| VirB10 |
| ID: | 1669744629 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 336 (200) | ||
| Sequences: | 1326 (802.9) | ||
| Seq/Len: | 6.630 | ||
| Nf(neff/√len): | 56.8 |
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 |
| 193_T | 218_L | 4.027 | 1.00 |
| 249_H | 308_T | 3.962 | 1.00 |
| 297_V | 300_E | 3.594 | 1.00 |
| 244_G | 309_M | 3.121 | 1.00 |
| 157_C | 173_C | 2.957 | 1.00 |
| 162_R | 239_E | 2.934 | 1.00 |
| 293_E | 296_K | 2.645 | 1.00 |
| 244_G | 312_N | 2.452 | 1.00 |
| 162_R | 313_Q | 2.432 | 1.00 |
| 160_T | 174_V | 2.402 | 1.00 |
| 155_I | 175_F | 2.360 | 1.00 |
| 195_A | 319_I | 2.358 | 1.00 |
| 247_D | 310_Y | 2.214 | 1.00 |
| 235_G | 239_E | 2.189 | 1.00 |
| 217_Q | 324_D | 2.176 | 1.00 |
| 175_F | 189_L | 2.127 | 1.00 |
| 158_A | 176_T | 2.011 | 1.00 |
| 215_W | 261_S | 1.968 | 1.00 |
| 165_S | 211_M | 1.893 | 1.00 |
| 178_D | 191_Q | 1.866 | 1.00 |
| 189_L | 218_L | 1.781 | 1.00 |
| 311_K | 315_D | 1.706 | 1.00 |
| 193_T | 220_T | 1.600 | 1.00 |
| 223_N | 228_M | 1.559 | 0.99 |
| 146_D | 183_N | 1.549 | 0.99 |
| 171_I | 197_G | 1.535 | 0.99 |
| 250_F | 254_F | 1.520 | 0.99 |
| 166_D | 308_T | 1.514 | 0.99 |
| 213_V | 242_I | 1.477 | 0.99 |
| 200_Q | 212_F | 1.435 | 0.99 |
| 175_F | 195_A | 1.423 | 0.99 |
| 260_L | 298_A | 1.400 | 0.99 |
| 156_P | 318_T | 1.395 | 0.99 |
| 149_I | 182_A | 1.391 | 0.98 |
| 155_I | 189_L | 1.387 | 0.98 |
| 197_G | 215_W | 1.376 | 0.98 |
| 189_L | 193_T | 1.348 | 0.98 |
| 197_G | 213_V | 1.342 | 0.98 |
| 215_W | 233_A | 1.340 | 0.98 |
| 265_D | 269_A | 1.330 | 0.98 |
| 198_R | 216_E | 1.328 | 0.98 |
| 164_V | 310_Y | 1.301 | 0.97 |
| 238_G | 314_G | 1.298 | 0.97 |
| 245_W | 310_Y | 1.298 | 0.97 |
| 155_I | 179_V | 1.285 | 0.97 |
| 178_D | 187_K | 1.276 | 0.97 |
| 150_E | 219_R | 1.271 | 0.97 |
| 242_I | 317_I | 1.268 | 0.97 |
| 163_F | 211_M | 1.262 | 0.97 |
| 139_T | 142_N | 1.238 | 0.96 |
| 252_E | 302_S | 1.224 | 0.96 |
| 163_F | 171_I | 1.203 | 0.95 |
| 160_T | 172_S | 1.201 | 0.95 |
| 149_I | 325_I | 1.186 | 0.95 |
| 296_K | 300_E | 1.181 | 0.95 |
| 156_P | 316_I | 1.181 | 0.95 |
| 237_L | 313_Q | 1.165 | 0.94 |
| 194_K | 219_R | 1.157 | 0.94 |
| 211_M | 309_M | 1.156 | 0.94 |
| 175_F | 179_V | 1.155 | 0.94 |
| 238_G | 241_G | 1.141 | 0.93 |
| 256_G | 299_L | 1.124 | 0.93 |
| 253_R | 257_S | 1.124 | 0.93 |
| 298_A | 302_S | 1.123 | 0.93 |
| 264_Q | 292_A | 1.122 | 0.93 |
| 295_A | 298_A | 1.113 | 0.92 |
| 261_S | 265_D | 1.109 | 0.92 |
| 270_A | 288_R | 1.102 | 0.92 |
| 145_P | 148_Y | 1.100 | 0.92 |
| 168_A | 212_F | 1.072 | 0.90 |
| 278_D | 317_I | 1.063 | 0.90 |
| 136_M | 140_A | 1.056 | 0.89 |
| 150_E | 182_A | 1.054 | 0.89 |
| 327_F | 330_I | 1.043 | 0.89 |
| 163_F | 311_K | 1.039 | 0.88 |
| 245_W | 312_N | 1.027 | 0.87 |
| 332_E | 335_V | 1.025 | 0.87 |
| 243_D | 309_M | 1.018 | 0.87 |
| 217_Q | 232_A | 1.015 | 0.87 |
| 173_C | 317_I | 1.013 | 0.87 |
| 152_N | 196_F | 1.004 | 0.86 |
| 215_W | 319_I | 1.003 | 0.86 |
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 | |
| 3jqoA | 14 | 0.5952 | 100 | 0.398 | Contact Map |
| 2bhvA | 6 | 0.5476 | 100 | 0.43 | Contact Map |
| 4pypA | 1 | 0.0744 | 14.4 | 0.964 | Contact Map |
| 2l16A | 1 | 0.0952 | 14 | 0.965 | Contact Map |
| 3wdoA | 1 | 0.253 | 11.5 | 0.966 | Contact Map |
| 4um9B | 1 | 0 | 11.4 | 0.966 | Contact Map |
| 1qleD | 1 | 0.0595 | 11.2 | 0.966 | Contact Map |
| 3rkoA | 2 | 0.0863 | 10.3 | 0.967 | Contact Map |
| 1m56D | 2 | 0.0595 | 9.7 | 0.967 | Contact Map |
| 2lonA | 1 | 0.1101 | 9.6 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)