| 1DBFA |
| ID: | 1411607651 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (120) | ||
| Sequences: | 288 (223.7) | ||
| Seq/Len: | 2.400 | ||
| Nf(neff/√len): | 20.4 |
HHblits Results: (2013_03)
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: 2.400).
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 |
| 44_Q | 94_T | 3.657 | 1.00 |
| 15_D | 54_H | 3.574 | 1.00 |
| 75_C | 78_E | 2.916 | 1.00 |
| 15_D | 55_A | 2.865 | 1.00 |
| 111_K | 114_V | 2.228 | 1.00 |
| 48_S | 76_M | 2.013 | 0.99 |
| 28_L | 62_V | 1.993 | 0.99 |
| 47_L | 62_V | 1.896 | 0.99 |
| 72_P | 119_L | 1.866 | 0.99 |
| 30_K | 34_E | 1.800 | 0.98 |
| 15_D | 20_I | 1.787 | 0.98 |
| 20_I | 55_A | 1.776 | 0.98 |
| 14_R | 19_E | 1.682 | 0.97 |
| 51_P | 80_D | 1.647 | 0.97 |
| 11_T | 88_C | 1.630 | 0.96 |
| 16_T | 19_E | 1.585 | 0.96 |
| 45_M | 93_M | 1.580 | 0.95 |
| 26_Q | 110_E | 1.534 | 0.94 |
| 5_G | 43_V | 1.518 | 0.94 |
| 4_R | 97_T | 1.446 | 0.92 |
| 99_V | 103_Q | 1.407 | 0.90 |
| 74_T | 81_V | 1.392 | 0.90 |
| 4_R | 71_V | 1.362 | 0.88 |
| 3_I | 73_V | 1.358 | 0.88 |
| 32_I | 68_W | 1.334 | 0.87 |
| 74_T | 92_M | 1.328 | 0.86 |
| 62_V | 73_V | 1.300 | 0.85 |
| 49_A | 79_M | 1.284 | 0.84 |
| 12_V | 53_L | 1.281 | 0.84 |
| 10_T | 26_Q | 1.278 | 0.83 |
| 32_I | 42_V | 1.272 | 0.83 |
| 51_P | 84_G | 1.264 | 0.83 |
| 21_L | 24_T | 1.255 | 0.82 |
| 23_K | 110_E | 1.245 | 0.81 |
| 51_P | 77_Q | 1.239 | 0.81 |
| 5_G | 37_T | 1.236 | 0.81 |
| 31_I | 91_V | 1.229 | 0.80 |
| 5_G | 101_Q | 1.219 | 0.79 |
| 6_I | 31_I | 1.188 | 0.77 |
| 10_T | 110_E | 1.188 | 0.77 |
| 23_K | 45_M | 1.180 | 0.76 |
| 49_A | 77_Q | 1.168 | 0.75 |
| 68_W | 92_M | 1.146 | 0.73 |
| 20_I | 53_L | 1.141 | 0.73 |
| 17_E | 55_A | 1.135 | 0.72 |
| 24_T | 60_K | 1.134 | 0.72 |
| 2_M | 31_I | 1.130 | 0.72 |
| 100_P | 103_Q | 1.127 | 0.71 |
| 5_G | 92_M | 1.123 | 0.71 |
| 79_M | 82_T | 1.122 | 0.71 |
| 43_V | 96_Q | 1.112 | 0.70 |
| 25_K | 64_E | 1.110 | 0.70 |
| 12_V | 72_P | 1.105 | 0.69 |
| 17_E | 60_K | 1.033 | 0.62 |
| 59_A | 73_V | 1.030 | 0.61 |
| 6_I | 104_I | 1.015 | 0.60 |
| 97_T | 104_I | 1.005 | 0.58 |
| 24_T | 61_A | 1.001 | 0.58 |
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 | |
| 1dbfA | 3 | 1 | 100 | 0.011 | Contact Map |
| 1xhoA | 3 | 0.8898 | 100 | 0.039 | Contact Map |
| 1ufyA | 1 | 0.9449 | 100 | 0.055 | Contact Map |
| 1wv8A | 1 | 0.4252 | 29.3 | 0.941 | Contact Map |
| 1igdA | 1 | 0.3701 | 24.2 | 0.943 | Contact Map |
| 4glnD | 2 | 0.0079 | 20 | 0.946 | Contact Map |
| 2rpvA | 1 | 0.3701 | 19.6 | 0.946 | Contact Map |
| 1mhxA | 1 | 0.3701 | 17.5 | 0.947 | Contact Map |
| 3mydA | 1 | 0.6693 | 12.8 | 0.95 | Contact Map |
| 3filA | 1 | 0.3622 | 12.3 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)