| ACTA1 |
| ID: | 1432285850 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 377 (368) | ||
| Sequences: | 5986 (2896.8) | ||
| Seq/Len: | 16.266 | ||
| Nf(neff/√len): | 151.0 |
HHblits Results: (2013_03)
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: 16.266).
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 |
| 104_P | 132_P | 4.724 | 1.00 |
| 212_R | 216_E | 4.270 | 1.00 |
| 157_S | 305_T | 3.173 | 1.00 |
| 155_L | 276_I | 2.953 | 1.00 |
| 316_Q | 330_K | 2.853 | 1.00 |
| 336_E | 339_Y | 2.850 | 1.00 |
| 157_S | 162_T | 2.812 | 1.00 |
| 213_D | 217_K | 2.658 | 1.00 |
| 68_T | 185_R | 2.651 | 1.00 |
| 314_R | 318_E | 2.611 | 1.00 |
| 280_T | 315_M | 2.556 | 1.00 |
| 198_R | 256_R | 2.540 | 1.00 |
| 305_T | 308_Y | 2.514 | 1.00 |
| 190_Y | 262_T | 2.419 | 1.00 |
| 313_D | 317_K | 2.337 | 1.00 |
| 166_P | 283_S | 2.280 | 1.00 |
| 123_Q | 127_E | 2.259 | 1.00 |
| 153_I | 164_N | 2.232 | 1.00 |
| 14_N | 88_W | 2.195 | 1.00 |
| 277_H | 318_E | 2.175 | 1.00 |
| 361_K | 365_D | 2.110 | 1.00 |
| 179_R | 275_G | 2.105 | 1.00 |
| 307_M | 338_K | 2.000 | 1.00 |
| 104_P | 134_M | 1.918 | 1.00 |
| 22_G | 346_S | 1.879 | 1.00 |
| 312_A | 333_A | 1.867 | 1.00 |
| 16_S | 160_G | 1.837 | 1.00 |
| 222_A | 228_E | 1.829 | 1.00 |
| 109_E | 118_R | 1.828 | 1.00 |
| 157_S | 311_I | 1.820 | 1.00 |
| 191_L | 252_I | 1.814 | 1.00 |
| 192_M | 208_R | 1.800 | 1.00 |
| 339_Y | 343_I | 1.800 | 1.00 |
| 57_G | 60_A | 1.767 | 1.00 |
| 85_E | 128_T | 1.765 | 1.00 |
| 155_L | 164_N | 1.764 | 1.00 |
| 107_L | 126_F | 1.731 | 1.00 |
| 195_L | 250_I | 1.725 | 1.00 |
| 278_E | 282_N | 1.724 | 1.00 |
| 299_N | 319_I | 1.705 | 1.00 |
| 125_M | 134_M | 1.703 | 1.00 |
| 119_E | 123_Q | 1.698 | 1.00 |
| 253_G | 256_R | 1.697 | 1.00 |
| 189_D | 193_K | 1.685 | 1.00 |
| 301_M | 315_M | 1.673 | 1.00 |
| 155_L | 162_T | 1.660 | 1.00 |
| 187_L | 259_C | 1.649 | 1.00 |
| 58_D | 62_S | 1.640 | 1.00 |
| 257_F | 305_T | 1.638 | 1.00 |
| 190_Y | 266_P | 1.630 | 1.00 |
| 25_G | 30_R | 1.627 | 1.00 |
| 19_V | 35_S | 1.608 | 1.00 |
| 264_F | 314_R | 1.602 | 1.00 |
| 89_H | 129_F | 1.596 | 1.00 |
| 25_G | 346_S | 1.594 | 1.00 |
| 137_A | 142_L | 1.587 | 1.00 |
| 194_I | 259_C | 1.572 | 1.00 |
| 156_D | 163_H | 1.570 | 1.00 |
| 150_T | 298_N | 1.556 | 1.00 |
| 336_E | 343_I | 1.554 | 1.00 |
| 144_L | 152_G | 1.551 | 1.00 |
| 104_P | 133_A | 1.542 | 1.00 |
| 298_N | 332_I | 1.535 | 1.00 |
