| 1lth |
| ID: | 1506711094 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 313 (308) | ||
| Sequences: | 5096 (2736.4) | ||
| Seq/Len: | 16.545 | ||
| Nf(neff/√len): | 155.9 |
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: 16.545).
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 |
| 5_A | 70_A | 4.115 | 1.00 |
| 72_M | 242_I | 2.976 | 1.00 |
| 214_Q | 218_N | 2.782 | 1.00 |
| 294_L | 298_K | 2.678 | 1.00 |
| 74_V | 242_I | 2.658 | 1.00 |
| 95_V | 127_V | 2.529 | 1.00 |
| 102_M | 128_A | 2.523 | 1.00 |
| 79_P | 93_A | 2.439 | 1.00 |
| 5_A | 67_C | 2.386 | 1.00 |
| 117_I | 238_G | 2.382 | 1.00 |
| 275_L | 283_N | 2.357 | 1.00 |
| 104_N | 107_K | 2.271 | 1.00 |
| 270_M | 297_L | 2.237 | 1.00 |
| 215_E | 222_K | 2.218 | 1.00 |
| 168_A | 185_A | 2.179 | 1.00 |
| 171_A | 181_L | 2.176 | 1.00 |
| 67_C | 109_A | 2.164 | 1.00 |
| 250_N | 277_N | 2.095 | 1.00 |
| 158_Q | 208_K | 2.074 | 1.00 |
| 302_E | 306_E | 2.067 | 1.00 |
| 134_L | 138_Q | 1.976 | 1.00 |
| 99_K | 103_P | 1.949 | 1.00 |
| 102_M | 132_T | 1.849 | 1.00 |
| 277_N | 282_N | 1.821 | 1.00 |
| 3_K | 28_E | 1.805 | 1.00 |
| 250_N | 282_N | 1.790 | 1.00 |
| 23_R | 243_E | 1.783 | 1.00 |
| 259_L | 272_V | 1.766 | 1.00 |
| 270_M | 301_A | 1.755 | 1.00 |
| 206_A | 210_E | 1.754 | 1.00 |
| 295_A | 299_R | 1.739 | 1.00 |
| 129_Q | 269_C | 1.737 | 1.00 |
| 16_L | 238_G | 1.722 | 1.00 |
| 100_A | 104_N | 1.715 | 1.00 |
| 126_H | 130_K | 1.702 | 1.00 |
| 98_L | 128_A | 1.693 | 1.00 |
| 113_I | 245_V | 1.689 | 1.00 |
| 265_I | 297_L | 1.657 | 1.00 |
| 3_K | 30_V | 1.654 | 1.00 |
| 103_P | 131_L | 1.652 | 1.00 |
| 274_T | 281_V | 1.650 | 1.00 |
| 141_G | 256_S | 1.638 | 1.00 |
| 298_K | 302_E | 1.636 | 1.00 |
| 39_V | 43_V | 1.623 | 1.00 |
| 291_D | 294_L | 1.614 | 1.00 |
| 211_E | 215_E | 1.605 | 1.00 |
| 114_Y | 128_A | 1.603 | 1.00 |
| 91_V | 307_T | 1.596 | 1.00 |
| 4_L | 20_A | 1.595 | 1.00 |
| 222_K | 225_N | 1.575 | 1.00 |
| 142_S | 238_G | 1.575 | 1.00 |
| 99_K | 131_L | 1.573 | 1.00 |
| 179_V | 293_E | 1.569 | 1.00 |
| 145_N | 253_L | 1.538 | 1.00 |
| 296_A | 299_R | 1.533 | 1.00 |
| 6_V | 17_A | 1.516 | 1.00 |
| 106_V | 133_G | 1.497 | 1.00 |
| 170_I | 180_P | 1.495 | 1.00 |
| 49_G | 236_M | 1.485 | 1.00 |
| 243_E | 247_H | 1.474 | 1.00 |
| 125_T | 269_C | 1.469 | 1.00 |
| 98_L | 102_M | 1.452 | 1.00 |
| 75_I | 116_L | 1.451 | 1.00 |
| 73_V | 105_L | 1.451 | 1.00 |
| 144_T | 271_S | 1.444 | 1.00 |
| 279_Q | 282_N | 1.444 | 1.00 |
| 103_P | 107_K | 1.440 | 1.00 |
| 47_Q | 157_Q | 1.433 | 1.00 |
| 96_N | 99_K | 1.429 | 1.00 |
| 79_P | 82_K | 1.414 | 1.00 |
| 222_K | 226_G | 1.411 | 1.00 |
| 258_M | 269_C | 1.402 | 0.99 |
| 18_F | 235_G | 1.399 | 0.99 |
| 126_H | 308_A | 1.390 | 0.99 |
| 3_K | 69_D | 1.386 | 0.99 |
| 20_A | 29_I | 1.383 | 0.99 |
| 93_A | 96_N | 1.381 | 0.99 |
| 116_L | 128_A | 1.381 | 0.99 |
| 47_Q | 153_F | 1.380 | 0.99 |
| 291_D | 295_A | 1.377 | 0.99 |
| 159_T | 187_I | 1.375 | 0.99 |
| 156_A | 166_V | 1.373 | 0.99 |
| 67_C | 70_A | 1.371 | 0.99 |
| 127_V | 131_L | 1.367 | 0.99 |
| 295_A | 298_K | 1.354 | 0.99 |
| 145_N | 237_S | 1.345 | 0.99 |
| 299_R | 302_E | 1.342 | 0.99 |
| 218_N | 221_Y | 1.337 | 0.99 |
| 113_I | 138_Q | 1.328 | 0.99 |
