| d2bv2b_ |
| ID: | 1448598590 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (82) | ||
| Sequences: | 958 (459.9) | ||
| Seq/Len: | 11.683 | ||
| Nf(neff/√len): | 50.8 |
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: 11.683).
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_I | 39_V | 2.572 | 1.00 |
| 57_Y | 70_W | 2.270 | 1.00 |
| 45_F | 58_K | 2.188 | 1.00 |
| 4_I | 40_E | 2.143 | 1.00 |
| 5_L | 18_L | 1.965 | 1.00 |
| 48_D | 55_P | 1.848 | 1.00 |
| 43_T | 58_K | 1.820 | 1.00 |
| 2_K | 17_E | 1.761 | 1.00 |
| 4_I | 17_E | 1.602 | 1.00 |
| 5_L | 34_V | 1.568 | 1.00 |
| 49_D | 55_P | 1.504 | 1.00 |
| 5_L | 80_V | 1.463 | 1.00 |
| 36_S | 39_V | 1.434 | 1.00 |
| 11_F | 17_E | 1.388 | 0.99 |
| 6_F | 13_G | 1.343 | 0.99 |
| 47_F | 56_S | 1.341 | 0.99 |
| 52_F | 79_S | 1.267 | 0.99 |
| 37_I | 46_V | 1.262 | 0.99 |
| 21_S | 82_Q | 1.255 | 0.99 |
| 3_I | 80_V | 1.237 | 0.98 |
| 18_L | 34_V | 1.226 | 0.98 |
| 57_Y | 67_P | 1.225 | 0.98 |
| 44_W | 59_L | 1.215 | 0.98 |
| 39_V | 42_G | 1.206 | 0.98 |
| 46_V | 61_P | 1.168 | 0.97 |
| 46_V | 60_T | 1.163 | 0.97 |
| 44_W | 54_G | 1.159 | 0.97 |
| 18_L | 80_V | 1.121 | 0.97 |
| 57_Y | 64_Y | 1.119 | 0.96 |
| 35_S | 70_W | 1.114 | 0.96 |
| 54_G | 62_G | 1.112 | 0.96 |
| 38_I | 63_K | 1.107 | 0.96 |
| 4_I | 15_K | 1.102 | 0.96 |
| 7_E | 17_E | 1.085 | 0.96 |
| 1_G | 41_S | 1.084 | 0.96 |
| 50_E | 53_S | 1.047 | 0.94 |
| 58_K | 76_E | 1.042 | 0.94 |
| 3_I | 20_T | 1.030 | 0.94 |
| 38_I | 69_S | 1.024 | 0.93 |
| 54_G | 59_L | 1.011 | 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 | |
| 1ha4A | 2 | 1 | 99.9 | 0.02 | Contact Map |
| 2bv2A | 2 | 1 | 99.9 | 0.026 | Contact Map |
| 2m3cA | 1 | 1 | 99.9 | 0.034 | Contact Map |
| 1zwmA | 1 | 1 | 99.9 | 0.037 | Contact Map |
| 2jdgA | 1 | 1 | 99.9 | 0.045 | Contact Map |
| 3hz2A | 4 | 0.988 | 99.9 | 0.046 | Contact Map |
| 2dadA | 1 | 0.9639 | 99.9 | 0.05 | Contact Map |
| 3qk3A | 3 | 1 | 99.9 | 0.051 | Contact Map |
| 1okiA | 2 | 1 | 99.9 | 0.052 | Contact Map |
| 1h4aX | 1 | 1 | 99.9 | 0.054 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)