| C1_rep |
| ID: | 1512073059 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 357 (347) | ||
| Sequences: | 577 (219.9) | ||
| Seq/Len: | 1.663 | ||
| Nf(neff/√len): | 11.8 |
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: 1.663).
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 |
| 134_E | 151_K | 2.339 | 1.00 |
| 43_K | 108_F | 2.155 | 0.99 |
| 152_A | 158_L | 2.116 | 0.99 |
| 103_E | 110_D | 1.921 | 0.98 |
| 157_I | 167_L | 1.906 | 0.98 |
| 43_K | 103_E | 1.897 | 0.98 |
| 132_Y | 158_L | 1.888 | 0.97 |
| 141_K | 164_S | 1.848 | 0.97 |
| 152_A | 155_D | 1.809 | 0.97 |
| 81_R | 84_H | 1.807 | 0.96 |
| 6_K | 67_Q | 1.803 | 0.96 |
| 141_K | 168_D | 1.803 | 0.96 |
| 132_Y | 154_K | 1.790 | 0.96 |
| 103_E | 108_F | 1.781 | 0.96 |
| 160_F | 164_S | 1.734 | 0.95 |
| 43_K | 110_D | 1.733 | 0.95 |
| 151_K | 157_I | 1.711 | 0.95 |
| 219_G | 225_K | 1.687 | 0.94 |
| 140_S | 143_E | 1.647 | 0.93 |
| 345_G | 348_Q | 1.634 | 0.93 |
| 230_R | 235_H | 1.628 | 0.93 |
| 173_P | 176_E | 1.621 | 0.93 |
| 78_S | 84_H | 1.610 | 0.92 |
| 132_Y | 152_A | 1.603 | 0.92 |
| 211_R | 214_S | 1.597 | 0.92 |
| 12_Y | 68_C | 1.566 | 0.91 |
| 80_N | 84_H | 1.495 | 0.88 |
| 138_S | 147_I | 1.490 | 0.88 |
| 108_F | 111_F | 1.470 | 0.87 |
| 7_I | 12_Y | 1.466 | 0.87 |
| 232_L | 235_H | 1.465 | 0.86 |
| 41_Y | 110_D | 1.453 | 0.86 |
| 138_S | 146_N | 1.440 | 0.85 |
| 219_G | 224_G | 1.425 | 0.84 |
| 279_W | 288_P | 1.424 | 0.84 |
| 273_M | 299_F | 1.416 | 0.84 |
| 48_L | 54_P | 1.408 | 0.83 |
| 92_A | 98_V | 1.405 | 0.83 |
| 77_V | 84_H | 1.403 | 0.83 |
| 211_R | 225_K | 1.391 | 0.82 |
| 155_D | 158_L | 1.389 | 0.82 |
| 244_L | 272_F | 1.388 | 0.82 |
| 50_E | 58_V | 1.375 | 0.81 |
| 100_T | 111_F | 1.366 | 0.81 |
| 236_N | 243_D | 1.340 | 0.79 |
| 272_F | 299_F | 1.335 | 0.79 |
| 282_N | 287_K | 1.333 | 0.78 |
| 66_Y | 73_F | 1.333 | 0.78 |
| 343_N | 347_T | 1.327 | 0.78 |
| 37_T | 73_F | 1.320 | 0.78 |
| 341_S | 345_G | 1.314 | 0.77 |
| 217_I | 300_L | 1.310 | 0.77 |
| 211_R | 219_G | 1.309 | 0.77 |
| 78_S | 81_R | 1.305 | 0.76 |
| 229_A | 233_G | 1.297 | 0.76 |
| 220_D | 227_M | 1.279 | 0.74 |
| 38_N | 69_K | 1.273 | 0.74 |
| 18_N | 53_E | 1.272 | 0.74 |
| 44_V | 108_F | 1.270 | 0.74 |
| 155_D | 167_L | 1.269 | 0.74 |
