| AAC4_auto |
| ID: | 1469021604 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 315 (299) | ||
| Sequences: | 16317 (9561.6) | ||
| Seq/Len: | 54.572 | ||
| Nf(neff/√len): | 553.0 |
Jackhmmer Results: (2016_04)
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: 54.572).
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 |
| 272_Y | 280_F | 3.341 | 1.00 |
| 177_A | 185_L | 3.097 | 1.00 |
| 74_P | 82_F | 2.905 | 1.00 |
| 71_V | 75_R | 2.827 | 1.00 |
| 266_D | 270_K | 2.824 | 1.00 |
| 171_D | 175_K | 2.726 | 1.00 |
| 174_M | 178_K | 2.704 | 1.00 |
| 271_I | 279_S | 2.701 | 1.00 |
| 269_V | 273_Q | 2.647 | 1.00 |
| 270_K | 274_H | 2.614 | 1.00 |
| 175_K | 179_S | 2.451 | 1.00 |
| 68_D | 72_R | 2.420 | 1.00 |
| 167_K | 171_D | 2.408 | 1.00 |
| 268_F | 280_F | 2.404 | 1.00 |
| 107_Y | 138_T | 2.388 | 1.00 |
| 107_Y | 134_A | 2.331 | 1.00 |
| 176_I | 184_G | 2.267 | 1.00 |
| 246_V | 268_F | 2.233 | 1.00 |
| 275_E | 279_S | 2.203 | 1.00 |
| 166_F | 172_C | 2.166 | 1.00 |
| 133_G | 197_I | 2.135 | 1.00 |
| 72_R | 76_E | 2.133 | 1.00 |
| 261_Y | 267_C | 2.113 | 1.00 |
| 238_I | 284_A | 2.084 | 1.00 |
| 214_L | 228_I | 1.984 | 1.00 |
| 166_F | 171_D | 1.982 | 1.00 |
| 261_Y | 266_D | 1.981 | 1.00 |
| 272_Y | 277_I | 1.969 | 1.00 |
| 129_L | 201_A | 1.955 | 1.00 |
| 173_I | 185_L | 1.933 | 1.00 |
| 263_G | 266_D | 1.932 | 1.00 |
| 63_Y | 69_C | 1.932 | 1.00 |
| 249_R | 275_E | 1.926 | 1.00 |
| 70_L | 82_F | 1.836 | 1.00 |
| 103_F | 107_Y | 1.828 | 1.00 |
| 180_D | 184_G | 1.826 | 1.00 |
| 303_K | 306_E | 1.798 | 1.00 |
| 47_L | 77_Q | 1.789 | 1.00 |
| 168_G | 171_D | 1.788 | 1.00 |
| 262_K | 266_D | 1.782 | 1.00 |
| 29_V | 304_I | 1.777 | 1.00 |
| 206_A | 235_C | 1.767 | 1.00 |
| 230_Q | 292_T | 1.766 | 1.00 |
| 50_V | 155_V | 1.764 | 1.00 |
| 64_K | 68_D | 1.728 | 1.00 |
| 115_V | 127_A | 1.701 | 1.00 |
| 265_L | 269_V | 1.700 | 1.00 |
| 296_L | 300_L | 1.697 | 1.00 |
| 152_R | 180_D | 1.683 | 1.00 |
| 63_Y | 68_D | 1.630 | 1.00 |
| 207_Y | 302_D | 1.623 | 1.00 |
| 171_D | 174_M | 1.611 | 1.00 |
| 45_K | 49_Q | 1.597 | 1.00 |
| 300_L | 304_I | 1.593 | 1.00 |
| 73_I | 81_S | 1.571 | 1.00 |
| 148_F | 152_R | 1.562 | 1.00 |
| 44_V | 70_L | 1.544 | 1.00 |
| 39_A | 43_R | 1.544 | 1.00 |
| 209_T | 213_L | 1.542 | 1.00 |
| 210_V | 231_V | 1.512 | 1.00 |
| 107_Y | 131_S | 1.507 | 1.00 |
| 220_T | 224_V | 1.500 | 1.00 |
| 177_A | 182_I | 1.474 | 1.00 |
| 182_I | 186_Y | 1.472 | 1.00 |
| 210_V | 228_I | 1.437 | 1.00 |
| 77_Q | 84_R | 1.436 | 1.00 |
| 275_E | 282_R | 1.402 | 0.99 |
| 221_P | 224_V | 1.400 | 0.99 |
| 170_G | 174_M | 1.389 | 0.99 |
| 202_S | 239_L | 1.376 | 0.99 |
| 265_L | 268_F | 1.372 | 0.99 |
| 33_V | 300_L | 1.368 | 0.99 |
| 111_F | 131_S | 1.367 | 0.99 |
| 133_G | 201_A | 1.358 | 0.99 |
| 149_A | 173_I | 1.339 | 0.99 |
| 42_E | 45_K | 1.336 | 0.99 |
| 99_L | 103_F | 1.334 | 0.99 |
| 180_D | 187_Q | 1.321 | 0.99 |
| 103_F | 138_T | 1.320 | 0.99 |
