| alex2 |
| ID: | 1452273634 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 347 (329) | ||
| Sequences: | 12172 (6734) | ||
| Seq/Len: | 36.997 | ||
| Nf(neff/√len): | 371.3 |
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: 36.997).
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 |
| 216_E | 220_H | 3.836 | 1.00 |
| 109_R | 136_R | 3.696 | 1.00 |
| 272_M | 310_E | 3.141 | 1.00 |
| 164_V | 267_I | 2.999 | 1.00 |
| 197_A | 262_E | 2.988 | 1.00 |
| 186_S | 266_G | 2.967 | 1.00 |
| 205_N | 255_E | 2.671 | 1.00 |
| 88_E | 132_G | 2.648 | 1.00 |
| 305_R | 309_E | 2.633 | 1.00 |
| 320_D | 323_T | 2.487 | 1.00 |
| 297_G | 300_L | 2.433 | 1.00 |
| 175_V | 274_A | 2.355 | 1.00 |
| 112_V | 130_A | 2.330 | 1.00 |
| 22_T | 37_S | 2.242 | 1.00 |
| 306_L | 309_E | 2.234 | 1.00 |
| 268_V | 310_E | 2.233 | 1.00 |
| 217_R | 221_E | 2.224 | 1.00 |
| 166_I | 171_T | 2.218 | 1.00 |
| 304_D | 317_V | 2.189 | 1.00 |
| 93_H | 97_Q | 2.166 | 1.00 |
| 124_R | 128_E | 2.165 | 1.00 |
| 166_I | 297_G | 2.084 | 1.00 |
| 22_T | 94_F | 2.067 | 1.00 |
| 194_F | 263_P | 2.048 | 1.00 |
| 113_C | 329_G | 2.028 | 1.00 |
| 269_S | 273_V | 2.022 | 1.00 |
| 299_L | 322_L | 2.021 | 1.00 |
| 255_E | 258_E | 2.013 | 1.00 |
| 20_A | 168_G | 1.943 | 1.00 |
| 95_I | 99_H | 1.926 | 1.00 |
| 261_Q | 265_T | 1.921 | 1.00 |
| 195_D | 219_K | 1.896 | 1.00 |
| 260_L | 264_L | 1.886 | 1.00 |
| 323_T | 327_R | 1.880 | 1.00 |
| 252_N | 255_E | 1.861 | 1.00 |
| 271_V | 307_L | 1.857 | 1.00 |
| 162_M | 175_V | 1.843 | 1.00 |
| 197_A | 200_N | 1.842 | 1.00 |
| 25_Y | 326_A | 1.822 | 1.00 |
| 19_T | 169_G | 1.730 | 1.00 |
| 304_D | 308_M | 1.714 | 1.00 |
| 306_L | 310_E | 1.712 | 1.00 |
| 165_D | 172_E | 1.697 | 1.00 |
| 258_E | 261_Q | 1.684 | 1.00 |
| 159_T | 289_R | 1.684 | 1.00 |
| 25_Y | 330_G | 1.662 | 1.00 |
| 253_S | 257_L | 1.656 | 1.00 |
| 92_Q | 96_K | 1.652 | 1.00 |
| 261_Q | 306_L | 1.645 | 1.00 |
| 293_L | 307_L | 1.640 | 1.00 |
| 260_L | 300_L | 1.636 | 1.00 |
| 173_V | 270_A | 1.635 | 1.00 |
| 141_I | 146_A | 1.635 | 1.00 |
| 260_L | 263_P | 1.631 | 1.00 |
| 202_V | 249_F | 1.596 | 1.00 |
| 41_I | 89_K | 1.591 | 1.00 |
| 202_V | 215_A | 1.582 | 1.00 |
| 116_V | 144_P | 1.580 | 1.00 |
