| asd |
| ID: | 1480701017 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 48 (48) | ||
| Sequences: | 2839 (1411.2) | ||
| Seq/Len: | 59.146 | ||
| Nf(neff/√len): | 203.7 |
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: 59.146).
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 |
| 2_K | 20_E | 2.950 | 1.00 |
| 26_A | 31_I | 2.420 | 1.00 |
| 5_L | 13_G | 2.352 | 1.00 |
| 7_K | 35_L | 2.306 | 1.00 |
| 30_L | 36_A | 2.093 | 1.00 |
| 45_K | 48_E | 1.904 | 1.00 |
| 5_L | 19_V | 1.859 | 1.00 |
| 8_D | 14_K | 1.770 | 1.00 |
| 9_V | 35_L | 1.736 | 1.00 |
| 37_V | 43_N | 1.629 | 1.00 |
| 42_E | 46_Q | 1.599 | 1.00 |
| 5_L | 12_L | 1.570 | 1.00 |
| 8_D | 15_K | 1.553 | 1.00 |
| 39_A | 44_L | 1.505 | 1.00 |
| 41_P | 45_K | 1.483 | 1.00 |
| 44_L | 48_E | 1.443 | 1.00 |
| 18_I | 44_L | 1.400 | 0.99 |
| 43_N | 46_Q | 1.394 | 0.99 |
| 25_Y | 29_F | 1.393 | 0.99 |
| 2_K | 18_I | 1.378 | 0.99 |
| 4_I | 43_N | 1.290 | 0.99 |
| 1_M | 23_P | 1.254 | 0.99 |
| 4_I | 39_A | 1.236 | 0.98 |
| 2_K | 44_L | 1.202 | 0.98 |
| 42_E | 45_K | 1.152 | 0.97 |
| 6_L | 37_V | 1.133 | 0.97 |
| 1_M | 26_A | 1.102 | 0.96 |
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 | |
| 3j7yH | 1 | 1 | 99.7 | -0.111 | Contact Map |
| 3bboJ | 1 | 1 | 99.7 | -0.108 | Contact Map |
| 4rb6I | 1 | 1 | 99.7 | -0.104 | Contact Map |
| 4tp9H | 1 | 1 | 99.7 | -0.1 | Contact Map |
| 1divA | 1 | 1 | 99.7 | -0.1 | Contact Map |
| 1nkwF | 1 | 0.9792 | 99.6 | -0.069 | Contact Map |
| 2hbaA | 2 | 1 | 99.6 | -0.064 | Contact Map |
| 1vw4G | 1 | 0.9375 | 99.6 | -0.007 | Contact Map |
| 4qjty | 1 | 1 | 99.4 | 0.103 | Contact Map |
| 1m55A | 2 | 0.8958 | 11.9 | 0.83 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)