| 1403tk1 |
| ID: | 1500560722 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (89) | ||
| Sequences: | 650 (459.9) | ||
| Seq/Len: | 7.303 | ||
| Nf(neff/√len): | 48.7 |
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: 7.303).
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 |
| 3_L | 82_V | 4.006 | 1.00 |
| 27_V | 43_A | 2.088 | 1.00 |
| 54_W | 82_V | 2.021 | 1.00 |
| 58_V | 62_S | 1.930 | 1.00 |
| 25_L | 78_V | 1.868 | 1.00 |
| 42_V | 56_L | 1.805 | 1.00 |
| 27_V | 57_L | 1.699 | 1.00 |
| 15_R | 21_H | 1.687 | 1.00 |
| 42_V | 75_D | 1.592 | 1.00 |
| 48_G | 53_E | 1.549 | 1.00 |
| 47_I | 81_I | 1.481 | 0.99 |
| 43_A | 78_V | 1.459 | 0.99 |
| 3_L | 10_I | 1.452 | 0.99 |
| 22_D | 44_I | 1.452 | 0.99 |
| 58_V | 77_C | 1.423 | 0.99 |
| 2_K | 29_M | 1.370 | 0.99 |
| 49_A | 81_I | 1.365 | 0.99 |
| 63_A | 75_D | 1.311 | 0.98 |
| 6_V | 27_V | 1.306 | 0.98 |
| 5_V | 54_W | 1.292 | 0.98 |
| 18_G | 73_P | 1.263 | 0.97 |
| 47_I | 78_V | 1.214 | 0.96 |
| 28_E | 40_C | 1.188 | 0.96 |
| 41_A | 76_L | 1.183 | 0.96 |
| 29_M | 41_A | 1.167 | 0.95 |
| 30_I | 54_W | 1.149 | 0.95 |
| 50_G | 53_E | 1.143 | 0.94 |
| 18_G | 21_H | 1.127 | 0.94 |
| 61_S | 64_R | 1.124 | 0.94 |
| 11_V | 44_I | 1.122 | 0.94 |
| 59_S | 76_L | 1.113 | 0.93 |
| 4_A | 41_A | 1.105 | 0.93 |
| 7_T | 40_C | 1.091 | 0.93 |
| 28_E | 38_G | 1.066 | 0.91 |
| 2_K | 59_S | 1.066 | 0.91 |
| 12_C | 80_G | 1.057 | 0.91 |
| 65_Q | 71_T | 1.049 | 0.90 |
| 53_E | 58_V | 1.044 | 0.90 |
| 8_G | 50_G | 1.044 | 0.90 |
| 5_V | 27_V | 1.034 | 0.90 |
| 23_K | 49_A | 1.025 | 0.89 |
| 30_I | 37_D | 1.020 | 0.89 |
| 9_Q | 51_T | 1.014 | 0.88 |
| 23_K | 50_G | 1.014 | 0.88 |
| 11_V | 14_V | 1.011 | 0.88 |
| 54_W | 85_V | 1.005 | 0.88 |
| 53_E | 81_I | 1.003 | 0.88 |
| 65_Q | 70_E | 1.001 | 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 | |
| 2qw7A | 10 | 1 | 100 | 0.019 | Contact Map |
| 4n8fA | 5 | 1 | 100 | 0.021 | Contact Map |
| 4jw0B | 5 | 1 | 100 | 0.022 | Contact Map |
| 2hd3A | 12 | 1 | 100 | 0.024 | Contact Map |
| 4i7aA | 5 | 0.9158 | 100 | 0.081 | Contact Map |
| 2rcfA | 5 | 0.8632 | 100 | 0.135 | Contact Map |
| 4umwA | 1 | 0.8211 | 9.5 | 0.919 | Contact Map |
| 3j09A | 2 | 0.8316 | 7.7 | 0.922 | Contact Map |
| 4w23L | 1 | 0.8632 | 7.4 | 0.923 | Contact Map |
| 3r4rA | 2 | 0.4526 | 7 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)