| sep3 |
| ID: | 1447421570 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 251 (244) | ||
| Sequences: | 1868 (1430.5) | ||
| Seq/Len: | 7.656 | ||
| Nf(neff/√len): | 91.6 |
Jackhmmer Results: (2015_08)
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: 7.656).
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 |
| 197_R | 200_H | 2.170 | 1.00 |
| 219_L | 222_G | 2.081 | 1.00 |
| 186_N | 189_Q | 1.942 | 1.00 |
| 226_Q | 230_M | 1.698 | 1.00 |
| 42_E | 69_R | 1.610 | 1.00 |
| 206_S | 209_F | 1.540 | 1.00 |
| 145_L | 149_F | 1.540 | 1.00 |
| 212_P | 215_C | 1.529 | 1.00 |
| 30_K | 34_E | 1.521 | 1.00 |
| 230_M | 234_P | 1.510 | 0.99 |
| 207_Q | 211_Q | 1.503 | 0.99 |
| 193_D | 196_G | 1.465 | 0.99 |
| 213_L | 216_E | 1.462 | 0.99 |
| 214_E | 218_I | 1.459 | 0.99 |
| 214_E | 217_P | 1.457 | 0.99 |
| 217_P | 221_I | 1.453 | 0.99 |
| 148_Q | 152_D | 1.450 | 0.99 |
| 210_F | 213_L | 1.446 | 0.99 |
| 198_H | 201_Q | 1.422 | 0.99 |
| 199_H | 203_Q | 1.406 | 0.99 |
| 232_A | 235_S | 1.385 | 0.99 |
| 218_I | 221_I | 1.382 | 0.99 |
| 217_P | 222_G | 1.376 | 0.99 |
| 235_S | 239_Y | 1.365 | 0.99 |
| 209_F | 212_P | 1.360 | 0.99 |
| 210_F | 217_P | 1.351 | 0.99 |
| 219_L | 224_Q | 1.346 | 0.99 |
| 2_G | 7_E | 1.336 | 0.98 |
| 112_Q | 116_L | 1.332 | 0.98 |
| 206_S | 210_F | 1.324 | 0.98 |
| 2_G | 16_N | 1.319 | 0.98 |
| 215_C | 221_I | 1.316 | 0.98 |
| 234_P | 238_N | 1.303 | 0.98 |
| 214_E | 219_L | 1.302 | 0.98 |
| 2_G | 6_V | 1.286 | 0.98 |
| 227_Q | 230_M | 1.284 | 0.98 |
| 21_F | 55_Y | 1.283 | 0.98 |
| 26_N | 33_Y | 1.283 | 0.98 |
| 198_H | 202_Q | 1.273 | 0.98 |
| 208_A | 214_E | 1.273 | 0.98 |
| 213_L | 220_Q | 1.272 | 0.98 |
| 207_Q | 212_P | 1.272 | 0.98 |
| 195_Y | 198_H | 1.256 | 0.97 |
| 216_E | 220_Q | 1.256 | 0.97 |
| 187_P | 190_E | 1.248 | 0.97 |
| 188_N | 191_E | 1.239 | 0.97 |
| 58_C | 63_M | 1.236 | 0.97 |
| 215_C | 218_I | 1.235 | 0.97 |
| 3_R | 11_I | 1.233 | 0.97 |
| 225_G | 229_G | 1.231 | 0.97 |
| 201_Q | 205_H | 1.228 | 0.97 |
| 200_H | 203_Q | 1.226 | 0.97 |
| 216_E | 224_Q | 1.225 | 0.97 |
| 231_G | 234_P | 1.219 | 0.97 |
| 192_V | 195_Y | 1.219 | 0.97 |
| 225_G | 230_M | 1.216 | 0.97 |
| 183_L | 187_P | 1.205 | 0.97 |
| 233_G | 239_Y | 1.204 | 0.97 |
| 202_Q | 205_H | 1.199 | 0.96 |
| 10_R | 18_Q | 1.193 | 0.96 |
| 211_Q | 214_E | 1.188 | 0.96 |
| 195_Y | 199_H | 1.187 | 0.96 |
| 228_D | 231_G | 1.181 | 0.96 |
| 199_H | 202_Q | 1.180 | 0.96 |
| 222_G | 225_G | 1.180 | 0.96 |
| 230_M | 233_G | 1.177 | 0.96 |
| 228_D | 232_A | 1.172 | 0.96 |
| 205_H | 212_P | 1.169 | 0.96 |
| 225_G | 228_D | 1.165 | 0.96 |
| 236_V | 239_Y | 1.164 | 0.96 |
| 212_P | 217_P | 1.163 | 0.96 |
| 147_T | 150_M | 1.155 | 0.95 |
| 227_Q | 232_A | 1.152 | 0.95 |
| 241_L | 244_L | 1.151 | 0.95 |
| 183_L | 186_N | 1.148 | 0.95 |
| 231_G | 236_V | 1.148 | 0.95 |
| 228_D | 233_G | 1.144 | 0.95 |
| 208_A | 213_L | 1.143 | 0.95 |
