| Q9H1A3 -force run |
| ID: | 1510652751 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 318 (275) | ||
| Sequences: | 205 (165.5) | ||
| Seq/Len: | 0.745 | ||
| Nf(neff/√len): | 10.0 |
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: 0.745).
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 |
| 152_L | 211_L | 3.087 | 1.00 |
| 75_S | 291_T | 1.998 | 0.92 |
| 229_L | 234_G | 1.984 | 0.92 |
| 286_V | 316_K | 1.716 | 0.82 |
| 300_D | 306_Y | 1.656 | 0.79 |
| 235_R | 288_E | 1.652 | 0.78 |
| 171_Y | 203_Y | 1.633 | 0.77 |
| 118_N | 121_L | 1.609 | 0.76 |
| 273_V | 280_F | 1.605 | 0.76 |
| 156_D | 179_M | 1.600 | 0.75 |
| 75_S | 293_L | 1.589 | 0.75 |
| 231_P | 234_G | 1.585 | 0.74 |
| 269_W | 311_A | 1.582 | 0.74 |
| 157_G | 173_T | 1.533 | 0.71 |
| 130_S | 133_Q | 1.521 | 0.70 |
| 210_N | 241_V | 1.490 | 0.68 |
| 97_I | 237_I | 1.480 | 0.67 |
| 303_N | 307_V | 1.468 | 0.66 |
| 130_S | 248_V | 1.439 | 0.64 |
| 104_V | 305_Y | 1.407 | 0.61 |
| 125_S | 130_S | 1.407 | 0.61 |
| 152_L | 196_W | 1.397 | 0.60 |
| 160_T | 173_T | 1.388 | 0.60 |
| 80_G | 268_N | 1.385 | 0.59 |
| 196_W | 211_L | 1.379 | 0.59 |
| 280_F | 313_F | 1.365 | 0.58 |
| 125_S | 134_F | 1.350 | 0.56 |
| 208_C | 215_C | 1.348 | 0.56 |
| 125_S | 140_I | 1.345 | 0.56 |
| 126_M | 130_S | 1.333 | 0.55 |
| 137_L | 314_V | 1.324 | 0.54 |
| 90_E | 236_V | 1.320 | 0.54 |
| 92_S | 119_G | 1.315 | 0.53 |
| 119_G | 124_G | 1.308 | 0.53 |
| 231_P | 314_V | 1.299 | 0.52 |
| 196_W | 272_Q | 1.294 | 0.52 |
| 154_A | 173_T | 1.294 | 0.52 |
| 124_G | 130_S | 1.289 | 0.51 |
| 215_C | 234_G | 1.288 | 0.51 |
| 241_V | 249_E | 1.287 | 0.51 |
| 301_M | 311_A | 1.278 | 0.50 |
| 56_W | 117_I | 1.267 | 0.49 |
| 164_S | 287_I | 1.260 | 0.49 |
| 229_L | 314_V | 1.248 | 0.48 |
| 72_F | 81_T | 1.247 | 0.48 |
| 98_Q | 123_R | 1.244 | 0.47 |
| 219_L | 316_K | 1.241 | 0.47 |
| 264_I | 276_L | 1.240 | 0.47 |
| 210_N | 270_E | 1.238 | 0.47 |
| 234_G | 314_V | 1.234 | 0.46 |
| 165_P | 205_V | 1.233 | 0.46 |
| 141_N | 311_A | 1.230 | 0.46 |
| 128_V | 159_V | 1.230 | 0.46 |
| 164_S | 170_I | 1.229 | 0.46 |
| 155_G | 173_T | 1.226 | 0.46 |
| 117_I | 205_V | 1.226 | 0.46 |
| 152_L | 227_S | 1.212 | 0.45 |
| 293_L | 312_V | 1.211 | 0.45 |
| 124_G | 210_N | 1.201 | 0.44 |
| 241_V | 270_E | 1.198 | 0.43 |
| 173_T | 179_M | 1.196 | 0.43 |
| 171_Y | 280_F | 1.193 | 0.43 |
| 206_I | 228_V | 1.186 | 0.42 |
| 192_G | 195_E | 1.173 | 0.41 |
| 150_L | 237_I | 1.172 | 0.41 |
| 291_T | 312_V | 1.171 | 0.41 |
| 180_I | 307_V | 1.168 | 0.41 |
| 243_P | 249_E | 1.157 | 0.40 |
| 98_Q | 211_L | 1.154 | 0.40 |
| 239_A | 310_D | 1.154 | 0.40 |
| 115_T | 130_S | 1.153 | 0.40 |
| 156_D | 305_Y | 1.144 | 0.39 |
| 56_W | 247_Y | 1.143 | 0.39 |
| 209_L | 239_A | 1.134 | 0.38 |
| 55_Q | 62_E | 1.128 | 0.38 |
| 64_L | 203_Y | 1.128 | 0.38 |
| 49_G | 239_A | 1.127 | 0.38 |
| 181_W | 276_L | 1.127 | 0.38 |
