| bshA from L acidophilus |
| ID: | 1453511498 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 325 (325) | ||
| Sequences: | 1159 (812.7) | ||
| Seq/Len: | 3.566 | ||
| Nf(neff/√len): | 45.1 |
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: 3.566).
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 |
| 109_C | 118_L | 3.788 | 1.00 |
| 240_T | 243_E | 3.333 | 1.00 |
| 142_I | 152_V | 3.202 | 1.00 |
| 75_M | 102_I | 3.146 | 1.00 |
| 33_R | 70_E | 2.806 | 1.00 |
| 218_G | 223_S | 2.574 | 1.00 |
| 148_T | 163_D | 2.460 | 1.00 |
| 71_K | 110_S | 2.457 | 1.00 |
| 299_D | 302_K | 2.319 | 1.00 |
| 155_D | 160_H | 2.264 | 1.00 |
| 116_K | 163_D | 2.260 | 1.00 |
| 68_T | 74_G | 2.233 | 1.00 |
| 115_V | 142_I | 2.226 | 1.00 |
| 110_S | 114_E | 2.226 | 1.00 |
| 181_N | 226_V | 2.218 | 1.00 |
| 75_M | 142_I | 2.190 | 1.00 |
| 105_I | 142_I | 2.118 | 1.00 |
| 259_K | 271_Y | 2.089 | 1.00 |
| 113_S | 117_D | 2.087 | 1.00 |
| 67_A | 106_L | 2.051 | 1.00 |
| 162_Y | 176_P | 2.045 | 1.00 |
| 31_T | 64_Y | 2.000 | 1.00 |
| 279_N | 282_K | 1.997 | 1.00 |
| 82_G | 172_N | 1.993 | 1.00 |
| 249_F | 277_G | 1.958 | 1.00 |
| 181_N | 184_N | 1.935 | 1.00 |
| 249_F | 295_I | 1.902 | 1.00 |
| 112_I | 147_G | 1.868 | 1.00 |
| 51_M | 107_G | 1.850 | 0.99 |
| 81_P | 221_S | 1.838 | 0.99 |
| 36_T | 46_K | 1.788 | 0.99 |
| 3_T | 228_V | 1.772 | 0.99 |
| 85_T | 156_K | 1.764 | 0.99 |
| 238_A | 243_E | 1.753 | 0.99 |
| 145_K | 283_G | 1.740 | 0.99 |
| 253_H | 256_E | 1.735 | 0.99 |
| 284_I | 297_V | 1.728 | 0.99 |
| 49_Y | 70_E | 1.718 | 0.99 |
| 181_N | 185_Y | 1.685 | 0.99 |
| 113_S | 148_T | 1.683 | 0.99 |
| 74_G | 280_L | 1.646 | 0.99 |
| 160_H | 176_P | 1.643 | 0.99 |
| 214_N | 218_G | 1.606 | 0.98 |
| 17_N | 275_S | 1.603 | 0.98 |
| 101_F | 152_V | 1.599 | 0.98 |
| 20_L | 137_S | 1.554 | 0.98 |
| 248_Y | 277_G | 1.543 | 0.98 |
| 80_Y | 155_D | 1.534 | 0.97 |
| 4_S | 78_L | 1.527 | 0.97 |
| 49_Y | 71_K | 1.523 | 0.97 |
| 283_G | 301_N | 1.521 | 0.97 |
| 30_I | 303_E | 1.510 | 0.97 |
| 68_T | 278_T | 1.464 | 0.96 |
| 50_A | 70_E | 1.461 | 0.96 |
| 98_S | 124_I | 1.455 | 0.96 |
| 9_P | 13_Y | 1.448 | 0.96 |
| 150_L | 161_I | 1.444 | 0.96 |
| 294_Q | 320_K | 1.423 | 0.95 |
| 145_K | 281_D | 1.422 | 0.95 |
| 50_A | 305_L | 1.413 | 0.95 |
| 181_N | 222_E | 1.386 | 0.95 |
| 278_T | 285_F | 1.384 | 0.94 |
| 73_L | 111_T | 1.383 | 0.94 |
| 30_I | 311_I | 1.375 | 0.94 |
| 2_C | 16_R | 1.373 | 0.94 |
| 26_Q | 54_I | 1.369 | 0.94 |
| 53_G | 64_Y | 1.357 | 0.94 |
| 45_L | 107_G | 1.346 | 0.93 |
| 157_D | 160_H | 1.345 | 0.93 |
| 49_Y | 110_S | 1.336 | 0.93 |
| 47_K | 107_G | 1.333 | 0.93 |
| 165_P | 175_F | 1.331 | 0.93 |
| 33_R | 304_D | 1.327 | 0.93 |
| 95_N | 123_N | 1.319 | 0.92 |
| 48_H | 108_Q | 1.310 | 0.92 |