| 155_I | 166_V | 1.326 | 0.99 |
| 109_A | 112_A | 1.323 | 0.99 |
| 105_L | 114_Y | 1.319 | 0.99 |
| 158_Q | 211_E | 1.310 | 0.99 |
| 86_S | 89_E | 1.304 | 0.99 |
| 2_T | 246_L | 1.298 | 0.99 |
| 48_H | 219_A | 1.297 | 0.99 |
| 214_Q | 217_K | 1.294 | 0.99 |
| 16_L | 242_I | 1.289 | 0.99 |
| 121_V | 141_G | 1.280 | 0.99 |
| 28_E | 57_S | 1.265 | 0.99 |
| 305_K | 309_A | 1.260 | 0.99 |
| 90_L | 94_T | 1.257 | 0.99 |
| 180_P | 213_H | 1.248 | 0.99 |
| 41_A | 226_G | 1.244 | 0.98 |
| 16_L | 235_G | 1.225 | 0.98 |
| 177_S | 303_T | 1.225 | 0.98 |
| 129_Q | 139_I | 1.221 | 0.98 |
| 16_L | 74_V | 1.210 | 0.98 |
| 125_T | 141_G | 1.210 | 0.98 |
| 83_P | 225_N | 1.209 | 0.98 |
| 85_Q | 93_A | 1.201 | 0.98 |
| 183_E | 293_E | 1.200 | 0.98 |
| 257_S | 274_T | 1.197 | 0.98 |
| 59_D | 66_I | 1.186 | 0.98 |
| 306_E | 309_A | 1.177 | 0.98 |
| 81_Q | 220_A | 1.174 | 0.98 |
| 205_D | 208_K | 1.172 | 0.98 |
| 14_S | 42_E | 1.169 | 0.97 |
| 135_P | 138_Q | 1.157 | 0.97 |
| 18_F | 22_Q | 1.157 | 0.97 |
| 105_L | 134_L | 1.155 | 0.97 |
| 30_V | 66_I | 1.148 | 0.97 |
| 73_V | 112_A | 1.142 | 0.97 |
| 100_A | 103_P | 1.141 | 0.97 |
| 75_I | 128_A | 1.140 | 0.97 |
| 272_V | 284_T | 1.139 | 0.97 |
| 162_N | 165_N | 1.139 | 0.97 |
| 292_K | 296_A | 1.135 | 0.97 |
| 240_D | 251_R | 1.125 | 0.97 |
| 32_E | 64_P | 1.118 | 0.96 |
| 89_E | 92_G | 1.117 | 0.96 |
| 248_D | 278_R | 1.115 | 0.96 |
| 252_I | 275_L | 1.114 | 0.96 |
| 266_S | 305_K | 1.113 | 0.96 |
| 11_A | 231_N | 1.112 | 0.96 |
| 85_Q | 89_E | 1.111 | 0.96 |
| 208_K | 211_E | 1.111 | 0.96 |
| 65_E | 68_R | 1.104 | 0.96 |
| 87_R | 174_H | 1.103 | 0.96 |
| 289_V | 297_L | 1.100 | 0.96 |
| 306_E | 310_Q | 1.099 | 0.96 |
| 292_K | 295_A | 1.094 | 0.96 |
| 220_A | 224_I | 1.091 | 0.96 |
| 299_R | 303_T | 1.090 | 0.96 |
| 75_I | 101_I | 1.087 | 0.96 |
| 298_K | 301_A | 1.087 | 0.96 |
| 30_V | 70_A | 1.083 | 0.96 |
| 183_E | 290_S | 1.075 | 0.95 |
| 102_M | 131_L | 1.070 | 0.95 |
| 38_R | 42_E | 1.068 | 0.95 |
| 121_V | 125_T | 1.055 | 0.95 |
| 154_L | 157_Q | 1.051 | 0.94 |
| 92_G | 96_N | 1.048 | 0.94 |
| 241_I | 255_V | 1.047 | 0.94 |
| 119_N | 174_H | 1.043 | 0.94 |
| 210_E | 214_Q | 1.040 | 0.94 |
| 265_I | 298_K | 1.038 | 0.94 |
| 98_L | 124_A | 1.031 | 0.94 |
| 154_L | 215_E | 1.029 | 0.94 |
| 156_A | 163_V | 1.027 | 0.94 |
| 87_R | 119_N | 1.026 | 0.94 |
| 115_M | 241_I | 1.024 | 0.93 |
| 223_I | 233_A | 1.023 | 0.93 |
| 262_F | 286_N | 1.023 | 0.93 |
| 243_E | 249_T | 1.016 | 0.93 |
| 74_V | 115_M | 1.013 | 0.93 |
| 161_V | 166_V | 1.008 | 0.93 |
| 72_M | 115_M | 1.005 | 0.93 |
| 106_V | 132_T | 1.002 | 0.92 |
| 17_A | 31_L | 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 | |
| 2d4aB | 4 | 0.9649 | 100 | 0.183 | Contact Map |
| 1a5zA | 1 | 0.9872 | 100 | 0.189 | Contact Map |
| 4cl3A | 2 | 0.9712 | 100 | 0.194 | Contact Map |
| 3nepX | 1 | 0.9489 | 100 | 0.195 | Contact Map |
| 1lldA | 2 | 0.9904 | 100 | 0.196 | Contact Map |
| 4aj2A | 4 | 0.9904 | 100 | 0.198 | Contact Map |
| 4plzA | 1 | 0.9617 | 100 | 0.202 | Contact Map |
| 1guzA | 4 | 0.9649 | 100 | 0.205 | Contact Map |
| 3vpgA | 4 | 0.9904 | 100 | 0.21 | Contact Map |
| 2v6bA | 4 | 0.9042 | 100 | 0.211 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)