| 303_N | 317_P | 1.120 | 0.37 |
| 124_G | 133_Q | 1.116 | 0.37 |
| 215_C | 235_R | 1.112 | 0.36 |
| 179_M | 213_D | 1.111 | 0.36 |
| 47_A | 52_E | 1.108 | 0.36 |
| 232_T | 318_V | 1.108 | 0.36 |
| 211_L | 272_Q | 1.108 | 0.36 |
| 47_A | 50_R | 1.106 | 0.36 |
| 249_E | 270_E | 1.106 | 0.36 |
| 179_M | 211_L | 1.104 | 0.36 |
| 159_V | 210_N | 1.102 | 0.36 |
| 175_L | 180_I | 1.102 | 0.36 |
| 130_S | 138_L | 1.100 | 0.35 |
| 189_R | 312_V | 1.096 | 0.35 |
| 129_F | 293_L | 1.095 | 0.35 |
| 204_D | 230_E | 1.094 | 0.35 |
| 78_D | 243_P | 1.089 | 0.35 |
| 47_A | 210_N | 1.087 | 0.34 |
| 125_S | 135_Q | 1.086 | 0.34 |
| 128_V | 133_Q | 1.085 | 0.34 |
| 188_Y | 279_V | 1.080 | 0.34 |
| 115_T | 118_N | 1.079 | 0.34 |
| 172_A | 186_K | 1.079 | 0.34 |
| 45_A | 49_G | 1.079 | 0.34 |
| 75_S | 188_Y | 1.074 | 0.33 |
| 156_D | 297_C | 1.071 | 0.33 |
| 301_M | 307_V | 1.070 | 0.33 |
| 153_G | 173_T | 1.068 | 0.33 |
| 217_Q | 220_T | 1.064 | 0.33 |
| 124_G | 241_V | 1.063 | 0.33 |
| 99_L | 190_V | 1.060 | 0.32 |
| 288_E | 314_V | 1.059 | 0.32 |
| 302_Y | 307_V | 1.056 | 0.32 |
| 219_L | 282_K | 1.054 | 0.32 |
| 214_R | 218_P | 1.054 | 0.32 |
| 163_M | 237_I | 1.052 | 0.32 |
| 152_L | 225_I | 1.051 | 0.32 |
| 46_A | 49_G | 1.051 | 0.32 |
| 133_Q | 138_L | 1.051 | 0.32 |
| 183_L | 213_D | 1.051 | 0.32 |
| 243_P | 270_E | 1.050 | 0.32 |
| 122_G | 130_S | 1.049 | 0.32 |
| 58_V | 61_R | 1.042 | 0.31 |
| 254_K | 302_Y | 1.041 | 0.31 |
| 209_L | 243_P | 1.036 | 0.31 |
| 59_C | 269_W | 1.034 | 0.30 |
| 124_G | 179_M | 1.033 | 0.30 |
| 44_A | 241_V | 1.031 | 0.30 |
| 84_F | 88_S | 1.030 | 0.30 |
| 49_G | 241_V | 1.028 | 0.30 |
| 47_A | 237_I | 1.026 | 0.30 |
| 164_S | 254_K | 1.024 | 0.30 |
| 192_G | 301_M | 1.024 | 0.30 |
| 157_G | 160_T | 1.021 | 0.29 |
| 130_S | 134_F | 1.021 | 0.29 |
| 113_S | 260_E | 1.020 | 0.29 |
| 220_T | 224_D | 1.019 | 0.29 |
| 78_D | 126_M | 1.016 | 0.29 |
| 161_K | 164_S | 1.015 | 0.29 |
| 50_R | 53_N | 1.014 | 0.29 |
| 45_A | 243_P | 1.013 | 0.29 |
| 202_Q | 305_Y | 1.007 | 0.29 |
| 51_K | 126_M | 1.006 | 0.28 |
| 277_P | 281_R | 1.006 | 0.28 |
| 69_Q | 237_I | 1.004 | 0.28 |
| 44_A | 279_V | 1.004 | 0.28 |
| 90_E | 273_V | 1.001 | 0.28 |
| 46_A | 241_V | 1.001 | 0.28 |
| 68_L | 309_D | 1.001 | 0.28 |
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 | |
| 2vz8A | 2 | 0.522 | 100 | 0.756 | Contact Map |
| 4pivA | 2 | 0.7296 | 100 | 0.766 | Contact Map |
| 1xtpA | 1 | 0.7296 | 99.8 | 0.825 | Contact Map |
| 3busA | 2 | 0.6415 | 99.8 | 0.826 | Contact Map |
| 4pneA | 2 | 0.6981 | 99.8 | 0.827 | Contact Map |
| 4krgA | 2 | 0.7044 | 99.8 | 0.827 | Contact Map |
| 3g5lA | 2 | 0.5943 | 99.8 | 0.827 | Contact Map |
| 3e8sA | 1 | 0.6541 | 99.8 | 0.829 | Contact Map |
| 3cc8A | 1 | 0.5786 | 99.8 | 0.829 | Contact Map |
| 3bkwA | 2 | 0.5943 | 99.8 | 0.829 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)