| 185_S | 273_V | 1.569 | 1.00 |
| 162_M | 271_V | 1.569 | 1.00 |
| 273_V | 277_Q | 1.558 | 1.00 |
| 264_L | 302_N | 1.552 | 1.00 |
| 198_I | 215_A | 1.550 | 1.00 |
| 274_A | 278_C | 1.549 | 1.00 |
| 166_I | 194_F | 1.543 | 1.00 |
| 201_Y | 259_A | 1.543 | 1.00 |
| 227_P | 250_T | 1.536 | 1.00 |
| 308_M | 314_P | 1.532 | 1.00 |
| 89_K | 92_Q | 1.529 | 1.00 |
| 109_R | 138_V | 1.515 | 1.00 |
| 198_I | 251_L | 1.512 | 1.00 |
| 17_L | 91_L | 1.507 | 1.00 |
| 291_M | 311_T | 1.506 | 1.00 |
| 24_I | 94_F | 1.498 | 1.00 |
| 199_I | 212_E | 1.486 | 1.00 |
| 114_V | 123_R | 1.481 | 1.00 |
| 175_V | 278_C | 1.474 | 1.00 |
| 142_E | 145_M | 1.470 | 1.00 |
| 268_V | 306_L | 1.458 | 1.00 |
| 199_I | 215_A | 1.450 | 1.00 |
| 114_V | 140_L | 1.448 | 1.00 |
| 164_V | 171_T | 1.428 | 1.00 |
| 191_G | 297_G | 1.421 | 1.00 |
| 196_E | 200_N | 1.395 | 0.99 |
| 194_F | 260_L | 1.393 | 0.99 |
| 219_K | 297_G | 1.390 | 0.99 |
| 93_H | 96_K | 1.385 | 0.99 |
| 191_G | 219_K | 1.383 | 0.99 |
| 201_Y | 205_N | 1.381 | 0.99 |
| 173_V | 274_A | 1.376 | 0.99 |
| 164_V | 173_V | 1.372 | 0.99 |
| 56_G | 59_A | 1.369 | 0.99 |
| 162_M | 173_V | 1.367 | 0.99 |
| 143_E | 172_E | 1.367 | 0.99 |
| 109_R | 137_E | 1.359 | 0.99 |
| 87_T | 91_L | 1.356 | 0.99 |
| 259_A | 262_E | 1.350 | 0.99 |
| 128_E | 131_Q | 1.317 | 0.99 |
| 127_R | 131_Q | 1.315 | 0.99 |
| 305_R | 308_M | 1.314 | 0.99 |
| 320_D | 327_R | 1.309 | 0.99 |
| 17_L | 87_T | 1.296 | 0.99 |
| 124_R | 127_R | 1.294 | 0.99 |
| 256_I | 300_L | 1.292 | 0.99 |
| 96_K | 100_S | 1.291 | 0.99 |
| 160_G | 177_S | 1.289 | 0.99 |
| 62_M | 66_T | 1.283 | 0.99 |
| 10_S | 109_R | 1.280 | 0.99 |
| 168_G | 192_D | 1.280 | 0.99 |
| 264_L | 306_L | 1.275 | 0.99 |
| 268_V | 272_M | 1.267 | 0.99 |
| 85_F | 132_G | 1.262 | 0.99 |
| 37_S | 90_M | 1.261 | 0.99 |
| 201_Y | 255_E | 1.252 | 0.99 |
| 194_F | 297_G | 1.246 | 0.98 |
| 307_L | 315_V | 1.246 | 0.98 |
| 119_T | 122_E | 1.243 | 0.98 |
| 214_T | 217_R | 1.239 | 0.98 |
| 12_D | 138_V | 1.231 | 0.98 |
| 166_I | 303_L | 1.225 | 0.98 |
| 94_F | 97_Q | 1.220 | 0.98 |
| 141_I | 332_A | 1.214 | 0.98 |
| 13_L | 24_I | 1.208 | 0.98 |
| 229_D | 248_G | 1.208 | 0.98 |
| 269_S | 272_M | 1.201 | 0.98 |
