| SubsetJordan20 |
| ID: | 1478288120 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 58 (58) | ||
| Sequences: | 499 (499) | ||
| Seq/Len: | 8.603 | ||
| Nf(neff/√len): | 65.5 |
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: 8.603).
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 |
| 40_G | 55_A | 1.635 | 1.00 |
| 11_Y | 22_G | 1.609 | 1.00 |
| 1_Q | 16_D | 1.589 | 1.00 |
| 7_I | 56_G | 1.586 | 1.00 |
| 2_P | 47_D | 1.439 | 0.99 |
| 14_E | 22_G | 1.419 | 0.99 |
| 7_I | 39_C | 1.365 | 0.99 |
| 18_E | 58_M | 1.355 | 0.99 |
| 7_I | 18_E | 1.270 | 0.98 |
| 19_I | 33_G | 1.246 | 0.98 |
| 3_G | 44_C | 1.242 | 0.98 |
| 37_M | 45_Y | 1.224 | 0.98 |
| 23_R | 50_L | 1.186 | 0.97 |
| 16_D | 33_G | 1.166 | 0.97 |
| 9_A | 22_G | 1.146 | 0.96 |
| 22_G | 52_T | 1.141 | 0.96 |
| 2_P | 50_L | 1.137 | 0.96 |
| 8_M | 35_T | 1.133 | 0.96 |
| 22_G | 57_M | 1.132 | 0.96 |
| 41_Q | 58_M | 1.123 | 0.95 |
| 6_R | 10_C | 1.117 | 0.95 |
| 2_P | 41_Q | 1.087 | 0.94 |
| 1_Q | 4_Y | 1.073 | 0.94 |
| 2_P | 56_G | 1.069 | 0.94 |
| 18_E | 24_D | 1.068 | 0.94 |
| 4_Y | 9_A | 1.067 | 0.93 |
| 9_A | 39_C | 1.052 | 0.93 |
| 13_A | 31_N | 1.043 | 0.92 |
| 6_R | 35_T | 1.019 | 0.91 |
| 5_V | 27_V | 1.018 | 0.91 |
| 30_I | 55_A | 1.018 | 0.91 |
| 9_A | 53_Y | 1.010 | 0.91 |
| 29_V | 55_A | 1.008 | 0.91 |
| 8_M | 53_Y | 1.000 | 0.90 |
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 | |
| 4n78F | 1 | 0 | 96.7 | 0.686 | Contact Map |
| 2h8hA | 1 | 0.9483 | 96.7 | 0.687 | Contact Map |
| 4xi2A | 1 | 1 | 96.4 | 0.695 | Contact Map |
| 1fmkA | 1 | 1 | 96.3 | 0.698 | Contact Map |
| 4mt7A | 1 | 0 | 96.3 | 0.698 | Contact Map |
| 3tvtA | 1 | 0.8276 | 96.3 | 0.7 | Contact Map |
| 1opkA | 1 | 0.9655 | 96.2 | 0.702 | Contact Map |
| 3qwxX | 1 | 0.9828 | 96.2 | 0.703 | Contact Map |
| 2dvjA | 1 | 1 | 96.2 | 0.703 | Contact Map |
| 1griA | 2 | 1 | 96.1 | 0.704 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)