| ccka_hk_rd |
| ID: | 1493839566 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 381 (373) | ||
| Sequences: | 24365 (18587.1) | ||
| Seq/Len: | 65.322 | ||
| Nf(neff/√len): | 962.4 |
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: 65.322).
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 |
| 288_L | 307_I | 3.494 | 1.00 |
| 25_L | 45_I | 3.151 | 1.00 |
| 73_L | 109_A | 3.138 | 1.00 |
| 273_R | 289_E | 3.098 | 1.00 |
| 219_R | 222_E | 2.858 | 1.00 |
| 292_D | 318_G | 2.847 | 1.00 |
| 179_M | 216_V | 2.741 | 1.00 |
| 312_S | 324_L | 2.704 | 1.00 |
| 215_H | 227_R | 2.696 | 1.00 |
| 294_E | 318_G | 2.673 | 1.00 |
| 168_S | 225_A | 2.621 | 1.00 |
| 320_D | 323_T | 2.619 | 1.00 |
| 175_P | 178_V | 2.567 | 1.00 |
| 291_A | 295_E | 2.544 | 1.00 |
| 262_R | 286_E | 2.498 | 1.00 |
| 204_Y | 208_K | 2.479 | 1.00 |
| 327_K | 330_G | 2.344 | 1.00 |
| 266_V | 296_A | 2.298 | 1.00 |
| 262_R | 288_L | 2.286 | 1.00 |
| 164_F | 229_F | 2.270 | 1.00 |
| 72_V | 108_R | 2.261 | 1.00 |
| 301_E | 331_Y | 2.227 | 1.00 |
| 359_T | 373_R | 2.210 | 1.00 |
| 71_E | 111_K | 2.204 | 1.00 |
| 164_F | 227_R | 2.181 | 1.00 |
| 273_R | 291_A | 2.177 | 1.00 |
| 283_R | 371_A | 2.161 | 1.00 |
| 277_A | 289_E | 2.156 | 1.00 |
| 22_Q | 49_G | 2.143 | 1.00 |
| 99_D | 141_R | 2.134 | 1.00 |
| 166_E | 225_A | 2.133 | 1.00 |
| 325_L | 337_V | 2.112 | 1.00 |
| 203_V | 214_I | 2.104 | 1.00 |
| 129_V | 170_D | 2.085 | 1.00 |
| 174_I | 178_V | 2.024 | 1.00 |
| 29_L | 43_N | 1.995 | 1.00 |
| 29_L | 46_R | 1.962 | 1.00 |
| 109_A | 210_S | 1.936 | 1.00 |
| 141_R | 168_S | 1.901 | 1.00 |
| 74_D | 77_E | 1.893 | 1.00 |
| 162_T | 229_F | 1.884 | 1.00 |
| 277_A | 281_R | 1.861 | 1.00 |
| 141_R | 166_E | 1.844 | 1.00 |
| 329_R | 358_V | 1.830 | 1.00 |
| 97_I | 137_V | 1.822 | 1.00 |
| 31_R | 38_S | 1.816 | 1.00 |
| 292_D | 295_E | 1.814 | 1.00 |
| 217_H | 225_A | 1.807 | 1.00 |
| 216_V | 226_F | 1.802 | 1.00 |
| 288_L | 299_I | 1.778 | 1.00 |
| 178_V | 181_K | 1.764 | 1.00 |
| 166_E | 227_R | 1.759 | 1.00 |
| 290_A | 299_I | 1.742 | 1.00 |
| 143_A | 164_F | 1.720 | 1.00 |
| 208_K | 213_W | 1.714 | 1.00 |
| 175_P | 220_P | 1.710 | 1.00 |
| 325_L | 357_G | 1.706 | 1.00 |
| 99_D | 139_R | 1.686 | 1.00 |
| 294_E | 298_I | 1.682 | 1.00 |
| 97_I | 139_R | 1.677 | 1.00 |
| 359_T | 376_Q | 1.671 | 1.00 |
| 339_F | 357_G | 1.663 | 1.00 |
| 297_L | 324_L | 1.662 | 1.00 |
| 176_P | 179_M | 1.647 | 1.00 |
| 46_R | 50_V | 1.627 | 1.00 |
| 95_K | 137_V | 1.626 | 1.00 |