| 26_A | 29_Q | 1.267 | 0.73 |
| 90_Q | 98_V | 1.264 | 0.73 |
| 256_N | 293_G | 1.261 | 0.73 |
| 343_N | 348_Q | 1.258 | 0.73 |
| 35_T | 73_F | 1.254 | 0.72 |
| 49_H | 55_H | 1.254 | 0.72 |
| 269_F | 272_F | 1.245 | 0.71 |
| 148_L | 152_A | 1.240 | 0.71 |
| 239_C | 269_F | 1.238 | 0.71 |
| 269_F | 283_T | 1.233 | 0.70 |
| 278_D | 281_S | 1.233 | 0.70 |
| 4_L | 69_K | 1.233 | 0.70 |
| 59_L | 102_V | 1.230 | 0.70 |
| 272_F | 305_P | 1.230 | 0.70 |
| 191_P | 198_V | 1.229 | 0.70 |
| 147_I | 151_K | 1.228 | 0.70 |
| 222_R | 225_K | 1.225 | 0.70 |
| 164_S | 167_L | 1.223 | 0.70 |
| 164_S | 168_D | 1.223 | 0.70 |
| 269_F | 305_P | 1.220 | 0.69 |
| 151_K | 158_L | 1.217 | 0.69 |
| 298_I | 302_N | 1.216 | 0.69 |
| 244_L | 297_T | 1.215 | 0.69 |
| 289_I | 339_F | 1.197 | 0.67 |
| 245_S | 283_T | 1.196 | 0.67 |
| 225_K | 229_A | 1.195 | 0.67 |
| 221_S | 327_K | 1.192 | 0.67 |
| 238_L | 248_V | 1.191 | 0.67 |
| 26_A | 56_L | 1.186 | 0.66 |
| 239_C | 297_T | 1.183 | 0.66 |
| 148_L | 155_D | 1.180 | 0.66 |
| 271_E | 281_S | 1.177 | 0.65 |
| 269_F | 325_T | 1.176 | 0.65 |
| 131_A | 152_A | 1.170 | 0.65 |
| 251_N | 289_I | 1.158 | 0.63 |
| 68_C | 73_F | 1.158 | 0.63 |
| 306_T | 317_K | 1.157 | 0.63 |
| 225_K | 228_W | 1.157 | 0.63 |
| 14_L | 30_L | 1.156 | 0.63 |
| 278_D | 282_N | 1.155 | 0.63 |
| 12_Y | 37_T | 1.154 | 0.63 |
| 315_E | 340_A | 1.151 | 0.63 |
| 154_K | 157_I | 1.151 | 0.63 |
| 100_T | 115_Q | 1.149 | 0.62 |
| 38_N | 53_E | 1.149 | 0.62 |
| 187_F | 191_P | 1.148 | 0.62 |
| 139_G | 167_L | 1.139 | 0.61 |
| 267_K | 281_S | 1.137 | 0.61 |
| 324_W | 328_N | 1.135 | 0.61 |
| 33_L | 73_F | 1.128 | 0.60 |
| 236_N | 249_Y | 1.128 | 0.60 |
| 49_H | 57_H | 1.121 | 0.60 |
| 279_W | 282_N | 1.113 | 0.59 |
| 230_R | 233_G | 1.110 | 0.59 |
| 236_N | 282_N | 1.110 | 0.59 |
| 304_G | 308_S | 1.109 | 0.58 |
| 223_T | 227_M | 1.106 | 0.58 |
| 159_Q | 162_N | 1.102 | 0.58 |
| 340_A | 343_N | 1.095 | 0.57 |
| 187_F | 190_V | 1.093 | 0.57 |
| 195_E | 200_E | 1.093 | 0.57 |
| 236_N | 256_N | 1.092 | 0.57 |
| 119_R | 122_R | 1.092 | 0.57 |
| 238_L | 242_L | 1.087 | 0.56 |
| 43_K | 111_F | 1.083 | 0.56 |
| 311_E | 315_E | 1.081 | 0.56 |
| 225_K | 231_S | 1.080 | 0.55 |
| 230_R | 237_Y | 1.078 | 0.55 |
| 269_F | 273_M | 1.076 | 0.55 |
