| T0800 -force run |
| ID: | 1401726898 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 247 (241) | ||
| Sequences: | 64 (59) | ||
| Seq/Len: | 0.266 | ||
| Nf(neff/√len): | 3.8 |
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: 0.266).
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 |
| 120_W | 160_G | 2.079 | 0.74 |
| 130_T | 166_I | 1.953 | 0.67 |
| 137_G | 158_G | 1.920 | 0.65 |
| 160_G | 183_G | 1.859 | 0.61 |
| 60_V | 138_T | 1.825 | 0.59 |
| 120_W | 183_G | 1.767 | 0.56 |
| 13_V | 17_F | 1.662 | 0.49 |
| 120_W | 240_G | 1.608 | 0.45 |
| 59_G | 158_G | 1.601 | 0.45 |
| 61_G | 239_V | 1.551 | 0.42 |
| 160_G | 240_G | 1.494 | 0.38 |
| 167_S | 192_S | 1.467 | 0.36 |
| 202_G | 238_G | 1.460 | 0.36 |
| 52_T | 72_L | 1.411 | 0.33 |
| 155_V | 239_V | 1.379 | 0.31 |
| 194_G | 224_Y | 1.374 | 0.31 |
| 161_K | 197_I | 1.366 | 0.31 |
| 46_P | 173_N | 1.364 | 0.31 |
| 164_L | 178_I | 1.349 | 0.30 |
| 184_E | 217_N | 1.337 | 0.29 |
| 139_G | 183_G | 1.332 | 0.29 |
| 180_G | 204_G | 1.330 | 0.29 |
| 124_L | 144_D | 1.315 | 0.28 |
| 158_G | 238_G | 1.314 | 0.28 |
| 210_G | 239_V | 1.304 | 0.27 |
| 150_L | 202_G | 1.298 | 0.27 |
| 76_K | 94_D | 1.292 | 0.27 |
| 183_G | 240_G | 1.286 | 0.26 |
| 134_L | 220_K | 1.273 | 0.26 |
| 101_I | 132_I | 1.271 | 0.26 |
| 159_V | 183_G | 1.263 | 0.25 |
| 183_G | 239_V | 1.247 | 0.24 |
| 159_V | 203_V | 1.237 | 0.24 |
| 104_P | 184_E | 1.236 | 0.24 |
| 149_N | 206_V | 1.235 | 0.24 |
| 159_V | 167_S | 1.235 | 0.24 |
| 210_G | 221_N | 1.226 | 0.23 |
| 132_I | 246_Q | 1.223 | 0.23 |
| 145_L | 166_I | 1.218 | 0.23 |
| 9_I | 27_K | 1.207 | 0.23 |
| 187_V | 216_E | 1.201 | 0.22 |
| 143_A | 244_I | 1.191 | 0.22 |
| 86_P | 149_N | 1.178 | 0.21 |
| 49_A | 122_I | 1.176 | 0.21 |
| 60_V | 180_G | 1.176 | 0.21 |
| 144_D | 189_L | 1.174 | 0.21 |
| 154_N | 217_N | 1.173 | 0.21 |
| 143_A | 150_L | 1.165 | 0.21 |
| 138_T | 167_S | 1.162 | 0.21 |
| 222_S | 230_S | 1.160 | 0.21 |
| 74_K | 152_E | 1.157 | 0.20 |
| 59_G | 138_T | 1.155 | 0.20 |
| 54_L | 132_I | 1.149 | 0.20 |
| 107_K | 244_I | 1.147 | 0.20 |
| 61_G | 66_S | 1.147 | 0.20 |
| 122_I | 242_I | 1.139 | 0.20 |
| 64_N | 173_N | 1.137 | 0.20 |
| 15_L | 35_E | 1.135 | 0.19 |
| 99_L | 208_A | 1.134 | 0.19 |
| 8_S | 12_L | 1.128 | 0.19 |
| 75_G | 196_K | 1.128 | 0.19 |
| 62_K | 221_N | 1.126 | 0.19 |
| 198_K | 202_G | 1.126 | 0.19 |
| 189_L | 194_G | 1.126 | 0.19 |
| 55_N | 162_V | 1.124 | 0.19 |
| 197_I | 224_Y | 1.119 | 0.19 |
| 104_P | 134_L | 1.110 | 0.18 |
| 171_K | 200_E | 1.106 | 0.18 |
| 72_L | 196_K | 1.106 | 0.18 |
