| 1lth-jackhmmer |
| ID: | 1506720722 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 313 (306) | ||
| Sequences: | 6516 (3665.5) | ||
| Seq/Len: | 21.294 | ||
| Nf(neff/√len): | 209.5 |
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: 21.294).
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 | 3.954 | 1.00 |
| 72_M | 242_I | 2.732 | 1.00 |
| 294_L | 298_K | 2.722 | 1.00 |
| 214_Q | 218_N | 2.601 | 1.00 |
| 74_V | 242_I | 2.366 | 1.00 |
| 23_R | 243_E | 2.357 | 1.00 |
| 95_V | 127_V | 2.327 | 1.00 |
| 79_P | 93_A | 2.295 | 1.00 |
| 250_N | 277_N | 2.233 | 1.00 |
| 302_E | 306_E | 2.147 | 1.00 |
| 104_N | 107_K | 2.147 | 1.00 |
| 67_C | 109_A | 2.142 | 1.00 |
| 215_E | 222_K | 2.142 | 1.00 |
| 117_I | 238_G | 2.136 | 1.00 |
| 5_A | 67_C | 2.109 | 1.00 |
| 136_E | 260_K | 2.098 | 1.00 |
| 206_A | 210_E | 2.087 | 1.00 |
| 265_I | 297_L | 2.085 | 1.00 |
| 158_Q | 208_K | 2.059 | 1.00 |
| 171_A | 181_L | 2.050 | 1.00 |
| 102_M | 128_A | 2.039 | 1.00 |
| 277_N | 282_N | 2.020 | 1.00 |
| 270_M | 297_L | 2.000 | 1.00 |
| 168_A | 185_A | 1.953 | 1.00 |
| 250_N | 282_N | 1.943 | 1.00 |
| 275_L | 283_N | 1.911 | 1.00 |
| 129_Q | 269_C | 1.904 | 1.00 |
| 159_T | 187_I | 1.880 | 1.00 |
| 106_V | 134_L | 1.863 | 1.00 |
| 106_V | 133_G | 1.862 | 1.00 |
| 99_K | 103_P | 1.853 | 1.00 |
| 259_L | 272_V | 1.808 | 1.00 |
| 274_T | 281_V | 1.801 | 1.00 |
| 211_E | 215_E | 1.779 | 1.00 |
| 103_P | 131_L | 1.758 | 1.00 |
| 100_A | 104_N | 1.756 | 1.00 |
| 134_L | 138_Q | 1.740 | 1.00 |
| 295_A | 299_R | 1.735 | 1.00 |
| 298_K | 302_E | 1.712 | 1.00 |
| 270_M | 301_A | 1.710 | 1.00 |
| 257_S | 274_T | 1.698 | 1.00 |
| 102_M | 132_T | 1.694 | 1.00 |
| 114_Y | 128_A | 1.684 | 1.00 |
| 228_G | 231_N | 1.672 | 1.00 |
| 91_V | 307_T | 1.667 | 1.00 |
| 4_L | 26_A | 1.666 | 1.00 |
| 279_Q | 282_N | 1.660 | 1.00 |
| 113_I | 245_V | 1.649 | 1.00 |
| 85_Q | 93_A | 1.648 | 1.00 |
| 144_T | 271_S | 1.607 | 1.00 |
| 296_A | 299_R | 1.590 | 1.00 |
| 258_M | 269_C | 1.581 | 1.00 |
| 125_T | 269_C | 1.576 | 1.00 |
| 103_P | 107_K | 1.566 | 1.00 |
| 179_V | 293_E | 1.558 | 1.00 |
| 64_P | 108_V | 1.541 | 1.00 |
| 6_V | 17_A | 1.539 | 1.00 |
| 265_I | 298_K | 1.531 | 1.00 |
| 291_D | 295_A | 1.528 | 1.00 |
| 291_D | 294_L | 1.524 | 1.00 |
| 16_L | 238_G | 1.503 | 1.00 |
| 126_H | 130_K | 1.496 | 1.00 |
| 141_G | 256_S | 1.496 | 1.00 |
| 47_Q | 157_Q | 1.488 | 1.00 |
| 98_L | 128_A | 1.486 | 1.00 |
| 39_V | 43_V | 1.469 | 1.00 |
| 142_S | 238_G | 1.460 | 1.00 |
| 96_N | 99_K | 1.459 | 1.00 |
| 243_E | 247_H | 1.455 | 1.00 |
| 4_L | 20_A | 1.423 | 1.00 |
| 299_R | 302_E | 1.420 | 1.00 |
| 205_D | 208_K | 1.413 | 1.00 |
| 81_Q | 220_A | 1.395 | 0.99 |
| 9_A | 31_L | 1.379 | 0.99 |
| 145_N | 237_S | 1.374 | 0.99 |
| 145_N | 253_L | 1.364 | 0.99 |
| 113_I | 138_Q | 1.360 | 0.99 |
| 210_E | 214_Q | 1.354 | 0.99 |
| 292_K | 296_A | 1.351 | 0.99 |
| 170_I | 180_P | 1.351 | 0.99 |
| 72_M | 115_M | 1.341 | 0.99 |
| 65_E | 68_R | 1.339 | 0.99 |
| 3_K | 30_V | 1.339 | 0.99 |
| 47_Q | 153_F | 1.321 | 0.99 |
| 73_V | 105_L | 1.319 | 0.99 |
| 98_L | 102_M | 1.312 | 0.99 |
| 177_S | 303_T | 1.297 | 0.99 |
| 127_V | 131_L | 1.294 | 0.99 |
