| PopZH2H3H4_104-177 |
| ID: | 1440143540 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (72) | ||
| Sequences: | 222 (142.2) | ||
| Seq/Len: | 3.083 | ||
| Nf(neff/√len): | 16.8 |
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: 3.083).
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 |
| 42_L | 46_L | 1.825 | 0.99 |
| 61_K | 66_V | 1.721 | 0.99 |
| 48_E | 64_E | 1.714 | 0.99 |
| 51_D | 62_V | 1.677 | 0.98 |
| 37_V | 45_L | 1.639 | 0.98 |
| 40_E | 46_L | 1.617 | 0.98 |
| 54_L | 62_V | 1.613 | 0.98 |
| 33_T | 38_V | 1.607 | 0.98 |
| 51_D | 54_L | 1.576 | 0.97 |
| 57_I | 61_K | 1.575 | 0.97 |
| 60_T | 67_Q | 1.542 | 0.97 |
| 4_Q | 40_E | 1.380 | 0.93 |
| 38_V | 47_K | 1.373 | 0.92 |
| 43_R | 63_E | 1.273 | 0.88 |
| 68_R | 71_R | 1.256 | 0.87 |
| 45_L | 59_E | 1.191 | 0.83 |
| 41_L | 44_P | 1.184 | 0.83 |
| 57_I | 66_V | 1.183 | 0.83 |
| 3_E | 57_I | 1.176 | 0.82 |
| 41_L | 66_V | 1.157 | 0.81 |
| 20_S | 24_A | 1.148 | 0.80 |
| 4_Q | 9_S | 1.136 | 0.79 |
| 43_R | 59_E | 1.129 | 0.78 |
| 42_L | 50_L | 1.112 | 0.77 |
| 41_L | 53_N | 1.107 | 0.76 |
| 41_L | 45_L | 1.103 | 0.76 |
| 3_E | 72_G | 1.101 | 0.76 |
| 34_L | 38_V | 1.100 | 0.76 |
| 4_Q | 8_V | 1.100 | 0.76 |
| 39_R | 64_E | 1.099 | 0.76 |
| 13_A | 20_S | 1.080 | 0.74 |
| 43_R | 65_E | 1.075 | 0.73 |
| 4_Q | 23_S | 1.071 | 0.73 |
| 55_P | 59_E | 1.070 | 0.73 |
| 3_E | 6_V | 1.043 | 0.70 |
| 18_F | 21_L | 1.042 | 0.70 |
| 59_E | 65_E | 1.036 | 0.69 |
| 12_S | 27_M | 1.034 | 0.69 |
| 58_V | 71_R | 1.019 | 0.68 |
| 58_V | 62_V | 1.010 | 0.67 |
| 60_T | 66_V | 1.007 | 0.66 |
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 | |
| 4hy1A | 2 | 0.8933 | 64.1 | 0.835 | Contact Map |
| 1kijA | 2 | 0.9467 | 63 | 0.836 | Contact Map |
| 4wubA | 1 | 0.9467 | 60.7 | 0.838 | Contact Map |
| 3zkbA | 16 | 0.9467 | 56 | 0.842 | Contact Map |
| 4urlA | 2 | 0.9067 | 53.6 | 0.845 | Contact Map |
| 3lnuA | 1 | 0.8533 | 51.7 | 0.847 | Contact Map |
| 1s16A | 2 | 0.92 | 51.4 | 0.847 | Contact Map |
| 3oghB | 2 | 0.88 | 35.2 | 0.861 | Contact Map |
| 4i3hA | 2 | 0.9467 | 33.1 | 0.863 | Contact Map |
| 3cwvA | 2 | 0.6533 | 31.6 | 0.864 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)