| P21156 test |
| ID: | 1502090861 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 302 (301) | ||
| Sequences: | 1189 (435.5) | ||
| Seq/Len: | 3.950 | ||
| Nf(neff/√len): | 25.1 |
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: 3.950).
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 |
| 10_R | 200_L | 5.555 | 1.00 |
| 93_P | 97_A | 4.419 | 1.00 |
| 263_Q | 267_E | 4.330 | 1.00 |
| 199_W | 266_P | 4.161 | 1.00 |
| 78_R | 82_A | 3.698 | 1.00 |
| 61_L | 122_A | 3.665 | 1.00 |
| 213_E | 241_K | 3.238 | 1.00 |
| 45_H | 48_R | 3.220 | 1.00 |
| 242_R | 259_E | 2.801 | 1.00 |
| 31_V | 61_L | 2.752 | 1.00 |
| 74_E | 78_R | 2.632 | 1.00 |
| 56_L | 85_C | 2.528 | 1.00 |
| 151_F | 181_I | 2.352 | 1.00 |
| 18_H | 171_Y | 2.267 | 1.00 |
| 32_M | 43_M | 2.254 | 1.00 |
| 20_I | 132_F | 2.233 | 1.00 |
| 264_T | 267_E | 2.175 | 1.00 |
| 218_E | 223_L | 2.171 | 1.00 |
| 90_H | 122_A | 2.168 | 1.00 |
| 43_M | 132_F | 2.166 | 1.00 |
| 219_R | 237_E | 2.139 | 1.00 |
| 101_N | 104_V | 2.123 | 1.00 |
| 243_M | 261_N | 2.105 | 1.00 |
| 218_E | 240_K | 2.093 | 1.00 |
| 90_H | 126_Y | 2.082 | 1.00 |
| 48_R | 83_Y | 2.027 | 1.00 |
| 79_T | 82_A | 1.940 | 1.00 |
| 31_V | 122_A | 1.876 | 1.00 |
| 261_N | 267_E | 1.859 | 1.00 |
| 196_Q | 273_L | 1.849 | 1.00 |
| 26_E | 173_G | 1.838 | 1.00 |
| 213_E | 243_M | 1.828 | 1.00 |
| 215_P | 241_K | 1.734 | 0.99 |
| 49_K | 201_E | 1.722 | 0.99 |
| 31_V | 131_A | 1.721 | 0.99 |
| 27_F | 173_G | 1.706 | 0.99 |
| 175_I | 181_I | 1.684 | 0.99 |
| 243_M | 263_Q | 1.667 | 0.99 |
| 218_E | 221_G | 1.660 | 0.99 |
| 157_R | 298_R | 1.626 | 0.99 |
| 95_G | 114_M | 1.614 | 0.99 |
| 79_T | 83_Y | 1.613 | 0.99 |
| 23_V | 130_A | 1.609 | 0.99 |
| 78_R | 204_D | 1.606 | 0.99 |
| 284_V | 287_R | 1.586 | 0.98 |
| 95_G | 118_G | 1.565 | 0.98 |
| 27_F | 130_A | 1.563 | 0.98 |
| 61_L | 88_L | 1.549 | 0.98 |
| 283_R | 287_R | 1.487 | 0.97 |
| 148_I | 171_Y | 1.459 | 0.97 |
| 205_I | 210_L | 1.457 | 0.97 |
| 100_I | 121_Q | 1.450 | 0.97 |
| 68_K | 72_M | 1.447 | 0.97 |
| 270_E | 274_V | 1.446 | 0.97 |
| 151_F | 175_I | 1.440 | 0.97 |
| 8_H | 196_Q | 1.432 | 0.96 |
| 123_L | 131_A | 1.401 | 0.96 |
| 90_H | 125_K | 1.347 | 0.94 |
| 283_R | 289_Q | 1.341 | 0.94 |
| 112_D | 117_E | 1.337 | 0.94 |
| 222_M | 256_G | 1.318 | 0.94 |
| 217_L | 226_I | 1.309 | 0.93 |
| 68_K | 115_K | 1.308 | 0.93 |
| 103_F | 231_I | 1.280 | 0.92 |
| 297_K | 302_F | 1.279 | 0.92 |
| 42_V | 194_I | 1.244 | 0.91 |
| 282_G | 290_A | 1.235 | 0.90 |
| 233_L | 237_E | 1.214 | 0.89 |
| 114_M | 254_L | 1.207 | 0.89 |
| 36_I | 206_V | 1.205 | 0.89 |
