| A |
| ID: | 1457413725 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 377 (370) | ||
| Sequences: | 1118 (807.3) | ||
| Seq/Len: | 3.022 | ||
| Nf(neff/√len): | 42.0 |
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: 3.022).
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 |
| 78_T | 98_P | 4.669 | 1.00 |
| 76_H | 88_S | 4.029 | 1.00 |
| 125_A | 208_V | 3.750 | 1.00 |
| 45_L | 125_A | 3.614 | 1.00 |
| 123_I | 208_V | 3.608 | 1.00 |
| 58_G | 121_Y | 3.576 | 1.00 |
| 32_K | 56_R | 3.424 | 1.00 |
| 151_A | 200_L | 3.269 | 1.00 |
| 62_S | 108_M | 3.117 | 1.00 |
| 38_T | 59_L | 3.113 | 1.00 |
| 93_L | 102_I | 2.949 | 1.00 |
| 35_C | 46_A | 2.923 | 1.00 |
| 294_L | 333_V | 2.915 | 1.00 |
| 83_K | 91_E | 2.820 | 1.00 |
| 170_C | 173_C | 2.659 | 1.00 |
| 124_V | 141_C | 2.631 | 1.00 |
| 56_R | 103_V | 2.593 | 1.00 |
| 43_S | 75_I | 2.580 | 1.00 |
| 170_C | 244_C | 2.555 | 1.00 |
| 173_C | 244_C | 2.497 | 1.00 |
| 11_Y | 97_N | 2.384 | 1.00 |
| 90_A | 94_R | 2.372 | 1.00 |
| 244_C | 247_C | 2.341 | 1.00 |
| 48_Y | 198_G | 2.328 | 1.00 |
| 139_D | 172_R | 2.307 | 1.00 |
| 14_H | 71_Q | 2.287 | 1.00 |
| 105_H | 121_Y | 2.282 | 1.00 |
| 278_A | 370_V | 2.274 | 1.00 |
| 206_T | 226_F | 2.245 | 1.00 |
| 7_E | 29_K | 2.196 | 1.00 |
| 20_V | 24_G | 2.188 | 1.00 |
| 170_C | 247_C | 2.147 | 1.00 |
| 207_E | 210_K | 2.098 | 1.00 |
| 315_L | 344_A | 2.095 | 1.00 |
| 118_C | 141_C | 2.041 | 1.00 |
| 20_V | 213_L | 2.030 | 1.00 |
| 128_T | 137_I | 2.011 | 1.00 |
| 31_A | 212_I | 1.959 | 1.00 |
| 173_C | 247_C | 1.946 | 1.00 |
| 75_I | 89_A | 1.945 | 1.00 |
| 58_G | 105_H | 1.934 | 0.99 |
| 141_C | 148_N | 1.915 | 0.99 |
| 34_L | 118_C | 1.910 | 0.99 |
| 128_T | 133_T | 1.883 | 0.99 |
| 44_P | 47_L | 1.831 | 0.99 |
| 281_A | 291_V | 1.828 | 0.99 |
| 86_I | 104_K | 1.823 | 0.99 |
| 75_I | 93_L | 1.818 | 0.99 |
| 80_D | 83_K | 1.801 | 0.99 |
| 28_L | 209_I | 1.801 | 0.99 |
| 56_R | 101_E | 1.781 | 0.99 |
| 298_E | 316_G | 1.775 | 0.99 |
| 333_V | 345_L | 1.773 | 0.99 |
| 169_P | 221_G | 1.756 | 0.99 |
| 118_C | 124_V | 1.749 | 0.99 |
| 84_P | 106_E | 1.737 | 0.99 |
| 36_V | 137_I | 1.726 | 0.99 |
| 332_I | 359_L | 1.694 | 0.98 |
| 319_A | 347_I | 1.666 | 0.98 |
| 125_A | 151_A | 1.662 | 0.98 |
| 79_A | 95_D | 1.652 | 0.98 |
| 124_V | 146_K | 1.650 | 0.98 |
| 109_L | 114_A | 1.645 | 0.98 |
| 259_Y | 262_F | 1.641 | 0.98 |
| 46_A | 59_L | 1.639 | 0.98 |
| 118_C | 144_L | 1.588 | 0.97 |
| 345_L | 356_V | 1.578 | 0.97 |
| 206_T | 228_A | 1.578 | 0.97 |
| 86_I | 106_E | 1.574 | 0.97 |
| 46_A | 89_A | 1.569 | 0.97 |
| 33_V | 208_V | 1.559 | 0.97 |
| 341_G | 358_N | 1.559 | 0.97 |
| 123_I | 212_I | 1.509 | 0.96 |
| 333_V | 348_L | 1.486 | 0.95 |
| 160_A | 203_V | 1.466 | 0.95 |
| 281_A | 359_L | 1.427 | 0.94 |
| 345_L | 358_N | 1.423 | 0.94 |
| 90_A | 104_K | 1.414 | 0.94 |
| 299_P | 303_D | 1.411 | 0.93 |
| 259_Y | 263_C | 1.410 | 0.93 |
| 50_A | 102_I | 1.408 | 0.93 |