| 300_A | 328_A | 1.596 | 1.00 |
| 30_H | 282_A | 1.589 | 1.00 |
| 174_I | 182_I | 1.587 | 1.00 |
| 350_D | 354_G | 1.578 | 1.00 |
| 319_I | 327_K | 1.578 | 1.00 |
| 261_G | 285_Y | 1.569 | 1.00 |
| 312_S | 325_L | 1.567 | 1.00 |
| 315_I | 343_Y | 1.541 | 1.00 |
| 139_R | 168_S | 1.527 | 1.00 |
| 309_L | 374_V | 1.525 | 1.00 |
| 338_M | 373_R | 1.523 | 1.00 |
| 319_I | 323_T | 1.521 | 1.00 |
| 258_S | 285_Y | 1.509 | 1.00 |
| 143_A | 166_E | 1.501 | 1.00 |
| 323_T | 327_K | 1.499 | 1.00 |
| 366_D | 369_T | 1.494 | 1.00 |
| 267_E | 273_R | 1.491 | 1.00 |
| 28_L | 42_L | 1.490 | 1.00 |
| 165_I | 228_I | 1.462 | 1.00 |
| 265_F | 276_A | 1.458 | 1.00 |
| 279_L | 367_I | 1.455 | 1.00 |
| 117_A | 207_V | 1.438 | 1.00 |
| 26_D | 46_R | 1.427 | 1.00 |
| 181_K | 187_F | 1.425 | 1.00 |
| 81_E | 115_E | 1.420 | 1.00 |
| 359_T | 377_Q | 1.405 | 0.99 |
| 40_E | 274_S | 1.401 | 0.99 |
| 137_V | 170_D | 1.391 | 0.99 |
| 117_A | 206_I | 1.379 | 0.99 |
| 270_D | 273_R | 1.372 | 0.99 |
| 130_R | 135_G | 1.367 | 0.99 |
| 184_D | 187_F | 1.359 | 0.99 |
| 217_H | 227_R | 1.339 | 0.99 |
| 263_I | 285_Y | 1.339 | 0.99 |
| 314_V | 322_P | 1.329 | 0.99 |
| 118_V | 165_I | 1.327 | 0.99 |
| 373_R | 376_Q | 1.323 | 0.99 |
| 293_G | 324_L | 1.321 | 0.99 |
| 263_I | 309_L | 1.319 | 0.99 |
| 28_L | 38_S | 1.313 | 0.99 |
| 207_V | 228_I | 1.311 | 0.99 |
| 179_M | 218_S | 1.309 | 0.99 |
| 37_P | 278_R | 1.306 | 0.99 |
| 83_E | 96_L | 1.289 | 0.99 |
| 145_L | 164_F | 1.284 | 0.99 |
| 297_L | 327_K | 1.281 | 0.99 |
| 169_D | 173_G | 1.281 | 0.99 |
| 162_T | 231_P | 1.278 | 0.99 |
| 264_L | 290_A | 1.273 | 0.99 |
| 70_R | 108_R | 1.270 | 0.99 |
| 293_G | 319_I | 1.264 | 0.99 |
| 323_T | 326_K | 1.263 | 0.99 |
| 183_F | 214_I | 1.256 | 0.99 |
| 70_R | 233_Y | 1.251 | 0.99 |
| 265_F | 287_V | 1.251 | 0.99 |
| 373_R | 377_Q | 1.247 | 0.99 |
| 30_H | 367_I | 1.244 | 0.98 |
| 105_P | 144_R | 1.241 | 0.98 |
| 83_E | 87_R | 1.236 | 0.98 |
| 86_L | 119_M | 1.233 | 0.98 |
| 182_I | 216_V | 1.228 | 0.98 |
| 29_L | 39_Y | 1.227 | 0.98 |
| 117_A | 228_I | 1.227 | 0.98 |
| 310_L | 328_A | 1.227 | 0.98 |
| 24_R | 275_V | 1.226 | 0.98 |
| 261_G | 378_L | 1.224 | 0.98 |
| 314_V | 339_F | 1.219 | 0.98 |
| 299_I | 307_I | 1.215 | 0.98 |
| 83_E | 98_T | 1.210 | 0.98 |
| 117_A | 203_V | 1.209 | 0.98 |
| 19_T | 272_V | 1.204 | 0.98 |
| 86_L | 122_A | 1.201 | 0.98 |
| 109_A | 114_L | 1.198 | 0.98 |
| 312_S | 339_F | 1.197 | 0.98 |
| 122_A | 140_I | 1.193 | 0.98 |
| 41_G | 278_R | 1.185 | 0.98 |
