| d3whoc_ |
| ID: | 1448506772 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (99) | ||
| Sequences: | 271 (209.2) | ||
| Seq/Len: | 2.737 | ||
| Nf(neff/√len): | 21.0 |
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: 2.737).
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 |
| 8_N | 11_G | 2.655 | 1.00 |
| 27_R | 79_G | 2.569 | 1.00 |
| 48_C | 82_C | 2.415 | 1.00 |
| 96_F | 99_C | 2.406 | 1.00 |
| 26_A | 75_Y | 2.173 | 1.00 |
| 48_C | 76_D | 2.115 | 1.00 |
| 38_Y | 41_F | 1.810 | 0.99 |
| 7_C | 81_F | 1.706 | 0.98 |
| 76_D | 82_C | 1.685 | 0.98 |
| 86_T | 89_G | 1.595 | 0.97 |
| 74_I | 85_L | 1.559 | 0.96 |
| 23_I | 75_Y | 1.543 | 0.96 |
| 57_V | 84_C | 1.537 | 0.96 |
| 7_C | 98_E | 1.529 | 0.95 |
| 7_C | 84_C | 1.521 | 0.95 |
| 92_S | 95_G | 1.464 | 0.94 |
| 32_G | 40_N | 1.456 | 0.94 |
| 76_D | 79_G | 1.444 | 0.93 |
| 22_A | 73_V | 1.386 | 0.91 |
| 87_H | 96_F | 1.345 | 0.90 |
| 75_Y | 82_C | 1.335 | 0.89 |
| 54_E | 87_H | 1.314 | 0.88 |
| 75_Y | 79_G | 1.303 | 0.88 |
| 57_V | 74_I | 1.294 | 0.87 |
| 52_F | 83_A | 1.290 | 0.87 |
| 16_G | 20_T | 1.283 | 0.87 |
| 5_R | 13_S | 1.282 | 0.86 |
| 14_F | 71_D | 1.271 | 0.86 |
| 39_N | 51_T | 1.249 | 0.84 |
| 15_T | 18_D | 1.245 | 0.84 |
| 46_F | 85_L | 1.221 | 0.83 |
| 18_D | 84_C | 1.192 | 0.80 |
| 79_G | 82_C | 1.190 | 0.80 |
| 26_A | 79_G | 1.140 | 0.76 |
| 63_Y | 66_G | 1.103 | 0.73 |
| 40_N | 54_E | 1.076 | 0.70 |
| 38_Y | 85_L | 1.049 | 0.67 |
| 44_F | 66_G | 1.047 | 0.67 |
| 38_Y | 53_F | 1.044 | 0.67 |
| 23_I | 79_G | 1.026 | 0.65 |
| 40_N | 83_A | 1.017 | 0.64 |
| 71_D | 86_T | 1.009 | 0.63 |
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 | |
| 1rdsA | 1 | 0.9703 | 100 | 0.101 | Contact Map |
| 1fusA | 1 | 0.9505 | 100 | 0.117 | Contact Map |
| 3wr2A | 6 | 1 | 100 | 0.117 | Contact Map |
| 1i0vA | 1 | 0.9505 | 100 | 0.122 | Contact Map |
| 3agnA | 1 | 0.9901 | 100 | 0.146 | Contact Map |
| 2kaaA | 1 | 0.9505 | 99.9 | 0.268 | Contact Map |
| 1aqzA | 2 | 0.9406 | 99.9 | 0.356 | Contact Map |
| 2c4bA | 2 | 0.901 | 63.1 | 0.884 | Contact Map |
| 1pylA | 2 | 0.8614 | 35.1 | 0.902 | Contact Map |
| 1lniA | 2 | 0.8515 | 30.7 | 0.905 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)