| ProX or BamE |
| ID: | 1457619884 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (102) | ||
| Sequences: | 199 (96.8) | ||
| Seq/Len: | 1.951 | ||
| Nf(neff/√len): | 9.6 |
HHblits Results: (2015_06)
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: 1.951).
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 |
| 44_T | 51_K | 3.851 | 1.00 |
| 90_A | 101_M | 3.144 | 1.00 |
| 26_P | 40_L | 1.873 | 0.98 |
| 48_I | 52_E | 1.812 | 0.98 |
| 86_K | 108_S | 1.690 | 0.96 |
| 53_P | 96_N | 1.637 | 0.95 |
| 60_D | 88_F | 1.588 | 0.94 |
| 76_N | 79_S | 1.523 | 0.92 |
| 53_P | 111_A | 1.461 | 0.89 |
| 50_A | 81_G | 1.455 | 0.89 |
| 29_L | 33_I | 1.406 | 0.87 |
| 79_S | 102_P | 1.398 | 0.86 |
| 22_Y | 25_S | 1.394 | 0.86 |
| 26_P | 77_G | 1.380 | 0.85 |
| 34_A | 64_L | 1.366 | 0.84 |
| 53_P | 89_S | 1.336 | 0.83 |
| 15_S | 51_K | 1.306 | 0.81 |
| 13_L | 69_S | 1.302 | 0.80 |
| 86_K | 96_N | 1.301 | 0.80 |
| 53_P | 101_M | 1.300 | 0.80 |
| 9_V | 58_A | 1.240 | 0.76 |
| 22_Y | 69_S | 1.239 | 0.75 |
| 7_F | 39_E | 1.226 | 0.74 |
| 53_P | 90_A | 1.194 | 0.72 |
| 78_K | 85_R | 1.184 | 0.71 |
| 16_I | 80_D | 1.182 | 0.70 |
| 51_K | 116_L | 1.173 | 0.70 |
| 15_S | 44_T | 1.172 | 0.70 |
| 23_I | 82_T | 1.169 | 0.69 |
| 35_T | 55_Q | 1.163 | 0.69 |
| 41_F | 70_A | 1.153 | 0.68 |
| 20_K | 62_L | 1.146 | 0.67 |
| 67_S | 89_S | 1.141 | 0.67 |
| 8_D | 69_S | 1.141 | 0.67 |
| 79_S | 103_R | 1.112 | 0.64 |
| 46_A | 79_S | 1.094 | 0.62 |
| 79_S | 105_D | 1.090 | 0.61 |
| 53_P | 78_K | 1.071 | 0.59 |
| 25_S | 100_P | 1.064 | 0.59 |
| 41_F | 73_R | 1.064 | 0.59 |
| 65_L | 74_M | 1.062 | 0.58 |
| 38_T | 45_P | 1.060 | 0.58 |
| 34_A | 39_E | 1.030 | 0.55 |
| 24_R | 101_M | 1.029 | 0.55 |
| 31_K | 77_G | 1.026 | 0.54 |
| 55_Q | 58_A | 1.012 | 0.53 |
| 58_A | 85_R | 1.011 | 0.53 |
| 26_P | 38_T | 1.001 | 0.52 |
| 45_P | 49_S | 1.000 | 0.52 |
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 | |
| 2pxgA | 1 | 0.6983 | 99.4 | 0.649 | Contact Map |
| 2km7A | 1 | 0.7069 | 99.2 | 0.678 | Contact Map |
| 2yh9A | 3 | 0.4914 | 98.4 | 0.761 | Contact Map |
| 4dm5A | 4 | 0.6293 | 98.2 | 0.777 | Contact Map |
| 3tlkA | 3 | 0.6379 | 30.1 | 0.922 | Contact Map |
| 4kysA | 2 | 0.6552 | 20.2 | 0.928 | Contact Map |
| 3zbiC | 14 | 0.2414 | 15.2 | 0.932 | Contact Map |
| 4q8wA | 1 | 0 | 13.7 | 0.933 | Contact Map |
| 2qgmA | 1 | 0.6897 | 12.8 | 0.934 | Contact Map |
| 3d4eA | 1 | 0.8103 | 12.4 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)