| 288_T | 293_K | 1.306 | 0.92 |
| 177_K | 181_N | 1.305 | 0.92 |
| 182_L | 229_A | 1.298 | 0.92 |
| 117_D | 120_S | 1.295 | 0.92 |
| 9_P | 244_N | 1.291 | 0.91 |
| 284_I | 299_D | 1.286 | 0.91 |
| 19_D | 256_E | 1.275 | 0.91 |
| 227_R | 258_Q | 1.262 | 0.90 |
| 293_K | 319_T | 1.257 | 0.90 |
| 14_F | 278_T | 1.238 | 0.89 |
| 303_E | 311_I | 1.224 | 0.88 |
| 105_I | 115_V | 1.218 | 0.88 |
| 97_A | 135_A | 1.217 | 0.88 |
| 33_R | 50_A | 1.216 | 0.88 |
| 167_G | 232_K | 1.202 | 0.87 |
| 92_N | 111_T | 1.201 | 0.87 |
| 87_Y | 154_T | 1.189 | 0.86 |
| 17_N | 256_E | 1.188 | 0.86 |
| 180_F | 183_N | 1.187 | 0.86 |
| 154_T | 159_M | 1.178 | 0.85 |
| 75_M | 105_I | 1.176 | 0.85 |
| 143_A | 149_S | 1.173 | 0.85 |
| 13_Y | 244_N | 1.173 | 0.85 |
| 126_D | 135_A | 1.172 | 0.85 |
| 109_C | 142_I | 1.168 | 0.85 |
| 213_H | 218_G | 1.157 | 0.84 |
| 183_N | 222_E | 1.142 | 0.83 |
| 36_T | 44_S | 1.140 | 0.83 |
| 5_I | 228_V | 1.138 | 0.83 |
| 3_T | 16_R | 1.137 | 0.83 |
| 252_L | 275_S | 1.127 | 0.82 |
| 54_I | 285_F | 1.124 | 0.82 |
| 164_N | 175_F | 1.110 | 0.80 |
| 101_F | 124_I | 1.109 | 0.80 |
| 235_A | 247_T | 1.109 | 0.80 |
| 12_H | 281_D | 1.104 | 0.80 |
| 88_E | 126_D | 1.104 | 0.80 |
| 217_G | 226_V | 1.104 | 0.80 |
| 248_Y | 252_L | 1.104 | 0.80 |
| 198_S | 203_M | 1.089 | 0.79 |
| 253_H | 288_T | 1.081 | 0.78 |
| 98_S | 135_A | 1.078 | 0.78 |
| 155_D | 162_Y | 1.077 | 0.78 |
| 166_V | 179_L | 1.075 | 0.77 |
| 166_V | 182_L | 1.073 | 0.77 |
| 275_S | 288_T | 1.072 | 0.77 |
| 119_L | 152_V | 1.072 | 0.77 |
| 24_F | 273_I | 1.067 | 0.77 |
| 73_L | 112_I | 1.057 | 0.76 |
| 108_Q | 118_L | 1.055 | 0.75 |
| 208_R | 270_E | 1.054 | 0.75 |
| 241_E | 282_K | 1.050 | 0.75 |
| 242_E | 318_K | 1.044 | 0.74 |
| 228_V | 251_I | 1.041 | 0.74 |
| 19_D | 255_V | 1.040 | 0.74 |
| 30_I | 33_R | 1.033 | 0.73 |
| 250_H | 253_H | 1.032 | 0.73 |
| 250_H | 290_Y | 1.030 | 0.73 |
| 245_I | 277_G | 1.028 | 0.73 |
| 235_A | 251_I | 1.027 | 0.73 |
| 117_D | 121_R | 1.024 | 0.72 |
| 173_P | 178_Q | 1.021 | 0.72 |
| 178_Q | 181_N | 1.015 | 0.71 |
| 185_Y | 226_V | 1.007 | 0.71 |
| 96_I | 105_I | 1.005 | 0.70 |
| 101_F | 104_W | 1.004 | 0.70 |
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 | |
| 2oqcA | 2 | 0.9631 | 100 | 0.161 | Contact Map |
| 2bjfA | 1 | 0.9969 | 100 | 0.173 | Contact Map |
| 2quyA | 8 | 0.9969 | 100 | 0.187 | Contact Map |
| 2hf0A | 2 | 0.96 | 100 | 0.196 | Contact Map |
| 3hbcA | 1 | 0.8892 | 100 | 0.273 | Contact Map |
| 2x1dA | 4 | 0.7446 | 100 | 0.543 | Contact Map |
| 3gvzA | 2 | 0.7415 | 100 | 0.578 | Contact Map |
| 2cx7A | 2 | 0.3785 | 3 | 0.976 | Contact Map |
| 4hwxA | 1 | 0.12 | 2.6 | 0.977 | Contact Map |
| 4y04A | 1 | 0 | 2.4 | 0.977 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)