| cckA |
| ID: | 1446558196 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 380 (376) | ||
| Sequences: | 21444 (16674.1) | ||
| Seq/Len: | 57.032 | ||
| Nf(neff/√len): | 859.9 |
HHblits Results: (2015_06)
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: 57.032).
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_H | 307_V | 4.155 | 1.00 |
| 273_R | 289_E | 3.355 | 1.00 |
| 292_S | 318_E | 3.259 | 1.00 |
| 312_S | 324_L | 3.214 | 1.00 |
| 72_L | 108_V | 3.184 | 1.00 |
| 176_L | 213_C | 3.089 | 1.00 |
| 216_E | 219_K | 3.045 | 1.00 |
| 212_F | 224_R | 2.946 | 1.00 |
| 24_S | 44_I | 2.942 | 1.00 |
| 320_D | 323_T | 2.873 | 1.00 |
| 291_S | 295_E | 2.857 | 1.00 |
| 294_V | 318_E | 2.805 | 1.00 |
| 172_A | 175_V | 2.791 | 1.00 |
| 201_Y | 205_K | 2.692 | 1.00 |
| 165_E | 222_T | 2.605 | 1.00 |
| 262_T | 286_T | 2.522 | 1.00 |
| 327_E | 330_K | 2.367 | 1.00 |
| 171_I | 175_V | 2.343 | 1.00 |
| 108_V | 207_T | 2.297 | 1.00 |
| 262_T | 288_H | 2.278 | 1.00 |
| 266_V | 296_A | 2.255 | 1.00 |
| 359_G | 373_V | 2.251 | 1.00 |
| 161_V | 226_F | 2.243 | 1.00 |
| 200_V | 211_I | 2.223 | 1.00 |
| 128_M | 167_S | 2.211 | 1.00 |
| 273_R | 291_S | 2.184 | 1.00 |
| 71_V | 107_K | 2.149 | 1.00 |
| 283_R | 371_A | 2.142 | 1.00 |
| 325_L | 337_F | 2.100 | 1.00 |
| 161_V | 224_R | 2.097 | 1.00 |
| 21_I | 48_A | 2.071 | 1.00 |
| 277_S | 289_E | 2.048 | 1.00 |
| 163_E | 222_T | 2.041 | 1.00 |
| 70_E | 110_I | 2.010 | 1.00 |
| 290_A | 299_V | 2.005 | 1.00 |
| 301_E | 331_R | 1.999 | 1.00 |
| 277_S | 281_T | 1.964 | 1.00 |
| 205_K | 210_F | 1.931 | 1.00 |
| 297_L | 324_L | 1.916 | 1.00 |
| 137_R | 165_E | 1.910 | 1.00 |
| 213_C | 223_F | 1.908 | 1.00 |
| 175_V | 178_K | 1.894 | 1.00 |
| 98_D | 137_R | 1.879 | 1.00 |
| 288_H | 299_V | 1.878 | 1.00 |
| 294_V | 298_E | 1.877 | 1.00 |
| 73_N | 76_D | 1.877 | 1.00 |
| 137_R | 163_E | 1.867 | 1.00 |
| 172_A | 217_V | 1.851 | 1.00 |
| 163_E | 224_R | 1.834 | 1.00 |
| 214_D | 222_T | 1.781 | 1.00 |
| 312_S | 325_L | 1.778 | 1.00 |
| 267_E | 273_R | 1.768 | 1.00 |
| 159_Y | 226_F | 1.765 | 1.00 |
| 339_F | 357_Q | 1.764 | 1.00 |
| 323_T | 327_E | 1.720 | 1.00 |
| 325_L | 357_Q | 1.719 | 1.00 |
| 292_S | 295_E | 1.718 | 1.00 |
| 352_L | 355_D | 1.697 | 1.00 |
| 309_I | 374_V | 1.696 | 1.00 |
| 300_F | 328_L | 1.670 | 1.00 |
| 139_R | 161_V | 1.651 | 1.00 |
| 116_V | 204_I | 1.646 | 1.00 |
| 263_V | 285_Y | 1.605 | 1.00 |
| 351_N | 355_D | 1.604 | 1.00 |