| 130_T | 240_G | 1.105 | 0.18 |
| 125_N | 203_V | 1.104 | 0.18 |
| 101_I | 129_P | 1.104 | 0.18 |
| 142_K | 167_S | 1.103 | 0.18 |
| 79_Y | 97_G | 1.103 | 0.18 |
| 19_T | 25_S | 1.101 | 0.18 |
| 12_L | 23_N | 1.100 | 0.18 |
| 22_T | 25_S | 1.094 | 0.18 |
| 12_L | 28_A | 1.093 | 0.18 |
| 79_Y | 168_G | 1.092 | 0.18 |
| 207_N | 223_Q | 1.092 | 0.18 |
| 12_L | 27_K | 1.091 | 0.18 |
| 39_E | 86_P | 1.088 | 0.18 |
| 127_K | 166_I | 1.087 | 0.18 |
| 132_I | 155_V | 1.086 | 0.18 |
| 65_I | 238_G | 1.082 | 0.17 |
| 100_E | 242_I | 1.077 | 0.17 |
| 48_G | 185_A | 1.074 | 0.17 |
| 9_I | 12_L | 1.073 | 0.17 |
| 10_F | 29_T | 1.073 | 0.17 |
| 114_N | 154_N | 1.072 | 0.17 |
| 122_I | 125_N | 1.071 | 0.17 |
| 138_T | 158_G | 1.068 | 0.17 |
| 69_E | 120_W | 1.067 | 0.17 |
| 28_A | 34_N | 1.066 | 0.17 |
| 132_I | 241_A | 1.066 | 0.17 |
| 52_T | 56_L | 1.064 | 0.17 |
| 162_V | 208_A | 1.062 | 0.17 |
| 124_L | 137_G | 1.062 | 0.17 |
| 9_I | 22_T | 1.058 | 0.17 |
| 86_P | 96_D | 1.056 | 0.16 |
| 163_D | 176_V | 1.056 | 0.16 |
| 27_K | 34_N | 1.056 | 0.16 |
| 187_V | 197_I | 1.050 | 0.16 |
| 61_G | 120_W | 1.047 | 0.16 |
| 120_W | 130_T | 1.045 | 0.16 |
| 50_E | 152_E | 1.043 | 0.16 |
| 19_T | 32_D | 1.040 | 0.16 |
| 124_L | 233_V | 1.040 | 0.16 |
| 9_I | 30_V | 1.036 | 0.16 |
| 86_P | 103_Q | 1.035 | 0.16 |
| 131_E | 192_S | 1.033 | 0.16 |
| 64_N | 221_N | 1.032 | 0.16 |
| 77_F | 160_G | 1.031 | 0.16 |
| 14_I | 29_T | 1.031 | 0.16 |
| 18_A | 25_S | 1.027 | 0.15 |
| 100_E | 221_N | 1.025 | 0.15 |
| 176_V | 238_G | 1.025 | 0.15 |
| 60_V | 159_V | 1.020 | 0.15 |
| 159_V | 222_S | 1.020 | 0.15 |
| 63_L | 150_L | 1.018 | 0.15 |
| 6_L | 14_I | 1.017 | 0.15 |
| 65_I | 191_K | 1.016 | 0.15 |
| 115_N | 139_G | 1.014 | 0.15 |
| 217_N | 237_A | 1.013 | 0.15 |
| 14_I | 22_T | 1.011 | 0.15 |
| 149_N | 204_G | 1.005 | 0.15 |
| 82_N | 225_G | 1.004 | 0.15 |
| 124_L | 130_T | 1.004 | 0.15 |
| 54_L | 215_G | 1.000 | 0.15 |
| 228_K | 244_I | 1.000 | 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 | |
| 4qrkA | 1 | 0.8583 | 100 | 0.469 | Contact Map |
| 4yguA | 4 | 0.6761 | 97 | 0.896 | Contact Map |
| 3jx8A | 6 | 0.7935 | 95.5 | 0.91 | Contact Map |
| 3petA | 2 | 0.7692 | 95.4 | 0.911 | Contact Map |
| 3lycA | 16 | 0.7854 | 95 | 0.913 | Contact Map |
| 4opwA | 2 | 0.7814 | 94.4 | 0.916 | Contact Map |
| 3glaA | 2 | 0.2834 | 28.5 | 0.955 | Contact Map |
| 3l1eA | 1 | 0.332 | 23.3 | 0.956 | Contact Map |
| 3zbiC | 14 | 0.1093 | 22.2 | 0.957 | Contact Map |
| 4mjhA | 2 | 0.2551 | 13.9 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)