| HD SYNTH low coverage |
| ID: | 1425313177 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 322 (319) | ||
| Sequences: | 1226 (608.5) | ||
| Seq/Len: | 3.843 | ||
| Nf(neff/√len): | 34.1 |
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: 3.843).
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 |
| 39_L | 112_L | 4.298 | 1.00 |
| 53_I | 60_K | 4.167 | 1.00 |
| 64_A | 69_D | 3.850 | 1.00 |
| 129_K | 132_A | 3.577 | 1.00 |
| 125_L | 168_H | 3.336 | 1.00 |
| 199_I | 259_V | 3.046 | 1.00 |
| 247_D | 304_E | 2.990 | 1.00 |
| 248_S | 251_D | 2.834 | 1.00 |
| 245_I | 304_E | 2.784 | 1.00 |
| 123_R | 160_E | 2.679 | 1.00 |
| 60_K | 76_E | 2.654 | 1.00 |
| 42_A | 70_E | 2.490 | 1.00 |
| 213_F | 307_D | 2.449 | 1.00 |
| 211_R | 304_E | 2.364 | 1.00 |
| 180_R | 233_F | 2.320 | 1.00 |
| 202_R | 205_S | 2.302 | 1.00 |
| 3_R | 66_L | 2.271 | 1.00 |
| 139_R | 143_D | 2.262 | 1.00 |
| 231_I | 236_M | 2.222 | 1.00 |
| 7_Y | 58_V | 2.160 | 1.00 |
| 53_I | 76_E | 2.111 | 1.00 |
| 74_L | 113_V | 2.101 | 1.00 |
| 53_I | 63_I | 2.086 | 1.00 |
| 209_P | 247_D | 2.021 | 1.00 |
| 181_L | 219_P | 2.020 | 1.00 |
| 1_M | 44_I | 1.991 | 1.00 |
| 170_N | 173_A | 1.980 | 1.00 |
| 2_N | 6_V | 1.897 | 1.00 |
| 8_A | 24_Y | 1.890 | 1.00 |
| 46_T | 113_V | 1.883 | 1.00 |
| 177_I | 219_P | 1.872 | 1.00 |
| 176_A | 180_R | 1.869 | 1.00 |
| 31_A | 44_I | 1.859 | 1.00 |
| 192_V | 214_G | 1.844 | 1.00 |
| 131_Q | 134_R | 1.838 | 1.00 |
| 131_Q | 135_E | 1.834 | 1.00 |
| 134_R | 168_H | 1.813 | 0.99 |
| 73_E | 106_K | 1.813 | 0.99 |
| 122_M | 164_L | 1.806 | 0.99 |
| 104_I | 108_V | 1.787 | 0.99 |
| 259_V | 289_V | 1.785 | 0.99 |
| 166_F | 219_P | 1.732 | 0.99 |
| 53_I | 72_G | 1.698 | 0.99 |
| 34_L | 47_A | 1.645 | 0.99 |
| 251_D | 254_R | 1.641 | 0.99 |
| 166_F | 170_N | 1.589 | 0.98 |
| 194_L | 293_R | 1.587 | 0.98 |
| 10_R | 13_G | 1.580 | 0.98 |
| 178_I | 219_P | 1.573 | 0.98 |
| 18_A | 128_I | 1.568 | 0.98 |
| 60_K | 72_G | 1.565 | 0.98 |
| 255_A | 258_V | 1.562 | 0.98 |
| 46_T | 74_L | 1.546 | 0.98 |
| 142_R | 220_Y | 1.528 | 0.98 |
| 175_N | 178_I | 1.516 | 0.98 |
| 159_T | 185_R | 1.515 | 0.98 |
| 41_T | 45_V | 1.508 | 0.97 |
| 250_E | 254_R | 1.503 | 0.97 |
| 239_I | 275_S | 1.503 | 0.97 |
| 202_R | 262_A | 1.503 | 0.97 |
| 128_I | 137_I | 1.492 | 0.97 |
| 200_A | 204_E | 1.481 | 0.97 |
| 185_R | 216_E | 1.477 | 0.97 |
| 244_V | 255_A | 1.477 | 0.97 |
| 201_A | 205_S | 1.450 | 0.97 |
| 166_F | 173_A | 1.448 | 0.97 |
| 246_V | 255_A | 1.430 | 0.96 |
| 39_L | 43_T | 1.403 | 0.96 |
| 34_L | 43_T | 1.399 | 0.96 |
| 33_I | 123_R | 1.389 | 0.95 |
| 247_D | 251_D | 1.384 | 0.95 |
