| gremlindata |
| ID: | 1411751735 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 310 (310) | ||
| Sequences: | 517 (361) | ||
| Seq/Len: | 1.668 | ||
| Nf(neff/√len): | 20.5 |
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: 1.668).
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 |
| 98_W | 101_G | 2.567 | 1.00 |
| 126_I | 243_F | 2.349 | 1.00 |
| 122_H | 152_I | 2.159 | 0.99 |
| 53_V | 283_N | 1.782 | 0.96 |
| 48_V | 157_L | 1.779 | 0.96 |
| 247_W | 283_N | 1.773 | 0.96 |
| 166_P | 169_S | 1.726 | 0.95 |
| 165_P | 197_P | 1.700 | 0.95 |
| 98_W | 120_I | 1.653 | 0.93 |
| 53_V | 77_A | 1.614 | 0.92 |
| 68_N | 294_F | 1.602 | 0.92 |
| 73_S | 122_H | 1.567 | 0.91 |
| 46_T | 82_A | 1.556 | 0.90 |
| 190_S | 255_S | 1.547 | 0.90 |
| 119_S | 126_I | 1.545 | 0.90 |
| 101_G | 105_C | 1.542 | 0.90 |
| 147_R | 236_L | 1.511 | 0.89 |
| 73_S | 156_W | 1.506 | 0.88 |
| 134_V | 245_V | 1.494 | 0.88 |
| 283_N | 287_Y | 1.492 | 0.88 |
| 43_I | 117_T | 1.489 | 0.88 |
| 49_G | 105_C | 1.474 | 0.87 |
| 53_V | 247_W | 1.460 | 0.86 |
| 54_V | 75_A | 1.443 | 0.85 |
| 98_W | 105_C | 1.412 | 0.84 |
| 131_Y | 205_Y | 1.371 | 0.81 |
| 83_T | 127_S | 1.362 | 0.81 |
| 49_G | 281_S | 1.362 | 0.81 |
| 168_L | 191_M | 1.354 | 0.80 |
| 115_F | 152_I | 1.333 | 0.79 |
| 129_D | 231_R | 1.326 | 0.78 |
| 247_W | 276_G | 1.320 | 0.78 |
| 194_F | 243_F | 1.318 | 0.77 |
| 85_V | 115_F | 1.314 | 0.77 |
| 73_S | 201_M | 1.310 | 0.77 |
| 119_S | 279_N | 1.310 | 0.77 |
| 213_K | 233_T | 1.308 | 0.77 |
| 110_A | 114_L | 1.296 | 0.76 |
| 105_C | 197_P | 1.292 | 0.75 |
| 86_M | 152_I | 1.291 | 0.75 |
| 64_K | 72_V | 1.283 | 0.75 |
| 46_T | 86_M | 1.282 | 0.75 |
| 67_Q | 205_Y | 1.282 | 0.75 |
| 53_V | 129_D | 1.282 | 0.75 |
| 137_A | 239_V | 1.280 | 0.74 |
| 200_I | 204_V | 1.276 | 0.74 |
| 146_K | 150_C | 1.275 | 0.74 |
| 54_V | 72_V | 1.272 | 0.74 |
| 139_Y | 235_V | 1.271 | 0.74 |
| 128_L | 208_I | 1.269 | 0.74 |
| 43_I | 204_V | 1.256 | 0.73 |
| 159_S | 283_N | 1.254 | 0.72 |
| 1_M | 4_L | 1.253 | 0.72 |
| 71_L | 159_S | 1.245 | 0.72 |
| 85_V | 276_G | 1.235 | 0.71 |
| 260_C | 263_Y | 1.233 | 0.71 |
| 135_T | 208_I | 1.233 | 0.71 |
| 127_S | 198_C | 1.233 | 0.71 |
