| b2ar |
| ID: | 1436276333 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 413 (366) | ||
| Sequences: | 8106 (5437.3) | ||
| Seq/Len: | 22.148 | ||
| Nf(neff/√len): | 284.2 |
Jackhmmer Results: (2015_01_07)
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: 22.148).
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 |
| 47_I | 83_G | 5.444 | 1.00 |
| 74_S | 158_W | 3.455 | 1.00 |
| 217_F | 221_R | 3.406 | 1.00 |
| 132_Y | 137_S | 3.043 | 1.00 |
| 126_V | 157_V | 2.777 | 1.00 |
| 74_S | 123_T | 2.745 | 1.00 |
| 70_Y | 154_I | 2.636 | 1.00 |
| 104_F | 108_F | 2.549 | 1.00 |
| 99_W | 102_G | 2.410 | 1.00 |
| 111_S | 115_L | 2.372 | 1.00 |
| 126_V | 153_I | 2.289 | 1.00 |
| 55_I | 73_T | 2.257 | 1.00 |
| 214_I | 218_V | 2.224 | 1.00 |
| 281_T | 325_I | 2.110 | 1.00 |
| 64_L | 69_N | 2.028 | 1.00 |
| 132_Y | 221_R | 2.018 | 1.00 |
| 79_D | 322_N | 1.988 | 1.00 |
| 103_N | 107_E | 1.973 | 1.00 |
| 132_Y | 136_T | 1.852 | 1.00 |
| 286_W | 315_G | 1.830 | 1.00 |
| 58_I | 73_T | 1.820 | 1.00 |
| 115_L | 162_G | 1.799 | 1.00 |
| 50_G | 320_G | 1.797 | 1.00 |
| 212_L | 283_T | 1.697 | 1.00 |
| 58_I | 64_L | 1.694 | 1.00 |
| 148_N | 152_V | 1.680 | 1.00 |
| 221_R | 224_Q | 1.679 | 1.00 |
| 71_F | 150_A | 1.677 | 1.00 |
| 220_S | 224_Q | 1.664 | 1.00 |
| 137_S | 140_K | 1.647 | 1.00 |
| 52_V | 56_T | 1.643 | 1.00 |
| 31_V | 35_G | 1.578 | 1.00 |
| 81_V | 116_C | 1.559 | 1.00 |
| 132_Y | 218_V | 1.555 | 1.00 |
| 119_A | 161_S | 1.550 | 1.00 |
| 184_C | 187_N | 1.525 | 1.00 |
| 34_V | 38_I | 1.515 | 1.00 |
| 52_V | 80_L | 1.512 | 1.00 |
| 71_F | 127_I | 1.491 | 1.00 |
| 186_A | 190_C | 1.482 | 1.00 |
| 47_I | 320_G | 1.475 | 1.00 |
| 224_Q | 228_R | 1.454 | 1.00 |
| 74_S | 154_I | 1.450 | 1.00 |
| 204_S | 209_Y | 1.443 | 1.00 |
| 299_Q | 302_L | 1.434 | 1.00 |
| 291_I | 295_V | 1.431 | 1.00 |
| 216_V | 220_S | 1.430 | 1.00 |
| 48_V | 83_G | 1.425 | 1.00 |
| 184_C | 189_T | 1.418 | 1.00 |
| 54_V | 323_P | 1.404 | 0.99 |
| 225_E | 228_R | 1.395 | 0.99 |
| 106_C | 184_C | 1.390 | 0.99 |
| 46_A | 320_G | 1.386 | 0.99 |
| 221_R | 225_E | 1.386 | 0.99 |
| 115_L | 165_S | 1.382 | 0.99 |
| 54_V | 322_N | 1.380 | 0.99 |
| 130_D | 145_L | 1.379 | 0.99 |