| 260_K | 266_S | 1.291 | 0.99 |
| 105_L | 114_Y | 1.288 | 0.99 |
| 49_G | 236_M | 1.280 | 0.99 |
| 248_D | 278_R | 1.278 | 0.99 |
| 41_A | 226_G | 1.275 | 0.99 |
| 37_E | 225_N | 1.270 | 0.99 |
| 75_I | 116_L | 1.266 | 0.99 |
| 214_Q | 217_K | 1.265 | 0.99 |
| 16_L | 242_I | 1.264 | 0.99 |
| 265_I | 301_A | 1.263 | 0.99 |
| 183_E | 293_E | 1.260 | 0.99 |
| 20_A | 29_I | 1.255 | 0.99 |
| 218_N | 221_Y | 1.249 | 0.99 |
| 208_K | 211_E | 1.245 | 0.98 |
| 155_I | 166_V | 1.227 | 0.98 |
| 222_K | 225_N | 1.224 | 0.98 |
| 100_A | 103_P | 1.222 | 0.98 |
| 36_K | 63_D | 1.222 | 0.98 |
| 64_P | 107_K | 1.219 | 0.98 |
| 37_E | 226_G | 1.211 | 0.98 |
| 162_N | 165_N | 1.197 | 0.98 |
| 86_S | 89_E | 1.193 | 0.98 |
| 180_P | 213_H | 1.188 | 0.98 |
| 275_L | 282_N | 1.186 | 0.98 |
| 295_A | 298_K | 1.186 | 0.98 |
| 93_A | 96_N | 1.170 | 0.97 |
| 259_L | 262_F | 1.167 | 0.97 |
| 156_A | 166_V | 1.166 | 0.97 |
| 37_E | 40_E | 1.155 | 0.97 |
| 158_Q | 211_E | 1.154 | 0.97 |
| 167_H | 186_T | 1.154 | 0.97 |
| 109_A | 112_A | 1.151 | 0.97 |
| 16_L | 74_V | 1.142 | 0.97 |
| 38_R | 42_E | 1.140 | 0.97 |
| 79_P | 82_K | 1.138 | 0.97 |
| 3_K | 28_E | 1.138 | 0.97 |
| 35_A | 38_R | 1.132 | 0.97 |
| 292_K | 295_A | 1.127 | 0.97 |
| 257_S | 281_V | 1.124 | 0.97 |
| 3_K | 69_D | 1.123 | 0.97 |
| 73_V | 112_A | 1.122 | 0.97 |
| 18_F | 235_G | 1.119 | 0.96 |
| 129_Q | 258_M | 1.118 | 0.96 |
| 48_H | 219_A | 1.116 | 0.96 |
| 99_K | 131_L | 1.113 | 0.96 |
| 67_C | 70_A | 1.112 | 0.96 |
| 299_R | 303_T | 1.111 | 0.96 |
| 116_L | 128_A | 1.106 | 0.96 |
| 183_E | 290_S | 1.102 | 0.96 |
| 165_N | 188_G | 1.101 | 0.96 |
| 255_V | 274_T | 1.096 | 0.96 |
| 85_Q | 89_E | 1.094 | 0.96 |
| 56_V | 59_D | 1.093 | 0.96 |
| 18_F | 22_Q | 1.092 | 0.96 |
| 30_V | 66_I | 1.091 | 0.96 |
| 89_E | 92_G | 1.070 | 0.95 |
| 32_E | 64_P | 1.068 | 0.95 |
| 20_A | 25_I | 1.064 | 0.95 |
| 71_D | 111_N | 1.054 | 0.95 |
| 153_F | 157_Q | 1.050 | 0.94 |
| 121_V | 141_G | 1.042 | 0.94 |
| 177_S | 300_S | 1.040 | 0.94 |
| 243_E | 249_T | 1.038 | 0.94 |
| 87_R | 119_N | 1.038 | 0.94 |
| 90_L | 94_T | 1.038 | 0.94 |
| 252_I | 275_L | 1.032 | 0.94 |
| 222_K | 226_G | 1.031 | 0.94 |
| 154_L | 215_E | 1.029 | 0.94 |
| 14_S | 42_E | 1.027 | 0.94 |
| 30_V | 70_A | 1.026 | 0.94 |
| 181_L | 289_V | 1.021 | 0.93 |
| 190_V | 194_D | 1.019 | 0.93 |
| 11_A | 231_N | 1.018 | 0.93 |
| 75_I | 128_A | 1.012 | 0.93 |
| 121_V | 125_T | 1.010 | 0.93 |
| 240_D | 251_R | 1.003 | 0.93 |
| 74_V | 115_M | 1.001 | 0.92 |
| 63_D | 66_I | 1.000 | 0.92 |
| 106_V | 132_T | 1.000 | 0.92 |
| 92_G | 96_N | 1.000 | 0.92 |
| 171_A | 179_V | 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 | 0.229 | Contact Map |
| 1lldA | 2 | 0.9936 | 100 | 0.236 | Contact Map |
| 1a5zA | 1 | 0.9872 | 100 | 0.241 | Contact Map |
| 3nepX | 1 | 0.9489 | 100 | 0.243 | Contact Map |
| 4plzA | 1 | 0.9617 | 100 | 0.245 | Contact Map |
| 4cl3A | 2 | 0.9712 | 100 | 0.248 | Contact Map |
| 4aj2A | 4 | 0.9968 | 100 | 0.25 | Contact Map |
| 1guzA | 4 | 0.9649 | 100 | 0.256 | Contact Map |
| 2v6bA | 4 | 0.9042 | 100 | 0.258 | Contact Map |
| 3vpgA | 4 | 0.9904 | 100 | 0.258 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)