| 2WOZ_A non default parameters |
| ID: | 1482669867 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 318 (274) | ||
| Sequences: | 4914 (3466.4) | ||
| Seq/Len: | 17.934 | ||
| Nf(neff/√len): | 209.4 |
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: 17.934).
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 |
| 111_K | 131_C | 3.652 | 1.00 |
| 227_F | 232_N | 3.593 | 1.00 |
| 83_L | 88_S | 3.494 | 1.00 |
| 132_Y | 137_A | 3.348 | 1.00 |
| 58_Q | 82_Q | 3.346 | 1.00 |
| 208_K | 226_A | 3.188 | 1.00 |
| 160_M | 179_I | 3.088 | 1.00 |
| 180_Y | 185_G | 3.047 | 1.00 |
| 283_Y | 288_K | 2.713 | 1.00 |
| 153_N | 202_V | 2.669 | 1.00 |
| 58_Q | 84_D | 2.449 | 1.00 |
| 104_G | 154_V | 2.365 | 1.00 |
| 97_P | 130_L | 2.291 | 1.00 |
| 202_V | 211_I | 2.275 | 1.00 |
| 208_K | 228_D | 2.247 | 1.00 |
| 105_L | 114_V | 2.156 | 1.00 |
| 111_K | 133_D | 2.146 | 1.00 |
| 152_H | 163_C | 2.136 | 1.00 |
| 201_G | 249_L | 2.119 | 1.00 |
| 29_Y | 34_N | 2.091 | 1.00 |
| 255_S | 284_E | 2.069 | 1.00 |
| 113_Y | 131_C | 2.003 | 1.00 |
| 149_V | 176_R | 1.975 | 1.00 |
| 155_I | 209_I | 1.973 | 1.00 |
| 255_S | 282_K | 1.954 | 1.00 |
| 160_M | 181_N | 1.882 | 1.00 |
| 179_I | 190_L | 1.875 | 1.00 |
| 149_V | 178_F | 1.848 | 1.00 |
| 203_A | 256_L | 1.793 | 1.00 |
| 155_I | 204_I | 1.788 | 1.00 |
| 82_Q | 93_L | 1.786 | 1.00 |
| 249_L | 258_A | 1.784 | 1.00 |
| 113_Y | 161_I | 1.762 | 1.00 |
| 197_R | 225_E | 1.724 | 1.00 |
| 104_G | 152_H | 1.698 | 1.00 |
| 106_G | 154_V | 1.678 | 1.00 |
| 146_P | 178_F | 1.672 | 1.00 |
| 153_N | 200_F | 1.667 | 1.00 |
| 162_Y | 177_V | 1.663 | 1.00 |
| 201_G | 247_I | 1.648 | 1.00 |
| 100_R | 128_S | 1.637 | 1.00 |
| 60_Y | 112_I | 1.598 | 1.00 |
| 52_I | 61_V | 1.591 | 1.00 |
| 53_V | 112_I | 1.581 | 1.00 |
| 207_G | 230_K | 1.565 | 1.00 |
| 131_C | 142_V | 1.564 | 1.00 |
| 210_V | 226_A | 1.560 | 1.00 |
| 106_G | 161_I | 1.528 | 1.00 |
| 226_A | 237_M | 1.523 | 1.00 |
| 203_A | 251_S | 1.520 | 1.00 |
| 200_F | 211_I | 1.512 | 1.00 |
| 210_V | 256_L | 1.510 | 1.00 |
| 154_V | 163_C | 1.505 | 1.00 |
| 212_A | 224_V | 1.472 | 1.00 |
| 110_D | 135_V | 1.469 | 1.00 |
| 284_E | 287_K | 1.406 | 0.99 |
| 51_S | 105_L | 1.403 | 0.99 |
| 162_Y | 209_I | 1.399 | 0.99 |
| 203_A | 249_L | 1.391 | 0.99 |
| 94_P | 137_A | 1.388 | 0.99 |
| 155_I | 202_V | 1.385 | 0.99 |
| 115_V | 161_I | 1.376 | 0.99 |
| 161_I | 182_P | 1.370 | 0.99 |
| 133_D | 136_A | 1.347 | 0.99 |
| 93_L | 137_A | 1.346 | 0.99 |
| 110_D | 134_P | 1.338 | 0.99 |
| 143_K | 185_G | 1.334 | 0.99 |
| 60_Y | 82_Q | 1.324 | 0.99 |
| 194_K | 225_E | 1.320 | 0.99 |
| 108_V | 156_S | 1.319 | 0.99 |
| 142_V | 185_G | 1.303 | 0.99 |
| 247_I | 258_A | 1.303 | 0.99 |
| 154_V | 161_I | 1.301 | 0.99 |
