| PopZH2H3H4_104-177 |
| ID: | 1440142174 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (71) | ||
| Sequences: | 202 (123.8) | ||
| Seq/Len: | 2.845 | ||
| Nf(neff/√len): | 14.7 |
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: 2.845).
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 |
| 61_K | 66_V | 2.144 | 1.00 |
| 37_V | 45_L | 1.898 | 0.99 |
| 4_Q | 40_E | 1.617 | 0.97 |
| 45_L | 59_E | 1.594 | 0.97 |
| 48_E | 64_E | 1.580 | 0.97 |
| 40_E | 46_L | 1.566 | 0.96 |
| 60_T | 66_V | 1.450 | 0.94 |
| 60_T | 67_Q | 1.375 | 0.91 |
| 3_E | 57_I | 1.348 | 0.90 |
| 39_R | 64_E | 1.346 | 0.90 |
| 3_E | 72_G | 1.303 | 0.88 |
| 38_V | 47_K | 1.300 | 0.88 |
| 41_L | 53_N | 1.283 | 0.87 |
| 7_G | 46_L | 1.261 | 0.86 |
| 33_T | 47_K | 1.231 | 0.84 |
| 57_I | 61_K | 1.215 | 0.83 |
| 57_I | 66_V | 1.210 | 0.83 |
| 33_T | 38_V | 1.204 | 0.82 |
| 6_V | 43_R | 1.178 | 0.80 |
| 6_V | 46_L | 1.172 | 0.80 |
| 21_L | 51_D | 1.145 | 0.78 |
| 7_G | 67_Q | 1.125 | 0.76 |
| 43_R | 66_V | 1.121 | 0.76 |
| 58_V | 71_R | 1.097 | 0.73 |
| 37_V | 41_L | 1.087 | 0.72 |
| 68_R | 71_R | 1.080 | 0.72 |
| 43_R | 59_E | 1.079 | 0.72 |
| 51_D | 62_V | 1.075 | 0.71 |
| 24_A | 31_G | 1.071 | 0.71 |
| 35_E | 38_V | 1.060 | 0.70 |
| 41_L | 69_I | 1.060 | 0.70 |
| 42_L | 46_L | 1.057 | 0.69 |
| 20_S | 24_A | 1.039 | 0.67 |
| 18_F | 21_L | 1.030 | 0.66 |
| 4_Q | 8_V | 1.022 | 0.65 |
| 3_E | 37_V | 1.021 | 0.65 |
| 33_T | 37_V | 1.018 | 0.65 |
| 18_F | 64_E | 1.016 | 0.65 |
| 3_E | 6_V | 1.014 | 0.65 |
| 4_Q | 9_S | 1.011 | 0.64 |
| 7_G | 61_K | 1.008 | 0.64 |
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 | |
| 1kijA | 2 | 0.7867 | 58.6 | 0.853 | Contact Map |
| 4hy1A | 2 | 0.8933 | 55.6 | 0.855 | Contact Map |
| 4wubA | 1 | 0.9467 | 50.8 | 0.859 | Contact Map |
| 1s16A | 2 | 0.9067 | 47.7 | 0.862 | Contact Map |
| 3zkbA | 16 | 0.96 | 45.8 | 0.864 | Contact Map |
| 4urlA | 2 | 0.8667 | 45.8 | 0.864 | Contact Map |
| 3lnuA | 1 | 0.8533 | 43.4 | 0.865 | Contact Map |
| 3oghB | 2 | 0.88 | 33.6 | 0.874 | Contact Map |
| 3cwvA | 2 | 0.6533 | 32.9 | 0.874 | Contact Map |
| 3t38A | 2 | 0.84 | 24.9 | 0.882 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)