| 148_V | 273_F | 1.221 | 0.69 |
| 165_P | 281_S | 1.209 | 0.68 |
| 206_I | 231_R | 1.208 | 0.68 |
| 71_L | 233_T | 1.208 | 0.68 |
| 139_Y | 212_A | 1.207 | 0.68 |
| 278_C | 282_L | 1.205 | 0.68 |
| 12_F | 153_V | 1.196 | 0.67 |
| 49_G | 294_F | 1.189 | 0.66 |
| 276_G | 282_L | 1.183 | 0.66 |
| 123_L | 201_M | 1.182 | 0.66 |
| 63_L | 68_N | 1.177 | 0.65 |
| 252_F | 292_R | 1.173 | 0.65 |
| 14_A | 25_S | 1.170 | 0.65 |
| 194_F | 251_F | 1.167 | 0.64 |
| 86_M | 115_F | 1.157 | 0.63 |
| 84_L | 125_A | 1.149 | 0.63 |
| 115_F | 172_S | 1.147 | 0.62 |
| 205_Y | 234_F | 1.137 | 0.61 |
| 156_W | 287_Y | 1.136 | 0.61 |
| 111_L | 225_S | 1.135 | 0.61 |
| 58_L | 252_F | 1.134 | 0.61 |
| 86_M | 122_H | 1.133 | 0.61 |
| 217_R | 220_A | 1.131 | 0.61 |
| 112_D | 277_Y | 1.128 | 0.60 |
| 277_Y | 283_N | 1.128 | 0.60 |
| 39_V | 275_I | 1.126 | 0.60 |
| 3_P | 8_G | 1.124 | 0.60 |
| 159_S | 247_W | 1.122 | 0.60 |
| 117_T | 251_F | 1.122 | 0.60 |
| 49_G | 240_M | 1.118 | 0.59 |
| 153_V | 157_L | 1.118 | 0.59 |
| 138_V | 143_R | 1.117 | 0.59 |
| 65_A | 99_Y | 1.112 | 0.59 |
| 73_S | 81_V | 1.111 | 0.59 |
| 44_L | 220_A | 1.106 | 0.58 |
| 72_V | 134_V | 1.105 | 0.58 |
| 188_S | 233_T | 1.104 | 0.58 |
| 67_Q | 254_Y | 1.104 | 0.58 |
| 105_C | 294_F | 1.102 | 0.58 |
| 42_L | 298_F | 1.102 | 0.58 |
| 40_S | 107_I | 1.101 | 0.58 |
| 75_A | 247_W | 1.100 | 0.58 |
| 204_V | 281_S | 1.099 | 0.57 |
| 204_V | 276_G | 1.099 | 0.57 |
| 6_A | 10_D | 1.098 | 0.57 |
| 5_N | 8_G | 1.096 | 0.57 |
| 185_Y | 270_F | 1.096 | 0.57 |
| 77_A | 119_S | 1.096 | 0.57 |
| 145_P | 153_V | 1.093 | 0.57 |
| 129_D | 193_S | 1.092 | 0.57 |
| 48_V | 208_I | 1.091 | 0.57 |
| 77_A | 287_Y | 1.091 | 0.57 |
| 158_I | 301_I | 1.088 | 0.56 |
| 116_C | 276_G | 1.084 | 0.56 |
| 51_I | 200_I | 1.084 | 0.56 |
| 288_T | 291_N | 1.083 | 0.56 |
| 134_V | 295_R | 1.083 | 0.56 |
| 156_W | 247_W | 1.082 | 0.56 |
| 125_A | 152_I | 1.079 | 0.55 |
| 118_S | 304_K | 1.077 | 0.55 |
| 273_F | 279_N | 1.076 | 0.55 |
| 54_V | 63_L | 1.075 | 0.55 |
| 49_G | 283_N | 1.075 | 0.55 |
| 96_G | 245_V | 1.074 | 0.55 |
| 101_G | 197_P | 1.074 | 0.55 |
| 150_C | 154_I | 1.071 | 0.55 |