| 79_I | 142_T | 1.184 | 0.98 |
| 213_W | 229_F | 1.177 | 0.98 |
| 188_T | 192_V | 1.171 | 0.98 |
| 129_V | 136_G | 1.163 | 0.97 |
| 310_L | 335_A | 1.160 | 0.97 |
| 348_F | 351_L | 1.156 | 0.97 |
| 298_I | 301_E | 1.154 | 0.97 |
| 25_L | 46_R | 1.152 | 0.97 |
| 262_R | 307_I | 1.151 | 0.97 |
| 260_A | 286_E | 1.140 | 0.97 |
| 113_Q | 116_T | 1.126 | 0.97 |
| 181_K | 184_D | 1.120 | 0.96 |
| 262_R | 308_D | 1.115 | 0.96 |
| 26_D | 367_I | 1.112 | 0.96 |
| 207_V | 212_G | 1.103 | 0.96 |
| 327_K | 331_Y | 1.101 | 0.96 |
| 295_E | 298_I | 1.094 | 0.96 |
| 294_E | 319_I | 1.093 | 0.96 |
| 76_G | 142_T | 1.092 | 0.96 |
| 260_A | 285_Y | 1.091 | 0.96 |
| 53_A | 57_R | 1.088 | 0.96 |
| 298_I | 302_E | 1.088 | 0.96 |
| 176_P | 219_R | 1.087 | 0.96 |
| 218_S | 224_A | 1.079 | 0.95 |
| 129_V | 138_V | 1.077 | 0.95 |
| 343_Y | 348_F | 1.070 | 0.95 |
| 322_P | 352_L | 1.068 | 0.95 |
| 297_L | 319_I | 1.067 | 0.95 |
| 314_V | 352_L | 1.067 | 0.95 |
| 39_Y | 43_N | 1.067 | 0.95 |
| 340_I | 365_I | 1.065 | 0.95 |
| 72_V | 106_Q | 1.065 | 0.95 |
| 266_V | 324_L | 1.064 | 0.95 |
| 218_S | 222_E | 1.062 | 0.95 |
| 23_L | 275_V | 1.060 | 0.95 |
| 137_V | 168_S | 1.057 | 0.95 |
| 50_V | 366_D | 1.057 | 0.95 |
| 70_R | 109_A | 1.053 | 0.95 |
| 24_R | 41_G | 1.044 | 0.94 |
| 270_D | 291_A | 1.043 | 0.94 |
| 75_L | 163_A | 1.038 | 0.94 |
| 188_T | 193_G | 1.038 | 0.94 |
| 207_V | 214_I | 1.036 | 0.94 |
| 267_E | 316_M | 1.035 | 0.94 |
| 203_V | 207_V | 1.034 | 0.94 |
| 303_N | 307_I | 1.031 | 0.94 |
| 341_S | 360_F | 1.030 | 0.94 |
| 300_A | 335_A | 1.029 | 0.94 |
| 20_A | 48_T | 1.023 | 0.93 |
| 35_G | 38_S | 1.023 | 0.93 |
| 188_T | 191_P | 1.019 | 0.93 |
| 276_A | 340_I | 1.018 | 0.93 |
| 20_A | 271_A | 1.017 | 0.93 |
| 290_A | 296_A | 1.002 | 0.92 |
| 108_R | 233_Y | 1.001 | 0.92 |
| 185_P | 205_G | 1.000 | 0.92 |
| 261_G | 308_D | 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 | |
| 4i5sA | 2 | 0.5486 | 100 | 0.539 | Contact Map |
| 4gczA | 2 | 0.5906 | 100 | 0.539 | Contact Map |
| 3a0rA | 1 | 0.5512 | 100 | 0.545 | Contact Map |
| 3jz3A | 2 | 0.4121 | 100 | 0.546 | Contact Map |
| 4mpcA | 1 | 0.6142 | 100 | 0.558 | Contact Map |
| 4e01A | 1 | 0.5591 | 100 | 0.559 | Contact Map |
| 4q20A | 2 | 0.5591 | 100 | 0.559 | Contact Map |
| 3d36A | 2 | 0.5512 | 100 | 0.559 | Contact Map |
| 2q8gA | 1 | 0.6142 | 100 | 0.561 | Contact Map |
| 4bixA | 2 | 0.5459 | 100 | 0.571 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)