| small domain |
| ID: | 1383353193 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 66 (61) | ||
| Sequences: | 92 (63.7) | ||
| Seq/Len: | 1.508 | ||
| Nf(neff/√len): | 8.2 |
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: 1.508).
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 |
| 1_K | 57_S | 1.832 | 0.96 |
| 1_K | 56_L | 1.678 | 0.93 |
| 33_A | 36_G | 1.592 | 0.90 |
| 24_I | 31_S | 1.590 | 0.90 |
| 2_L | 65_V | 1.478 | 0.85 |
| 8_D | 52_S | 1.462 | 0.84 |
| 3_K | 7_V | 1.409 | 0.81 |
| 6_F | 10_E | 1.406 | 0.81 |
| 8_D | 53_R | 1.406 | 0.81 |
| 50_S | 56_L | 1.390 | 0.80 |
| 32_A | 36_G | 1.388 | 0.80 |
| 32_A | 38_I | 1.338 | 0.76 |
| 3_K | 54_A | 1.311 | 0.74 |
| 55_F | 62_P | 1.277 | 0.71 |
| 7_V | 10_E | 1.277 | 0.71 |
| 51_Q | 62_P | 1.264 | 0.70 |
| 44_E | 48_R | 1.233 | 0.68 |
| 47_L | 50_S | 1.227 | 0.67 |
| 3_K | 8_D | 1.197 | 0.64 |
| 8_D | 54_A | 1.187 | 0.63 |
| 10_E | 62_P | 1.175 | 0.62 |
| 2_L | 11_F | 1.168 | 0.61 |
| 38_I | 41_A | 1.144 | 0.59 |
| 56_L | 61_L | 1.141 | 0.59 |
| 3_K | 10_E | 1.097 | 0.54 |
| 51_Q | 54_A | 1.088 | 0.53 |
| 23_Q | 30_T | 1.086 | 0.53 |
| 2_L | 20_Q | 1.084 | 0.53 |
| 7_V | 62_P | 1.080 | 0.52 |
| 7_V | 54_A | 1.050 | 0.49 |
| 9_V | 26_H | 1.030 | 0.47 |
| 24_I | 61_L | 1.005 | 0.45 |
| 21_Q | 42_P | 1.001 | 0.44 |
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 | |
| 4ee6A | 1 | 0.7879 | 8.7 | 0.89 | Contact Map |
| 2nu8B | 2 | 0.3333 | 6.4 | 0.896 | Contact Map |
| 3ufxB | 4 | 0.3333 | 6.3 | 0.896 | Contact Map |
| 2fp4B | 1 | 0.3333 | 4.8 | 0.902 | Contact Map |
| 1zdyA | 1 | 0.7121 | 2.4 | 0.916 | Contact Map |
| 4hvfA | 4 | 0.8939 | 2.3 | 0.917 | Contact Map |
| 2iovA | 4 | 0.8788 | 2.2 | 0.917 | Contact Map |
| 4h3dA | 4 | 0.6667 | 2.2 | 0.918 | Contact Map |
| 2yr1A | 2 | 0.6515 | 2.1 | 0.918 | Contact Map |
| 2gw3A | 2 | 0.8788 | 2.1 | 0.918 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)