| d3llba_ |
| ID: | 1451193989 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (78) | ||
| Sequences: | 4431 (2964.6) | ||
| Seq/Len: | 56.808 | ||
| Nf(neff/√len): | 335.7 |
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: 56.808).
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 |
| 48_H | 54_E | 3.546 | 1.00 |
| 13_V | 78_L | 3.163 | 1.00 |
| 12_I | 66_L | 2.299 | 1.00 |
| 57_E | 62_R | 2.227 | 1.00 |
| 42_V | 76_L | 2.206 | 1.00 |
| 12_I | 75_L | 2.108 | 1.00 |
| 10_D | 77_R | 1.974 | 1.00 |
| 55_V | 62_R | 1.914 | 1.00 |
| 67_N | 74_H | 1.887 | 1.00 |
| 45_A | 58_L | 1.885 | 1.00 |
| 41_L | 58_L | 1.864 | 1.00 |
| 22_F | 26_F | 1.861 | 1.00 |
| 12_I | 77_R | 1.794 | 1.00 |
| 66_L | 77_R | 1.764 | 1.00 |
| 38_V | 76_L | 1.680 | 1.00 |
| 55_V | 64_R | 1.631 | 1.00 |
| 67_N | 75_L | 1.624 | 1.00 |
| 35_F | 44_S | 1.620 | 1.00 |
| 62_R | 79_S | 1.611 | 1.00 |
| 64_R | 79_S | 1.537 | 1.00 |
| 42_V | 65_V | 1.451 | 1.00 |
| 61_F | 80_P | 1.385 | 0.99 |
| 17_T | 22_F | 1.338 | 0.99 |
| 10_D | 79_S | 1.305 | 0.99 |
| 22_F | 78_L | 1.290 | 0.99 |
| 43_M | 49_L | 1.287 | 0.99 |
| 5_P | 11_F | 1.222 | 0.98 |
| 69_D | 74_H | 1.221 | 0.98 |
| 22_F | 38_V | 1.183 | 0.98 |
| 6_L | 10_D | 1.180 | 0.98 |
| 13_V | 38_V | 1.177 | 0.98 |
| 19_V | 23_N | 1.175 | 0.98 |
| 37_T | 40_G | 1.151 | 0.97 |
| 23_N | 28_S | 1.133 | 0.97 |
| 64_R | 77_R | 1.129 | 0.97 |
| 9_G | 80_P | 1.105 | 0.96 |
| 17_T | 38_V | 1.096 | 0.96 |
| 28_S | 61_F | 1.095 | 0.96 |
| 7_P | 10_D | 1.065 | 0.95 |
| 61_F | 78_L | 1.042 | 0.94 |
| 39_G | 72_R | 1.016 | 0.93 |
| 63_F | 76_L | 1.015 | 0.93 |
| 46_F | 50_P | 1.010 | 0.93 |
| 39_G | 43_M | 1.009 | 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 | |
| 3llbA | 1 | 1 | 99.8 | 0.009 | Contact Map |
| 3laeA | 1 | 1 | 99.8 | 0.014 | Contact Map |
| 2plsA | 12 | 1 | 99.8 | 0.024 | Contact Map |
| 2pliA | 4 | 1 | 99.7 | 0.028 | Contact Map |
| 2nqwA | 1 | 1 | 99.7 | 0.032 | Contact Map |
| 2r2zA | 1 | 1 | 99.7 | 0.034 | Contact Map |
| 3dedA | 6 | 1 | 99.7 | 0.034 | Contact Map |
| 2p3hA | 1 | 1 | 99.7 | 0.041 | Contact Map |
| 2oaiA | 1 | 0.9383 | 99.7 | 0.045 | Contact Map |
| 2p4pA | 2 | 0.9136 | 99.7 | 0.045 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)