| d4p7tc_ |
| ID: | 1448470967 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (74) | ||
| Sequences: | 1141 (676.3) | ||
| Seq/Len: | 15.419 | ||
| Nf(neff/√len): | 78.6 |
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: 15.419).
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 |
| 19_M | 42_V | 3.980 | 1.00 |
| 57_A | 69_V | 2.591 | 1.00 |
| 46_V | 73_P | 2.491 | 1.00 |
| 53_T | 71_V | 2.461 | 1.00 |
| 50_K | 54_D | 1.805 | 1.00 |
| 12_A | 40_V | 1.720 | 1.00 |
| 42_V | 53_T | 1.704 | 1.00 |
| 37_L | 67_K | 1.686 | 1.00 |
| 7_K | 67_K | 1.558 | 1.00 |
| 45_D | 48_A | 1.548 | 1.00 |
| 53_T | 69_V | 1.526 | 1.00 |
| 4_V | 53_T | 1.504 | 1.00 |
| 58_A | 61_R | 1.413 | 1.00 |
| 16_A | 27_L | 1.379 | 0.99 |
| 54_D | 58_A | 1.372 | 0.99 |
| 57_A | 66_V | 1.352 | 0.99 |
| 60_A | 66_V | 1.310 | 0.99 |
| 56_G | 60_A | 1.302 | 0.99 |
| 19_M | 56_G | 1.291 | 0.99 |
| 9_L | 13_I | 1.232 | 0.98 |
| 28_V | 43_R | 1.210 | 0.98 |
| 18_A | 59_A | 1.160 | 0.97 |
| 34_G | 38_V | 1.158 | 0.97 |
| 18_A | 22_S | 1.155 | 0.97 |
| 18_A | 56_G | 1.147 | 0.97 |
| 31_E | 39_T | 1.122 | 0.97 |
| 57_A | 61_R | 1.112 | 0.96 |
| 54_D | 57_A | 1.109 | 0.96 |
| 34_G | 37_L | 1.063 | 0.95 |
| 25_V | 42_V | 1.047 | 0.94 |
| 15_A | 55_A | 1.040 | 0.94 |
| 32_K | 38_V | 1.033 | 0.94 |
| 6_T | 12_A | 1.028 | 0.94 |
| 1_L | 41_I | 1.027 | 0.94 |
| 12_A | 38_V | 1.021 | 0.93 |
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 | |
| 4qifA | 9 | 1 | 99.8 | 0.024 | Contact Map |
| 3mpyA | 1 | 1 | 99.8 | 0.047 | Contact Map |
| 4ox6A | 2 | 1 | 99.8 | 0.055 | Contact Map |
| 4ox7A | 6 | 1 | 99.8 | 0.057 | Contact Map |
| 4ox8A | 6 | 1 | 99.8 | 0.059 | Contact Map |
| 4axjA | 3 | 1 | 99.8 | 0.059 | Contact Map |
| 4p7tA | 6 | 1 | 99.8 | 0.061 | Contact Map |
| 2a10A | 6 | 1 | 99.8 | 0.073 | Contact Map |
| 3gv2A | 6 | 0 | 99.8 | 0.073 | Contact Map |
| 3ssqA | 6 | 1 | 99.8 | 0.075 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)