| LEF1 |
| ID: | 1401712138 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 399 (268) | ||
| Sequences: | 14909 (14653.6) | ||
| Seq/Len: | 55.631 | ||
| Nf(neff/√len): | 895.1 |
Jackhmmer Results: (2014_04_16)
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: 55.631).
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 |
| 294_P | 297_P | 1.577 | 1.00 |
| 251_P | 254_H | 1.509 | 1.00 |
| 180_S | 183_G | 1.472 | 1.00 |
| 147_P | 150_A | 1.439 | 1.00 |
| 204_V | 207_I | 1.419 | 1.00 |
| 155_T | 158_I | 1.407 | 0.99 |
| 154_L | 157_L | 1.397 | 0.99 |
| 197_Y | 201_P | 1.397 | 0.99 |
| 245_H | 248_P | 1.385 | 0.99 |
| 143_P | 146_Q | 1.384 | 0.99 |
| 149_H | 152_H | 1.383 | 0.99 |
| 249_G | 252_G | 1.380 | 0.99 |
| 248_P | 251_P | 1.349 | 0.99 |
| 97_P | 101_L | 1.332 | 0.99 |
| 145_V | 149_H | 1.308 | 0.99 |
| 206_Q | 209_P | 1.308 | 0.99 |
| 191_P | 195_T | 1.304 | 0.99 |
| 247_I | 250_P | 1.298 | 0.99 |
| 158_I | 162_D | 1.287 | 0.99 |
| 114_Y | 118_P | 1.286 | 0.99 |
| 203_G | 207_I | 1.278 | 0.99 |
| 170_H | 174_I | 1.271 | 0.99 |
| 271_E | 274_H | 1.268 | 0.99 |
| 112_S | 115_I | 1.265 | 0.99 |
| 181_K | 184_M | 1.260 | 0.99 |
| 158_I | 161_S | 1.258 | 0.99 |
| 199_L | 203_G | 1.249 | 0.99 |
| 118_P | 121_N | 1.248 | 0.99 |
| 224_G | 228_P | 1.246 | 0.98 |
| 196_F | 199_L | 1.243 | 0.98 |
| 146_Q | 149_H | 1.239 | 0.98 |
| 241_R | 244_H | 1.237 | 0.98 |
| 150_A | 153_P | 1.236 | 0.98 |
| 101_L | 105_G | 1.235 | 0.98 |
| 135_I | 138_T | 1.229 | 0.98 |
| 256_T | 259_P | 1.228 | 0.98 |
| 129_G | 132_S | 1.227 | 0.98 |
| 259_P | 262_A | 1.226 | 0.98 |
| 179_N | 182_Q | 1.224 | 0.98 |
| 189_P | 192_D | 1.222 | 0.98 |
| 246_M | 250_P | 1.216 | 0.98 |
| 255_T | 259_P | 1.216 | 0.98 |
| 156_P | 159_T | 1.215 | 0.98 |
| 252_G | 255_T | 1.213 | 0.98 |
| 195_T | 198_P | 1.211 | 0.98 |
| 246_M | 249_G | 1.210 | 0.98 |
| 185_S | 188_P | 1.207 | 0.98 |
| 201_P | 205_G | 1.201 | 0.98 |
| 139_S | 143_P | 1.199 | 0.98 |
| 165_F | 168_G | 1.198 | 0.98 |
| 147_P | 151_V | 1.197 | 0.98 |
| 141_K | 145_V | 1.195 | 0.98 |
| 140_N | 143_P | 1.194 | 0.98 |
| 204_V | 208_T | 1.191 | 0.98 |
| 203_G | 206_Q | 1.184 | 0.98 |
| 216_Q | 219_Y | 1.180 | 0.98 |
| 195_T | 199_L | 1.179 | 0.98 |
