| PV2B-2 |
| ID: | 1463095512 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 97 (97) | ||
| Sequences: | 199 (124.9) | ||
| Seq/Len: | 2.052 | ||
| Nf(neff/√len): | 12.7 |
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: 2.052).
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 |
| 64_V | 68_L | 2.156 | 1.00 |
| 49_S | 66_A | 1.817 | 0.98 |
| 15_S | 20_Q | 1.500 | 0.91 |
| 53_I | 70_L | 1.401 | 0.87 |
| 47_I | 71_L | 1.369 | 0.86 |
| 42_K | 53_I | 1.357 | 0.85 |
| 44_L | 51_L | 1.353 | 0.85 |
| 7_E | 57_N | 1.349 | 0.84 |
| 20_Q | 25_I | 1.348 | 0.84 |
| 61_T | 65_L | 1.326 | 0.83 |
| 35_T | 46_K | 1.324 | 0.83 |
| 49_S | 67_T | 1.322 | 0.83 |
| 10_G | 16_G | 1.319 | 0.83 |
| 49_S | 73_C | 1.318 | 0.83 |
| 56_R | 67_T | 1.285 | 0.80 |
| 57_N | 64_V | 1.269 | 0.79 |
| 15_S | 25_I | 1.260 | 0.78 |
| 55_T | 74_D | 1.249 | 0.78 |
| 53_I | 77_P | 1.240 | 0.77 |
| 56_R | 60_D | 1.239 | 0.77 |
| 42_K | 70_L | 1.239 | 0.77 |
| 63_T | 66_A | 1.223 | 0.75 |
| 53_I | 67_T | 1.215 | 0.75 |
| 11_A | 26_T | 1.214 | 0.75 |
| 60_D | 72_G | 1.212 | 0.75 |
| 73_C | 78_W | 1.211 | 0.74 |
| 62_T | 65_L | 1.187 | 0.72 |
| 52_V | 72_G | 1.179 | 0.72 |
| 89_L | 92_P | 1.167 | 0.71 |
| 23_D | 26_T | 1.157 | 0.70 |
| 39_K | 42_K | 1.142 | 0.68 |
| 46_K | 54_I | 1.134 | 0.67 |
| 18_T | 30_N | 1.130 | 0.67 |
| 67_T | 73_C | 1.124 | 0.66 |
| 43_N | 88_V | 1.113 | 0.65 |
| 68_L | 78_W | 1.108 | 0.65 |
| 58_Y | 61_T | 1.107 | 0.65 |
| 27_E | 45_I | 1.099 | 0.64 |
| 33_T | 44_L | 1.085 | 0.62 |
| 66_A | 73_C | 1.070 | 0.61 |
| 18_T | 66_A | 1.066 | 0.60 |
| 24_K | 59_E | 1.064 | 0.60 |
| 41_L | 83_K | 1.054 | 0.59 |
| 62_T | 69_A | 1.050 | 0.59 |
| 77_P | 84_K | 1.043 | 0.58 |
| 44_L | 84_K | 1.035 | 0.57 |
| 41_L | 47_I | 1.034 | 0.57 |
| 10_G | 72_G | 1.032 | 0.57 |
| 29_T | 32_V | 1.018 | 0.55 |
| 85_A | 93_Y | 1.016 | 0.55 |
| 6_I | 75_A | 1.014 | 0.55 |
| 80_W | 84_K | 1.008 | 0.54 |
| 84_K | 88_V | 1.008 | 0.54 |
| 14_G | 59_E | 1.006 | 0.54 |
| 66_A | 82_R | 1.004 | 0.54 |
| 25_I | 52_V | 1.004 | 0.54 |
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 | |
| 3ikmA | 2 | 0.9485 | 4.5 | 0.903 | Contact Map |
| 2ap3A | 1 | 0.3608 | 4.2 | 0.904 | Contact Map |
| 1up7A | 8 | 0.9897 | 3.2 | 0.91 | Contact Map |
| 4gehB | 2 | 0.4124 | 3.1 | 0.911 | Contact Map |
| 1yqfA | 6 | 0.4433 | 3.1 | 0.911 | Contact Map |
| 3jv1A | 1 | 0.4433 | 2.6 | 0.914 | Contact Map |
| 4pjwA | 1 | 0.8969 | 2.4 | 0.915 | Contact Map |
| 2pjhA | 1 | 0.4433 | 2.1 | 0.918 | Contact Map |
| 4qinA | 1 | 0.866 | 2.1 | 0.918 | Contact Map |
| 3qv0A | 1 | 0.4433 | 2 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)