| 331-384 |
| ID: | 1479414696 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 54 (53) | ||
| Sequences: | 64 (49) | ||
| Seq/Len: | 1.208 | ||
| Nf(neff/√len): | 6.7 |
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: 1.208).
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 |
| 4_Y | 25_P | 1.759 | 0.92 |
| 8_T | 14_Q | 1.752 | 0.92 |
| 5_D | 32_E | 1.729 | 0.91 |
| 2_Y | 28_P | 1.688 | 0.90 |
| 6_M | 20_I | 1.646 | 0.89 |
| 1_M | 9_A | 1.451 | 0.78 |
| 30_G | 43_D | 1.395 | 0.74 |
| 38_Q | 53_F | 1.327 | 0.69 |
| 31_S | 48_L | 1.294 | 0.66 |
| 14_Q | 38_Q | 1.272 | 0.64 |
| 33_N | 37_C | 1.267 | 0.64 |
| 35_N | 38_Q | 1.232 | 0.61 |
| 13_Q | 33_N | 1.210 | 0.59 |
| 24_I | 31_S | 1.205 | 0.58 |
| 8_T | 46_T | 1.195 | 0.57 |
| 22_N | 44_N | 1.179 | 0.56 |
| 1_M | 46_T | 1.153 | 0.53 |
| 5_D | 17_Q | 1.147 | 0.53 |
| 21_F | 25_P | 1.136 | 0.51 |
| 7_N | 12_S | 1.108 | 0.49 |
| 16_D | 20_I | 1.082 | 0.46 |
| 14_Q | 18_K | 1.069 | 0.45 |
| 42_D | 47_S | 1.053 | 0.43 |
| 48_L | 51_L | 1.043 | 0.42 |
| 7_N | 42_D | 1.030 | 0.41 |
| 1_M | 26_P | 1.010 | 0.39 |
| 43_D | 52_N | 1.005 | 0.39 |
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 | |
| 1qtqA | 1 | 0.4815 | 14.4 | 0.876 | Contact Map |
| 5bnzA | 2 | 0 | 12 | 0.88 | Contact Map |
| 4h3sA | 1 | 0.5185 | 4.8 | 0.9 | Contact Map |
| 4r3zC | 1 | 0.463 | 4.6 | 0.901 | Contact Map |
| 4p2bA | 1 | 0.3889 | 3.3 | 0.907 | Contact Map |
| 2hz7A | 1 | 0.4444 | 2.5 | 0.913 | Contact Map |
| 4j07A | 5 | 0.963 | 2.4 | 0.914 | Contact Map |
| 4lr4A | 4 | 0.9259 | 2.4 | 0.914 | Contact Map |
| 1hqkA | 5 | 1 | 1.7 | 0.921 | Contact Map |
| 2b99A | 5 | 0.9074 | 1.6 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)