| 135_T | 165_E | 1.592 | 1.00 |
| 319_M | 327_E | 1.589 | 1.00 |
| 319_M | 323_T | 1.586 | 1.00 |
| 171_I | 179_I | 1.580 | 1.00 |
| 173_P | 176_L | 1.562 | 1.00 |
| 329_R | 358_F | 1.551 | 1.00 |
| 112_Q | 115_Q | 1.542 | 1.00 |
| 162_V | 225_I | 1.525 | 1.00 |
| 261_A | 285_Y | 1.524 | 1.00 |
| 96_K | 133_D | 1.521 | 1.00 |
| 366_S | 369_Q | 1.521 | 1.00 |
| 338_V | 373_V | 1.514 | 1.00 |
| 352_L | 356_A | 1.512 | 1.00 |
| 28_L | 45_K | 1.502 | 1.00 |
| 34_S | 38_F | 1.471 | 1.00 |
| 28_L | 42_M | 1.466 | 1.00 |
| 293_G | 324_L | 1.445 | 1.00 |
| 94_K | 133_D | 1.442 | 1.00 |
| 133_D | 167_S | 1.439 | 1.00 |
| 267_E | 316_M | 1.437 | 1.00 |
| 265_L | 276_G | 1.436 | 1.00 |
| 310_V | 335_I | 1.432 | 1.00 |
| 265_L | 287_V | 1.423 | 1.00 |
| 314_V | 322_P | 1.415 | 1.00 |
| 33_P | 37_S | 1.413 | 1.00 |
| 204_I | 225_I | 1.409 | 1.00 |
| 178_K | 184_F | 1.403 | 0.99 |
| 359_G | 376_D | 1.401 | 0.99 |
| 315_V | 343_Y | 1.390 | 0.99 |
| 96_K | 135_T | 1.390 | 0.99 |
| 181_E | 184_F | 1.387 | 0.99 |
| 299_V | 307_V | 1.381 | 0.99 |
| 264_L | 290_A | 1.376 | 0.99 |
| 23_A | 275_G | 1.373 | 0.99 |
| 353_P | 356_A | 1.366 | 0.99 |
| 116_V | 203_I | 1.365 | 0.99 |
| 262_T | 307_V | 1.364 | 0.99 |
| 45_K | 49_N | 1.364 | 0.99 |
| 323_T | 326_G | 1.359 | 0.99 |
| 98_D | 135_T | 1.349 | 0.99 |
| 279_A | 367_L | 1.349 | 0.99 |
| 314_V | 339_F | 1.349 | 0.99 |
| 166_D | 170_G | 1.343 | 0.99 |
| 180_F | 211_I | 1.328 | 0.99 |
| 25_D | 45_K | 1.321 | 0.99 |
| 117_V | 162_V | 1.320 | 0.99 |
| 34_S | 37_S | 1.317 | 0.99 |
| 176_L | 215_S | 1.300 | 0.99 |
| 270_D | 273_R | 1.285 | 0.99 |
| 263_V | 309_I | 1.280 | 0.99 |
| 85_L | 121_A | 1.280 | 0.99 |
| 312_S | 339_F | 1.277 | 0.99 |
| 29_T | 282_S | 1.275 | 0.99 |
| 52_A | 56_R | 1.268 | 0.99 |
| 139_R | 163_E | 1.268 | 0.99 |
| 204_I | 209_G | 1.267 | 0.99 |
| 300_F | 335_I | 1.262 | 0.99 |
| 359_G | 377_V | 1.257 | 0.99 |
| 80_D | 114_E | 1.244 | 0.98 |
| 19_A | 23_A | 1.244 | 0.98 |
| 214_D | 224_R | 1.236 | 0.98 |
| 297_L | 327_E | 1.235 | 0.98 |
| 310_V | 328_L | 1.231 | 0.98 |
| 88_L | 91_N | 1.224 | 0.98 |
| 215_S | 221_S | 1.216 | 0.98 |
| 293_G | 319_M | 1.213 | 0.98 |
| 187_K | 190_G | 1.213 | 0.98 |
| 18_T | 272_V | 1.213 | 0.98 |
| 179_I | 213_C | 1.208 | 0.98 |
| 116_V | 200_V | 1.204 | 0.98 |
| 35_D | 38_F | 1.197 | 0.98 |
| 215_S | 219_K | 1.190 | 0.98 |
| 200_V | 204_I | 1.188 | 0.98 |
| 121_A | 136_V | 1.182 | 0.98 |
| 141_V | 161_V | 1.177 | 0.98 |
