| prmt5n |
| ID: | 1486546059 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 293 (284) | ||
| Sequences: | 338 (242.3) | ||
| Seq/Len: | 1.190 | ||
| Nf(neff/√len): | 14.4 |
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: 1.190).
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 |
| 84_G | 119_L | 3.689 | 1.00 |
| 226_I | 257_L | 3.050 | 1.00 |
| 253_L | 257_L | 2.196 | 0.98 |
| 142_I | 202_I | 1.931 | 0.96 |
| 89_W | 103_S | 1.794 | 0.93 |
| 212_L | 250_H | 1.719 | 0.91 |
| 229_A | 257_L | 1.708 | 0.91 |
| 239_N | 251_Q | 1.671 | 0.89 |
| 265_I | 284_L | 1.640 | 0.88 |
| 47_H | 52_R | 1.637 | 0.88 |
| 73_L | 78_W | 1.607 | 0.87 |
| 107_M | 111_L | 1.607 | 0.87 |
| 89_W | 110_E | 1.579 | 0.85 |
| 186_W | 189_W | 1.553 | 0.84 |
| 221_W | 224_E | 1.534 | 0.83 |
| 153_M | 185_T | 1.514 | 0.82 |
| 90_I | 103_S | 1.514 | 0.82 |
| 103_S | 110_E | 1.496 | 0.81 |
| 237_L | 247_S | 1.482 | 0.80 |
| 89_W | 106_A | 1.463 | 0.79 |
| 121_A | 152_W | 1.459 | 0.79 |
| 286_Y | 290_N | 1.433 | 0.77 |
| 122_F | 199_S | 1.421 | 0.76 |
| 196_C | 202_I | 1.417 | 0.76 |
| 203_A | 227_K | 1.416 | 0.76 |
| 78_W | 82_I | 1.402 | 0.75 |
| 73_L | 80_T | 1.395 | 0.74 |
| 127_N | 134_L | 1.386 | 0.73 |
| 125_P | 212_L | 1.385 | 0.73 |
| 118_G | 258_L | 1.379 | 0.73 |
| 272_H | 280_Y | 1.366 | 0.72 |
| 84_G | 122_F | 1.357 | 0.71 |
| 125_P | 154_R | 1.352 | 0.71 |
| 189_W | 193_R | 1.337 | 0.70 |
| 103_S | 107_M | 1.326 | 0.69 |
| 90_I | 110_E | 1.321 | 0.68 |
| 213_P | 250_H | 1.308 | 0.67 |
| 41_L | 276_E | 1.298 | 0.66 |
| 173_T | 176_T | 1.297 | 0.66 |
| 65_P | 68_R | 1.292 | 0.66 |
| 117_L | 228_A | 1.291 | 0.66 |
| 155_V | 203_A | 1.289 | 0.65 |
| 185_T | 217_V | 1.289 | 0.65 |
| 186_W | 193_R | 1.288 | 0.65 |
| 39_D | 281_L | 1.281 | 0.65 |
| 185_T | 188_W | 1.273 | 0.64 |
| 126_L | 134_L | 1.271 | 0.64 |
| 167_I | 170_N | 1.267 | 0.63 |
| 19_D | 42_C | 1.262 | 0.63 |
| 95_K | 204_V | 1.259 | 0.63 |
| 118_G | 157_L | 1.255 | 0.62 |
| 73_L | 94_S | 1.255 | 0.62 |
| 190_H | 193_R | 1.250 | 0.62 |
| 45_V | 235_I | 1.247 | 0.62 |
| 19_D | 113_F | 1.246 | 0.62 |
| 70_D | 157_L | 1.242 | 0.61 |
| 138_L | 252_R | 1.238 | 0.61 |
| 160_P | 209_G | 1.235 | 0.61 |
| 152_W | 263_Q | 1.229 | 0.60 |
| 92_P | 123_L | 1.229 | 0.60 |
| 128_Q | 253_L | 1.217 | 0.59 |
| 99_I | 113_F | 1.215 | 0.59 |
| 113_F | 198_Y | 1.210 | 0.58 |
| 173_T | 177_E | 1.202 | 0.57 |
| 187_M | 253_L | 1.197 | 0.57 |
| 70_D | 73_L | 1.192 | 0.56 |
| 193_R | 196_C | 1.191 | 0.56 |
| 241_K | 245_V | 1.190 | 0.56 |
| 10_G | 13_R | 1.178 | 0.55 |
| 239_N | 283_Y | 1.177 | 0.55 |
| 87_S | 196_C | 1.174 | 0.55 |
| 171_A | 174_T | 1.171 | 0.54 |
