| adometpro |
| ID: | 1456764109 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 325 (299) | ||
| Sequences: | 476 (325.5) | ||
| Seq/Len: | 1.592 | ||
| Nf(neff/√len): | 18.8 |
HHblits Results: (2015_06)
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: 1.592).
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 |
| 165_Y | 168_G | 2.159 | 0.99 |
| 52_G | 80_H | 2.072 | 0.99 |
| 204_N | 273_E | 1.975 | 0.98 |
| 40_R | 44_N | 1.954 | 0.98 |
| 176_F | 201_Y | 1.684 | 0.94 |
| 64_E | 69_S | 1.661 | 0.93 |
| 40_R | 128_S | 1.646 | 0.93 |
| 156_K | 178_F | 1.618 | 0.92 |
| 231_Y | 250_T | 1.575 | 0.90 |
| 72_Q | 218_K | 1.565 | 0.90 |
| 63_M | 68_E | 1.534 | 0.89 |
| 267_L | 318_Q | 1.531 | 0.89 |
| 91_F | 94_K | 1.516 | 0.88 |
| 36_G | 39_K | 1.509 | 0.88 |
| 162_G | 168_G | 1.501 | 0.87 |
| 90_V | 94_K | 1.486 | 0.87 |
| 112_P | 115_E | 1.475 | 0.86 |
| 24_G | 27_T | 1.451 | 0.85 |
| 65_R | 112_P | 1.439 | 0.84 |
| 40_R | 71_R | 1.436 | 0.84 |
| 51_I | 210_E | 1.429 | 0.84 |
| 97_V | 130_M | 1.412 | 0.83 |
| 24_G | 29_S | 1.405 | 0.82 |
| 76_E | 219_E | 1.403 | 0.82 |
| 105_M | 243_H | 1.398 | 0.82 |
| 68_E | 84_F | 1.389 | 0.81 |
| 198_I | 266_L | 1.385 | 0.81 |
| 204_N | 274_R | 1.377 | 0.80 |
| 217_T | 223_L | 1.362 | 0.79 |
| 24_G | 28_Q | 1.343 | 0.78 |
| 89_L | 100_S | 1.334 | 0.77 |
| 206_Q | 271_Y | 1.319 | 0.76 |
| 54_V | 88_L | 1.317 | 0.76 |
| 70_L | 236_V | 1.307 | 0.75 |
| 129_F | 134_Y | 1.306 | 0.75 |
| 39_K | 42_E | 1.299 | 0.75 |
| 195_D | 314_Y | 1.290 | 0.74 |
| 34_D | 38_E | 1.285 | 0.74 |
| 173_D | 274_R | 1.283 | 0.73 |
| 68_E | 98_V | 1.282 | 0.73 |
| 200_V | 266_L | 1.273 | 0.73 |
| 199_N | 203_Y | 1.260 | 0.72 |
| 148_M | 223_L | 1.256 | 0.71 |
| 59_L | 90_V | 1.256 | 0.71 |
| 195_D | 231_Y | 1.250 | 0.71 |
| 35_S | 39_K | 1.247 | 0.70 |
| 95_Q | 163_H | 1.245 | 0.70 |
| 225_S | 232_E | 1.243 | 0.70 |
| 76_E | 105_M | 1.237 | 0.70 |
| 195_D | 251_N | 1.233 | 0.69 |
| 38_E | 42_E | 1.229 | 0.69 |
| 199_N | 205_V | 1.224 | 0.68 |
| 111_H | 115_E | 1.224 | 0.68 |
| 88_L | 122_I | 1.218 | 0.68 |
| 162_G | 165_Y | 1.215 | 0.68 |
| 119_S | 322_A | 1.215 | 0.68 |
| 219_E | 223_L | 1.210 | 0.67 |
| 165_Y | 302_V | 1.209 | 0.67 |
| 83_K | 148_M | 1.206 | 0.67 |
| 161_T | 210_E | 1.191 | 0.65 |
| 162_G | 251_N | 1.191 | 0.65 |
| 44_N | 278_V | 1.183 | 0.64 |
| 223_L | 232_E | 1.179 | 0.64 |
| 35_S | 38_E | 1.179 | 0.64 |
| 24_G | 30_K | 1.178 | 0.64 |
| 231_Y | 251_N | 1.177 | 0.64 |
| 25_G | 28_Q | 1.167 | 0.63 |
| 195_D | 280_L | 1.161 | 0.62 |
| 106_L | 137_P | 1.157 | 0.62 |
| 261_K | 301_T | 1.155 | 0.62 |
| 87_S | 99_R | 1.154 | 0.62 |
| 37_L | 41_F | 1.153 | 0.62 |
| 59_L | 147_I | 1.150 | 0.61 |
| 301_T | 323_R | 1.147 | 0.61 |
| 271_Y | 323_R | 1.146 | 0.61 |
| 105_M | 109_A | 1.142 | 0.60 |
| 114_L | 117_M | 1.141 | 0.60 |
| 94_K | 215_G | 1.138 | 0.60 |
| 198_I | 263_V | 1.130 | 0.59 |
| 178_F | 239_Y | 1.129 | 0.59 |
| 43_L | 78_G | 1.124 | 0.59 |
| 165_Y | 316_F | 1.124 | 0.59 |
