| 4ku0 |
| ID: | 1501760672 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 96 (88) | ||
| Sequences: | 630 (598.8) | ||
| Seq/Len: | 7.159 | ||
| Nf(neff/√len): | 63.8 |
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: 7.159).
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 |
| 75_Q | 78_D | 3.366 | 1.00 |
| 37_V | 40_D | 3.263 | 1.00 |
| 5_Y | 8_C | 3.112 | 1.00 |
| 59_T | 74_V | 2.936 | 1.00 |
| 6_D | 24_T | 2.521 | 1.00 |
| 4_S | 21_V | 2.187 | 1.00 |
| 68_V | 73_A | 2.177 | 1.00 |
| 39_G | 71_K | 2.078 | 1.00 |
| 32_G | 70_G | 1.949 | 1.00 |
| 36_L | 59_T | 1.948 | 1.00 |
| 28_V | 66_V | 1.758 | 1.00 |
| 25_Q | 69_T | 1.757 | 1.00 |
| 27_K | 69_T | 1.747 | 1.00 |
| 58_V | 81_S | 1.714 | 1.00 |
| 31_G | 90_S | 1.709 | 1.00 |
| 59_T | 86_V | 1.638 | 1.00 |
| 31_G | 92_K | 1.603 | 1.00 |
| 23_A | 40_D | 1.591 | 1.00 |
| 12_G | 15_A | 1.541 | 1.00 |
| 63_T | 75_Q | 1.507 | 0.99 |
| 35_V | 73_A | 1.427 | 0.99 |
| 23_A | 41_P | 1.396 | 0.99 |
| 61_P | 78_D | 1.387 | 0.99 |
| 74_V | 86_V | 1.350 | 0.98 |
| 42_I | 80_I | 1.346 | 0.98 |
| 93_V | 96_K | 1.335 | 0.98 |
| 73_A | 95_I | 1.326 | 0.98 |
| 10_T | 14_E | 1.295 | 0.98 |
| 21_V | 36_L | 1.284 | 0.98 |
| 57_G | 80_I | 1.234 | 0.97 |
| 37_V | 71_K | 1.207 | 0.96 |
| 9_V | 20_V | 1.188 | 0.96 |
| 29_F | 67_Y | 1.187 | 0.96 |
| 80_I | 84_D | 1.132 | 0.94 |
| 38_A | 72_K | 1.122 | 0.94 |
| 30_T | 35_V | 1.083 | 0.92 |
| 57_G | 84_D | 1.020 | 0.88 |
| 42_I | 57_G | 1.016 | 0.88 |
| 25_Q | 37_V | 1.005 | 0.87 |
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 | |
| 4ku0D | 1 | 1 | 99.9 | -0.03 | Contact Map |
| 4jiwD | 4 | 0.9688 | 99.9 | 0.048 | Contact Map |
| 4jivD | 1 | 0.9688 | 99.9 | 0.049 | Contact Map |
| 4zjmA | 1 | 0 | 1.7 | 0.921 | Contact Map |
| 4xinA | 2 | 0.6042 | 1.2 | 0.928 | Contact Map |
| 3zqjA | 6 | 0.8854 | 1 | 0.932 | Contact Map |
| 2kddA | 2 | 0.1146 | 0.9 | 0.933 | Contact Map |
| 3sk3A | 2 | 0.3958 | 0.9 | 0.934 | Contact Map |
| 2r6fA | 2 | 0.7812 | 0.8 | 0.936 | Contact Map |
| 4om9A | 1 | 0.8958 | 0.7 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)