| 114_G | 239_N | 1.169 | 0.54 |
| 193_R | 198_Y | 1.163 | 0.54 |
| 276_E | 279_S | 1.161 | 0.53 |
| 208_I | 253_L | 1.160 | 0.53 |
| 194_T | 198_Y | 1.158 | 0.53 |
| 95_K | 266_I | 1.158 | 0.53 |
| 42_C | 126_L | 1.158 | 0.53 |
| 118_G | 209_G | 1.154 | 0.53 |
| 221_W | 225_P | 1.153 | 0.53 |
| 177_E | 181_G | 1.152 | 0.53 |
| 99_I | 153_M | 1.149 | 0.52 |
| 184_K | 220_R | 1.144 | 0.52 |
| 90_I | 243_F | 1.142 | 0.52 |
| 99_I | 198_Y | 1.137 | 0.51 |
| 212_L | 249_M | 1.135 | 0.51 |
| 74_S | 113_F | 1.133 | 0.51 |
| 248_K | 251_Q | 1.133 | 0.51 |
| 251_Q | 283_Y | 1.127 | 0.50 |
| 83_V | 121_A | 1.124 | 0.50 |
| 283_Y | 287_L | 1.120 | 0.50 |
| 257_L | 289_Q | 1.120 | 0.50 |
| 19_D | 23_V | 1.118 | 0.49 |
| 75_G | 209_G | 1.109 | 0.48 |
| 233_T | 268_G | 1.109 | 0.48 |
| 96_V | 192_F | 1.096 | 0.47 |
| 266_I | 284_L | 1.095 | 0.47 |
| 25_E | 31_G | 1.076 | 0.45 |
| 168_I | 171_A | 1.075 | 0.45 |
| 90_I | 156_P | 1.063 | 0.44 |
| 189_W | 225_P | 1.061 | 0.44 |
| 175_H | 178_E | 1.060 | 0.44 |
| 26_I | 68_R | 1.060 | 0.44 |
| 91_R | 106_A | 1.059 | 0.44 |
| 82_I | 286_Y | 1.057 | 0.43 |
| 175_H | 179_Y | 1.055 | 0.43 |
| 178_E | 181_G | 1.054 | 0.43 |
| 133_N | 136_R | 1.049 | 0.43 |
| 151_F | 155_V | 1.048 | 0.43 |
| 26_I | 65_P | 1.044 | 0.42 |
| 84_G | 157_L | 1.040 | 0.42 |
| 61_N | 266_I | 1.035 | 0.41 |
| 71_L | 133_N | 1.032 | 0.41 |
| 39_D | 44_P | 1.032 | 0.41 |
| 79_N | 174_T | 1.031 | 0.41 |
| 121_A | 223_G | 1.028 | 0.41 |
| 176_T | 273_S | 1.028 | 0.41 |
| 66_Q | 133_N | 1.026 | 0.40 |
| 232_P | 253_L | 1.023 | 0.40 |
| 116_Y | 190_H | 1.020 | 0.40 |
| 21_N | 268_G | 1.019 | 0.40 |
| 190_H | 194_T | 1.016 | 0.40 |
| 177_E | 180_S | 1.016 | 0.40 |
| 48_P | 287_L | 1.015 | 0.39 |
| 274_E | 284_L | 1.015 | 0.39 |
| 239_N | 244_P | 1.013 | 0.39 |
| 87_S | 90_I | 1.013 | 0.39 |
| 125_P | 250_H | 1.010 | 0.39 |
| 173_T | 180_S | 1.006 | 0.39 |
| 63_P | 187_M | 1.005 | 0.39 |
| 52_R | 109_Q | 1.003 | 0.38 |
| 248_K | 283_Y | 1.003 | 0.38 |
| 49_R | 52_R | 1.002 | 0.38 |
| 187_M | 222_L | 1.000 | 0.38 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4gqbA | 1 | 0.959 | 100 | 0.214 | Contact Map |
| 3ua3A | 2 | 0.9181 | 100 | 0.256 | Contact Map |
| 4hnoA | 1 | 0.8635 | 77 | 0.954 | Contact Map |
| 3tc3A | 2 | 0.8157 | 60.6 | 0.959 | Contact Map |
| 1qtwA | 1 | 0.8601 | 52 | 0.961 | Contact Map |
| 3aamA | 1 | 0.8191 | 35.7 | 0.965 | Contact Map |
| 3aalA | 1 | 0.8669 | 33.9 | 0.965 | Contact Map |
| 2qw5A | 2 | 0.7679 | 31.2 | 0.966 | Contact Map |
| 2zvrA | 2 | 0.8362 | 25.1 | 0.967 | Contact Map |
| 1xlaA | 2 | 0.7952 | 23.8 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)