| 227_Q | 231_G | 1.143 | 0.95 |
| 213_L | 217_P | 1.141 | 0.95 |
| 232_A | 237_N | 1.140 | 0.95 |
| 34_E | 39_C | 1.137 | 0.95 |
| 209_F | 213_L | 1.136 | 0.95 |
| 208_A | 212_P | 1.130 | 0.95 |
| 8_L | 15_I | 1.129 | 0.95 |
| 233_G | 236_V | 1.127 | 0.94 |
| 83_P | 86_E | 1.126 | 0.94 |
| 207_Q | 210_F | 1.126 | 0.94 |
| 196_G | 199_H | 1.125 | 0.94 |
| 189_Q | 194_H | 1.124 | 0.94 |
| 8_L | 51_R | 1.124 | 0.94 |
| 216_E | 222_G | 1.124 | 0.94 |
| 211_Q | 216_E | 1.122 | 0.94 |
| 228_D | 235_S | 1.120 | 0.94 |
| 215_C | 220_Q | 1.117 | 0.94 |
| 44_A | 58_C | 1.112 | 0.94 |
| 211_Q | 219_L | 1.108 | 0.94 |
| 18_Q | 22_A | 1.104 | 0.94 |
| 211_Q | 217_P | 1.101 | 0.93 |
| 232_A | 239_Y | 1.101 | 0.93 |
| 32_A | 43_V | 1.099 | 0.93 |
| 6_V | 15_I | 1.087 | 0.93 |
| 204_Q | 208_A | 1.085 | 0.93 |
| 226_Q | 229_G | 1.084 | 0.93 |
| 216_E | 221_I | 1.080 | 0.93 |
| 231_G | 235_S | 1.080 | 0.93 |
| 219_L | 223_Y | 1.079 | 0.93 |
| 205_H | 213_L | 1.079 | 0.93 |
| 205_H | 208_A | 1.078 | 0.93 |
| 33_Y | 37_V | 1.078 | 0.93 |
| 196_G | 201_Q | 1.077 | 0.92 |
| 189_Q | 192_V | 1.074 | 0.92 |
| 26_N | 29_L | 1.072 | 0.92 |
| 203_Q | 206_S | 1.069 | 0.92 |
| 194_H | 197_R | 1.068 | 0.92 |
| 230_M | 237_N | 1.065 | 0.92 |
| 216_E | 219_L | 1.063 | 0.92 |
| 31_K | 34_E | 1.060 | 0.92 |
| 225_G | 232_A | 1.058 | 0.92 |
| 229_G | 232_A | 1.058 | 0.92 |
| 35_L | 153_Q | 1.055 | 0.91 |
| 204_Q | 207_Q | 1.053 | 0.91 |
| 206_S | 211_Q | 1.045 | 0.91 |
| 211_Q | 215_C | 1.044 | 0.91 |
| 214_E | 221_I | 1.042 | 0.91 |
| 217_P | 220_Q | 1.042 | 0.91 |
| 226_Q | 233_G | 1.041 | 0.91 |
| 240_M | 245_P | 1.040 | 0.91 |
| 200_H | 206_S | 1.038 | 0.91 |
| 229_G | 234_P | 1.037 | 0.91 |
| 236_V | 241_L | 1.036 | 0.90 |
| 204_Q | 210_F | 1.036 | 0.90 |
| 220_Q | 223_Y | 1.036 | 0.90 |
| 213_L | 218_I | 1.033 | 0.90 |
| 218_I | 223_Y | 1.032 | 0.90 |
| 221_I | 225_G | 1.030 | 0.90 |
| 215_C | 219_L | 1.029 | 0.90 |
| 9_K | 12_E | 1.025 | 0.90 |
| 83_P | 87_A | 1.024 | 0.90 |
| 182_P | 185_L | 1.022 | 0.90 |
| 205_H | 214_E | 1.018 | 0.89 |
| 224_Q | 227_Q | 1.018 | 0.89 |
| 230_M | 236_V | 1.015 | 0.89 |
| 229_G | 233_G | 1.013 | 0.89 |
| 231_G | 237_N | 1.011 | 0.89 |
| 190_E | 193_D | 1.011 | 0.89 |
| 221_I | 226_Q | 1.010 | 0.89 |
| 224_Q | 228_D | 1.003 | 0.88 |
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 | |
| 3p57A | 6 | 0.3586 | 100 | 0.482 | Contact Map |
| 1mnmA | 2 | 0.3347 | 100 | 0.498 | Contact Map |
| 1egwA | 4 | 0.2869 | 100 | 0.499 | Contact Map |
| 1hbxA | 4 | 0.3307 | 100 | 0.509 | Contact Map |
| 1k6oB | 2 | 0.3227 | 100 | 0.513 | Contact Map |
| 4ox0A | 4 | 0.3825 | 98.7 | 0.823 | Contact Map |
| 3mlfA | 5 | 0.255 | 15.6 | 0.954 | Contact Map |
| 1k20A | 2 | 0.3865 | 15.6 | 0.954 | Contact Map |
| 2ostA | 4 | 0.3865 | 9.8 | 0.958 | Contact Map |
| 2eb0A | 2 | 0.3825 | 9.6 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)