| trial |
| ID: | 1499258957 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 53 (53) | ||
| Sequences: | 825 (745.8) | ||
| Seq/Len: | 15.566 | ||
| Nf(neff/√len): | 102.4 |
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: 15.566).
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 |
| 39_T | 42_E | 2.525 | 1.00 |
| 39_T | 53_A | 2.137 | 1.00 |
| 8_V | 44_K | 1.794 | 1.00 |
| 14_L | 31_N | 1.769 | 1.00 |
| 12_V | 26_S | 1.692 | 1.00 |
| 2_R | 14_L | 1.664 | 1.00 |
| 11_I | 18_F | 1.615 | 1.00 |
| 42_E | 53_A | 1.589 | 1.00 |
| 2_R | 24_D | 1.461 | 1.00 |
| 17_I | 44_K | 1.404 | 0.99 |
| 12_V | 15_Q | 1.324 | 0.99 |
| 5_E | 15_Q | 1.307 | 0.99 |
| 8_V | 12_V | 1.223 | 0.98 |
| 9_S | 30_T | 1.209 | 0.98 |
| 2_R | 41_T | 1.181 | 0.98 |
| 26_S | 30_T | 1.176 | 0.98 |
| 20_E | 24_D | 1.167 | 0.97 |
| 31_N | 46_G | 1.129 | 0.97 |
| 47_N | 53_A | 1.124 | 0.97 |
| 13_N | 21_K | 1.114 | 0.96 |
| 1_V | 35_D | 1.109 | 0.96 |
| 18_F | 22_V | 1.082 | 0.96 |
| 21_K | 24_D | 1.065 | 0.95 |
| 6_V | 43_V | 1.062 | 0.95 |
| 19_T | 46_G | 1.049 | 0.94 |
| 40_Q | 43_V | 1.044 | 0.94 |
| 7_R | 11_I | 1.040 | 0.94 |
| 40_Q | 48_K | 1.029 | 0.94 |
| 24_D | 40_Q | 1.025 | 0.93 |
| 24_D | 53_A | 1.022 | 0.93 |
| 7_R | 31_N | 1.018 | 0.93 |
| 1_V | 38_S | 1.014 | 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 | |
| 2m8rA | 1 | 1 | 97.8 | 0.442 | Contact Map |
| 2xheB | 1 | 0.8113 | 97.8 | 0.451 | Contact Map |
| 1jthB | 2 | 1 | 97.8 | 0.452 | Contact Map |
| 5buzC | 2 | 0 | 97.8 | 0.452 | Contact Map |
| 3c98B | 1 | 0.8868 | 97.7 | 0.46 | Contact Map |
| 1gl2B | 1 | 1 | 97.6 | 0.467 | Contact Map |
| 2npsB | 1 | 1 | 97.5 | 0.475 | Contact Map |
| 4jehB | 1 | 0.8679 | 97.5 | 0.482 | Contact Map |
| 1sfcB | 3 | 1 | 97.4 | 0.489 | Contact Map |
| 1n7sB | 1 | 1 | 97.4 | 0.491 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)