| 686_2 |
| ID: | 1433411808 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (83) | ||
| Sequences: | 602 (475.3) | ||
| Seq/Len: | 7.253 | ||
| Nf(neff/√len): | 52.2 |
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: 7.253).
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 |
| 80_E | 85_R | 3.969 | 1.00 |
| 31_N | 34_S | 3.137 | 1.00 |
| 66_E | 84_N | 2.934 | 1.00 |
| 4_R | 51_V | 2.595 | 1.00 |
| 19_F | 72_K | 2.320 | 1.00 |
| 23_N | 65_I | 2.309 | 1.00 |
| 73_Q | 76_T | 2.059 | 1.00 |
| 38_M | 50_S | 1.876 | 1.00 |
| 20_I | 50_S | 1.846 | 1.00 |
| 24_I | 65_I | 1.723 | 1.00 |
| 21_V | 70_I | 1.692 | 1.00 |
| 42_K | 45_Y | 1.623 | 1.00 |
| 18_L | 71_I | 1.613 | 1.00 |
| 79_W | 84_N | 1.588 | 1.00 |
| 32_A | 70_I | 1.507 | 0.99 |
| 12_T | 15_G | 1.477 | 0.99 |
| 23_N | 29_N | 1.461 | 0.99 |
| 12_T | 18_L | 1.401 | 0.99 |
| 35_A | 70_I | 1.395 | 0.99 |
| 12_T | 45_Y | 1.391 | 0.99 |
| 10_A | 71_I | 1.388 | 0.99 |
| 44_R | 49_D | 1.312 | 0.98 |
| 12_T | 46_P | 1.284 | 0.98 |
| 42_K | 46_P | 1.271 | 0.97 |
| 25_P | 29_N | 1.237 | 0.97 |
| 19_F | 35_A | 1.228 | 0.97 |
| 66_E | 79_W | 1.194 | 0.96 |
| 62_L | 89_L | 1.146 | 0.95 |
| 36_L | 70_I | 1.120 | 0.94 |
| 17_N | 37_P | 1.092 | 0.92 |
| 19_F | 70_I | 1.087 | 0.92 |
| 23_N | 66_E | 1.081 | 0.92 |
| 19_F | 37_P | 1.074 | 0.92 |
| 43_S | 49_D | 1.072 | 0.92 |
| 36_L | 60_E | 1.062 | 0.91 |
| 18_L | 38_M | 1.054 | 0.91 |
| 16_E | 73_Q | 1.031 | 0.89 |
| 68_K | 84_N | 1.011 | 0.88 |
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 | |
| 4jcmA | 1 | 0.9286 | 99.9 | 0.187 | Contact Map |
| 2vn4A | 1 | 0.9184 | 99.9 | 0.189 | Contact Map |
| 1cygA | 1 | 0.9184 | 99.9 | 0.198 | Contact Map |
| 4jclA | 1 | 0.9184 | 99.9 | 0.2 | Contact Map |
| 3bmvA | 1 | 0.949 | 99.9 | 0.208 | Contact Map |
| 1d3cA | 1 | 0.9286 | 99.9 | 0.216 | Contact Map |
| 1gcyA | 1 | 0 | 99.9 | 0.225 | Contact Map |
| 1qhoA | 1 | 0.9184 | 99.9 | 0.232 | Contact Map |
| 1vemA | 1 | 0.9184 | 99.9 | 0.254 | Contact Map |
| 1ac0A | 1 | 0.9184 | 99.9 | 0.256 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)