| actino |
| ID: | 1512137223 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (124) | ||
| Sequences: | 139 (129.3) | ||
| Seq/Len: | 1.121 | ||
| Nf(neff/√len): | 11.6 |
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: 1.121).
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_E | 59_P | 2.133 | 0.98 |
| 23_A | 27_V | 2.034 | 0.97 |
| 62_W | 65_R | 1.885 | 0.94 |
| 65_R | 69_C | 1.774 | 0.92 |
| 11_L | 52_L | 1.741 | 0.91 |
| 2_E | 5_L | 1.671 | 0.88 |
| 7_I | 75_A | 1.602 | 0.85 |
| 87_D | 91_L | 1.600 | 0.85 |
| 120_Q | 123_S | 1.528 | 0.81 |
| 17_V | 52_L | 1.483 | 0.79 |
| 114_V | 117_S | 1.469 | 0.78 |
| 52_L | 109_A | 1.463 | 0.77 |
| 120_Q | 124_F | 1.430 | 0.75 |
| 111_G | 115_G | 1.361 | 0.70 |
| 58_D | 68_A | 1.334 | 0.67 |
| 21_D | 83_A | 1.326 | 0.67 |
| 6_V | 11_L | 1.325 | 0.67 |
| 93_G | 96_P | 1.317 | 0.66 |
| 103_V | 106_L | 1.316 | 0.66 |
| 93_G | 102_T | 1.303 | 0.65 |
| 96_P | 104_V | 1.294 | 0.64 |
| 117_S | 121_H | 1.285 | 0.63 |
| 114_V | 119_V | 1.285 | 0.63 |
| 14_G | 23_A | 1.284 | 0.63 |
| 106_L | 109_A | 1.283 | 0.63 |
| 34_L | 85_A | 1.259 | 0.61 |
| 17_V | 21_D | 1.251 | 0.60 |
| 49_E | 53_A | 1.238 | 0.59 |
| 18_G | 83_A | 1.238 | 0.59 |
| 21_D | 28_Q | 1.228 | 0.58 |
| 16_G | 79_A | 1.197 | 0.55 |
| 31_Y | 35_R | 1.168 | 0.52 |
| 86_Q | 95_E | 1.164 | 0.52 |
| 94_R | 97_G | 1.146 | 0.50 |
| 83_A | 100_G | 1.142 | 0.50 |
| 113_Q | 118_N | 1.131 | 0.49 |
| 59_P | 68_A | 1.119 | 0.48 |
| 51_A | 54_G | 1.115 | 0.47 |
| 38_V | 76_A | 1.107 | 0.47 |
| 34_L | 38_V | 1.094 | 0.45 |
| 113_Q | 124_F | 1.089 | 0.45 |
| 61_A | 68_A | 1.088 | 0.45 |
| 24_S | 83_A | 1.084 | 0.44 |
| 13_A | 20_R | 1.069 | 0.43 |
| 9_S | 30_A | 1.060 | 0.42 |
| 113_Q | 122_N | 1.052 | 0.41 |
| 4_V | 25_A | 1.052 | 0.41 |
| 33_A | 98_Q | 1.049 | 0.41 |
| 28_Q | 35_R | 1.049 | 0.41 |
| 50_D | 54_G | 1.047 | 0.41 |
| 14_G | 22_V | 1.045 | 0.41 |
| 16_G | 60_E | 1.044 | 0.41 |
| 101_E | 109_A | 1.040 | 0.40 |
| 70_L | 99_A | 1.032 | 0.40 |
| 41_R | 106_L | 1.030 | 0.39 |
| 82_L | 86_Q | 1.029 | 0.39 |
| 80_A | 109_A | 1.028 | 0.39 |
| 21_D | 27_V | 1.015 | 0.38 |
| 104_V | 111_G | 1.015 | 0.38 |
| 16_G | 74_G | 1.015 | 0.38 |
| 102_T | 113_Q | 1.010 | 0.38 |
| 7_I | 85_A | 1.007 | 0.37 |
| 100_G | 105_D | 1.000 | 0.37 |
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 | |
| 4fgvA | 1 | 0.7097 | 8.6 | 0.939 | Contact Map |
| 4jkvA | 2 | 0.7903 | 8.5 | 0.939 | Contact Map |
| 2c1wA | 3 | 0.3548 | 7.5 | 0.94 | Contact Map |
| 1xg8A | 1 | 0.7419 | 5.7 | 0.943 | Contact Map |
| 3m0mA | 4 | 0.879 | 5.5 | 0.944 | Contact Map |
| 2xd3A | 1 | 0.2984 | 5.3 | 0.944 | Contact Map |
| 3kxqA | 2 | 0.5726 | 5 | 0.945 | Contact Map |
| 4nvtA | 4 | 0.621 | 4.9 | 0.945 | Contact Map |
| 3rh3A | 2 | 0.7742 | 4.2 | 0.947 | Contact Map |
| 2ww9C | 1 | 0.1613 | 3.9 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)