| 261_Q | 302_N | 1.191 | 0.98 |
| 83_D | 86_V | 1.191 | 0.98 |
| 87_T | 126_I | 1.185 | 0.98 |
| 143_E | 325_V | 1.184 | 0.98 |
| 196_E | 212_E | 1.180 | 0.98 |
| 302_N | 305_R | 1.173 | 0.98 |
| 197_A | 263_P | 1.170 | 0.97 |
| 171_T | 267_I | 1.169 | 0.97 |
| 173_V | 271_V | 1.159 | 0.97 |
| 257_L | 305_R | 1.159 | 0.97 |
| 53_A | 89_K | 1.149 | 0.97 |
| 272_M | 276_E | 1.149 | 0.97 |
| 197_A | 260_L | 1.139 | 0.97 |
| 191_G | 195_D | 1.136 | 0.97 |
| 110_V | 135_A | 1.131 | 0.97 |
| 151_A | 292_V | 1.130 | 0.97 |
| 273_V | 276_E | 1.121 | 0.97 |
| 214_T | 218_I | 1.119 | 0.96 |
| 194_F | 256_I | 1.114 | 0.96 |
| 66_T | 70_I | 1.109 | 0.96 |
| 195_D | 216_E | 1.109 | 0.96 |
| 41_I | 86_V | 1.103 | 0.96 |
| 17_L | 126_I | 1.103 | 0.96 |
| 57_H | 61_Q | 1.100 | 0.96 |
| 127_R | 140_L | 1.093 | 0.96 |
| 175_V | 287_S | 1.083 | 0.96 |
| 95_I | 110_V | 1.082 | 0.96 |
| 148_A | 176_I | 1.080 | 0.95 |
| 66_T | 69_N | 1.079 | 0.95 |
| 14_S | 326_A | 1.069 | 0.95 |
| 164_V | 271_V | 1.062 | 0.95 |
| 293_L | 298_A | 1.062 | 0.95 |
| 255_E | 259_A | 1.059 | 0.95 |
| 294_T | 324_C | 1.055 | 0.95 |
| 62_M | 65_R | 1.053 | 0.95 |
| 63_L | 66_T | 1.052 | 0.95 |
| 254_N | 257_L | 1.052 | 0.95 |
| 88_E | 92_Q | 1.047 | 0.94 |
| 213_A | 216_E | 1.045 | 0.94 |
| 147_A | 294_T | 1.042 | 0.94 |
| 61_Q | 64_G | 1.042 | 0.94 |
| 128_E | 132_G | 1.037 | 0.94 |
| 22_T | 90_M | 1.027 | 0.94 |
| 81_I | 84_F | 1.021 | 0.93 |
| 150_G | 327_R | 1.020 | 0.93 |
| 118_A | 122_E | 1.018 | 0.93 |
| 256_I | 297_G | 1.018 | 0.93 |
| 148_A | 161_S | 1.009 | 0.93 |
| 204_R | 207_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 | |
| 1jceA | 1 | 0.9481 | 100 | 0.176 | Contact Map |
| 4czgA | 1 | 0.9193 | 100 | 0.219 | Contact Map |
| 2v7yA | 1 | 0.9395 | 100 | 0.253 | Contact Map |
| 4fl9A | 1 | 0.9078 | 100 | 0.254 | Contact Map |
| 1k8kA | 1 | 0.9424 | 100 | 0.254 | Contact Map |
| 4jneA | 2 | 0.9366 | 100 | 0.256 | Contact Map |
| 3dwlA | 2 | 0.8991 | 100 | 0.258 | Contact Map |
| 4pl7A | 2 | 0.8847 | 100 | 0.269 | Contact Map |
| 5afuA | 8 | 0.9395 | 100 | 0.27 | Contact Map |
| 4b1yB | 1 | 0.9222 | 100 | 0.273 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)