| AAC4_manual |
| ID: | 1469021898 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 315 (294) | ||
| Sequences: | 11960 (7019) | ||
| Seq/Len: | 40.680 | ||
| Nf(neff/√len): | 409.4 |
HHblits Results: (2016_02)
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: 40.680).
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 | 3.793 | 1.00 |
| 177_A | 185_L | 3.523 | 1.00 |
| 74_P | 82_F | 3.042 | 1.00 |
| 266_D | 270_K | 2.994 | 1.00 |
| 271_I | 279_S | 2.813 | 1.00 |
| 171_D | 175_K | 2.790 | 1.00 |
| 174_M | 178_K | 2.775 | 1.00 |
| 269_V | 273_Q | 2.746 | 1.00 |
| 71_V | 75_R | 2.641 | 1.00 |
| 176_I | 184_G | 2.581 | 1.00 |
| 268_F | 280_F | 2.521 | 1.00 |
| 270_K | 274_H | 2.516 | 1.00 |
| 68_D | 72_R | 2.456 | 1.00 |
| 175_K | 179_S | 2.403 | 1.00 |
| 173_I | 185_L | 2.297 | 1.00 |
| 107_Y | 134_A | 2.259 | 1.00 |
| 249_R | 275_E | 2.245 | 1.00 |
| 167_K | 171_D | 2.238 | 1.00 |
| 275_E | 279_S | 2.231 | 1.00 |
| 246_V | 268_F | 2.168 | 1.00 |
| 107_Y | 138_T | 2.108 | 1.00 |
| 72_R | 76_E | 2.049 | 1.00 |
| 133_G | 197_I | 2.034 | 1.00 |
| 45_K | 49_Q | 2.017 | 1.00 |
| 73_I | 81_S | 1.984 | 1.00 |
| 238_I | 284_A | 1.967 | 1.00 |
| 152_R | 180_D | 1.932 | 1.00 |
| 263_G | 266_D | 1.920 | 1.00 |
| 166_F | 172_C | 1.887 | 1.00 |
| 47_L | 77_Q | 1.832 | 1.00 |
| 206_A | 235_C | 1.826 | 1.00 |
| 261_Y | 266_D | 1.806 | 1.00 |
| 300_L | 304_I | 1.788 | 1.00 |
| 129_L | 201_A | 1.763 | 1.00 |
| 214_L | 228_I | 1.755 | 1.00 |
| 70_L | 82_F | 1.745 | 1.00 |
| 42_E | 45_K | 1.740 | 1.00 |
| 261_Y | 267_C | 1.718 | 1.00 |
| 103_F | 107_Y | 1.714 | 1.00 |
| 272_Y | 277_I | 1.713 | 1.00 |
| 63_Y | 69_C | 1.710 | 1.00 |
| 180_D | 184_G | 1.709 | 1.00 |
| 303_K | 306_E | 1.674 | 1.00 |
| 168_G | 171_D | 1.659 | 1.00 |
| 29_V | 304_I | 1.650 | 1.00 |
| 207_Y | 302_D | 1.638 | 1.00 |
| 77_Q | 84_R | 1.623 | 1.00 |
| 50_V | 155_V | 1.619 | 1.00 |
| 107_Y | 131_S | 1.612 | 1.00 |
| 111_F | 131_S | 1.611 | 1.00 |
| 44_V | 70_L | 1.589 | 1.00 |
| 39_A | 43_R | 1.588 | 1.00 |
| 275_E | 282_R | 1.585 | 1.00 |
| 262_K | 266_D | 1.573 | 1.00 |
| 230_Q | 292_T | 1.558 | 1.00 |
| 63_Y | 68_D | 1.553 | 1.00 |
| 166_F | 171_D | 1.520 | 1.00 |
| 247_R | 251_M | 1.519 | 1.00 |
| 171_D | 174_M | 1.486 | 1.00 |
| 64_K | 68_D | 1.483 | 1.00 |
| 148_F | 152_R | 1.479 | 1.00 |
| 210_V | 228_I | 1.474 | 1.00 |
| 27_G | 31_A | 1.442 | 1.00 |
| 68_D | 71_V | 1.433 | 1.00 |
| 177_A | 182_I | 1.430 | 1.00 |
| 210_V | 231_V | 1.425 | 1.00 |
| 180_D | 187_Q | 1.422 | 1.00 |
| 206_A | 210_V | 1.394 | 0.99 |
| 108_K | 208_D | 1.367 | 0.99 |
| 265_L | 269_V | 1.355 | 0.99 |
| 199_Y | 236_S | 1.351 | 0.99 |
| 220_T | 224_V | 1.343 | 0.99 |
| 99_L | 103_F | 1.333 | 0.99 |
| 106_K | 110_L | 1.333 | 0.99 |
| 77_Q | 81_S | 1.324 | 0.99 |
| 202_S | 239_L | 1.324 | 0.99 |
| 304_I | 308_F | 1.316 | 0.99 |
| 265_L | 268_F | 1.311 | 0.99 |
| 181_G | 184_G | 1.298 | 0.99 |
