| C -force run |
| ID: | 1510157215 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 250 (236) | ||
| Sequences: | 216 (148.2) | ||
| Seq/Len: | 0.915 | ||
| Nf(neff/√len): | 9.6 |
Jackhmmer Results: (2016_04)
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: 0.915).
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 |
| 76_N | 141_N | 2.326 | 0.98 |
| 101_D | 105_V | 2.309 | 0.98 |
| 134_S | 142_V | 2.163 | 0.97 |
| 88_Q | 153_Q | 2.039 | 0.95 |
| 214_N | 231_L | 1.888 | 0.92 |
| 94_A | 170_A | 1.827 | 0.90 |
| 99_A | 105_V | 1.820 | 0.90 |
| 101_D | 106_F | 1.746 | 0.88 |
| 95_I | 160_I | 1.675 | 0.85 |
| 22_A | 26_P | 1.605 | 0.81 |
| 122_N | 185_N | 1.603 | 0.81 |
| 73_S | 138_S | 1.598 | 0.80 |
| 63_N | 128_N | 1.571 | 0.79 |
| 48_Q | 53_N | 1.520 | 0.76 |
| 70_L | 77_L | 1.494 | 0.74 |
| 172_S | 181_N | 1.489 | 0.74 |
| 222_G | 225_N | 1.436 | 0.70 |
| 90_D | 157_N | 1.436 | 0.70 |
| 198_V | 207_S | 1.435 | 0.70 |
| 105_V | 109_A | 1.417 | 0.68 |
| 95_I | 138_S | 1.417 | 0.68 |
| 220_A | 227_Q | 1.408 | 0.67 |
| 34_P | 37_T | 1.405 | 0.67 |
| 214_N | 227_Q | 1.386 | 0.66 |
| 70_L | 135_A | 1.382 | 0.65 |
| 76_N | 231_L | 1.380 | 0.65 |
| 222_G | 229_N | 1.377 | 0.65 |
| 65_G | 130_L | 1.376 | 0.65 |
| 7_L | 12_F | 1.373 | 0.65 |
| 69_S | 77_L | 1.363 | 0.64 |
| 89_Q | 154_Q | 1.360 | 0.64 |
| 52_D | 180_D | 1.360 | 0.64 |
| 129_A | 148_A | 1.360 | 0.64 |
| 231_L | 234_G | 1.341 | 0.62 |
| 78_G | 143_G | 1.337 | 0.62 |
| 227_Q | 234_G | 1.336 | 0.61 |
| 114_E | 221_A | 1.333 | 0.61 |
| 135_A | 138_S | 1.333 | 0.61 |
| 218_N | 225_N | 1.332 | 0.61 |
| 213_G | 229_N | 1.326 | 0.61 |
| 99_A | 103_A | 1.316 | 0.60 |
| 76_N | 214_N | 1.307 | 0.59 |
| 102_A | 105_V | 1.299 | 0.58 |
| 80_N | 145_N | 1.299 | 0.58 |
| 217_V | 220_A | 1.283 | 0.57 |
| 211_A | 215_I | 1.269 | 0.56 |
| 57_D | 185_N | 1.268 | 0.56 |
| 111_I | 203_G | 1.268 | 0.56 |
| 213_G | 218_N | 1.268 | 0.56 |
| 105_V | 111_I | 1.263 | 0.55 |
| 88_Q | 226_Q | 1.259 | 0.55 |
| 128_N | 201_N | 1.255 | 0.54 |
| 20_V | 134_S | 1.246 | 0.54 |
| 15_A | 19_A | 1.244 | 0.53 |
| 202_A | 218_N | 1.243 | 0.53 |
| 99_A | 102_A | 1.233 | 0.52 |
| 111_I | 157_N | 1.231 | 0.52 |
| 141_N | 214_N | 1.230 | 0.52 |
| 216_G | 220_A | 1.228 | 0.52 |
| 138_S | 142_V | 1.226 | 0.52 |
| 6_A | 12_F | 1.226 | 0.52 |
| 218_N | 222_G | 1.219 | 0.51 |
| 5_M | 8_K | 1.218 | 0.51 |
| 140_G | 149_G | 1.207 | 0.50 |
| 67_N | 132_N | 1.201 | 0.49 |
| 203_G | 211_A | 1.198 | 0.49 |
| 89_Q | 145_N | 1.198 | 0.49 |
| 73_S | 77_L | 1.196 | 0.49 |
| 140_G | 156_N | 1.192 | 0.49 |
| 227_Q | 231_L | 1.189 | 0.48 |