| 117_M | 121_N | 1.179 | 0.98 |
| 112_S | 116_M | 1.175 | 0.98 |
| 192_D | 196_F | 1.173 | 0.98 |
| 123_D | 126_M | 1.172 | 0.98 |
| 184_M | 187_H | 1.168 | 0.97 |
| 242_F | 245_H | 1.168 | 0.97 |
| 209_P | 213_W | 1.167 | 0.97 |
| 201_P | 204_V | 1.161 | 0.97 |
| 228_P | 232_S | 1.161 | 0.97 |
| 284_P | 288_Q | 1.161 | 0.97 |
| 164_H | 167_P | 1.159 | 0.97 |
| 202_G | 205_G | 1.157 | 0.97 |
| 226_R | 229_Y | 1.155 | 0.97 |
| 182_Q | 185_S | 1.153 | 0.97 |
| 111_Y | 114_Y | 1.152 | 0.97 |
| 117_M | 120_M | 1.148 | 0.97 |
| 148_S | 152_H | 1.148 | 0.97 |
| 116_M | 119_N | 1.145 | 0.97 |
| 126_M | 129_G | 1.145 | 0.97 |
| 144_V | 148_S | 1.145 | 0.97 |
| 145_V | 148_S | 1.144 | 0.97 |
| 115_I | 118_P | 1.139 | 0.97 |
| 134_P | 137_R | 1.137 | 0.97 |
| 130_S | 133_P | 1.135 | 0.97 |
| 228_P | 231_S | 1.134 | 0.97 |
| 189_P | 193_I | 1.128 | 0.97 |
| 209_P | 212_G | 1.127 | 0.97 |
| 223_G | 226_R | 1.127 | 0.97 |
| 119_N | 122_N | 1.124 | 0.97 |
| 179_N | 183_G | 1.124 | 0.97 |
| 255_T | 258_I | 1.122 | 0.97 |
| 144_V | 147_P | 1.119 | 0.96 |
| 150_A | 154_L | 1.116 | 0.96 |
| 177_D | 180_S | 1.114 | 0.96 |
| 138_T | 142_V | 1.112 | 0.96 |
| 272_H | 275_T | 1.110 | 0.96 |
| 223_G | 227_Q | 1.110 | 0.96 |
| 177_D | 181_K | 1.110 | 0.96 |
| 210_P | 213_W | 1.109 | 0.96 |
| 127_S | 130_S | 1.108 | 0.96 |
| 257_G | 260_H | 1.107 | 0.96 |
| 230_P | 234_S | 1.106 | 0.96 |
| 129_G | 133_P | 1.106 | 0.96 |
| 152_H | 155_T | 1.104 | 0.96 |
| 293_E | 296_R | 1.099 | 0.96 |
| 251_P | 255_T | 1.098 | 0.96 |
| 137_R | 141_K | 1.097 | 0.96 |
| 47_E | 50_L | 1.096 | 0.96 |
| 138_T | 141_K | 1.095 | 0.96 |
| 205_G | 208_T | 1.094 | 0.96 |
| 175_P | 178_V | 1.093 | 0.96 |
| 98_D | 102_Y | 1.093 | 0.96 |
| 235_V | 239_M | 1.092 | 0.96 |
| 208_T | 211_L | 1.091 | 0.96 |
| 202_G | 206_Q | 1.087 | 0.96 |
| 207_I | 210_P | 1.087 | 0.96 |
| 124_P | 127_S | 1.087 | 0.96 |
| 217_P | 220_P | 1.084 | 0.96 |
| 137_R | 140_N | 1.084 | 0.96 |
| 231_S | 234_S | 1.083 | 0.96 |
| 257_G | 261_P | 1.079 | 0.95 |
| 226_R | 230_P | 1.078 | 0.95 |
| 258_I | 261_P | 1.077 | 0.95 |
| 98_D | 101_L | 1.076 | 0.95 |
| 222_T | 225_F | 1.075 | 0.95 |
| 29_E | 33_Q | 1.075 | 0.95 |
| 220_P | 224_G | 1.074 | 0.95 |
| 258_I | 262_A | 1.072 | 0.95 |