| 129_V | 218_V | 1.379 | 0.99 |
| 124_L | 215_M | 1.373 | 0.99 |
| 201_I | 298_I | 1.361 | 0.99 |
| 78_A | 119_A | 1.345 | 0.99 |
| 363_Q | 366_Y | 1.344 | 0.99 |
| 56_T | 339_L | 1.343 | 0.99 |
| 76_A | 79_D | 1.342 | 0.99 |
| 283_T | 287_L | 1.337 | 0.99 |
| 123_T | 158_W | 1.335 | 0.99 |
| 125_C | 214_I | 1.334 | 0.99 |
| 125_C | 218_V | 1.333 | 0.99 |
| 148_N | 151_R | 1.319 | 0.99 |
| 82_M | 319_S | 1.318 | 0.99 |
| 92_A | 101_F | 1.309 | 0.99 |
| 184_C | 188_E | 1.301 | 0.99 |
| 125_C | 215_M | 1.296 | 0.99 |
| 102_G | 105_W | 1.292 | 0.99 |
| 66_T | 69_N | 1.287 | 0.99 |
| 136_T | 225_E | 1.287 | 0.99 |
| 79_D | 120_S | 1.285 | 0.99 |
| 152_V | 156_M | 1.277 | 0.99 |
| 186_A | 189_T | 1.276 | 0.99 |
| 78_A | 120_S | 1.273 | 0.99 |
| 373_E | 376_L | 1.270 | 0.99 |
| 158_W | 323_P | 1.268 | 0.99 |
| 133_F | 144_L | 1.266 | 0.99 |
| 123_T | 154_I | 1.259 | 0.99 |
| 121_I | 282_F | 1.247 | 0.99 |
| 132_Y | 217_F | 1.242 | 0.98 |
| 277_I | 325_I | 1.240 | 0.98 |
| 292_V | 311_L | 1.237 | 0.98 |
| 368_V | 371_E | 1.236 | 0.98 |
| 61_F | 335_A | 1.235 | 0.98 |
| 306_E | 310_L | 1.234 | 0.98 |
| 268_E | 272_L | 1.225 | 0.98 |
| 71_F | 145_L | 1.225 | 0.98 |
| 119_A | 123_T | 1.223 | 0.98 |
| 55_I | 80_L | 1.222 | 0.98 |
| 287_L | 291_I | 1.216 | 0.98 |
| 223_F | 227_K | 1.215 | 0.98 |
| 75_L | 123_T | 1.212 | 0.98 |
| 289_F | 293_N | 1.209 | 0.98 |
| 153_I | 157_V | 1.209 | 0.98 |
| 151_R | 155_L | 1.206 | 0.98 |
| 141_Y | 145_L | 1.205 | 0.98 |
| 131_R | 134_A | 1.192 | 0.98 |
| 215_M | 279_M | 1.188 | 0.98 |
| 130_D | 134_A | 1.185 | 0.98 |
| 248_V | 251_D | 1.182 | 0.98 |
| 147_K | 151_R | 1.174 | 0.98 |
| 198_A | 202_A | 1.164 | 0.97 |
| 202_A | 206_V | 1.164 | 0.97 |
| 146_T | 149_K | 1.158 | 0.97 |
| 204_S | 294_I | 1.158 | 0.97 |
| 307_V | 311_L | 1.156 | 0.97 |
| 54_V | 332_F | 1.149 | 0.97 |
| 184_C | 190_C | 1.144 | 0.97 |
| 44_V | 91_A | 1.141 | 0.97 |
| 76_A | 322_N | 1.138 | 0.97 |
| 79_D | 318_N | 1.135 | 0.97 |
| 49_F | 52_V | 1.131 | 0.97 |
| 128_A | 219_Y | 1.128 | 0.97 |
| 317_V | 321_F | 1.124 | 0.97 |
| 197_Q | 298_I | 1.120 | 0.96 |
| 186_A | 191_C | 1.105 | 0.96 |
| 128_A | 218_V | 1.103 | 0.96 |
| 20_P | 23_D | 1.102 | 0.96 |
| 226_A | 271_A | 1.097 | 0.96 |
