| T0808 19-330 -force run -force run |
| ID: | 1405972752 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 312 (310) | ||
| Sequences: | 83 (71.7) | ||
| Seq/Len: | 0.268 | ||
| Nf(neff/√len): | 4.1 |
Jackhmmer Results: (2014_04_16)
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: 0.268).
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_F | 99_I | 2.368 | 0.86 |
| 197_L | 240_Q | 2.072 | 0.74 |
| 156_W | 272_Y | 1.920 | 0.65 |
| 221_L | 287_F | 1.915 | 0.65 |
| 172_S | 227_V | 1.871 | 0.62 |
| 208_N | 211_E | 1.807 | 0.58 |
| 202_S | 237_S | 1.806 | 0.58 |
| 155_E | 258_Q | 1.776 | 0.56 |
| 259_I | 296_Y | 1.762 | 0.56 |
| 168_E | 171_H | 1.723 | 0.53 |
| 243_L | 284_I | 1.680 | 0.50 |
| 251_N | 275_A | 1.653 | 0.48 |
| 157_F | 299_P | 1.625 | 0.47 |
| 156_W | 298_R | 1.621 | 0.46 |
| 257_M | 271_A | 1.610 | 0.46 |
| 7_V | 39_V | 1.601 | 0.45 |
| 131_D | 134_D | 1.585 | 0.44 |
| 16_T | 265_G | 1.572 | 0.43 |
| 234_N | 283_L | 1.561 | 0.43 |
| 230_G | 234_N | 1.482 | 0.38 |
| 101_L | 282_K | 1.470 | 0.37 |
| 99_I | 134_D | 1.450 | 0.36 |
| 7_V | 155_E | 1.389 | 0.32 |
| 272_Y | 299_P | 1.372 | 0.31 |
| 176_A | 255_F | 1.370 | 0.31 |
| 202_S | 209_P | 1.362 | 0.31 |
| 40_S | 100_D | 1.362 | 0.31 |
| 296_Y | 299_P | 1.313 | 0.28 |
| 157_F | 272_Y | 1.307 | 0.28 |
| 16_T | 40_S | 1.303 | 0.27 |
| 231_E | 269_Y | 1.301 | 0.27 |
| 181_E | 294_T | 1.301 | 0.27 |
| 202_S | 212_I | 1.299 | 0.27 |
| 44_Y | 114_I | 1.289 | 0.27 |
| 29_V | 300_H | 1.261 | 0.25 |
| 15_V | 196_I | 1.260 | 0.25 |
| 25_T | 63_I | 1.257 | 0.25 |
| 220_L | 276_T | 1.254 | 0.25 |
| 202_S | 206_T | 1.254 | 0.25 |
| 43_F | 119_A | 1.253 | 0.25 |
| 8_G | 132_F | 1.252 | 0.25 |
| 188_Y | 296_Y | 1.249 | 0.25 |
| 137_G | 202_S | 1.244 | 0.24 |
| 229_I | 297_K | 1.241 | 0.24 |
| 139_R | 289_R | 1.235 | 0.24 |
| 168_E | 188_Y | 1.233 | 0.24 |
| 38_I | 102_Q | 1.230 | 0.24 |
| 171_H | 207_Q | 1.228 | 0.24 |
| 136_W | 218_I | 1.224 | 0.23 |
| 91_I | 186_M | 1.211 | 0.23 |
| 243_L | 308_P | 1.210 | 0.23 |
| 91_I | 94_A | 1.205 | 0.23 |
| 10_S | 272_Y | 1.202 | 0.22 |
| 147_Y | 159_N | 1.199 | 0.22 |
| 140_G | 289_R | 1.179 | 0.21 |
| 193_E | 305_N | 1.179 | 0.21 |
| 14_Y | 310_Q | 1.176 | 0.21 |
| 135_Y | 292_T | 1.176 | 0.21 |
| 206_T | 213_P | 1.174 | 0.21 |
| 162_T | 252_T | 1.173 | 0.21 |
| 137_G | 212_I | 1.169 | 0.21 |
| 186_M | 196_I | 1.167 | 0.21 |
| 140_G | 203_P | 1.161 | 0.21 |
| 26_Q | 274_Y | 1.156 | 0.20 |
| 137_G | 287_F | 1.150 | 0.20 |
| 141_P | 164_P | 1.150 | 0.20 |
| 257_M | 296_Y | 1.149 | 0.20 |
| 188_Y | 223_Q | 1.149 | 0.20 |
| 171_H | 174_Y | 1.146 | 0.20 |
| 87_G | 242_Y | 1.146 | 0.20 |
| 195_R | 286_S | 1.142 | 0.20 |
| 259_I | 266_N | 1.141 | 0.20 |
| 108_G | 269_Y | 1.140 | 0.20 |
| 103_G | 111_F | 1.131 | 0.19 |
| 141_P | 240_Q | 1.130 | 0.19 |
| 128_Y | 300_H | 1.130 | 0.19 |
| 266_N | 288_L | 1.123 | 0.19 |
| 272_Y | 298_R | 1.122 | 0.19 |
| 12_N | 139_R | 1.121 | 0.19 |
| 104_V | 170_M | 1.118 | 0.19 |
| 141_P | 197_L | 1.117 | 0.19 |
| 186_M | 214_D | 1.116 | 0.19 |
| 270_T | 287_F | 1.114 | 0.19 |
| 122_V | 161_I | 1.114 | 0.19 |
| 74_V | 242_Y | 1.112 | 0.19 |
