| RelA Pass 2 |
| ID: | 1433283050 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 382 (324) | ||
| Sequences: | 1416 (784.7) | ||
| Seq/Len: | 4.370 | ||
| Nf(neff/√len): | 43.6 |
HHblits Results: (2013_03)
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: 4.370).
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 |
| 43_V | 61_I | 4.214 | 1.00 |
| 79_K | 153_A | 3.807 | 1.00 |
| 111_T | 150_G | 3.666 | 1.00 |
| 86_K | 119_Q | 3.506 | 1.00 |
| 230_I | 305_E | 3.281 | 1.00 |
| 86_K | 120_I | 3.146 | 1.00 |
| 137_T | 167_D | 3.125 | 1.00 |
| 19_V | 113_A | 3.098 | 1.00 |
| 153_A | 156_E | 3.032 | 1.00 |
| 119_Q | 157_A | 2.969 | 1.00 |
| 85_S | 88_Q | 2.783 | 1.00 |
| 235_N | 239_E | 2.716 | 1.00 |
| 130_G | 158_V | 2.595 | 1.00 |
| 105_M | 151_I | 2.541 | 1.00 |
| 158_V | 161_L | 2.528 | 1.00 |
| 236_R | 274_E | 2.526 | 1.00 |
| 232_T | 305_E | 2.334 | 1.00 |
| 262_M | 279_A | 2.314 | 1.00 |
| 134_R | 144_Q | 2.286 | 1.00 |
| 91_E | 94_K | 2.276 | 1.00 |
| 101_V | 114_A | 2.248 | 1.00 |
| 32_E | 54_K | 2.203 | 1.00 |
| 185_E | 188_N | 2.086 | 1.00 |
| 268_T | 300_E | 2.072 | 1.00 |
| 218_M | 313_T | 2.015 | 1.00 |
| 119_Q | 123_D | 1.965 | 1.00 |
| 86_K | 90_E | 1.954 | 1.00 |
| 141_R | 145_L | 1.899 | 1.00 |
| 90_E | 123_D | 1.889 | 1.00 |
| 15_K | 96_A | 1.884 | 1.00 |
| 130_G | 161_L | 1.865 | 1.00 |
| 200_L | 209_L | 1.843 | 1.00 |
| 217_I | 259_G | 1.802 | 1.00 |
| 41_I | 55_A | 1.747 | 0.99 |
| 24_N | 49_A | 1.690 | 0.99 |
| 59_M | 92_A | 1.655 | 0.99 |
| 215_K | 219_S | 1.643 | 0.99 |
| 238_A | 277_E | 1.639 | 0.99 |
| 188_N | 191_R | 1.626 | 0.99 |
| 152_S | 156_E | 1.618 | 0.99 |
| 93_L | 99_V | 1.617 | 0.99 |
| 80_K | 83_E | 1.614 | 0.99 |
| 239_E | 242_K | 1.594 | 0.99 |
| 270_L | 306_I | 1.583 | 0.99 |
| 28_N | 53_S | 1.578 | 0.99 |
| 160_T | 218_M | 1.571 | 0.99 |
| 177_T | 182_A | 1.556 | 0.99 |
| 79_K | 83_E | 1.550 | 0.98 |
| 191_R | 195_Q | 1.544 | 0.98 |
| 173_V | 185_E | 1.540 | 0.98 |
| 266_G | 270_L | 1.537 | 0.98 |
| 31_I | 55_A | 1.507 | 0.98 |
| 43_V | 117_I | 1.507 | 0.98 |
| 90_E | 120_I | 1.497 | 0.98 |
| 269_N | 304_D | 1.495 | 0.98 |
| 241_A | 282_V | 1.490 | 0.98 |
| 29_R | 187_D | 1.488 | 0.98 |
| 178_P | 181_E | 1.482 | 0.98 |
| 96_A | 99_V | 1.459 | 0.97 |
| 120_I | 124_L | 1.426 | 0.97 |
| 176_N | 273_Y | 1.425 | 0.97 |
| 17_I | 93_L | 1.418 | 0.97 |
| 88_Q | 91_E | 1.412 | 0.97 |
| 67_R | 97_D | 1.403 | 0.97 |
| 134_R | 148_A | 1.398 | 0.97 |
| 238_A | 242_K | 1.396 | 0.96 |
| 93_L | 124_L | 1.392 | 0.96 |
| 27_V | 42_A | 1.389 | 0.96 |
| 82_A | 113_A | 1.387 | 0.96 |
| 18_G | 23_G | 1.375 | 0.96 |
| 41_I | 57_V | 1.369 | 0.96 |
| 275_V | 294_F | 1.361 | 0.96 |
| 26_A | 30_M | 1.347 | 0.95 |
| 232_T | 304_D | 1.342 | 0.95 |
| 96_A | 126_A | 1.339 | 0.95 |