| 79_D | 319_S | 1.096 | 0.96 |
| 152_V | 155_L | 1.095 | 0.96 |
| 223_F | 272_L | 1.094 | 0.96 |
| 67_V | 150_A | 1.091 | 0.96 |
| 37_G | 95_L | 1.088 | 0.96 |
| 358_G | 361_G | 1.080 | 0.95 |
| 133_F | 137_S | 1.079 | 0.95 |
| 145_L | 149_K | 1.073 | 0.95 |
| 207_S | 211_P | 1.071 | 0.95 |
| 125_C | 211_P | 1.066 | 0.95 |
| 37_G | 41_S | 1.064 | 0.95 |
| 134_A | 138_P | 1.063 | 0.95 |
| 289_F | 315_G | 1.061 | 0.95 |
| 119_A | 158_W | 1.058 | 0.95 |
| 70_Y | 151_R | 1.058 | 0.95 |
| 62_E | 65_Q | 1.058 | 0.95 |
| 362_E | 366_Y | 1.055 | 0.95 |
| 44_V | 83_G | 1.053 | 0.95 |
| 48_V | 80_L | 1.052 | 0.95 |
| 219_Y | 222_V | 1.052 | 0.95 |
| 353_G | 359_N | 1.050 | 0.94 |
| 194_F | 198_A | 1.049 | 0.94 |
| 54_V | 327_C | 1.048 | 0.94 |
| 130_D | 275_L | 1.047 | 0.94 |
| 233_I | 236_S | 1.046 | 0.94 |
| 249_E | 253_R | 1.045 | 0.94 |
| 276_G | 280_G | 1.044 | 0.94 |
| 168_P | 174_Y | 1.044 | 0.94 |
| 73_T | 77_C | 1.042 | 0.94 |
| 358_G | 363_Q | 1.042 | 0.94 |
| 78_A | 158_W | 1.042 | 0.94 |
| 168_P | 172_H | 1.041 | 0.94 |
| 368_V | 373_E | 1.036 | 0.94 |
| 247_Q | 250_Q | 1.034 | 0.94 |
| 131_R | 318_N | 1.032 | 0.94 |
| 71_F | 123_T | 1.030 | 0.94 |
| 372_K | 377_L | 1.029 | 0.94 |
| 275_L | 279_M | 1.027 | 0.94 |
| 145_L | 153_I | 1.027 | 0.94 |
| 278_I | 325_I | 1.024 | 0.93 |
| 375_K | 380_D | 1.019 | 0.93 |
| 208_F | 287_L | 1.018 | 0.93 |
| 360_T | 363_Q | 1.018 | 0.93 |
| 29_D | 32_W | 1.017 | 0.93 |
| 372_K | 375_K | 1.016 | 0.93 |
| 377_L | 380_D | 1.012 | 0.93 |
| 122_E | 125_C | 1.009 | 0.93 |
| 136_T | 222_V | 1.007 | 0.93 |
| 122_E | 211_P | 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 | |
| 2rh1A | 1 | 0.7603 | 100 | 0.186 | Contact Map |
| 2r4rA | 1 | 0.523 | 100 | 0.238 | Contact Map |
| 2z73A | 2 | 0.8354 | 100 | 0.294 | Contact Map |
| 4pxzA | 1 | 0.7288 | 100 | 0.312 | Contact Map |
| 3uonA | 1 | 0.7409 | 100 | 0.322 | Contact Map |
| 4mbsA | 2 | 0.7676 | 100 | 0.322 | Contact Map |
| 4dklA | 1 | 0.7506 | 100 | 0.324 | Contact Map |
| 4grvA | 1 | 0.7433 | 100 | 0.326 | Contact Map |
| 3pblA | 2 | 0.7167 | 100 | 0.328 | Contact Map |
| 3emlA | 1 | 0.7579 | 100 | 0.329 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)