| 98_V | 175_C | 1.121 | 0.58 |
| 57_K | 184_D | 1.116 | 0.58 |
| 52_G | 245_F | 1.114 | 0.58 |
| 76_E | 83_K | 1.112 | 0.57 |
| 91_F | 120_H | 1.111 | 0.57 |
| 86_R | 100_S | 1.110 | 0.57 |
| 108_E | 236_V | 1.110 | 0.57 |
| 45_F | 151_E | 1.109 | 0.57 |
| 42_E | 249_E | 1.106 | 0.57 |
| 308_N | 321_Y | 1.104 | 0.57 |
| 92_T | 262_I | 1.102 | 0.56 |
| 106_L | 151_E | 1.101 | 0.56 |
| 137_P | 151_E | 1.100 | 0.56 |
| 234_L | 263_V | 1.099 | 0.56 |
| 220_Q | 301_T | 1.098 | 0.56 |
| 45_F | 98_V | 1.097 | 0.56 |
| 51_I | 216_N | 1.093 | 0.55 |
| 215_G | 288_T | 1.092 | 0.55 |
| 25_G | 29_S | 1.089 | 0.55 |
| 151_E | 175_C | 1.085 | 0.55 |
| 235_R | 238_T | 1.085 | 0.55 |
| 36_G | 42_E | 1.084 | 0.55 |
| 51_I | 255_A | 1.082 | 0.54 |
| 89_L | 101_S | 1.081 | 0.54 |
| 109_A | 236_V | 1.081 | 0.54 |
| 34_D | 39_K | 1.076 | 0.54 |
| 140_M | 238_T | 1.076 | 0.54 |
| 56_V | 60_A | 1.075 | 0.54 |
| 124_V | 300_F | 1.068 | 0.53 |
| 274_R | 297_L | 1.068 | 0.53 |
| 136_S | 246_A | 1.067 | 0.53 |
| 83_K | 219_E | 1.063 | 0.52 |
| 63_M | 98_V | 1.062 | 0.52 |
| 23_W | 28_Q | 1.061 | 0.52 |
| 303_V | 322_A | 1.059 | 0.52 |
| 110_V | 241_S | 1.057 | 0.52 |
| 132_V | 173_D | 1.054 | 0.51 |
| 222_L | 235_R | 1.049 | 0.51 |
| 33_T | 37_L | 1.048 | 0.51 |
| 175_C | 205_V | 1.048 | 0.51 |
| 256_A | 277_L | 1.046 | 0.51 |
| 74_S | 318_Q | 1.046 | 0.51 |
| 132_V | 144_T | 1.040 | 0.50 |
| 128_S | 169_P | 1.040 | 0.50 |
| 129_F | 278_V | 1.037 | 0.50 |
| 133_N | 176_F | 1.036 | 0.49 |
| 113_M | 255_A | 1.033 | 0.49 |
| 195_D | 248_F | 1.033 | 0.49 |
| 130_M | 143_E | 1.031 | 0.49 |
| 45_F | 175_C | 1.029 | 0.49 |
| 68_E | 175_C | 1.027 | 0.49 |
| 43_L | 95_Q | 1.027 | 0.49 |
| 43_L | 283_R | 1.026 | 0.48 |
| 134_Y | 175_C | 1.026 | 0.48 |
| 118_R | 323_R | 1.025 | 0.48 |
| 57_K | 60_A | 1.025 | 0.48 |
| 127_A | 250_T | 1.021 | 0.48 |
| 200_V | 263_V | 1.020 | 0.48 |
| 147_I | 285_A | 1.019 | 0.48 |
| 302_V | 319_A | 1.013 | 0.47 |
| 123_I | 216_N | 1.012 | 0.47 |
| 169_P | 172_R | 1.011 | 0.47 |
| 81_T | 84_F | 1.010 | 0.47 |
| 197_Q | 201_Y | 1.010 | 0.47 |
| 246_A | 300_F | 1.010 | 0.47 |
| 89_L | 99_R | 1.010 | 0.47 |
| 96_I | 259_I | 1.009 | 0.47 |
| 179_V | 274_R | 1.009 | 0.47 |
| 209_D | 234_L | 1.006 | 0.46 |
| 116_L | 278_V | 1.003 | 0.46 |
| 77_L | 211_Y | 1.003 | 0.46 |
| 60_A | 83_K | 1.002 | 0.46 |
| 101_S | 235_R | 1.001 | 0.46 |
| 127_A | 297_L | 1.001 | 0.46 |
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 | |
| 1jl0A | 2 | 0.8523 | 100 | 0.199 | Contact Map |
| 1mhmA | 1 | 0.6738 | 100 | 0.403 | Contact Map |
| 1mhmB | 1 | 0.1538 | 99.9 | 0.815 | Contact Map |
| 1vr7A | 2 | 0.3231 | 50.5 | 0.97 | Contact Map |
| 2iiiA | 1 | 0.3538 | 43.1 | 0.971 | Contact Map |
| 4jupA | 2 | 0.2462 | 16.7 | 0.976 | Contact Map |
| 4g6vB | 4 | 0.3077 | 5.9 | 0.981 | Contact Map |
| 2ookA | 2 | 0.2554 | 5.6 | 0.981 | Contact Map |
| 3oakC | 2 | 0.0954 | 5.5 | 0.981 | Contact Map |
| 1dgsA | 2 | 0.0892 | 5 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)