| SYNTH ACT low coverage reversed order |
| ID: | 1425308395 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 208 (205) | ||
| Sequences: | 1402 (882.5) | ||
| Seq/Len: | 6.839 | ||
| Nf(neff/√len): | 61.6 |
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: 6.839).
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 |
| 56_D | 113_E | 3.729 | 1.00 |
| 54_I | 113_E | 3.107 | 1.00 |
| 8_I | 68_V | 3.037 | 1.00 |
| 57_S | 60_D | 3.026 | 1.00 |
| 11_R | 14_S | 2.740 | 1.00 |
| 143_A | 149_Q | 2.679 | 1.00 |
| 22_F | 116_D | 2.633 | 1.00 |
| 18_P | 56_D | 2.521 | 1.00 |
| 20_R | 113_E | 2.397 | 1.00 |
| 192_S | 204_V | 2.298 | 1.00 |
| 1_V | 23_G | 2.174 | 1.00 |
| 40_I | 45_M | 2.153 | 1.00 |
| 3_L | 102_R | 2.088 | 1.00 |
| 53_V | 64_A | 1.976 | 1.00 |
| 68_V | 98_V | 1.952 | 1.00 |
| 55_V | 64_A | 1.899 | 1.00 |
| 9_A | 13_E | 1.825 | 1.00 |
| 159_G | 187_H | 1.811 | 1.00 |
| 4_V | 106_I | 1.758 | 1.00 |
| 143_A | 146_V | 1.711 | 1.00 |
| 138_A | 195_L | 1.671 | 1.00 |
| 11_R | 71_A | 1.662 | 1.00 |
| 136_L | 192_S | 1.661 | 1.00 |
| 135_R | 179_D | 1.616 | 1.00 |
| 64_A | 67_V | 1.602 | 1.00 |
| 10_A | 14_S | 1.594 | 1.00 |
| 154_I | 180_V | 1.576 | 1.00 |
| 48_I | 84_S | 1.565 | 1.00 |
| 59_E | 63_R | 1.552 | 0.99 |
| 69_H | 96_T | 1.534 | 0.99 |
| 60_D | 63_R | 1.478 | 0.99 |
| 55_V | 60_D | 1.472 | 0.99 |
| 113_E | 117_R | 1.472 | 0.99 |
| 92_R | 118_V | 1.448 | 0.99 |
| 140_I | 146_V | 1.408 | 0.99 |
| 78_R | 97_T | 1.401 | 0.99 |
| 137_H | 205_D | 1.394 | 0.99 |
| 147_L | 160_N | 1.389 | 0.99 |
| 152_T | 156_E | 1.384 | 0.99 |
| 4_V | 51_F | 1.377 | 0.98 |
| 33_R | 37_R | 1.369 | 0.98 |
| 164_L | 178_I | 1.369 | 0.98 |
| 151_C | 200_T | 1.357 | 0.98 |
| 5_S | 9_A | 1.352 | 0.98 |
| 2_A | 6_Q | 1.339 | 0.98 |
| 35_L | 82_F | 1.337 | 0.98 |
| 74_S | 84_S | 1.324 | 0.98 |
| 166_M | 176_V | 1.319 | 0.98 |
| 56_D | 60_D | 1.318 | 0.98 |
| 62_Y | 69_H | 1.316 | 0.98 |
| 5_S | 21_V | 1.302 | 0.98 |
| 135_R | 177_D | 1.284 | 0.97 |
| 80_K | 97_T | 1.270 | 0.97 |
| 58_E | 70_R | 1.265 | 0.97 |
| 149_Q | 198_C | 1.250 | 0.97 |
| 151_C | 161_I | 1.250 | 0.97 |
| 69_H | 79_F | 1.245 | 0.97 |
| 15_S | 67_V | 1.245 | 0.97 |
| 154_I | 178_I | 1.240 | 0.97 |
| 5_S | 51_F | 1.234 | 0.96 |
| 7_E | 72_W | 1.213 | 0.96 |
| 65_L | 69_H | 1.205 | 0.96 |
| 144_P | 160_N | 1.204 | 0.96 |
| 2_A | 5_S | 1.204 | 0.96 |
| 148_G | 155_G | 1.200 | 0.96 |
| 117_R | 121_E | 1.197 | 0.95 |
| 153_I | 191_I | 1.187 | 0.95 |
| 20_R | 35_L | 1.158 | 0.94 |
| 180_V | 191_I | 1.153 | 0.94 |
| 145_G | 160_N | 1.147 | 0.94 |
| 45_M | 163_N | 1.129 | 0.93 |
| 12_L | 64_A | 1.128 | 0.93 |
| 15_S | 64_A | 1.118 | 0.93 |
| 99_V | 103_G | 1.115 | 0.93 |
| 80_K | 93_S | 1.108 | 0.92 |
| 133_L | 162_V | 1.106 | 0.92 |
| 4_V | 72_W | 1.105 | 0.92 |
| 145_G | 151_C | 1.102 | 0.92 |
| 184_D | 187_H | 1.086 | 0.91 |
| 85_T | 90_N | 1.077 | 0.91 |
| 184_D | 190_N | 1.071 | 0.91 |
| 50_A | 106_I | 1.067 | 0.90 |
| 62_Y | 66_G | 1.063 | 0.90 |
| 143_A | 200_T | 1.062 | 0.90 |
| 154_I | 161_I | 1.059 | 0.90 |
| 19_A | 64_A | 1.058 | 0.90 |
| 40_I | 78_R | 1.049 | 0.89 |
| 157_A | 194_A | 1.044 | 0.89 |
| 201_V | 204_V | 1.037 | 0.89 |
| 142_N | 160_N | 1.036 | 0.89 |
| 116_D | 120_E | 1.035 | 0.89 |
| 62_Y | 65_L | 1.030 | 0.88 |
| 66_G | 69_H | 1.024 | 0.88 |
| 49_Y | 106_I | 1.011 | 0.87 |
| 13_E | 19_A | 1.011 | 0.87 |
| 8_I | 108_M | 1.004 | 0.86 |
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 | 0.6394 | 100 | 0.428 | Contact Map |
| 3l9dA | 2 | 0.8029 | 100 | 0.524 | Contact Map |
| 2be3A | 2 | 0.8125 | 100 | 0.549 | Contact Map |
| 1y7pA | 3 | 0.375 | 99.1 | 0.856 | Contact Map |
| 2ko1A | 2 | 0.3798 | 99.1 | 0.859 | Contact Map |
| 2lvwA | 2 | 0.399 | 98.8 | 0.873 | Contact Map |
| 2pc6A | 4 | 0.3702 | 98.8 | 0.875 | Contact Map |
| 2fgcA | 1 | 0.3606 | 98.7 | 0.877 | Contact Map |
| 2f1fA | 2 | 0.3654 | 98.7 | 0.878 | Contact Map |
| 1zpvA | 3 | 0.375 | 98.5 | 0.885 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)