| 165_A | 220_V | 1.404 | 0.93 |
| 203_V | 233_T | 1.401 | 0.93 |
| 199_L | 226_F | 1.389 | 0.93 |
| 43_S | 47_L | 1.376 | 0.92 |
| 275_E | 358_N | 1.356 | 0.92 |
| 151_A | 160_A | 1.353 | 0.91 |
| 162_V | 211_R | 1.352 | 0.91 |
| 367_V | 374_L | 1.335 | 0.91 |
| 209_I | 213_L | 1.332 | 0.91 |
| 77_H | 95_D | 1.328 | 0.90 |
| 185_P | 190_G | 1.326 | 0.90 |
| 302_W | 312_H | 1.319 | 0.90 |
| 244_C | 248_G | 1.283 | 0.88 |
| 302_W | 306_R | 1.278 | 0.88 |
| 325_L | 331_I | 1.277 | 0.88 |
| 222_R | 235_E | 1.276 | 0.88 |
| 304_I | 377_Y | 1.271 | 0.88 |
| 46_A | 93_L | 1.266 | 0.87 |
| 24_G | 213_L | 1.262 | 0.87 |
| 130_N | 133_T | 1.261 | 0.87 |
| 87_T | 104_K | 1.249 | 0.86 |
| 12_S | 16_L | 1.246 | 0.86 |
| 153_I | 196_L | 1.242 | 0.86 |
| 363_L | 374_L | 1.242 | 0.86 |
| 333_V | 358_N | 1.222 | 0.85 |
| 34_L | 60_V | 1.221 | 0.85 |
| 133_T | 137_I | 1.213 | 0.84 |
| 51_A | 71_Q | 1.211 | 0.84 |
| 198_G | 201_G | 1.210 | 0.84 |
| 3_L | 7_E | 1.204 | 0.84 |
| 149_V | 211_R | 1.199 | 0.83 |
| 197_P | 202_V | 1.188 | 0.82 |
| 45_L | 208_V | 1.182 | 0.82 |
| 109_L | 118_C | 1.176 | 0.82 |
| 75_I | 88_S | 1.173 | 0.81 |
| 151_A | 204_Q | 1.170 | 0.81 |
| 7_E | 99_D | 1.159 | 0.80 |
| 76_H | 80_D | 1.152 | 0.80 |
| 29_K | 99_D | 1.149 | 0.80 |
| 371_D | 375_P | 1.137 | 0.79 |
| 305_C | 377_Y | 1.127 | 0.78 |
| 65_V | 76_H | 1.126 | 0.78 |
| 371_D | 377_Y | 1.118 | 0.77 |
| 215_I | 229_L | 1.117 | 0.77 |
| 90_A | 102_I | 1.113 | 0.76 |
| 52_A | 209_I | 1.106 | 0.76 |
| 277_A | 280_E | 1.100 | 0.75 |
| 193_L | 228_A | 1.094 | 0.75 |
| 164_Y | 220_V | 1.093 | 0.75 |
| 60_V | 117_I | 1.086 | 0.74 |
| 138_N | 142_V | 1.086 | 0.74 |
| 203_V | 224_L | 1.084 | 0.74 |
| 301_E | 340_R | 1.083 | 0.74 |
| 117_I | 144_L | 1.080 | 0.73 |
| 150_H | 204_Q | 1.070 | 0.72 |
| 120_R | 146_K | 1.067 | 0.72 |
| 170_C | 248_G | 1.067 | 0.72 |
| 65_V | 88_S | 1.063 | 0.72 |
| 93_L | 100_I | 1.063 | 0.72 |
| 50_A | 100_I | 1.056 | 0.71 |
| 27_R | 213_L | 1.055 | 0.71 |
| 154_F | 190_G | 1.052 | 0.71 |
| 248_G | 251_P | 1.051 | 0.70 |
| 8_I | 12_S | 1.045 | 0.70 |
| 97_N | 100_I | 1.045 | 0.70 |
| 127_G | 131_F | 1.044 | 0.70 |
| 32_K | 58_G | 1.035 | 0.69 |
| 34_L | 144_L | 1.034 | 0.69 |
| 135_Y | 176_P | 1.029 | 0.68 |
| 140_V | 144_L | 1.026 | 0.68 |
| 38_T | 46_A | 1.025 | 0.68 |
| 358_N | 362_G | 1.001 | 0.65 |
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 | |
| 1zud1 | 2 | 0.634 | 100 | 0.512 | Contact Map |
| 1jw9B | 1 | 0.634 | 100 | 0.513 | Contact Map |
| 3h8vA | 2 | 0.565 | 100 | 0.531 | Contact Map |
| 4gslA | 2 | 0.7454 | 100 | 0.533 | Contact Map |
| 3ruiA | 1 | 0.7639 | 100 | 0.534 | Contact Map |
| 3h5nA | 4 | 0.6472 | 100 | 0.559 | Contact Map |
| 1tt5B | 2 | 0.8355 | 100 | 0.559 | Contact Map |
| 2nvuB | 1 | 0.8806 | 100 | 0.563 | Contact Map |
| 4d79A | 4 | 0 | 100 | 0.588 | Contact Map |
| 4v1tA | 2 | 0.8966 | 100 | 0.618 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)