| LarE |
| ID: | 1446058267 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 276 (250) | ||
| Sequences: | 839 (652.2) | ||
| Seq/Len: | 3.356 | ||
| Nf(neff/√len): | 41.2 |
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: 3.356).
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 |
| 98_Y | 141_E | 3.866 | 1.00 |
| 51_V | 76_V | 3.758 | 1.00 |
| 162_A | 169_N | 3.716 | 1.00 |
| 35_L | 74_A | 3.504 | 1.00 |
| 21_V | 121_L | 3.358 | 1.00 |
| 36_K | 40_D | 2.947 | 1.00 |
| 199_A | 213_V | 2.603 | 1.00 |
| 145_R | 150_E | 2.495 | 1.00 |
| 259_R | 265_D | 2.465 | 1.00 |
| 131_D | 264_N | 2.314 | 1.00 |
| 195_Q | 215_F | 2.289 | 1.00 |
| 182_F | 196_V | 2.245 | 1.00 |
| 186_T | 192_N | 2.146 | 1.00 |
| 61_E | 172_K | 2.094 | 1.00 |
| 56_L | 89_I | 2.086 | 1.00 |
| 37_M | 41_V | 2.015 | 1.00 |
| 95_D | 137_K | 1.974 | 1.00 |
| 242_Q | 245_S | 1.875 | 0.99 |
| 34_V | 158_V | 1.873 | 0.99 |
| 59_D | 197_M | 1.830 | 0.99 |
| 122_D | 146_S | 1.802 | 0.99 |
| 35_L | 47_V | 1.786 | 0.99 |
| 56_L | 179_S | 1.751 | 0.99 |
| 33_L | 162_A | 1.750 | 0.99 |
| 122_D | 139_R | 1.728 | 0.99 |
| 47_V | 74_A | 1.682 | 0.99 |
| 105_Y | 142_A | 1.673 | 0.99 |
| 95_D | 99_Y | 1.672 | 0.99 |
| 60_E | 201_K | 1.667 | 0.98 |
| 71_E | 168_T | 1.653 | 0.98 |
| 228_R | 231_D | 1.636 | 0.98 |
| 163_Q | 170_W | 1.591 | 0.98 |
| 202_Y | 242_Q | 1.582 | 0.98 |
| 33_L | 158_V | 1.571 | 0.98 |
| 153_F | 161_L | 1.569 | 0.98 |
| 216_H | 219_I | 1.563 | 0.97 |
| 129_E | 149_Q | 1.555 | 0.97 |
| 64_K | 172_K | 1.548 | 0.97 |
| 216_H | 221_R | 1.523 | 0.97 |
| 82_D | 85_S | 1.493 | 0.96 |
| 232_F | 253_L | 1.492 | 0.96 |
| 124_M | 136_L | 1.486 | 0.96 |
| 77_Q | 115_N | 1.475 | 0.96 |
| 216_H | 250_Y | 1.460 | 0.96 |
| 195_Q | 246_L | 1.452 | 0.96 |
| 56_L | 83_Y | 1.433 | 0.95 |
| 240_N | 256_G | 1.429 | 0.95 |
| 224_L | 232_F | 1.427 | 0.95 |
| 36_K | 165_L | 1.426 | 0.95 |
| 156_T | 160_A | 1.406 | 0.94 |
| 194_A | 198_A | 1.393 | 0.94 |
| 60_E | 204_R | 1.382 | 0.94 |
| 39_L | 72_L | 1.370 | 0.93 |
| 22_T | 108_L | 1.369 | 0.93 |
| 244_Q | 256_G | 1.368 | 0.93 |
| 221_R | 250_Y | 1.368 | 0.93 |
| 243_L | 246_L | 1.359 | 0.93 |
| 33_L | 165_L | 1.348 | 0.93 |
| 184_Y | 264_N | 1.340 | 0.92 |
| 111_I | 115_N | 1.339 | 0.92 |
| 204_R | 211_V | 1.331 | 0.92 |
| 23_V | 121_L | 1.326 | 0.92 |
| 102_K | 142_A | 1.293 | 0.91 |
| 52_A | 104_F | 1.292 | 0.90 |
| 126_K | 152_D | 1.282 | 0.90 |
| 209_P | 228_R | 1.265 | 0.89 |
| 34_V | 105_Y | 1.258 | 0.89 |
| 213_V | 220_A | 1.257 | 0.89 |
| 49_A | 74_A | 1.255 | 0.89 |
