
| 123_F | 130_M | 1.000 | 0.62 |
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 | |
| 2y4tA | 3 | 0.869 | 100 | 0.431 | Contact Map |
| 3iegA | 2 | 0.738 | 100 | 0.592 | Contact Map |
| 1w3bA | 2 | 0.7609 | 100 | 0.592 | Contact Map |
| 4ui9C | 2 | 0 | 100 | 0.616 | Contact Map |
| 3fp2A | 1 | 0.7277 | 100 | 0.625 | Contact Map |
| 4ui9J | 1 | 0 | 100 | 0.628 | Contact Map |
| 2gw1A | 2 | 0.8649 | 100 | 0.634 | Contact Map |
| 2xpiA | 2 | 0.6944 | 100 | 0.64 | Contact Map |
| 4rg9A | 2 | 0.5717 | 100 | 0.643 | Contact Map |
| 4ui9X | 2 | 0 | 100 | 0.646 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)