| 315_M | 331_I | 1.525 | 1.00 |
| 21_A | 91_T | 1.493 | 1.00 |
| 35_S | 42_H | 1.481 | 1.00 |
| 166_P | 287_C | 1.476 | 1.00 |
| 220_Y | 228_E | 1.475 | 1.00 |
| 11_V | 342_W | 1.471 | 1.00 |
| 26_D | 30_R | 1.467 | 1.00 |
| 9_A | 134_M | 1.458 | 1.00 |
| 333_A | 337_R | 1.451 | 1.00 |
| 9_A | 349_A | 1.448 | 1.00 |
| 80_N | 83_D | 1.445 | 1.00 |
| 78_I | 81_W | 1.436 | 1.00 |
| 187_L | 263_L | 1.433 | 1.00 |
| 11_V | 345_G | 1.426 | 1.00 |
| 188_T | 215_K | 1.424 | 1.00 |
| 178_M | 286_K | 1.414 | 1.00 |
| 312_A | 316_Q | 1.408 | 1.00 |
| 105_T | 125_M | 1.397 | 0.99 |
| 17_G | 159_D | 1.389 | 0.99 |
| 29_P | 343_I | 1.382 | 0.99 |
| 159_D | 185_R | 1.376 | 0.99 |
| 176_A | 283_S | 1.362 | 0.99 |
| 155_L | 280_T | 1.359 | 0.99 |
| 108_T | 345_G | 1.354 | 0.99 |
| 219_C | 260_P | 1.352 | 0.99 |
| 310_G | 313_D | 1.348 | 0.99 |
| 287_C | 295_L | 1.339 | 0.99 |
| 113_N | 117_N | 1.336 | 0.99 |
| 198_R | 255_E | 1.333 | 0.99 |
| 260_P | 308_Y | 1.325 | 0.99 |
| 126_F | 129_F | 1.320 | 0.99 |
| 164_N | 279_T | 1.320 | 0.99 |
| 35_S | 39_R | 1.315 | 0.99 |
| 281_Y | 318_E | 1.306 | 0.99 |
| 359_I | 371_I | 1.306 | 0.99 |
| 316_Q | 331_I | 1.303 | 0.99 |
| 184_G | 215_K | 1.286 | 0.99 |
| 122_T | 136_V | 1.283 | 0.99 |
| 219_C | 308_Y | 1.283 | 0.99 |
| 153_I | 280_T | 1.273 | 0.99 |
| 22_G | 342_W | 1.272 | 0.99 |
| 191_L | 211_V | 1.270 | 0.99 |
| 215_K | 305_T | 1.264 | 0.99 |
| 90_H | 94_N | 1.260 | 0.99 |
| 241_S | 249_V | 1.258 | 0.99 |
| 211_V | 214_I | 1.258 | 0.99 |
| 355_Q | 358_W | 1.256 | 0.99 |
| 9_A | 104_P | 1.253 | 0.99 |
| 184_G | 305_T | 1.246 | 0.98 |
| 192_M | 211_V | 1.245 | 0.98 |
| 15_G | 304_G | 1.244 | 0.98 |
| 224_D | 227_N | 1.242 | 0.98 |
| 175_H | 283_S | 1.238 | 0.98 |
| 89_H | 93_Y | 1.237 | 0.98 |
| 284_I | 296_Y | 1.213 | 0.98 |
| 182_L | 186_D | 1.201 | 0.98 |
| 225_F | 229_M | 1.197 | 0.98 |
| 88_W | 121_M | 1.196 | 0.98 |
| 149_R | 300_V | 1.182 | 0.98 |
| 306_T | 333_A | 1.174 | 0.98 |
| 209_E | 212_R | 1.170 | 0.97 |
| 24_A | 29_P | 1.170 | 0.97 |
| 142_L | 345_G | 1.169 | 0.97 |
| 166_P | 176_A | 1.167 | 0.97 |
| 187_L | 305_T | 1.167 | 0.97 |
| 103_H | 132_P | 1.164 | 0.97 |
| 301_M | 312_A | 1.156 | 0.97 |
| 153_I | 166_P | 1.156 | 0.97 |
| 264_F | 310_G | 1.153 | 0.97 |
| 20_K | 342_W | 1.146 | 0.97 |
| 178_M | 282_N | 1.145 | 0.97 |
| 260_P | 264_F | 1.143 | 0.97 |
| 34_P | 37_V | 1.127 | 0.97 |
| 157_S | 187_L | 1.126 | 0.97 |
