| PROK |
| ID: | 1687016087 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 279 (256) | ||
| Sequences: | 13169 (8912.8) | ||
| Seq/Len: | 51.441 | ||
| Nf(neff/√len): | 557.0 |
HHblits Results: (2016_02)
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 |
| 96_L | 102_G | 2.946 | 1.00 |
| 212_W | 218_R | 2.904 | 1.00 |
| 181_G | 202_F | 2.892 | 1.00 |
| 29_A | 87_K | 2.819 | 1.00 |
| 66_G | 98_D | 2.625 | 1.00 |
| 130_S | 227_T | 2.618 | 1.00 |
| 35_V | 77_V | 2.560 | 1.00 |
| 72_H | 225_M | 2.441 | 1.00 |
| 192_F | 206_T | 2.319 | 1.00 |
| 31_Q | 87_K | 2.316 | 1.00 |
| 182_A | 192_F | 2.289 | 1.00 |
| 72_H | 210_S | 2.279 | 1.00 |
| 75_G | 210_S | 2.279 | 1.00 |
| 93_V | 113_F | 2.196 | 1.00 |
| 93_V | 110_G | 2.193 | 1.00 |
| 75_G | 211_T | 2.164 | 1.00 |
| 190_S | 206_T | 2.135 | 1.00 |
| 34_C | 89_Q | 2.126 | 1.00 |
| 212_W | 220_I | 2.063 | 1.00 |
| 146_A | 176_S | 2.024 | 1.00 |
| 34_C | 91_F | 1.988 | 1.00 |
| 182_A | 190_S | 1.985 | 1.00 |
| 182_A | 205_G | 1.984 | 1.00 |
| 76_T | 229_H | 1.946 | 1.00 |
| 112_D | 147_R | 1.920 | 1.00 |
| 9_G | 229_H | 1.917 | 1.00 |
| 172_A | 179_T | 1.892 | 1.00 |
| 73_C | 130_S | 1.882 | 1.00 |
| 154_M | 234_A | 1.862 | 1.00 |
| 65_D | 68_G | 1.850 | 1.00 |
| 181_G | 193_S | 1.832 | 1.00 |
| 139_S | 143_S | 1.818 | 1.00 |
| 130_S | 231_A | 1.734 | 1.00 |
| 78_G | 90_L | 1.733 | 1.00 |
| 113_F | 117_D | 1.731 | 1.00 |
| 73_C | 228_P | 1.711 | 1.00 |
| 227_T | 231_A | 1.673 | 1.00 |
| 84_V | 232_G | 1.661 | 1.00 |
| 127_V | 238_M | 1.660 | 1.00 |
| 238_M | 248_A | 1.650 | 1.00 |
| 234_A | 248_A | 1.647 | 1.00 |
| 79_S | 211_T | 1.630 | 1.00 |
| 12_R | 187_D | 1.600 | 1.00 |
| 115_A | 148_L | 1.596 | 1.00 |
| 38_I | 95_V | 1.578 | 1.00 |
| 36_Y | 114_V | 1.570 | 1.00 |
| 36_Y | 126_G | 1.569 | 1.00 |
| 35_V | 235_A | 1.563 | 1.00 |
| 91_F | 126_G | 1.558 | 1.00 |
| 241_G | 244_T | 1.550 | 1.00 |
| 37_V | 77_V | 1.541 | 1.00 |
| 37_V | 73_C | 1.536 | 1.00 |
| 167_R | 198_V | 1.530 | 1.00 |
| 112_D | 116_S | 1.529 | 1.00 |
| 54_Q | 89_Q | 1.527 | 1.00 |
| 250_R | 254_D | 1.513 | 1.00 |
| 184_D | 188_R | 1.501 | 1.00 |
| 28_S | 239_T | 1.500 | 1.00 |
| 33_S | 238_M | 1.489 | 1.00 |
| 29_A | 239_T | 1.489 | 1.00 |
| 154_M | 178_C | 1.486 | 1.00 |
| 184_D | 206_T | 1.482 | 1.00 |
| 146_A | 150_S | 1.471 | 1.00 |
| 142_N | 146_A | 1.465 | 1.00 |
| 156_A | 234_A | 1.460 | 1.00 |
| 163_N | 189_R | 1.458 | 1.00 |
| 156_A | 227_T | 1.458 | 1.00 |
| 249_C | 253_A | 1.445 | 1.00 |
| 42_I | 92_G | 1.425 | 1.00 |
| 156_A | 230_V | 1.420 | 1.00 |
| 35_V | 88_T | 1.418 | 1.00 |