| 293_G | 301_C | 1.076 | 0.55 |
| 74_F | 86_H | 1.075 | 0.55 |
| 173_P | 177_V | 1.074 | 0.55 |
| 40_K | 46_R | 1.072 | 0.55 |
| 50_E | 63_E | 1.072 | 0.55 |
| 77_V | 80_N | 1.068 | 0.54 |
| 214_S | 219_G | 1.068 | 0.54 |
| 134_E | 143_E | 1.066 | 0.54 |
| 239_C | 244_L | 1.065 | 0.54 |
| 273_M | 297_T | 1.063 | 0.54 |
| 102_V | 111_F | 1.063 | 0.54 |
| 189_Q | 195_E | 1.056 | 0.53 |
| 101_Y | 104_K | 1.052 | 0.52 |
| 134_E | 152_A | 1.052 | 0.52 |
| 305_P | 315_E | 1.050 | 0.52 |
| 346_P | 349_D | 1.048 | 0.52 |
| 197_W | 201_N | 1.047 | 0.52 |
| 243_D | 282_N | 1.046 | 0.52 |
| 105_D | 124_G | 1.042 | 0.51 |
| 37_T | 68_C | 1.042 | 0.51 |
| 39_K | 50_E | 1.038 | 0.51 |
| 44_V | 58_V | 1.038 | 0.51 |
| 29_Q | 76_L | 1.037 | 0.51 |
| 271_E | 279_W | 1.036 | 0.51 |
| 75_D | 86_H | 1.036 | 0.51 |
| 269_F | 299_F | 1.034 | 0.51 |
| 299_F | 325_T | 1.034 | 0.51 |
| 343_N | 346_P | 1.033 | 0.50 |
| 216_V | 269_F | 1.031 | 0.50 |
| 294_G | 298_I | 1.028 | 0.50 |
| 342_I | 345_G | 1.026 | 0.50 |
| 89_I | 221_S | 1.024 | 0.49 |
| 283_T | 288_P | 1.020 | 0.49 |
| 142_S | 160_F | 1.019 | 0.49 |
| 226_T | 230_R | 1.016 | 0.49 |
| 267_K | 304_G | 1.016 | 0.49 |
| 217_I | 225_K | 1.012 | 0.48 |
| 67_Q | 70_N | 1.012 | 0.48 |
| 12_Y | 35_T | 1.012 | 0.48 |
| 284_K | 287_K | 1.011 | 0.48 |
| 152_A | 160_F | 1.010 | 0.48 |
| 259_D | 328_N | 1.010 | 0.48 |
| 24_E | 36_P | 1.008 | 0.48 |
| 195_E | 199_A | 1.007 | 0.48 |
| 271_E | 288_P | 1.003 | 0.47 |
| 283_T | 299_F | 1.003 | 0.47 |
| 26_A | 76_L | 1.002 | 0.47 |
| 255_Y | 259_D | 1.001 | 0.47 |
| 69_K | 73_F | 1.000 | 0.47 |
| 345_G | 349_D | 1.000 | 0.47 |
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 | |
| 1l2mA | 1 | 0.3305 | 100 | 0.668 | Contact Map |
| 2hwtA | 1 | 0.2465 | 99.8 | 0.856 | Contact Map |
| 2hw0A | 1 | 0.2969 | 99.7 | 0.871 | Contact Map |
| 1tueA | 6 | 0.5042 | 98.1 | 0.936 | Contact Map |
| 3ec2A | 1 | 0.4118 | 97.8 | 0.94 | Contact Map |
| 2w58A | 2 | 0.4454 | 97.8 | 0.94 | Contact Map |
| 1l8qA | 1 | 0.4566 | 97.4 | 0.946 | Contact Map |
| 2qgzA | 1 | 0.4118 | 97.1 | 0.948 | Contact Map |
| 4m4wJ | 6 | 0.5686 | 97.1 | 0.948 | Contact Map |
| 4qhsA | 7 | 0.4482 | 97 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)