| 52_A | 81_L | 1.255 | 0.89 |
| 53_N | 78_G | 1.247 | 0.88 |
| 97_W | 100_A | 1.241 | 0.88 |
| 219_I | 252_T | 1.237 | 0.88 |
| 171_N | 209_P | 1.210 | 0.86 |
| 90_K | 187_T | 1.210 | 0.86 |
| 32_T | 68_L | 1.209 | 0.86 |
| 33_L | 148_L | 1.196 | 0.85 |
| 48_T | 115_N | 1.195 | 0.85 |
| 184_Y | 260_S | 1.184 | 0.85 |
| 93_T | 99_Y | 1.182 | 0.84 |
| 68_L | 72_L | 1.181 | 0.84 |
| 203_L | 208_F | 1.180 | 0.84 |
| 126_K | 129_E | 1.176 | 0.84 |
| 188_L | 193_I | 1.173 | 0.84 |
| 91_N | 187_T | 1.164 | 0.83 |
| 100_A | 177_S | 1.155 | 0.82 |
| 124_M | 139_R | 1.146 | 0.82 |
| 69_A | 72_L | 1.140 | 0.81 |
| 229_I | 233_L | 1.140 | 0.81 |
| 39_L | 74_A | 1.137 | 0.81 |
| 148_L | 153_F | 1.137 | 0.81 |
| 97_W | 177_S | 1.131 | 0.81 |
| 83_Y | 104_F | 1.119 | 0.80 |
| 48_T | 77_Q | 1.113 | 0.79 |
| 179_S | 182_F | 1.110 | 0.79 |
| 106_S | 142_A | 1.108 | 0.79 |
| 126_K | 149_Q | 1.104 | 0.78 |
| 22_T | 50_V | 1.103 | 0.78 |
| 75_N | 115_N | 1.084 | 0.77 |
| 105_Y | 139_R | 1.082 | 0.76 |
| 62_F | 78_G | 1.081 | 0.76 |
| 176_C | 210_T | 1.081 | 0.76 |
| 126_K | 154_F | 1.080 | 0.76 |
| 151_A | 157_D | 1.078 | 0.76 |
| 210_T | 258_F | 1.074 | 0.76 |
| 202_Y | 243_L | 1.073 | 0.76 |
| 54_S | 83_Y | 1.072 | 0.75 |
| 96_S | 177_S | 1.065 | 0.75 |
| 83_Y | 180_S | 1.061 | 0.74 |
| 22_T | 111_I | 1.056 | 0.74 |
| 192_N | 195_Q | 1.048 | 0.73 |
| 189_T | 192_N | 1.045 | 0.73 |
| 53_N | 59_D | 1.041 | 0.72 |
| 182_F | 215_F | 1.040 | 0.72 |
| 86_D | 103_M | 1.039 | 0.72 |
| 22_T | 117_S | 1.038 | 0.72 |
| 84_L | 90_K | 1.035 | 0.72 |
| 89_I | 188_L | 1.032 | 0.71 |
| 67_S | 71_E | 1.028 | 0.71 |
| 89_I | 139_R | 1.025 | 0.71 |
| 139_R | 146_S | 1.024 | 0.71 |
| 215_F | 248_F | 1.019 | 0.70 |
| 63_D | 66_M | 1.012 | 0.69 |
| 29_I | 162_A | 1.010 | 0.69 |
| 87_D | 91_N | 1.010 | 0.69 |
| 96_S | 100_A | 1.010 | 0.69 |
| 225_P | 258_F | 1.006 | 0.69 |
| 107_R | 110_D | 1.002 | 0.68 |
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 | |
| 3uowA | 2 | 0.913 | 100 | 0.596 | Contact Map |
| 3tqiA | 4 | 0.8551 | 100 | 0.615 | Contact Map |
| 2dplA | 2 | 0.8659 | 100 | 0.632 | Contact Map |
| 1gpmA | 4 | 0.8949 | 100 | 0.638 | Contact Map |
| 2ywbA | 4 | 0.8913 | 100 | 0.644 | Contact Map |
| 2c5sA | 1 | 0.7428 | 100 | 0.68 | Contact Map |
| 2e18A | 2 | 0.8623 | 100 | 0.684 | Contact Map |
| 4kr6A | 2 | 0.7862 | 100 | 0.687 | Contact Map |
| 2vxoA | 2 | 0.9275 | 100 | 0.698 | Contact Map |
| 1wy5A | 2 | 0.9493 | 100 | 0.712 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)