| aaaaaaa |
| ID: | 1406005356 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 291 (269) | ||
| Sequences: | 1954 (1488.4) | ||
| Seq/Len: | 7.264 | ||
| Nf(neff/√len): | 90.7 |
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: 7.264).
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 |
| 91_Y | 97_D | 3.460 | 1.00 |
| 196_H | 201_Y | 3.384 | 1.00 |
| 157_D | 163_A | 3.282 | 1.00 |
| 27_G | 31_L | 2.970 | 1.00 |
| 91_Y | 94_R | 2.691 | 1.00 |
| 241_I | 245_F | 2.687 | 1.00 |
| 84_Q | 88_D | 2.557 | 1.00 |
| 88_D | 91_Y | 2.390 | 1.00 |
| 82_F | 86_M | 2.343 | 1.00 |
| 144_L | 203_L | 2.341 | 1.00 |
| 124_F | 128_S | 2.318 | 1.00 |
| 17_S | 22_A | 2.221 | 1.00 |
| 103_H | 263_G | 2.205 | 1.00 |
| 160_F | 163_A | 2.181 | 1.00 |
| 16_F | 23_L | 2.149 | 1.00 |
| 236_G | 271_I | 2.095 | 1.00 |
| 229_G | 274_G | 2.069 | 1.00 |
| 205_L | 238_F | 2.049 | 1.00 |
| 233_I | 274_G | 2.036 | 1.00 |
| 67_G | 112_V | 2.027 | 1.00 |
| 15_I | 23_L | 1.950 | 1.00 |
| 115_I | 119_R | 1.928 | 1.00 |
| 94_R | 97_D | 1.917 | 1.00 |
| 84_Q | 91_Y | 1.845 | 1.00 |
| 71_G | 108_G | 1.830 | 1.00 |
| 240_I | 264_Q | 1.805 | 1.00 |
| 86_M | 89_P | 1.779 | 1.00 |
| 45_A | 57_V | 1.777 | 1.00 |
| 210_L | 234_G | 1.732 | 1.00 |
| 146_N | 151_E | 1.726 | 1.00 |
| 233_I | 271_I | 1.714 | 1.00 |
| 56_E | 120_T | 1.713 | 1.00 |
| 15_I | 28_L | 1.679 | 1.00 |
| 53_T | 56_E | 1.677 | 1.00 |
| 67_G | 108_G | 1.660 | 1.00 |
| 240_I | 244_F | 1.657 | 1.00 |
| 139_L | 231_F | 1.657 | 1.00 |
| 117_A | 127_V | 1.629 | 1.00 |
| 29_M | 145_G | 1.599 | 1.00 |
| 44_R | 218_I | 1.586 | 1.00 |
| 276_I | 280_W | 1.583 | 1.00 |
| 226_A | 282_Y | 1.576 | 1.00 |
| 78_L | 82_F | 1.562 | 1.00 |
| 114_I | 118_R | 1.551 | 1.00 |
| 116_F | 120_T | 1.546 | 1.00 |
| 89_P | 93_F | 1.537 | 1.00 |
| 205_L | 242_V | 1.530 | 0.99 |
| 17_S | 20_P | 1.515 | 0.99 |
| 156_V | 193_L | 1.514 | 0.99 |
| 34_F | 68_V | 1.502 | 0.99 |
| 90_L | 93_F | 1.497 | 0.99 |
| 68_V | 109_V | 1.484 | 0.99 |
| 209_V | 234_G | 1.440 | 0.99 |
| 128_S | 228_S | 1.439 | 0.99 |
| 125_F | 225_G | 1.438 | 0.99 |
| 147_F | 200_L | 1.430 | 0.99 |
| 34_F | 65_F | 1.424 | 0.99 |
| 95_V | 98_G | 1.406 | 0.99 |
| 229_G | 277_M | 1.406 | 0.99 |
| 108_G | 112_V | 1.381 | 0.99 |
| 238_F | 242_V | 1.377 | 0.99 |
| 44_R | 47_R | 1.375 | 0.99 |
| 226_A | 278_M | 1.360 | 0.99 |
| 159_N | 163_A | 1.355 | 0.98 |
| 46_N | 54_K | 1.353 | 0.98 |
| 41_A | 134_L | 1.349 | 0.98 |
| 60_L | 127_V | 1.347 | 0.98 |
| 37_A | 64_G | 1.324 | 0.98 |
| 77_V | 92_L | 1.316 | 0.98 |
| 13_P | 24_H | 1.313 | 0.98 |
| 244_F | 264_Q | 1.313 | 0.98 |
| 15_I | 25_W | 1.295 | 0.98 |
| 113_M | 128_S | 1.281 | 0.98 |
| 146_N | 149_N | 1.271 | 0.97 |
| 233_I | 275_V | 1.265 | 0.97 |