| 199_Y | 236_S | 1.303 | 0.99 |
| 126_L | 130_A | 1.295 | 0.99 |
| 106_K | 110_L | 1.283 | 0.99 |
| 68_D | 71_V | 1.274 | 0.99 |
| 23_D | 105_D | 1.259 | 0.99 |
| 26_A | 304_I | 1.256 | 0.99 |
| 206_A | 210_V | 1.248 | 0.99 |
| 277_I | 281_F | 1.244 | 0.98 |
| 108_K | 208_D | 1.234 | 0.98 |
| 266_D | 269_V | 1.229 | 0.98 |
| 241_Y | 287_N | 1.225 | 0.98 |
| 39_A | 83_W | 1.223 | 0.98 |
| 27_G | 31_A | 1.220 | 0.98 |
| 209_T | 212_G | 1.212 | 0.98 |
| 111_F | 134_A | 1.212 | 0.98 |
| 150_R | 154_G | 1.207 | 0.98 |
| 77_Q | 81_S | 1.201 | 0.98 |
| 175_K | 178_K | 1.200 | 0.98 |
| 247_R | 251_M | 1.188 | 0.98 |
| 86_N | 90_V | 1.180 | 0.98 |
| 203_Y | 298_L | 1.169 | 0.97 |
| 227_F | 231_V | 1.169 | 0.97 |
| 134_A | 138_T | 1.167 | 0.97 |
| 50_V | 248_R | 1.164 | 0.97 |
| 191_V | 264_T | 1.153 | 0.97 |
| 270_K | 273_Q | 1.153 | 0.97 |
| 130_A | 134_A | 1.150 | 0.97 |
| 105_D | 305_K | 1.148 | 0.97 |
| 36_T | 86_N | 1.146 | 0.97 |
| 137_A | 193_V | 1.142 | 0.97 |
| 249_R | 271_I | 1.141 | 0.97 |
| 132_G | 201_A | 1.140 | 0.97 |
| 144_Y | 148_F | 1.137 | 0.97 |
| 21_G | 25_L | 1.135 | 0.97 |
| 43_R | 47_L | 1.132 | 0.97 |
| 25_L | 28_G | 1.129 | 0.97 |
| 29_V | 33_V | 1.125 | 0.97 |
| 67_V | 71_V | 1.123 | 0.97 |
| 73_I | 77_Q | 1.121 | 0.97 |
| 304_I | 308_F | 1.118 | 0.96 |
| 124_W | 127_A | 1.115 | 0.96 |
| 28_G | 94_F | 1.111 | 0.96 |
| 99_L | 142_V | 1.105 | 0.96 |
| 18_S | 22_K | 1.101 | 0.96 |
| 261_Y | 270_K | 1.088 | 0.96 |
| 225_S | 302_D | 1.085 | 0.96 |
| 39_A | 86_N | 1.085 | 0.96 |
| 213_L | 216_K | 1.078 | 0.95 |
| 148_F | 176_I | 1.073 | 0.95 |
| 37_A | 296_L | 1.072 | 0.95 |
| 32_A | 90_V | 1.069 | 0.95 |
| 44_V | 69_C | 1.065 | 0.95 |
| 272_Y | 275_E | 1.065 | 0.95 |
| 222_F | 303_K | 1.064 | 0.95 |
| 202_S | 206_A | 1.055 | 0.95 |
| 42_E | 150_R | 1.048 | 0.94 |
| 166_F | 175_K | 1.048 | 0.94 |
| 241_Y | 245_T | 1.045 | 0.94 |
| 246_V | 264_T | 1.041 | 0.94 |
| 155_V | 252_M | 1.040 | 0.94 |
| 151_T | 252_M | 1.039 | 0.94 |
| 226_F | 299_V | 1.037 | 0.94 |
| 65_G | 68_D | 1.037 | 0.94 |
| 63_Y | 72_R | 1.036 | 0.94 |
| 181_G | 184_G | 1.032 | 0.94 |
| 107_Y | 110_L | 1.030 | 0.94 |
| 43_R | 154_G | 1.015 | 0.93 |
| 189_F | 193_V | 1.012 | 0.93 |
| 284_A | 288_V | 1.008 | 0.93 |
| 227_F | 230_Q | 1.003 | 0.93 |
| 104_K | 208_D | 1.003 | 0.93 |
| 79_F | 83_W | 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 | |
| 1okcA | 1 | 0.9206 | 100 | 0.154 | Contact Map |
| 4c9gA | 1 | 0.8381 | 100 | 0.18 | Contact Map |
| 2lckA | 1 | 0.9111 | 100 | 0.192 | Contact Map |
| 4i5lB | 2 | 0.254 | 16.9 | 0.955 | Contact Map |
| 2kygA | 2 | 0.1587 | 5.3 | 0.964 | Contact Map |
| 2izyA | 8 | 0.1429 | 4.8 | 0.965 | Contact Map |
| 1t10A | 1 | 0.1841 | 4 | 0.966 | Contact Map |
| 4jjfA | 2 | 0.3587 | 2.9 | 0.968 | Contact Map |
| 3fblA | 1 | 0.2476 | 2.3 | 0.97 | Contact Map |
| 2jvwA | 1 | 0.2159 | 1.9 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)