| actino |
| ID: | 1512139109 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (113) | ||
| Sequences: | 680 (578.5) | ||
| Seq/Len: | 6.018 | ||
| Nf(neff/√len): | 54.4 |
Jackhmmer Results: (2016_04)
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: 6.018).
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 |
| 55_H | 59_P | 2.757 | 1.00 |
| 25_A | 28_Q | 2.339 | 1.00 |
| 17_V | 21_D | 2.013 | 1.00 |
| 21_D | 25_A | 1.988 | 1.00 |
| 56_E | 59_P | 1.960 | 1.00 |
| 54_G | 58_D | 1.949 | 1.00 |
| 111_G | 115_G | 1.902 | 1.00 |
| 106_L | 109_A | 1.846 | 1.00 |
| 86_Q | 90_R | 1.683 | 1.00 |
| 82_L | 86_Q | 1.667 | 1.00 |
| 41_R | 69_C | 1.653 | 1.00 |
| 17_V | 20_R | 1.643 | 1.00 |
| 113_Q | 116_H | 1.636 | 1.00 |
| 54_G | 59_P | 1.564 | 0.99 |
| 62_W | 65_R | 1.559 | 0.99 |
| 115_G | 118_N | 1.548 | 0.99 |
| 111_G | 114_V | 1.493 | 0.99 |
| 29_D | 35_R | 1.483 | 0.99 |
| 55_H | 58_D | 1.446 | 0.99 |
| 17_V | 24_S | 1.445 | 0.99 |
| 110_K | 114_V | 1.418 | 0.98 |
| 39_R | 81_L | 1.363 | 0.98 |
| 93_G | 96_P | 1.321 | 0.97 |
| 61_A | 65_R | 1.311 | 0.97 |
| 110_K | 113_Q | 1.296 | 0.97 |
| 46_R | 49_E | 1.281 | 0.96 |
| 44_G | 85_A | 1.279 | 0.96 |
| 42_F | 45_R | 1.277 | 0.96 |
| 87_D | 91_L | 1.273 | 0.96 |
| 73_A | 76_A | 1.269 | 0.96 |
| 53_A | 57_E | 1.225 | 0.95 |
| 18_G | 66_L | 1.224 | 0.95 |
| 113_Q | 118_N | 1.221 | 0.95 |
| 22_V | 27_V | 1.219 | 0.95 |
| 21_D | 28_Q | 1.183 | 0.94 |
| 104_V | 114_V | 1.182 | 0.94 |
| 69_C | 77_E | 1.173 | 0.93 |
| 102_T | 114_V | 1.149 | 0.93 |
| 106_L | 115_G | 1.148 | 0.92 |
| 102_T | 106_L | 1.139 | 0.92 |
| 19_A | 31_Y | 1.119 | 0.91 |
| 25_A | 68_A | 1.118 | 0.91 |
| 84_A | 88_V | 1.117 | 0.91 |
| 13_A | 16_G | 1.117 | 0.91 |
| 55_H | 60_E | 1.105 | 0.90 |
| 35_R | 39_R | 1.101 | 0.90 |
| 36_D | 43_S | 1.078 | 0.89 |
| 96_P | 100_G | 1.040 | 0.87 |
| 14_G | 31_Y | 1.035 | 0.86 |
| 11_L | 51_A | 1.033 | 0.86 |
| 104_V | 116_H | 1.018 | 0.85 |
| 37_S | 41_R | 1.016 | 0.85 |
| 23_A | 26_A | 1.008 | 0.84 |
| 19_A | 37_S | 1.004 | 0.84 |
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 | |
| 3wvzA | 2 | 0.6129 | 6 | 0.927 | Contact Map |
| 3mnfA | 1 | 0.5968 | 5.2 | 0.929 | Contact Map |
| 3dfzA | 2 | 0.7339 | 4.4 | 0.932 | Contact Map |
| 4pfbA | 1 | 0.7823 | 4.3 | 0.932 | Contact Map |
| 2ifoA | 1 | 0.3065 | 3.8 | 0.934 | Contact Map |
| 4fbdA | 2 | 0.379 | 3.1 | 0.937 | Contact Map |
| 3ldtA | 1 | 0.6774 | 3 | 0.937 | Contact Map |
| 2efkA | 1 | 0.6048 | 2.6 | 0.939 | Contact Map |
| 4n6tA | 1 | 0.3548 | 2.5 | 0.94 | Contact Map |
| 2yy0A | 4 | 0.4274 | 2.4 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)