| 210_L | 265_L | 1.202 | 0.89 |
| 287_R | 290_A | 1.201 | 0.89 |
| 199_W | 269_I | 1.196 | 0.88 |
| 94_E | 98_M | 1.195 | 0.88 |
| 19_I | 148_I | 1.195 | 0.88 |
| 267_E | 270_E | 1.193 | 0.88 |
| 63_V | 90_H | 1.189 | 0.88 |
| 7_T | 10_R | 1.185 | 0.88 |
| 80_A | 300_G | 1.185 | 0.88 |
| 70_R | 74_E | 1.182 | 0.88 |
| 283_R | 288_D | 1.177 | 0.87 |
| 110_H | 254_L | 1.158 | 0.86 |
| 120_K | 157_R | 1.150 | 0.86 |
| 104_V | 232_D | 1.136 | 0.85 |
| 149_Y | 183_V | 1.134 | 0.85 |
| 127_G | 175_I | 1.134 | 0.85 |
| 277_T | 282_G | 1.130 | 0.84 |
| 66_G | 91_K | 1.127 | 0.84 |
| 151_F | 180_S | 1.122 | 0.84 |
| 74_E | 82_A | 1.121 | 0.84 |
| 47_A | 58_F | 1.117 | 0.83 |
| 283_R | 290_A | 1.116 | 0.83 |
| 24_A | 27_F | 1.111 | 0.83 |
| 43_M | 186_L | 1.106 | 0.83 |
| 44_L | 79_T | 1.102 | 0.82 |
| 208_L | 249_L | 1.100 | 0.82 |
| 227_D | 230_R | 1.099 | 0.82 |
| 218_E | 239_I | 1.096 | 0.82 |
| 17_I | 186_L | 1.094 | 0.82 |
| 217_L | 236_G | 1.084 | 0.81 |
| 26_E | 149_Y | 1.076 | 0.80 |
| 295_L | 298_R | 1.075 | 0.80 |
| 159_D | 162_N | 1.071 | 0.80 |
| 60_L | 85_C | 1.071 | 0.80 |
| 111_T | 254_L | 1.067 | 0.79 |
| 114_M | 118_G | 1.064 | 0.79 |
| 20_I | 23_V | 1.062 | 0.79 |
| 48_R | 79_T | 1.061 | 0.79 |
| 222_M | 284_V | 1.060 | 0.79 |
| 110_H | 251_C | 1.060 | 0.79 |
| 233_L | 239_I | 1.049 | 0.78 |
| 217_L | 232_D | 1.047 | 0.77 |
| 24_A | 132_F | 1.044 | 0.77 |
| 48_R | 56_L | 1.042 | 0.77 |
| 123_L | 180_S | 1.042 | 0.77 |
| 66_G | 96_V | 1.040 | 0.77 |
| 216_V | 223_L | 1.040 | 0.77 |
| 44_L | 60_L | 1.035 | 0.76 |
| 297_K | 301_Y | 1.029 | 0.76 |
| 82_A | 204_D | 1.026 | 0.75 |
| 149_Y | 173_G | 1.024 | 0.75 |
| 151_F | 179_E | 1.024 | 0.75 |
| 124_N | 156_H | 1.022 | 0.75 |
| 218_E | 242_R | 1.019 | 0.75 |
| 273_L | 278_S | 1.018 | 0.75 |
| 7_T | 274_V | 1.016 | 0.74 |
| 93_P | 99_G | 1.016 | 0.74 |
| 29_N | 127_G | 1.014 | 0.74 |
| 263_Q | 266_P | 1.009 | 0.74 |
| 95_G | 101_N | 1.007 | 0.74 |
| 232_D | 239_I | 1.003 | 0.73 |
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 | |
| 1zunA | 1 | 0.6556 | 100 | 0.353 | Contact Map |
| 4bwvA | 2 | 0.7086 | 100 | 0.648 | Contact Map |
| 2oq2A | 4 | 0.7616 | 100 | 0.655 | Contact Map |
| 2wsiA | 1 | 0.6887 | 100 | 0.694 | Contact Map |
| 3fwkA | 1 | 0.702 | 100 | 0.695 | Contact Map |
| 2goyA | 8 | 0.6921 | 100 | 0.7 | Contact Map |
| 2o8vA | 1 | 0.6722 | 100 | 0.704 | Contact Map |
| 1surA | 1 | 0.6325 | 100 | 0.747 | Contact Map |
| 3bl5A | 6 | 0.6258 | 99.8 | 0.817 | Contact Map |
| 2ywbA | 4 | 0.7351 | 99.8 | 0.821 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)