| 249_G | 253_P | 1.072 | 0.95 |
| 180_S | 184_M | 1.071 | 0.95 |
| 194_P | 197_Y | 1.070 | 0.95 |
| 99_G | 102_Y | 1.069 | 0.95 |
| 211_L | 214_Q | 1.068 | 0.95 |
| 207_I | 211_L | 1.068 | 0.95 |
| 199_L | 202_G | 1.067 | 0.95 |
| 222_T | 226_R | 1.065 | 0.95 |
| 227_Q | 231_S | 1.063 | 0.95 |
| 248_P | 252_G | 1.063 | 0.95 |
| 274_H | 277_S | 1.062 | 0.95 |
| 293_E | 297_P | 1.060 | 0.95 |
| 148_S | 151_V | 1.058 | 0.95 |
| 196_F | 200_S | 1.054 | 0.95 |
| 146_Q | 150_A | 1.053 | 0.95 |
| 171_P | 174_I | 1.052 | 0.95 |
| 142_V | 145_V | 1.051 | 0.94 |
| 264_V | 267_Q | 1.047 | 0.94 |
| 254_H | 257_G | 1.047 | 0.94 |
| 74_R | 77_Q | 1.047 | 0.94 |
| 128_N | 131_L | 1.046 | 0.94 |
| 243_S | 246_M | 1.044 | 0.94 |
| 264_V | 268_V | 1.042 | 0.94 |
| 232_S | 235_V | 1.042 | 0.94 |
| 289_R | 292_Q | 1.041 | 0.94 |
| 272_H | 276_D | 1.041 | 0.94 |
| 192_D | 195_T | 1.036 | 0.94 |
| 169_S | 172_S | 1.034 | 0.94 |
| 149_H | 153_P | 1.034 | 0.94 |
| 37_I | 41_I | 1.033 | 0.94 |
| 168_G | 171_P | 1.033 | 0.94 |
| 183_G | 186_R | 1.033 | 0.94 |
| 198_P | 201_P | 1.032 | 0.94 |
| 190_A | 193_I | 1.029 | 0.94 |
| 159_T | 162_D | 1.028 | 0.94 |
| 96_H | 100_G | 1.027 | 0.94 |
| 164_H | 168_G | 1.026 | 0.94 |
| 205_G | 209_P | 1.024 | 0.93 |
| 270_Q | 274_H | 1.024 | 0.93 |
| 95_K | 99_G | 1.022 | 0.93 |
| 97_P | 100_G | 1.021 | 0.93 |
| 143_P | 147_P | 1.018 | 0.93 |
| 253_P | 257_G | 1.015 | 0.93 |
| 161_S | 164_H | 1.013 | 0.93 |
| 200_S | 203_G | 1.012 | 0.93 |
| 109_S | 112_S | 1.011 | 0.93 |
| 194_P | 198_P | 1.011 | 0.93 |
| 68_N | 71_E | 1.009 | 0.93 |
| 153_P | 156_P | 1.002 | 0.92 |
| 156_P | 160_Y | 1.001 | 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 | |
| 1j46A | 1 | 0.213 | 99.8 | 0.64 | Contact Map |
| 2lefA | 1 | 0.2155 | 99.8 | 0.642 | Contact Map |
| 1i11A | 1 | 0.1754 | 99.8 | 0.643 | Contact Map |
| 3f27D | 1 | 0.1855 | 99.8 | 0.645 | Contact Map |
| 3u2bC | 1 | 0.1905 | 99.8 | 0.647 | Contact Map |
| 2co9A | 1 | 0.2556 | 99.8 | 0.647 | Contact Map |
| 4euwA | 1 | 0.1805 | 99.8 | 0.647 | Contact Map |
| 3tmmA | 1 | 0.2707 | 99.8 | 0.647 | Contact Map |
| 1gt0D | 1 | 0.198 | 99.8 | 0.648 | Contact Map |
| 1wz6A | 1 | 0.2055 | 99.8 | 0.652 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)