| 131_C | 140_S | 1.300 | 0.99 |
| 249_L | 256_L | 1.288 | 0.99 |
| 181_N | 184_K | 1.280 | 0.99 |
| 103_F | 114_V | 1.279 | 0.99 |
| 162_Y | 179_I | 1.274 | 0.99 |
| 212_A | 256_L | 1.273 | 0.99 |
| 100_R | 130_L | 1.271 | 0.99 |
| 60_Y | 80_F | 1.269 | 0.99 |
| 197_R | 214_G | 1.262 | 0.99 |
| 164_L | 209_I | 1.257 | 0.99 |
| 106_G | 156_S | 1.255 | 0.99 |
| 207_G | 229_L | 1.253 | 0.99 |
| 164_L | 177_V | 1.239 | 0.98 |
| 244_R | 261_G | 1.234 | 0.98 |
| 179_I | 188_K | 1.227 | 0.98 |
| 57_N | 86_V | 1.213 | 0.98 |
| 157_H | 204_I | 1.205 | 0.98 |
| 129_V | 142_V | 1.202 | 0.98 |
| 84_D | 87_S | 1.198 | 0.98 |
| 61_V | 90_W | 1.193 | 0.98 |
| 159_G | 183_K | 1.188 | 0.98 |
| 100_R | 126_L | 1.183 | 0.98 |
| 197_R | 223_S | 1.173 | 0.98 |
| 97_P | 139_W | 1.173 | 0.98 |
| 241_P | 281_W | 1.168 | 0.97 |
| 112_I | 134_P | 1.163 | 0.97 |
| 114_V | 139_W | 1.159 | 0.97 |
| 30_D | 33_E | 1.156 | 0.97 |
| 157_H | 229_L | 1.154 | 0.97 |
| 129_V | 180_Y | 1.141 | 0.97 |
| 168_T | 174_T | 1.138 | 0.97 |
| 80_F | 132_Y | 1.137 | 0.97 |
| 163_C | 187_W | 1.126 | 0.97 |
| 173_C | 198_S | 1.123 | 0.97 |
| 191_A | 232_N | 1.122 | 0.97 |
| 119_D | 126_L | 1.117 | 0.96 |
| 298_R | 301_S | 1.116 | 0.96 |
| 216_T | 221_S | 1.113 | 0.96 |
| 55_Q | 107_E | 1.112 | 0.96 |
| 105_L | 112_I | 1.106 | 0.96 |
| 130_L | 141_E | 1.086 | 0.96 |
| 55_Q | 134_P | 1.073 | 0.95 |
| 242_Q | 281_W | 1.070 | 0.95 |
| 107_E | 134_P | 1.068 | 0.95 |
| 282_K | 291_A | 1.068 | 0.95 |
| 220_L | 245_S | 1.067 | 0.95 |
| 100_R | 103_F | 1.063 | 0.95 |
| 226_A | 235_E | 1.060 | 0.95 |
| 159_G | 182_P | 1.059 | 0.95 |
| 258_A | 290_W | 1.057 | 0.95 |
| 254_G | 285_D | 1.056 | 0.95 |
| 156_S | 182_P | 1.045 | 0.94 |
| 204_I | 229_L | 1.036 | 0.94 |
| 244_R | 281_W | 1.033 | 0.94 |
| 186_D | 233_K | 1.031 | 0.94 |
| 127_D | 148_K | 1.027 | 0.94 |
| 149_V | 174_T | 1.025 | 0.93 |
| 190_L | 232_N | 1.025 | 0.93 |
| 191_A | 227_F | 1.024 | 0.93 |
| 228_D | 231_T | 1.014 | 0.93 |
| 82_Q | 91_V | 1.012 | 0.93 |
| 108_V | 182_P | 1.010 | 0.93 |
| 164_L | 175_N | 1.005 | 0.93 |
| 149_V | 152_H | 1.003 | 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 | |
| 2wozA | 1 | 0.9654 | 100 | 0.168 | Contact Map |
| 4ascA | 1 | 0.934 | 100 | 0.257 | Contact Map |
| 4chbA | 2 | 0.8679 | 100 | 0.259 | Contact Map |
| 1zgkA | 1 | 0.8805 | 100 | 0.268 | Contact Map |
| 3ii7A | 1 | 0.8774 | 100 | 0.27 | Contact Map |
| 2vpjA | 1 | 0.8679 | 100 | 0.274 | Contact Map |
| 4yy8A | 2 | 0.9057 | 100 | 0.304 | Contact Map |
| 2uvkA | 2 | 0.8868 | 100 | 0.327 | Contact Map |
| 1k3iA | 1 | 0.9465 | 100 | 0.37 | Contact Map |
| 2zwaA | 2 | 0.8522 | 100 | 0.385 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)