| spo0A |
| ID: | 1492190745 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 211 (176) | ||
| Sequences: | 784 (551.2) | ||
| Seq/Len: | 4.455 | ||
| Nf(neff/√len): | 41.5 |
HHblits Results: (2016_02)
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: 4.455).
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 |
| 51_A | 79_R | 3.138 | 1.00 |
| 23_L | 39_A | 2.317 | 1.00 |
| 58_V | 85_V | 2.279 | 1.00 |
| 167_A | 170_A | 2.130 | 1.00 |
| 128_R | 131_G | 2.115 | 1.00 |
| 149_K | 156_G | 2.094 | 1.00 |
| 67_L | 71_G | 2.082 | 1.00 |
| 60_A | 72_L | 2.044 | 1.00 |
| 18_D | 61_D | 1.962 | 1.00 |
| 47_L | 72_L | 1.950 | 1.00 |
| 14_L | 50_L | 1.857 | 1.00 |
| 32_A | 115_L | 1.857 | 1.00 |
| 38_V | 53_D | 1.802 | 1.00 |
| 137_A | 142_P | 1.701 | 0.99 |
| 166_H | 170_A | 1.677 | 0.99 |
| 64_M | 69_G | 1.664 | 0.99 |
| 61_D | 90_A | 1.653 | 0.99 |
| 50_L | 76_T | 1.645 | 0.99 |
| 61_D | 111_K | 1.623 | 0.99 |
| 48_A | 52_T | 1.620 | 0.99 |
| 42_D | 66_H | 1.616 | 0.99 |
| 18_D | 64_M | 1.604 | 0.99 |
| 64_M | 68_D | 1.575 | 0.99 |
| 69_G | 111_K | 1.563 | 0.99 |
| 38_V | 55_F | 1.555 | 0.99 |
| 27_T | 39_A | 1.528 | 0.98 |
| 38_V | 49_L | 1.523 | 0.98 |
| 18_D | 69_G | 1.506 | 0.98 |
| 43_P | 112_P | 1.454 | 0.98 |
| 27_T | 31_R | 1.446 | 0.97 |
| 152_E | 156_G | 1.416 | 0.97 |
| 43_P | 67_L | 1.415 | 0.97 |
| 15_V | 27_T | 1.412 | 0.97 |
| 138_L | 141_E | 1.405 | 0.97 |
| 113_F | 117_T | 1.402 | 0.97 |
| 16_I | 58_V | 1.390 | 0.96 |
| 57_L | 126_L | 1.388 | 0.96 |
| 17_E | 111_K | 1.353 | 0.96 |
| 43_P | 69_G | 1.325 | 0.95 |
| 152_E | 155_E | 1.315 | 0.95 |
| 143_A | 147_C | 1.300 | 0.94 |
| 60_A | 73_L | 1.293 | 0.94 |
| 50_L | 72_L | 1.291 | 0.94 |
| 70_V | 100_A | 1.288 | 0.94 |
| 74_E | 99_E | 1.288 | 0.94 |
| 15_V | 26_L | 1.280 | 0.94 |
| 12_Q | 36_A | 1.270 | 0.93 |
| 40_T | 49_L | 1.269 | 0.93 |
| 16_I | 46_A | 1.236 | 0.92 |
| 64_M | 67_L | 1.231 | 0.92 |
| 18_D | 65_P | 1.230 | 0.92 |
| 58_V | 83_T | 1.220 | 0.91 |
| 18_D | 111_K | 1.214 | 0.91 |
| 68_D | 104_G | 1.202 | 0.91 |
| 18_D | 90_A | 1.177 | 0.89 |
| 121_R | 125_I | 1.176 | 0.89 |
| 134_E | 137_A | 1.169 | 0.89 |
| 128_R | 145_F | 1.144 | 0.88 |
| 45_Q | 48_A | 1.135 | 0.87 |
| 149_K | 154_G | 1.134 | 0.87 |
| 101_R | 123_R | 1.128 | 0.87 |
| 44_R | 48_A | 1.107 | 0.85 |
| 25_M | 91_Y | 1.100 | 0.85 |
| 65_P | 69_G | 1.094 | 0.84 |
| 148_T | 162_E | 1.094 | 0.84 |
| 57_L | 122_V | 1.092 | 0.84 |
| 67_L | 75_K | 1.085 | 0.84 |
| 64_M | 90_A | 1.078 | 0.83 |
| 61_D | 64_M | 1.070 | 0.82 |
| 64_M | 111_K | 1.060 | 0.82 |
| 61_D | 89_S | 1.059 | 0.82 |
| 43_P | 64_M | 1.056 | 0.81 |
| 73_L | 87_L | 1.047 | 0.80 |
| 58_V | 76_T | 1.038 | 0.80 |
| 68_D | 99_E | 1.038 | 0.80 |
| 166_H | 169_C | 1.037 | 0.80 |
| 176_C | 179_C | 1.037 | 0.80 |
| 161_K | 164_D | 1.034 | 0.79 |
| 63_V | 91_Y | 1.026 | 0.79 |
| 148_T | 155_E | 1.023 | 0.78 |
| 74_E | 95_G | 1.022 | 0.78 |
| 32_A | 79_R | 1.018 | 0.78 |
| 20_R | 93_T | 1.015 | 0.78 |
| 64_M | 72_L | 1.013 | 0.77 |
| 95_G | 98_R | 1.007 | 0.77 |
| 89_S | 111_K | 1.002 | 0.76 |
| 50_L | 58_V | 1.001 | 0.76 |
| 100_A | 105_A | 1.001 | 0.76 |
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 | |
| 1s8nA | 1 | 0.872 | 100 | 0.513 | Contact Map |
| 3eq2A | 2 | 0.9194 | 99.9 | 0.525 | Contact Map |
| 4g97A | 1 | 0.6493 | 99.9 | 0.527 | Contact Map |
| 3breA | 2 | 0.981 | 99.9 | 0.528 | Contact Map |
| 3n0rA | 1 | 0.6114 | 99.9 | 0.532 | Contact Map |
| 1w25A | 2 | 0.9526 | 99.9 | 0.534 | Contact Map |
| 3dzdA | 2 | 0.8863 | 99.9 | 0.554 | Contact Map |
| 2ayxA | 1 | 0.6398 | 99.9 | 0.555 | Contact Map |
| 1qo0D | 2 | 0.8626 | 99.9 | 0.562 | Contact Map |
| 3rqiA | 1 | 0.7915 | 99.9 | 0.565 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)