| ljp |
| ID: | 1487707240 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (97) | ||
| Sequences: | 164 (103.9) | ||
| Seq/Len: | 1.691 | ||
| Nf(neff/√len): | 10.5 |
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: 1.691).
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 |
| 30_D | 53_S | 2.785 | 1.00 |
| 3_C | 7_Q | 1.967 | 0.98 |
| 70_D | 85_Y | 1.838 | 0.97 |
| 50_M | 60_I | 1.773 | 0.96 |
| 4_T | 7_Q | 1.702 | 0.95 |
| 42_P | 50_M | 1.555 | 0.91 |
| 73_L | 87_Y | 1.495 | 0.88 |
| 14_T | 37_T | 1.389 | 0.83 |
| 76_P | 79_G | 1.378 | 0.82 |
| 42_P | 87_Y | 1.357 | 0.81 |
| 16_V | 34_S | 1.346 | 0.80 |
| 22_S | 28_S | 1.329 | 0.79 |
| 43_T | 46_Q | 1.326 | 0.78 |
| 14_T | 38_A | 1.325 | 0.78 |
| 25_S | 43_T | 1.292 | 0.76 |
| 21_E | 62_K | 1.259 | 0.73 |
| 7_Q | 11_A | 1.251 | 0.72 |
| 64_V | 70_D | 1.248 | 0.72 |
| 60_I | 68_P | 1.224 | 0.70 |
| 54_T | 57_N | 1.208 | 0.69 |
| 44_N | 48_K | 1.185 | 0.67 |
| 50_M | 87_Y | 1.173 | 0.65 |
| 33_Y | 57_N | 1.169 | 0.65 |
| 75_V | 80_L | 1.164 | 0.64 |
| 46_Q | 82_L | 1.145 | 0.63 |
| 72_D | 81_V | 1.140 | 0.62 |
| 22_S | 49_L | 1.131 | 0.61 |
| 63_I | 94_K | 1.110 | 0.59 |
| 25_S | 97_S | 1.108 | 0.59 |
| 24_F | 62_K | 1.095 | 0.57 |
| 45_A | 75_V | 1.095 | 0.57 |
| 21_E | 54_T | 1.094 | 0.57 |
| 44_N | 47_Y | 1.091 | 0.57 |
| 43_T | 94_K | 1.087 | 0.57 |
| 2_A | 5_A | 1.085 | 0.56 |
| 31_S | 68_P | 1.083 | 0.56 |
| 18_I | 87_Y | 1.073 | 0.55 |
| 35_M | 84_V | 1.067 | 0.55 |
| 30_D | 96_A | 1.064 | 0.54 |
| 49_L | 79_G | 1.062 | 0.54 |
| 49_L | 66_L | 1.059 | 0.54 |
| 29_K | 61_K | 1.048 | 0.53 |
| 19_L | 39_T | 1.045 | 0.52 |
| 44_N | 54_T | 1.043 | 0.52 |
| 69_P | 83_D | 1.043 | 0.52 |
| 37_T | 84_V | 1.039 | 0.52 |
| 44_N | 62_K | 1.033 | 0.51 |
| 19_L | 33_Y | 1.025 | 0.50 |
| 32_G | 65_A | 1.024 | 0.50 |
| 66_L | 90_G | 1.018 | 0.49 |
| 61_K | 73_L | 1.017 | 0.49 |
| 35_M | 61_K | 1.016 | 0.49 |
| 44_N | 58_T | 1.005 | 0.48 |
| 6_T | 52_A | 1.002 | 0.48 |
| 85_Y | 88_A | 1.001 | 0.48 |
| 5_A | 55_A | 1.001 | 0.48 |
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 | |
| 2aibA | 2 | 1 | 100 | 0.07 | Contact Map |
| 2posA | 4 | 0.9592 | 100 | 0.105 | Contact Map |
| 1up8A | 4 | 0.898 | 5.4 | 0.922 | Contact Map |
| 2dkaA | 2 | 0.4184 | 2.7 | 0.932 | Contact Map |
| 3ga1A | 2 | 0.5102 | 2.7 | 0.932 | Contact Map |
| 2wnkA | 1 | 0.6531 | 2.4 | 0.935 | Contact Map |
| 2ekmA | 3 | 0.4082 | 2 | 0.938 | Contact Map |
| 3ohuA | 6 | 0.551 | 1.8 | 0.939 | Contact Map |
| 2lmkA | 1 | 0.5102 | 1.6 | 0.941 | Contact Map |
| 1wrdA | 1 | 0.5102 | 1.5 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)