| 26_A | 40_Y | 1.334 | 0.95 |
| 76_E | 80_K | 1.326 | 0.95 |
| 230_I | 307_V | 1.324 | 0.95 |
| 299_N | 307_V | 1.302 | 0.94 |
| 169_I | 186_A | 1.287 | 0.94 |
| 245_I | 310_V | 1.285 | 0.94 |
| 258_Q | 287_D | 1.283 | 0.94 |
| 28_N | 54_K | 1.280 | 0.94 |
| 134_R | 251_E | 1.271 | 0.93 |
| 180_L | 298_I | 1.269 | 0.93 |
| 42_A | 50_L | 1.258 | 0.93 |
| 90_E | 124_L | 1.256 | 0.93 |
| 259_G | 287_D | 1.254 | 0.93 |
| 83_E | 119_Q | 1.247 | 0.92 |
| 63_A | 88_Q | 1.239 | 0.92 |
| 145_L | 149_G | 1.238 | 0.92 |
| 59_M | 89_I | 1.237 | 0.92 |
| 260_V | 286_S | 1.234 | 0.92 |
| 149_G | 152_S | 1.232 | 0.92 |
| 130_G | 154_M | 1.223 | 0.91 |
| 73_A | 216_T | 1.220 | 0.91 |
| 270_L | 275_V | 1.209 | 0.91 |
| 206_L | 296_S | 1.208 | 0.91 |
| 181_E | 184_R | 1.202 | 0.90 |
| 265_T | 302_L | 1.201 | 0.90 |
| 47_A | 51_N | 1.183 | 0.89 |
| 89_I | 120_I | 1.176 | 0.89 |
| 31_I | 40_Y | 1.171 | 0.89 |
| 278_A | 308_V | 1.171 | 0.89 |
| 90_E | 94_K | 1.168 | 0.89 |
| 42_A | 55_A | 1.157 | 0.88 |
| 82_A | 89_I | 1.153 | 0.88 |
| 153_A | 157_A | 1.149 | 0.88 |
| 205_G | 297_V | 1.146 | 0.87 |
| 87_E | 90_E | 1.141 | 0.87 |
| 87_E | 91_E | 1.136 | 0.87 |
| 266_G | 275_V | 1.135 | 0.87 |
| 149_G | 153_A | 1.134 | 0.87 |
| 34_E | 308_V | 1.118 | 0.86 |
| 280_D | 283_A | 1.113 | 0.85 |
| 19_V | 117_I | 1.109 | 0.85 |
| 221_K | 228_I | 1.107 | 0.85 |
| 101_V | 130_G | 1.103 | 0.85 |
| 255_D | 285_A | 1.095 | 0.84 |
| 269_N | 303_K | 1.076 | 0.82 |
| 142_K | 146_Q | 1.075 | 0.82 |
| 168_R | 247_S | 1.071 | 0.82 |
| 73_A | 293_I | 1.070 | 0.82 |
| 35_V | 191_R | 1.062 | 0.81 |
| 42_A | 53_S | 1.059 | 0.81 |
| 180_L | 268_T | 1.055 | 0.81 |
| 265_T | 297_V | 1.053 | 0.81 |
| 276_Q | 280_D | 1.052 | 0.80 |
| 179_M | 296_S | 1.052 | 0.80 |
| 99_V | 126_A | 1.050 | 0.80 |
| 168_R | 171_E | 1.041 | 0.80 |
| 178_P | 271_S | 1.037 | 0.79 |
| 259_G | 290_V | 1.036 | 0.79 |
| 42_A | 54_K | 1.036 | 0.79 |
| 53_S | 58_K | 1.024 | 0.78 |
| 17_I | 43_V | 1.019 | 0.77 |
| 262_M | 308_V | 1.012 | 0.77 |
| 16_V | 40_Y | 1.012 | 0.77 |
| 134_R | 311_I | 1.009 | 0.76 |
| 218_M | 259_G | 1.001 | 0.76 |
| 24_N | 42_A | 1.001 | 0.76 |
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 | |
| 2vawA | 1 | 0.822 | 100 | 0.064 | Contact Map |
| 2vxyA | 1 | 0.801 | 100 | 0.096 | Contact Map |
| 2vapA | 1 | 0.8534 | 100 | 0.142 | Contact Map |
| 2r751 | 1 | 0.8429 | 100 | 0.181 | Contact Map |
| 1rq2A | 2 | 0.788 | 100 | 0.264 | Contact Map |
| 4m8iA | 1 | 0.8141 | 100 | 0.264 | Contact Map |
| 1ofuA | 2 | 0.801 | 100 | 0.275 | Contact Map |
| 1w5fA | 2 | 0.8168 | 100 | 0.276 | Contact Map |
| 4ei7A | 2 | 0.877 | 100 | 0.351 | Contact Map |
| 4b45A | 1 | 0.8194 | 100 | 0.375 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)