| 195_V | 297_I | 1.376 | 0.95 |
| 304_E | 308_R | 1.359 | 0.95 |
| 6_V | 9_M | 1.331 | 0.94 |
| 11_M | 62_E | 1.326 | 0.94 |
| 159_T | 216_E | 1.310 | 0.93 |
| 183_T | 295_M | 1.301 | 0.93 |
| 7_Y | 66_L | 1.290 | 0.92 |
| 5_Y | 9_M | 1.287 | 0.92 |
| 167_E | 259_V | 1.264 | 0.91 |
| 13_G | 16_T | 1.251 | 0.91 |
| 271_K | 288_T | 1.243 | 0.90 |
| 118_R | 141_T | 1.243 | 0.90 |
| 62_E | 65_K | 1.242 | 0.90 |
| 101_I | 145_Y | 1.237 | 0.90 |
| 159_T | 218_S | 1.235 | 0.90 |
| 113_V | 150_R | 1.229 | 0.90 |
| 100_F | 265_S | 1.227 | 0.90 |
| 122_M | 125_L | 1.225 | 0.89 |
| 7_Y | 11_M | 1.223 | 0.89 |
| 125_L | 137_I | 1.221 | 0.89 |
| 61_E | 65_K | 1.218 | 0.89 |
| 265_S | 275_S | 1.210 | 0.89 |
| 31_A | 47_A | 1.204 | 0.88 |
| 45_V | 71_I | 1.200 | 0.88 |
| 11_M | 57_P | 1.200 | 0.88 |
| 56_T | 59_T | 1.197 | 0.88 |
| 269_R | 288_T | 1.164 | 0.86 |
| 61_E | 64_A | 1.153 | 0.85 |
| 167_E | 175_N | 1.147 | 0.85 |
| 11_M | 58_V | 1.142 | 0.85 |
| 177_I | 233_F | 1.139 | 0.84 |
| 53_I | 79_T | 1.136 | 0.84 |
| 125_L | 138_A | 1.136 | 0.84 |
| 55_D | 121_N | 1.133 | 0.84 |
| 55_D | 80_K | 1.128 | 0.84 |
| 260_H | 287_T | 1.126 | 0.83 |
| 60_K | 64_A | 1.122 | 0.83 |
| 224_R | 228_R | 1.121 | 0.83 |
| 58_V | 66_L | 1.117 | 0.83 |
| 283_R | 309_V | 1.090 | 0.81 |
| 54_E | 121_N | 1.086 | 0.80 |
| 246_V | 251_D | 1.086 | 0.80 |
| 206_S | 258_V | 1.084 | 0.80 |
| 256_L | 260_H | 1.076 | 0.79 |
| 184_L | 187_E | 1.075 | 0.79 |
| 181_L | 239_I | 1.063 | 0.78 |
| 253_Y | 260_H | 1.062 | 0.78 |
| 120_H | 124_T | 1.060 | 0.78 |
| 78_V | 81_L | 1.048 | 0.77 |
| 308_R | 312_E | 1.046 | 0.77 |
| 29_E | 32_G | 1.036 | 0.76 |
| 189_G | 275_S | 1.034 | 0.75 |
| 187_E | 191_A | 1.030 | 0.75 |
| 58_V | 62_E | 1.027 | 0.75 |
| 260_H | 270_F | 1.026 | 0.75 |
| 81_L | 148_L | 1.024 | 0.74 |
| 196_S | 242_F | 1.018 | 0.74 |
| 80_K | 121_N | 1.010 | 0.73 |
| 226_L | 273_F | 1.009 | 0.73 |
| 173_A | 176_A | 1.007 | 0.73 |
| 36_E | 156_R | 1.005 | 0.73 |
| 193_A | 196_S | 1.001 | 0.72 |
| 183_T | 240_Y | 1.001 | 0.72 |
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 | |
| 1vj7A | 2 | 0.941 | 100 | 0.216 | Contact Map |
| 3l9dA | 2 | 0.4596 | 100 | 0.645 | Contact Map |
| 3nr1A | 2 | 0.5217 | 100 | 0.707 | Contact Map |
| 3nqwA | 2 | 0.5093 | 100 | 0.718 | Contact Map |
| 2be3A | 2 | 0.472 | 100 | 0.747 | Contact Map |
| 2qgsA | 2 | 0.5714 | 90.9 | 0.966 | Contact Map |
| 2pq7A | 1 | 0.4503 | 85.9 | 0.969 | Contact Map |
| 2pjqA | 4 | 0.5404 | 83.7 | 0.97 | Contact Map |
| 4n6wA | 1 | 0.4814 | 79 | 0.971 | Contact Map |
| 3gw7A | 2 | 0.5621 | 75.9 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)