| bubr1_cassette |
| ID: | 1469454284 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 88 (76) | ||
| Sequences: | 343 (228.8) | ||
| Seq/Len: | 4.513 | ||
| Nf(neff/√len): | 26.2 |
HHblits Results: (2016_02)
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: 4.513).
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 |
| 47_A | 50_W | 2.732 | 1.00 |
| 64_T | 69_A | 2.380 | 1.00 |
| 48_G | 53_G | 2.064 | 1.00 |
| 12_F | 41_K | 2.029 | 1.00 |
| 52_T | 55_S | 1.377 | 0.96 |
| 15_N | 45_L | 1.369 | 0.96 |
| 5_N | 19_A | 1.229 | 0.92 |
| 32_W | 36_P | 1.222 | 0.92 |
| 65_A | 69_A | 1.207 | 0.91 |
| 27_P | 44_E | 1.187 | 0.90 |
| 65_A | 74_L | 1.183 | 0.90 |
| 44_E | 48_G | 1.180 | 0.90 |
| 71_P | 75_P | 1.176 | 0.90 |
| 76_S | 81_V | 1.168 | 0.89 |
| 13_D | 17_D | 1.166 | 0.89 |
| 8_R | 76_S | 1.148 | 0.88 |
| 79_P | 82_E | 1.143 | 0.88 |
| 65_A | 87_Q | 1.136 | 0.87 |
| 40_A | 52_T | 1.127 | 0.87 |
| 14_E | 71_P | 1.108 | 0.86 |
| 64_T | 70_V | 1.107 | 0.85 |
| 69_A | 74_L | 1.107 | 0.85 |
| 71_P | 74_L | 1.106 | 0.85 |
| 65_A | 85_A | 1.096 | 0.85 |
| 8_R | 53_G | 1.095 | 0.85 |
| 64_T | 75_P | 1.095 | 0.85 |
| 34_A | 38_P | 1.090 | 0.84 |
| 59_R | 69_A | 1.077 | 0.83 |
| 21_T | 72_A | 1.072 | 0.83 |
| 59_R | 64_T | 1.072 | 0.83 |
| 34_A | 40_A | 1.068 | 0.83 |
| 51_N | 54_R | 1.055 | 0.81 |
| 54_R | 58_H | 1.044 | 0.81 |
| 30_Q | 48_G | 1.039 | 0.80 |
| 48_G | 52_T | 1.039 | 0.80 |
| 6_N | 53_G | 1.024 | 0.79 |
| 15_N | 18_E | 1.015 | 0.78 |
| 23_E | 29_V | 1.005 | 0.77 |
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 | |
| 4xjnA | 13 | 0 | 3.2 | 0.885 | Contact Map |
| 3zdfC | 2 | 0.1818 | 1.1 | 0.912 | Contact Map |
| 2y9yA | 1 | 0.25 | 1.1 | 0.912 | Contact Map |
| 3b1jC | 2 | 0.1818 | 1 | 0.915 | Contact Map |
| 2kdoA | 1 | 0.4545 | 0.8 | 0.92 | Contact Map |
| 1t95A | 1 | 0.2841 | 0.7 | 0.922 | Contact Map |
| 3ujzA | 1 | 0.7614 | 0.6 | 0.926 | Contact Map |
| 1oxzA | 1 | 0.0795 | 0.6 | 0.927 | Contact Map |
| 4bh6I | 8 | 0.6705 | 0.6 | 0.928 | Contact Map |
| 3oqqA | 1 | 0.1818 | 0.6 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)