| 189_D | 208_R | 1.121 | 0.97 |
| 278_E | 281_Y | 1.117 | 0.96 |
| 109_E | 113_N | 1.116 | 0.96 |
| 19_V | 87_I | 1.111 | 0.96 |
| 194_I | 198_R | 1.110 | 0.96 |
| 106_L | 345_G | 1.107 | 0.96 |
| 114_P | 117_N | 1.104 | 0.96 |
| 261_E | 314_R | 1.097 | 0.96 |
| 39_R | 58_D | 1.095 | 0.96 |
| 24_A | 349_A | 1.093 | 0.96 |
| 193_K | 197_E | 1.091 | 0.96 |
| 314_R | 317_K | 1.084 | 0.96 |
| 125_M | 131_V | 1.082 | 0.96 |
| 343_I | 347_I | 1.079 | 0.95 |
| 137_A | 348_L | 1.079 | 0.95 |
| 224_D | 317_K | 1.076 | 0.95 |
| 135_Y | 348_L | 1.075 | 0.95 |
| 20_K | 32_V | 1.072 | 0.95 |
| 367_A | 371_I | 1.067 | 0.95 |
| 257_F | 308_Y | 1.064 | 0.95 |
| 12_C | 105_T | 1.062 | 0.95 |
| 191_L | 194_I | 1.061 | 0.95 |
| 127_E | 134_M | 1.059 | 0.95 |
| 166_P | 296_Y | 1.058 | 0.95 |
| 283_S | 287_C | 1.057 | 0.95 |
| 72_P | 78_I | 1.055 | 0.95 |
| 261_E | 266_P | 1.052 | 0.95 |
| 54_S | 90_H | 1.052 | 0.95 |
| 151_T | 291_I | 1.047 | 0.94 |
| 109_E | 138_I | 1.046 | 0.94 |
| 277_H | 314_R | 1.044 | 0.94 |
| 356_Q | 362_Q | 1.043 | 0.94 |
| 306_T | 337_R | 1.043 | 0.94 |
| 147_S | 340_S | 1.042 | 0.94 |
| 139_Q | 163_H | 1.039 | 0.94 |
| 69_L | 88_W | 1.038 | 0.94 |
| 115_K | 119_E | 1.037 | 0.94 |
| 262_T | 269_I | 1.032 | 0.94 |
| 35_S | 41_R | 1.030 | 0.94 |
| 306_T | 311_I | 1.030 | 0.94 |
| 39_R | 83_D | 1.028 | 0.94 |
| 96_L | 99_A | 1.028 | 0.94 |
| 84_M | 88_W | 1.028 | 0.94 |
| 289_I | 292_R | 1.027 | 0.94 |
| 354_F | 358_W | 1.022 | 0.93 |
| 138_I | 141_V | 1.019 | 0.93 |
| 154_V | 302_S | 1.018 | 0.93 |
| 93_Y | 100_P | 1.017 | 0.93 |
| 157_S | 306_T | 1.015 | 0.93 |
| 157_S | 276_I | 1.014 | 0.93 |
| 111_P | 140_A | 1.013 | 0.93 |
| 190_Y | 193_K | 1.010 | 0.93 |
| 72_P | 75_H | 1.007 | 0.93 |
| 264_F | 308_Y | 1.004 | 0.93 |
| 18_L | 338_K | 1.003 | 0.93 |
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 | |
| 4pl7A | 2 | 0.9178 | 100 | 0.128 | Contact Map |
| 4b1yB | 1 | 0.9655 | 100 | 0.153 | Contact Map |
| 4am6A | 2 | 0.9947 | 100 | 0.163 | Contact Map |
| 3qb0A | 4 | 0.9761 | 100 | 0.168 | Contact Map |
| 4fo0A | 1 | 0.9708 | 100 | 0.172 | Contact Map |
| 1k8kB | 1 | 0.4748 | 100 | 0.173 | Contact Map |
| 3dwlA | 2 | 0.9072 | 100 | 0.175 | Contact Map |
| 1k8kA | 1 | 0.9788 | 100 | 0.185 | Contact Map |
| 4i6mB | 1 | 0.8912 | 100 | 0.203 | Contact Map |
| 4i6mA | 1 | 0.9469 | 100 | 0.205 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)