| 147_F | 164_M | 1.265 | 0.97 |
| 85_F | 92_L | 1.261 | 0.97 |
| 212_I | 216_L | 1.260 | 0.97 |
| 203_L | 208_V | 1.255 | 0.97 |
| 153_W | 195_R | 1.254 | 0.97 |
| 278_M | 282_Y | 1.244 | 0.97 |
| 232_L | 274_G | 1.243 | 0.97 |
| 166_F | 199_Q | 1.243 | 0.97 |
| 230_L | 278_M | 1.236 | 0.97 |
| 44_R | 133_P | 1.235 | 0.97 |
| 102_F | 139_L | 1.230 | 0.97 |
| 195_R | 247_Q | 1.207 | 0.96 |
| 143_R | 239_R | 1.206 | 0.96 |
| 210_L | 214_L | 1.206 | 0.96 |
| 66_L | 70_L | 1.199 | 0.96 |
| 146_N | 152_L | 1.186 | 0.96 |
| 162_F | 196_H | 1.185 | 0.96 |
| 140_G | 203_L | 1.184 | 0.96 |
| 43_R | 47_R | 1.164 | 0.95 |
| 101_S | 152_L | 1.163 | 0.95 |
| 81_N | 85_F | 1.159 | 0.95 |
| 237_A | 271_I | 1.148 | 0.95 |
| 39_W | 43_R | 1.138 | 0.94 |
| 217_Y | 230_L | 1.137 | 0.94 |
| 260_I | 268_I | 1.135 | 0.94 |
| 114_I | 124_F | 1.135 | 0.94 |
| 263_G | 266_L | 1.133 | 0.94 |
| 111_V | 115_I | 1.132 | 0.94 |
| 141_A | 203_L | 1.122 | 0.94 |
| 26_Y | 146_N | 1.119 | 0.94 |
| 88_D | 94_R | 1.116 | 0.93 |
| 211_F | 214_L | 1.114 | 0.93 |
| 55_N | 58_E | 1.113 | 0.93 |
| 81_N | 84_Q | 1.109 | 0.93 |
| 84_Q | 87_A | 1.107 | 0.93 |
| 85_F | 91_Y | 1.100 | 0.93 |
| 106_L | 135_I | 1.092 | 0.92 |
| 229_G | 278_M | 1.092 | 0.92 |
| 133_P | 136_P | 1.086 | 0.92 |
| 170_R | 192_V | 1.083 | 0.92 |
| 15_I | 24_H | 1.079 | 0.92 |
| 42_T | 58_E | 1.073 | 0.92 |
| 36_F | 141_A | 1.071 | 0.92 |
| 129_D | 225_G | 1.068 | 0.91 |
| 198_S | 242_V | 1.067 | 0.91 |
| 122_R | 127_V | 1.058 | 0.91 |
| 237_A | 241_I | 1.058 | 0.91 |
| 38_M | 61_L | 1.055 | 0.91 |
| 163_A | 194_P | 1.055 | 0.91 |
| 230_L | 234_G | 1.052 | 0.91 |
| 45_A | 52_W | 1.050 | 0.90 |
| 60_L | 64_G | 1.049 | 0.90 |
| 74_I | 92_L | 1.046 | 0.90 |
| 151_E | 199_Q | 1.045 | 0.90 |
| 229_G | 281_A | 1.033 | 0.89 |
| 252_F | 262_M | 1.025 | 0.89 |
| 268_I | 272_V | 1.025 | 0.89 |
| 137_F | 140_G | 1.023 | 0.89 |
| 228_S | 232_L | 1.023 | 0.89 |
| 90_L | 94_R | 1.019 | 0.89 |
| 272_V | 276_I | 1.012 | 0.88 |
| 43_R | 46_N | 1.012 | 0.88 |
| 275_V | 279_V | 1.008 | 0.88 |
| 165_L | 194_P | 1.005 | 0.88 |
| 144_L | 148_I | 1.005 | 0.88 |
| 60_L | 116_F | 1.000 | 0.87 |
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 | |
| 2kluA | 1 | 0.1478 | 12.4 | 0.968 | Contact Map |
| 2m20A | 2 | 0.134 | 7 | 0.971 | Contact Map |
| 2l2tA | 2 | 0.1512 | 5.2 | 0.973 | Contact Map |
| 3ixzA | 1 | 0.2027 | 4.9 | 0.973 | Contact Map |
| 2ks1B | 1 | 0.1512 | 4.7 | 0.973 | Contact Map |
| 2ls4A | 1 | 0.0825 | 4.4 | 0.974 | Contact Map |
| 2zxeA | 1 | 0.2027 | 4.1 | 0.974 | Contact Map |
| 4o6yA | 2 | 0.3093 | 3.8 | 0.975 | Contact Map |
| 2rddB | 1 | 0.11 | 3.4 | 0.975 | Contact Map |
| 2i68A | 2 | 0.268 | 3.1 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)