| 212_I | 237_S | 1.107 | 0.18 |
| 137_G | 303_L | 1.103 | 0.18 |
| 64_K | 71_G | 1.103 | 0.18 |
| 10_S | 99_I | 1.099 | 0.18 |
| 164_P | 271_A | 1.099 | 0.18 |
| 175_M | 197_L | 1.093 | 0.18 |
| 189_N | 195_R | 1.093 | 0.18 |
| 200_V | 284_I | 1.092 | 0.18 |
| 161_I | 310_Q | 1.092 | 0.18 |
| 175_M | 240_Q | 1.089 | 0.18 |
| 108_G | 113_E | 1.086 | 0.18 |
| 40_S | 98_R | 1.086 | 0.18 |
| 204_F | 237_S | 1.085 | 0.18 |
| 57_A | 76_L | 1.084 | 0.18 |
| 7_V | 84_V | 1.082 | 0.17 |
| 166_E | 252_T | 1.082 | 0.17 |
| 209_P | 237_S | 1.082 | 0.17 |
| 21_G | 33_T | 1.081 | 0.17 |
| 218_I | 231_E | 1.077 | 0.17 |
| 35_P | 191_P | 1.077 | 0.17 |
| 87_G | 285_A | 1.075 | 0.17 |
| 206_T | 209_P | 1.075 | 0.17 |
| 146_G | 196_I | 1.073 | 0.17 |
| 209_P | 213_P | 1.072 | 0.17 |
| 237_S | 283_L | 1.070 | 0.17 |
| 203_P | 289_R | 1.068 | 0.17 |
| 194_R | 224_G | 1.067 | 0.17 |
| 203_P | 239_G | 1.066 | 0.17 |
| 218_I | 230_G | 1.065 | 0.17 |
| 55_L | 76_L | 1.065 | 0.17 |
| 36_K | 161_I | 1.063 | 0.17 |
| 76_L | 191_P | 1.056 | 0.17 |
| 206_T | 237_S | 1.053 | 0.16 |
| 253_Y | 273_F | 1.053 | 0.16 |
| 73_K | 149_L | 1.051 | 0.16 |
| 139_R | 203_P | 1.048 | 0.16 |
| 101_L | 204_F | 1.047 | 0.16 |
| 39_V | 74_V | 1.047 | 0.16 |
| 66_S | 125_K | 1.044 | 0.16 |
| 14_Y | 295_W | 1.044 | 0.16 |
| 7_V | 260_R | 1.044 | 0.16 |
| 262_D | 265_G | 1.043 | 0.16 |
| 16_T | 266_N | 1.042 | 0.16 |
| 11_G | 252_T | 1.042 | 0.16 |
| 57_A | 272_Y | 1.040 | 0.16 |
| 181_E | 204_F | 1.036 | 0.16 |
| 259_I | 295_W | 1.034 | 0.16 |
| 166_E | 177_A | 1.031 | 0.16 |
| 76_L | 167_G | 1.031 | 0.16 |
| 14_Y | 40_S | 1.030 | 0.16 |
| 166_E | 174_Y | 1.029 | 0.16 |
| 40_S | 102_Q | 1.029 | 0.16 |
| 117_L | 288_L | 1.028 | 0.16 |
| 288_L | 296_Y | 1.026 | 0.15 |
| 190_S | 194_R | 1.023 | 0.15 |
| 28_G | 184_F | 1.022 | 0.15 |
| 47_Q | 79_N | 1.020 | 0.15 |
| 259_I | 299_P | 1.019 | 0.15 |
| 270_T | 294_T | 1.016 | 0.15 |
| 195_R | 241_S | 1.015 | 0.15 |
| 197_L | 242_Y | 1.015 | 0.15 |
| 50_T | 67_Y | 1.015 | 0.15 |
| 13_G | 310_Q | 1.015 | 0.15 |
| 101_L | 242_Y | 1.013 | 0.15 |
| 202_S | 283_L | 1.013 | 0.15 |
| 147_Y | 162_T | 1.012 | 0.15 |
| 171_H | 257_M | 1.012 | 0.15 |
| 209_P | 212_I | 1.010 | 0.15 |
| 156_W | 299_P | 1.008 | 0.15 |
| 137_G | 189_N | 1.007 | 0.15 |
| 129_V | 300_H | 1.006 | 0.15 |
| 155_E | 260_R | 1.004 | 0.15 |
| 253_Y | 292_T | 1.004 | 0.15 |
| 218_I | 234_N | 1.003 | 0.15 |
| 28_G | 194_R | 1.002 | 0.15 |
| 33_T | 46_H | 1.002 | 0.15 |
| 231_E | 234_N | 1.002 | 0.15 |
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 | |
| 2bgoA | 1 | 0.3494 | 97.6 | 0.937 | Contact Map |
| 2vzsA | 2 | 0 | 97.1 | 0.941 | Contact Map |
| 4kmqA | 1 | 0.3622 | 97.1 | 0.942 | Contact Map |
| 2vzpA | 2 | 0.3558 | 96.6 | 0.945 | Contact Map |
| 2w87A | 2 | 0.3942 | 96.4 | 0.946 | Contact Map |
| 2y8kA | 1 | 0.3718 | 96.1 | 0.948 | Contact Map |
| 2w47A | 1 | 0.3814 | 96.1 | 0.948 | Contact Map |
| 2cdpA | 4 | 0.375 | 95.1 | 0.952 | Contact Map |
| 2wz8A | 1 | 0.3622 | 94.6 | 0.953 | Contact Map |
| 2w3jA | 1 | 0.391 | 94.5 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)