| 216_G | 227_Q | 1.184 | 0.48 |
| 73_S | 147_A | 1.183 | 0.48 |
| 69_S | 134_S | 1.181 | 0.48 |
| 141_N | 231_L | 1.176 | 0.47 |
| 87_N | 145_N | 1.171 | 0.47 |
| 145_N | 154_Q | 1.155 | 0.45 |
| 218_N | 227_Q | 1.153 | 0.45 |
| 226_Q | 230_T | 1.150 | 0.45 |
| 141_N | 158_L | 1.147 | 0.45 |
| 140_G | 145_N | 1.145 | 0.44 |
| 92_A | 155_K | 1.140 | 0.44 |
| 70_L | 73_S | 1.137 | 0.44 |
| 200_N | 216_G | 1.135 | 0.44 |
| 82_A | 147_A | 1.134 | 0.43 |
| 82_A | 89_Q | 1.133 | 0.43 |
| 91_N | 140_G | 1.125 | 0.43 |
| 214_N | 217_V | 1.120 | 0.42 |
| 85_S | 150_Q | 1.119 | 0.42 |
| 81_I | 146_V | 1.115 | 0.42 |
| 149_G | 156_N | 1.107 | 0.41 |
| 53_N | 118_N | 1.105 | 0.41 |
| 213_G | 222_G | 1.101 | 0.41 |
| 9_P | 12_F | 1.101 | 0.41 |
| 76_N | 89_Q | 1.096 | 0.40 |
| 48_Q | 118_N | 1.089 | 0.39 |
| 14_L | 19_A | 1.088 | 0.39 |
| 97_S | 100_G | 1.083 | 0.39 |
| 46_D | 157_N | 1.083 | 0.39 |
| 6_A | 18_M | 1.076 | 0.38 |
| 92_A | 230_T | 1.075 | 0.38 |
| 218_N | 229_N | 1.073 | 0.38 |
| 77_L | 138_S | 1.073 | 0.38 |
| 214_N | 218_N | 1.070 | 0.38 |
| 90_D | 155_K | 1.070 | 0.38 |
| 70_L | 79_A | 1.065 | 0.37 |
| 91_N | 152_N | 1.065 | 0.37 |
| 145_N | 149_G | 1.060 | 0.37 |
| 79_A | 94_A | 1.059 | 0.37 |
| 99_A | 106_F | 1.056 | 0.37 |
| 113_Q | 140_G | 1.052 | 0.36 |
| 11_V | 16_A | 1.049 | 0.36 |
| 31_K | 34_P | 1.045 | 0.36 |
| 225_N | 229_N | 1.044 | 0.36 |
| 32_P | 35_A | 1.036 | 0.35 |
| 62_N | 127_N | 1.031 | 0.35 |
| 42_A | 48_Q | 1.030 | 0.34 |
| 74_K | 212_S | 1.028 | 0.34 |
| 70_L | 211_A | 1.026 | 0.34 |
| 213_G | 225_N | 1.026 | 0.34 |
| 91_N | 149_G | 1.024 | 0.34 |
| 140_G | 152_N | 1.021 | 0.34 |
| 219_V | 227_Q | 1.021 | 0.34 |
| 134_S | 207_S | 1.021 | 0.34 |
| 87_N | 140_G | 1.020 | 0.34 |
| 149_G | 152_N | 1.017 | 0.33 |
| 143_G | 159_A | 1.015 | 0.33 |
| 224_G | 231_L | 1.008 | 0.33 |
| 202_A | 214_N | 1.008 | 0.33 |
| 131_L | 146_V | 1.006 | 0.33 |
| 145_N | 156_N | 1.004 | 0.32 |
| 214_N | 220_A | 1.002 | 0.32 |
| 48_Q | 170_A | 1.001 | 0.32 |
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 | |
| 2vdaB | 1 | 0.096 | 39.1 | 0.952 | Contact Map |
| 3ffvA | 2 | 0.236 | 10.1 | 0.963 | Contact Map |
| 4pdeA | 1 | 0 | 2.6 | 0.972 | Contact Map |
| 2pw9A | 4 | 0.196 | 2.6 | 0.972 | Contact Map |
| 4anjA | 1 | 0.192 | 2.2 | 0.973 | Contact Map |
| 3kl4B | 1 | 0 | 2.2 | 0.974 | Contact Map |
| 2pwaA | 1 | 0.24 | 1.9 | 0.974 | Contact Map |
| 1tzsX | 1 | 0.02 | 1.5 | 0.976 | Contact Map |
| 1c41A | 10 | 0.236 | 1.2 | 0.977 | Contact Map |
| 3v8hA | 4 | 0.18 | 1.1 | 0.978 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)