| 262_T | 308_D | 1.176 | 0.98 |
| 128_M | 132_G | 1.172 | 0.98 |
| 173_P | 216_E | 1.169 | 0.97 |
| 290_A | 296_A | 1.161 | 0.97 |
| 133_D | 165_E | 1.161 | 0.97 |
| 116_V | 225_I | 1.155 | 0.97 |
| 266_V | 324_L | 1.154 | 0.97 |
| 288_H | 305_G | 1.154 | 0.97 |
| 108_V | 113_F | 1.153 | 0.97 |
| 345_E | 348_F | 1.148 | 0.97 |
| 104_W | 140_N | 1.148 | 0.97 |
| 185_T | 188_E | 1.148 | 0.97 |
| 178_K | 181_E | 1.147 | 0.97 |
| 373_V | 376_D | 1.140 | 0.97 |
| 262_T | 305_G | 1.139 | 0.97 |
| 185_T | 190_G | 1.137 | 0.97 |
| 297_L | 319_M | 1.133 | 0.97 |
| 159_Y | 228_P | 1.131 | 0.97 |
| 128_M | 134_L | 1.121 | 0.97 |
| 341_S | 360_F | 1.119 | 0.96 |
| 25_D | 367_L | 1.116 | 0.96 |
| 78_L | 138_T | 1.106 | 0.96 |
| 27_L | 41_I | 1.106 | 0.96 |
| 298_E | 302_A | 1.095 | 0.96 |
| 24_S | 48_A | 1.091 | 0.96 |
| 298_E | 301_E | 1.082 | 0.96 |
| 351_N | 356_A | 1.081 | 0.95 |
| 19_A | 271_A | 1.071 | 0.95 |
| 373_V | 377_V | 1.068 | 0.95 |
| 85_L | 118_V | 1.067 | 0.95 |
| 210_F | 226_F | 1.066 | 0.95 |
| 347_A | 350_R | 1.058 | 0.95 |
| 314_V | 357_Q | 1.051 | 0.94 |
| 349_A | 353_P | 1.047 | 0.94 |
| 22_M | 275_G | 1.045 | 0.94 |
| 75_T | 138_T | 1.042 | 0.94 |
| 311_V | 370_L | 1.039 | 0.94 |
| 112_Q | 203_I | 1.032 | 0.94 |
| 57_Q | 112_Q | 1.031 | 0.94 |
| 276_G | 365_F | 1.029 | 0.94 |
| 24_S | 45_K | 1.029 | 0.94 |
| 131_G | 134_L | 1.028 | 0.94 |
| 296_A | 324_L | 1.027 | 0.94 |
| 300_F | 310_V | 1.027 | 0.94 |
| 215_S | 218_G | 1.018 | 0.93 |
| 171_I | 176_L | 1.013 | 0.93 |
| 334_D | 358_F | 1.011 | 0.93 |
| 295_E | 298_E | 1.010 | 0.93 |
| 82_R | 86_A | 1.009 | 0.93 |
| 69_P | 108_V | 1.009 | 0.93 |
| 340_V | 365_F | 1.006 | 0.93 |
| 19_A | 47_N | 1.003 | 0.93 |
| 182_P | 202_G | 1.002 | 0.92 |
| 171_I | 177_K | 1.000 | 0.92 |
| 369_Q | 372_T | 1.000 | 0.92 |
| 128_M | 131_G | 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 | |
| 4gczA | 2 | 0.5895 | 100 | 0.553 | Contact Map |
| 4i5sA | 2 | 0.5447 | 100 | 0.559 | Contact Map |
| 3a0rA | 1 | 0.55 | 100 | 0.566 | Contact Map |
| 3jz3A | 2 | 0.4132 | 100 | 0.571 | Contact Map |
| 3d36A | 2 | 0.5526 | 100 | 0.574 | Contact Map |
| 4e01A | 1 | 0.5579 | 100 | 0.577 | Contact Map |
| 4mpcA | 1 | 0.6132 | 100 | 0.577 | Contact Map |
| 4q20A | 2 | 0.5579 | 100 | 0.58 | Contact Map |
| 2q8gA | 1 | 0.6105 | 100 | 0.582 | Contact Map |
| 2e0aA | 2 | 0.6132 | 100 | 0.589 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)