| 241_G | 250_F | 1.070 | 0.54 |
| 90_L | 148_V | 1.070 | 0.54 |
| 166_P | 170_I | 1.069 | 0.54 |
| 80_L | 107_I | 1.068 | 0.54 |
| 73_S | 86_M | 1.067 | 0.54 |
| 121_V | 282_L | 1.065 | 0.54 |
| 216_K | 219_I | 1.065 | 0.54 |
| 53_V | 294_F | 1.063 | 0.54 |
| 144_T | 147_R | 1.060 | 0.53 |
| 120_I | 198_C | 1.058 | 0.53 |
| 47_V | 199_L | 1.057 | 0.53 |
| 129_D | 232_F | 1.056 | 0.53 |
| 216_K | 220_A | 1.054 | 0.53 |
| 86_M | 274_W | 1.054 | 0.53 |
| 243_F | 294_F | 1.051 | 0.52 |
| 104_W | 259_V | 1.050 | 0.52 |
| 69_L | 152_I | 1.041 | 0.51 |
| 120_I | 185_Y | 1.039 | 0.51 |
| 85_V | 118_S | 1.035 | 0.51 |
| 70_F | 295_R | 1.034 | 0.51 |
| 73_S | 284_P | 1.032 | 0.50 |
| 98_W | 119_S | 1.032 | 0.50 |
| 5_N | 13_T | 1.031 | 0.50 |
| 117_T | 193_S | 1.030 | 0.50 |
| 37_A | 245_V | 1.029 | 0.50 |
| 74_L | 78_D | 1.028 | 0.50 |
| 155_V | 250_F | 1.028 | 0.50 |
| 4_L | 11_A | 1.023 | 0.49 |
| 253_S | 272_F | 1.023 | 0.49 |
| 112_D | 276_G | 1.019 | 0.49 |
| 143_R | 193_S | 1.018 | 0.49 |
| 125_A | 153_V | 1.017 | 0.49 |
| 129_D | 186_I | 1.015 | 0.49 |
| 48_V | 255_S | 1.015 | 0.49 |
| 185_Y | 197_P | 1.014 | 0.48 |
| 49_G | 70_F | 1.013 | 0.48 |
| 112_D | 247_W | 1.012 | 0.48 |
| 196_A | 200_I | 1.012 | 0.48 |
| 116_C | 251_F | 1.010 | 0.48 |
| 77_A | 198_C | 1.008 | 0.48 |
| 151_I | 239_V | 1.008 | 0.48 |
| 153_V | 245_V | 1.007 | 0.48 |
| 44_L | 61_R | 1.006 | 0.48 |
| 222_K | 289_I | 1.005 | 0.48 |
| 67_Q | 201_M | 1.004 | 0.47 |
| 4_L | 14_A | 1.004 | 0.47 |
| 90_L | 128_L | 1.002 | 0.47 |
| 39_V | 229_E | 1.002 | 0.47 |
| 157_L | 198_C | 1.001 | 0.47 |
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 | |
| 4iarA | 1 | 0.9 | 100 | 0.224 | Contact Map |
| 1u19A | 2 | 1 | 100 | 0.238 | Contact Map |
| 2r4rA | 1 | 0.6742 | 100 | 0.247 | Contact Map |
| 4buoA | 2 | 0.929 | 100 | 0.247 | Contact Map |
| 4phuA | 1 | 0.8258 | 100 | 0.265 | Contact Map |
| 4bvnA | 1 | 0.8806 | 100 | 0.267 | Contact Map |
| 4grvA | 1 | 0.8903 | 100 | 0.273 | Contact Map |
| 3uonA | 1 | 0.8871 | 100 | 0.273 | Contact Map |
| 3v2yA | 1 | 0.9484 | 100 | 0.275 | Contact Map |
| 2rh1A | 1 | 0.8903 | 100 | 0.275 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)