| 103_Q | 106_T | 1.406 | 0.99 |
| 111_M | 148_L | 1.403 | 0.99 |
| 159_A | 179_T | 1.401 | 0.99 |
| 220_I | 225_M | 1.399 | 0.99 |
| 43_E | 213_I | 1.388 | 0.99 |
| 189_R | 193_S | 1.384 | 0.99 |
| 241_G | 251_Y | 1.371 | 0.99 |
| 128_V | 231_A | 1.352 | 0.99 |
| 183_S | 202_F | 1.338 | 0.99 |
| 148_L | 155_V | 1.336 | 0.99 |
| 142_N | 173_S | 1.334 | 0.99 |
| 244_T | 251_Y | 1.329 | 0.99 |
| 182_A | 206_T | 1.328 | 0.99 |
| 149_Q | 176_S | 1.318 | 0.99 |
| 85_A | 235_A | 1.312 | 0.99 |
| 209_L | 219_S | 1.299 | 0.99 |
| 189_R | 202_F | 1.297 | 0.99 |
| 181_G | 199_L | 1.286 | 0.99 |
| 180_V | 201_I | 1.273 | 0.99 |
| 108_I | 144_A | 1.243 | 0.98 |
| 72_H | 220_I | 1.221 | 0.98 |
| 132_S | 228_P | 1.220 | 0.98 |
| 33_S | 235_A | 1.218 | 0.98 |
| 76_T | 225_M | 1.213 | 0.98 |
| 178_C | 249_C | 1.208 | 0.98 |
| 154_M | 248_A | 1.205 | 0.98 |
| 201_I | 252_I | 1.204 | 0.98 |
| 85_A | 88_T | 1.200 | 0.98 |
| 251_Y | 255_T | 1.196 | 0.98 |
| 162_N | 194_N | 1.190 | 0.98 |
| 115_A | 153_V | 1.188 | 0.98 |
| 206_T | 221_S | 1.185 | 0.98 |
| 234_A | 252_I | 1.183 | 0.98 |
| 74_A | 90_L | 1.177 | 0.98 |
| 158_A | 227_T | 1.177 | 0.98 |
| 74_A | 92_G | 1.176 | 0.98 |
| 107_I | 133_L | 1.175 | 0.98 |
| 52_R | 80_R | 1.174 | 0.98 |
| 131_L | 155_V | 1.163 | 0.97 |
| 58_T | 94_K | 1.150 | 0.97 |
| 129_A | 153_V | 1.149 | 0.97 |
| 147_R | 150_S | 1.142 | 0.97 |
| 59_Y | 113_F | 1.133 | 0.97 |
| 46_H | 217_T | 1.130 | 0.97 |
| 50_E | 80_R | 1.122 | 0.97 |
| 131_L | 157_V | 1.108 | 0.96 |
| 108_I | 140_S | 1.101 | 0.96 |
| 142_N | 174_E | 1.101 | 0.96 |
| 146_A | 175_P | 1.100 | 0.96 |
| 54_Q | 91_F | 1.082 | 0.96 |
| 116_S | 147_R | 1.077 | 0.95 |
| 237_L | 244_T | 1.070 | 0.95 |
| 95_V | 133_L | 1.070 | 0.95 |
| 147_R | 151_S | 1.062 | 0.95 |
| 69_H | 224_S | 1.059 | 0.95 |
| 40_T | 67_N | 1.057 | 0.95 |
| 39_D | 69_H | 1.032 | 0.94 |
| 111_M | 131_L | 1.030 | 0.94 |
| 157_V | 177_V | 1.028 | 0.94 |
| 145_A | 177_V | 1.027 | 0.94 |
| 44_A | 53_A | 1.023 | 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 | |
| 2pwaA | 1 | 1 | 100 | 0.052 | Contact Map |
| 3f7mA | 1 | 0.9964 | 100 | 0.059 | Contact Map |
| 4dztA | 1 | 0.9713 | 100 | 0.099 | Contact Map |
| 2b6nA | 1 | 0.9713 | 100 | 0.112 | Contact Map |
| 1sh7A | 2 | 0.9677 | 100 | 0.117 | Contact Map |
| 2p4eP | 2 | 0.957 | 100 | 0.141 | Contact Map |
| 2qtwB | 1 | 0.9427 | 100 | 0.142 | Contact Map |
| 1r6vA | 1 | 0.957 | 100 | 0.145 | Contact Map |
| 3whiA | 2 | 0.9355 | 100 | 0.157 | Contact Map |
| 1thmA | 1 | 0.9391 | 100 | 0.164 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)