| Q8U3S5_PYRFU |
| ID: | 1417479940 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 242 (201) | ||
| Sequences: | 3491 (2753.2) | ||
| Seq/Len: | 17.368 | ||
| Nf(neff/√len): | 194.2 |
Jackhmmer Results: (2014_04_16)
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: 17.368).
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 |
| 15_K | 84_R | 4.223 | 1.00 |
| 67_I | 74_W | 3.408 | 1.00 |
| 22_E | 64_E | 3.163 | 1.00 |
| 21_I | 67_I | 2.991 | 1.00 |
| 120_E | 124_V | 2.856 | 1.00 |
| 41_I | 79_K | 2.786 | 1.00 |
| 139_I | 142_A | 2.720 | 1.00 |
| 49_I | 77_L | 2.484 | 1.00 |
| 54_M | 85_A | 2.468 | 1.00 |
| 20_F | 64_E | 2.389 | 1.00 |
| 130_A | 144_I | 2.329 | 1.00 |
| 149_F | 152_P | 2.262 | 1.00 |
| 17_E | 20_F | 2.247 | 1.00 |
| 188_D | 192_G | 2.243 | 1.00 |
| 36_E | 108_G | 2.237 | 1.00 |
| 57_A | 66_L | 2.170 | 1.00 |
| 56_L | 87_S | 2.135 | 1.00 |
| 16_V | 87_S | 1.983 | 1.00 |
| 154_G | 157_E | 1.954 | 1.00 |
| 37_L | 79_K | 1.934 | 1.00 |
| 54_M | 67_I | 1.873 | 1.00 |
| 49_I | 86_P | 1.869 | 1.00 |
| 149_F | 153_G | 1.845 | 1.00 |
| 16_V | 56_L | 1.819 | 1.00 |
| 38_E | 42_E | 1.817 | 1.00 |
| 77_L | 80_L | 1.808 | 1.00 |
| 22_E | 66_L | 1.790 | 1.00 |
| 38_E | 79_K | 1.755 | 1.00 |
| 121_G | 125_I | 1.752 | 1.00 |
| 153_G | 157_E | 1.693 | 1.00 |
| 194_I | 202_A | 1.673 | 1.00 |
| 74_W | 78_Q | 1.662 | 1.00 |
| 21_I | 56_L | 1.661 | 1.00 |
| 37_L | 41_I | 1.642 | 1.00 |
| 77_L | 82_A | 1.639 | 1.00 |
| 54_M | 87_S | 1.635 | 1.00 |
| 189_M | 199_I | 1.625 | 1.00 |
| 92_Y | 99_V | 1.584 | 1.00 |
| 18_Y | 74_W | 1.571 | 1.00 |
| 153_G | 156_E | 1.548 | 1.00 |
| 71_H | 75_A | 1.489 | 1.00 |
| 34_Q | 79_K | 1.485 | 1.00 |
| 50_F | 55_L | 1.447 | 1.00 |
| 57_A | 94_D | 1.412 | 1.00 |
| 186_K | 190_E | 1.371 | 0.99 |
| 17_E | 84_R | 1.362 | 0.99 |
| 182_K | 186_K | 1.360 | 0.99 |
| 59_I | 66_L | 1.347 | 0.99 |
| 28_P | 100_Y | 1.339 | 0.99 |
| 181_L | 184_D | 1.316 | 0.99 |
| 34_Q | 38_E | 1.309 | 0.99 |
| 146_E | 167_E | 1.308 | 0.99 |
| 132_E | 135_E | 1.308 | 0.99 |
| 169_D | 172_K | 1.287 | 0.99 |
| 149_F | 157_E | 1.273 | 0.99 |
| 123_E | 133_K | 1.270 | 0.99 |
| 140_A | 168_M | 1.267 | 0.99 |
| 42_E | 45_T | 1.262 | 0.99 |
| 176_L | 185_A | 1.257 | 0.99 |
| 44_V | 49_I | 1.236 | 0.98 |
| 69_D | 103_Y | 1.231 | 0.98 |
| 200_R | 203_P | 1.224 | 0.98 |
| 24_D | 96_G | 1.224 | 0.98 |
| 59_I | 64_E | 1.219 | 0.98 |
| 131_E | 135_E | 1.208 | 0.98 |
| 58_K | 91_D | 1.206 | 0.98 |
| 197_V | 200_R | 1.194 | 0.98 |
| 68_V | 92_Y | 1.188 | 0.98 |
| 190_E | 195_D | 1.187 | 0.98 |
| 178_Y | 181_L | 1.185 | 0.98 |
| 149_F | 156_E | 1.179 | 0.98 |
| 38_E | 41_I | 1.176 | 0.98 |
| 22_E | 59_I | 1.175 | 0.98 |
| 33_V | 36_E | 1.160 | 0.97 |
| 141_F | 144_I | 1.156 | 0.97 |
| 148_S | 152_P | 1.137 | 0.97 |
| 152_P | 156_E | 1.123 | 0.97 |
| 169_D | 173_E | 1.117 | 0.96 |
| 167_E | 171_A | 1.116 | 0.96 |
| 169_D | 196_Y | 1.115 | 0.96 |
| 103_Y | 107_K | 1.114 | 0.96 |
| 70_G | 73_R | 1.112 | 0.96 |
| 98_K | 136_K | 1.105 | 0.96 |
| 168_M | 173_E | 1.096 | 0.96 |
| 20_F | 63_D | 1.093 | 0.96 |
| 57_A | 96_G | 1.093 | 0.96 |
| 49_I | 80_L | 1.092 | 0.96 |
| 151_I | 157_E | 1.088 | 0.96 |
| 41_I | 80_L | 1.078 | 0.95 |
| 32_L | 75_A | 1.066 | 0.95 |
| 194_I | 198_F | 1.061 | 0.95 |
| 190_E | 193_E | 1.056 | 0.95 |
| 190_E | 194_I | 1.053 | 0.95 |
| 14_K | 89_I | 1.043 | 0.94 |
| 117_L | 158_Q | 1.041 | 0.94 |
| 24_D | 100_Y | 1.036 | 0.94 |
| 192_G | 195_D | 1.033 | 0.94 |
| 30_E | 117_L | 1.032 | 0.94 |
| 23_L | 74_W | 1.030 | 0.94 |
| 58_K | 63_D | 1.029 | 0.94 |
| 46_G | 135_E | 1.028 | 0.94 |
| 49_I | 54_M | 1.026 | 0.94 |
| 32_L | 71_H | 1.019 | 0.93 |
| 152_P | 157_E | 1.018 | 0.93 |
| 140_A | 146_E | 1.016 | 0.93 |
| 27_K | 71_H | 1.007 | 0.93 |
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 | |
| 1vk1A | 1 | 0.8512 | 100 | 0.366 | Contact Map |
| 1vz0A | 8 | 0.781 | 99.9 | 0.416 | Contact Map |
| 1yzsA | 1 | 0.4298 | 99.7 | 0.587 | Contact Map |
| 1xw3A | 1 | 0.4298 | 99.7 | 0.591 | Contact Map |
| 1r71A | 4 | 0.4711 | 99 | 0.723 | Contact Map |
| 2hwjA | 6 | 0.7438 | 97.4 | 0.823 | Contact Map |
| 3mkyB | 2 | 0.4421 | 94.9 | 0.861 | Contact Map |
| 1t77A | 4 | 0.2562 | 5.6 | 0.947 | Contact Map |
| 1xg8A | 1 | 0.2769 | 3.2 | 0.953 | Contact Map |
| 1x4pA | 1 | 0.2686 | 2.2 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)