| 43_R | 47_L | 1.294 | 0.99 |
| 209_T | 213_L | 1.286 | 0.99 |
| 144_Y | 148_F | 1.284 | 0.99 |
| 111_F | 134_A | 1.278 | 0.99 |
| 33_V | 300_L | 1.277 | 0.99 |
| 170_G | 174_M | 1.271 | 0.99 |
| 150_R | 154_G | 1.271 | 0.99 |
| 36_T | 86_N | 1.264 | 0.99 |
| 133_G | 201_A | 1.263 | 0.99 |
| 189_F | 193_V | 1.261 | 0.99 |
| 182_I | 186_Y | 1.254 | 0.99 |
| 209_T | 212_G | 1.254 | 0.99 |
| 149_A | 173_I | 1.253 | 0.99 |
| 73_I | 77_Q | 1.247 | 0.99 |
| 50_V | 248_R | 1.246 | 0.98 |
| 241_Y | 287_N | 1.230 | 0.98 |
| 276_G | 279_S | 1.229 | 0.98 |
| 26_A | 304_I | 1.223 | 0.98 |
| 202_S | 206_A | 1.210 | 0.98 |
| 172_C | 176_I | 1.209 | 0.98 |
| 137_A | 193_V | 1.202 | 0.98 |
| 39_A | 83_W | 1.198 | 0.98 |
| 132_G | 201_A | 1.192 | 0.98 |
| 105_D | 108_K | 1.181 | 0.98 |
| 233_T | 244_D | 1.164 | 0.97 |
| 86_N | 90_V | 1.162 | 0.97 |
| 134_A | 138_T | 1.158 | 0.97 |
| 103_F | 138_T | 1.156 | 0.97 |
| 25_L | 28_G | 1.154 | 0.97 |
| 175_K | 178_K | 1.150 | 0.97 |
| 96_T | 100_N | 1.146 | 0.97 |
| 227_F | 231_V | 1.146 | 0.97 |
| 191_V | 264_T | 1.145 | 0.97 |
| 115_V | 127_A | 1.144 | 0.97 |
| 126_L | 130_A | 1.141 | 0.97 |
| 67_V | 71_V | 1.140 | 0.97 |
| 281_F | 284_A | 1.139 | 0.97 |
| 208_D | 211_K | 1.137 | 0.97 |
| 29_V | 33_V | 1.135 | 0.97 |
| 28_G | 94_F | 1.126 | 0.97 |
| 107_Y | 111_F | 1.125 | 0.97 |
| 302_D | 305_K | 1.123 | 0.97 |
| 229_A | 233_T | 1.116 | 0.96 |
| 241_Y | 245_T | 1.115 | 0.96 |
| 51_Q | 63_Y | 1.107 | 0.96 |
| 272_Y | 275_E | 1.103 | 0.96 |
| 277_I | 281_F | 1.095 | 0.96 |
| 261_Y | 270_K | 1.093 | 0.96 |
| 132_G | 136_G | 1.090 | 0.96 |
| 231_V | 235_C | 1.086 | 0.96 |
| 221_P | 224_V | 1.084 | 0.96 |
| 203_Y | 298_L | 1.076 | 0.95 |
| 39_A | 86_N | 1.073 | 0.95 |
| 238_I | 288_V | 1.073 | 0.95 |
| 297_V | 300_L | 1.072 | 0.95 |
| 95_P | 98_A | 1.071 | 0.95 |
| 249_R | 279_S | 1.066 | 0.95 |
| 141_C | 189_F | 1.060 | 0.95 |
| 65_G | 68_D | 1.058 | 0.95 |
| 74_P | 79_F | 1.056 | 0.95 |
| 284_A | 288_V | 1.055 | 0.95 |
| 104_K | 208_D | 1.045 | 0.94 |
| 23_D | 105_D | 1.044 | 0.94 |
| 99_L | 142_V | 1.044 | 0.94 |
| 151_T | 252_M | 1.033 | 0.94 |
| 266_D | 269_V | 1.032 | 0.94 |
| 128_N | 208_D | 1.022 | 0.93 |
| 270_K | 273_Q | 1.015 | 0.93 |
| 21_G | 25_L | 1.015 | 0.93 |
| 176_I | 180_D | 1.008 | 0.93 |
| 105_D | 305_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 | |
| 1okcA | 1 | 0.9206 | 100 | 0.193 | Contact Map |
| 4c9gA | 1 | 0.8381 | 100 | 0.224 | Contact Map |
| 2lckA | 1 | 0.9111 | 100 | 0.232 | Contact Map |
| 4i5lB | 2 | 0.2508 | 22.2 | 0.955 | Contact Map |
| 2k6iA | 1 | 0.0857 | 6.1 | 0.965 | Contact Map |
| 3q98A | 1 | 0.1905 | 5.8 | 0.965 | Contact Map |
| 2kygA | 2 | 0.1587 | 4.9 | 0.966 | Contact Map |
| 2izyA | 8 | 0.1429 | 3.8 | 0.968 | Contact Map |
| 4amuA | 4 | 0.1905 | 2.5 | 0.971 | Contact Map |
| 1fa2A | 1 | 0.273 | 2.1 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)