| den1b |
| ID: | 1433426506 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 60 (60) | ||
| Sequences: | 62 (36.4) | ||
| Seq/Len: | 1.033 | ||
| Nf(neff/√len): | 4.7 |
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: 1.033).
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_P | 8_P | 1.631 | 0.85 |
| 1_P | 4_L | 1.616 | 0.84 |
| 8_P | 13_D | 1.560 | 0.81 |
| 25_F | 59_L | 1.459 | 0.75 |
| 31_R | 40_H | 1.430 | 0.73 |
| 52_Q | 59_L | 1.422 | 0.72 |
| 48_I | 51_K | 1.398 | 0.70 |
| 32_V | 60_T | 1.363 | 0.67 |
| 28_D | 31_R | 1.354 | 0.67 |
| 14_Q | 27_F | 1.352 | 0.67 |
| 34_Q | 60_T | 1.324 | 0.64 |
| 37_V | 51_K | 1.320 | 0.64 |
| 41_F | 47_D | 1.319 | 0.64 |
| 8_P | 11_F | 1.280 | 0.60 |
| 1_P | 7_F | 1.255 | 0.58 |
| 15_E | 21_P | 1.255 | 0.58 |
| 17_L | 20_V | 1.249 | 0.57 |
| 38_G | 41_F | 1.216 | 0.54 |
| 38_G | 50_S | 1.215 | 0.54 |
| 44_V | 50_S | 1.207 | 0.54 |
| 2_V | 25_F | 1.204 | 0.53 |
| 31_R | 60_T | 1.203 | 0.53 |
| 21_P | 30_E | 1.191 | 0.52 |
| 1_P | 6_K | 1.187 | 0.52 |
| 1_P | 10_D | 1.168 | 0.50 |
| 1_P | 9_E | 1.159 | 0.49 |
| 39_Q | 56_F | 1.133 | 0.47 |
| 21_P | 49_E | 1.120 | 0.45 |
| 10_D | 49_E | 1.115 | 0.45 |
| 36_Q | 48_I | 1.091 | 0.43 |
| 6_K | 20_V | 1.082 | 0.42 |
| 36_Q | 51_K | 1.065 | 0.40 |
| 19_S | 41_F | 1.062 | 0.40 |
| 37_V | 48_I | 1.049 | 0.39 |
| 40_H | 49_E | 1.028 | 0.37 |
| 38_G | 48_I | 1.026 | 0.37 |
| 36_Q | 50_S | 1.019 | 0.36 |
| 25_F | 29_V | 1.018 | 0.36 |
| 20_V | 40_H | 1.016 | 0.36 |
| 12_G | 44_V | 1.002 | 0.35 |
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 | |
| 3tw8A | 2 | 1 | 99.5 | 0.468 | Contact Map |
| 2ywkA | 1 | 0.7833 | 5.9 | 0.921 | Contact Map |
| 4eo2A | 6 | 1 | 5 | 0.924 | Contact Map |
| 3wjmB | 3 | 0.9833 | 4.2 | 0.927 | Contact Map |
| 2xs2A | 1 | 0.7833 | 4.1 | 0.927 | Contact Map |
| 2zrrA | 1 | 0.75 | 4 | 0.927 | Contact Map |
| 2r47A | 5 | 0.75 | 3.7 | 0.928 | Contact Map |
| 2zf8A | 1 | 0.3833 | 3.7 | 0.928 | Contact Map |
| 1qtqA | 1 | 0.8 | 3.6 | 0.929 | Contact Map |
| 3hhsB | 1 | 0.9667 | 3.4 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)