| strepto |
| ID: | 1509090514 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (118) | ||
| Sequences: | 261 (227.1) | ||
| Seq/Len: | 2.212 | ||
| Nf(neff/√len): | 20.9 |
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: 2.212).
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 |
| 117_V | 120_H | 3.451 | 1.00 |
| 70_L | 81_D | 2.295 | 1.00 |
| 23_A | 27_E | 1.819 | 0.98 |
| 36_A | 39_A | 1.736 | 0.97 |
| 31_M | 34_R | 1.687 | 0.97 |
| 109_L | 112_A | 1.547 | 0.94 |
| 115_V | 120_H | 1.517 | 0.93 |
| 90_T | 101_E | 1.483 | 0.92 |
| 25_G | 37_Y | 1.454 | 0.91 |
| 114_G | 117_V | 1.371 | 0.87 |
| 31_M | 72_T | 1.368 | 0.87 |
| 36_A | 83_Q | 1.346 | 0.86 |
| 54_T | 81_D | 1.339 | 0.85 |
| 14_T | 77_R | 1.332 | 0.85 |
| 27_E | 31_M | 1.332 | 0.85 |
| 64_G | 103_A | 1.321 | 0.84 |
| 56_L | 74_L | 1.304 | 0.83 |
| 41_R | 45_S | 1.291 | 0.82 |
| 23_A | 31_M | 1.273 | 0.81 |
| 62_A | 70_L | 1.268 | 0.81 |
| 40_L | 56_L | 1.250 | 0.80 |
| 112_A | 118_G | 1.223 | 0.78 |
| 8_D | 26_T | 1.222 | 0.77 |
| 54_T | 60_E | 1.199 | 0.76 |
| 60_E | 91_L | 1.192 | 0.75 |
| 22_A | 96_P | 1.184 | 0.74 |
| 80_R | 95_L | 1.177 | 0.74 |
| 90_T | 94_R | 1.164 | 0.72 |
| 24_G | 38_T | 1.160 | 0.72 |
| 66_N | 109_L | 1.146 | 0.71 |
| 24_G | 35_D | 1.138 | 0.70 |
| 90_T | 102_H | 1.134 | 0.70 |
| 63_P | 72_T | 1.131 | 0.69 |
| 47_D | 73_T | 1.112 | 0.67 |
| 20_G | 37_Y | 1.104 | 0.67 |
| 74_L | 83_Q | 1.095 | 0.66 |
| 45_S | 84_L | 1.094 | 0.66 |
| 82_Q | 88_A | 1.090 | 0.65 |
| 45_S | 85_Q | 1.078 | 0.64 |
| 120_H | 123_Q | 1.073 | 0.63 |
| 19_A | 22_A | 1.068 | 0.63 |
| 117_V | 122_T | 1.067 | 0.63 |
| 83_Q | 99_R | 1.066 | 0.63 |
| 40_L | 47_D | 1.060 | 0.62 |
| 44_L | 49_D | 1.058 | 0.62 |
| 37_Y | 88_A | 1.056 | 0.62 |
| 35_D | 59_N | 1.044 | 0.60 |
| 115_V | 121_N | 1.042 | 0.60 |
| 113_R | 122_T | 1.038 | 0.60 |
| 24_G | 107_I | 1.035 | 0.59 |
| 33_V | 37_Y | 1.035 | 0.59 |
| 33_V | 82_Q | 1.034 | 0.59 |
| 91_L | 118_G | 1.030 | 0.59 |
| 25_G | 113_R | 1.025 | 0.58 |
| 18_I | 51_G | 1.024 | 0.58 |
| 21_A | 110_R | 1.023 | 0.58 |
| 56_L | 69_E | 1.022 | 0.58 |
| 70_L | 80_R | 1.007 | 0.56 |
| 23_A | 30_S | 1.005 | 0.56 |
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 | |
| 3a7mA | 2 | 0.8906 | 14.3 | 0.912 | Contact Map |
| 4pfbA | 1 | 0.7656 | 9.4 | 0.919 | Contact Map |
| 3mnfA | 1 | 0.6328 | 9.3 | 0.919 | Contact Map |
| 3tu3B | 1 | 0.9062 | 9.2 | 0.919 | Contact Map |
| 2c6xA | 4 | 0.9688 | 6.3 | 0.925 | Contact Map |
| 2hkuA | 2 | 0.8828 | 6 | 0.926 | Contact Map |
| 2wwwA | 4 | 0.6797 | 5.9 | 0.926 | Contact Map |
| 1a59A | 1 | 0.9453 | 5.1 | 0.928 | Contact Map |
| 4qmkA | 2 | 0.9062 | 4.9 | 0.928 | Contact Map |
| 3nkzA | 4 | 0.7344 | 4.2 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)