| 8826_1 |
| ID: | 1433409111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (59) | ||
| Sequences: | 69 (36.7) | ||
| Seq/Len: | 1.169 | ||
| Nf(neff/√len): | 4.8 |
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: 1.169).
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 |
| 25_A | 28_I | 1.713 | 0.91 |
| 2_L | 6_L | 1.676 | 0.89 |
| 3_Q | 9_E | 1.604 | 0.86 |
| 43_E | 56_E | 1.602 | 0.86 |
| 24_K | 33_K | 1.507 | 0.81 |
| 30_T | 50_R | 1.431 | 0.76 |
| 5_A | 8_A | 1.420 | 0.75 |
| 12_A | 20_L | 1.403 | 0.74 |
| 42_S | 56_E | 1.388 | 0.73 |
| 22_K | 34_L | 1.374 | 0.72 |
| 34_L | 41_N | 1.352 | 0.70 |
| 6_L | 9_E | 1.342 | 0.69 |
| 11_R | 26_A | 1.318 | 0.67 |
| 41_N | 44_L | 1.258 | 0.62 |
| 1_E | 31_E | 1.251 | 0.61 |
| 29_S | 45_L | 1.240 | 0.60 |
| 21_N | 32_C | 1.229 | 0.59 |
| 34_L | 37_G | 1.215 | 0.58 |
| 3_Q | 6_L | 1.211 | 0.58 |
| 16_I | 58_I | 1.203 | 0.57 |
| 3_Q | 12_A | 1.182 | 0.55 |
| 3_Q | 20_L | 1.115 | 0.49 |
| 2_L | 9_E | 1.104 | 0.47 |
| 4_S | 13_K | 1.088 | 0.46 |
| 30_T | 54_E | 1.087 | 0.46 |
| 1_E | 5_A | 1.082 | 0.45 |
| 28_I | 43_E | 1.082 | 0.45 |
| 40_R | 45_L | 1.082 | 0.45 |
| 41_N | 47_D | 1.064 | 0.44 |
| 1_E | 14_Q | 1.062 | 0.43 |
| 2_L | 8_A | 1.046 | 0.42 |
| 33_K | 42_S | 1.039 | 0.41 |
| 25_A | 54_E | 1.032 | 0.41 |
| 1_E | 9_E | 1.025 | 0.40 |
| 9_E | 20_L | 1.023 | 0.40 |
| 16_I | 39_K | 1.023 | 0.40 |
| 31_E | 51_L | 1.018 | 0.39 |
| 23_V | 43_E | 1.001 | 0.38 |
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 | |
| 1wt6A | 3 | 0.9836 | 93.7 | 0.692 | Contact Map |
| 4q4gX | 1 | 0 | 63 | 0.787 | Contact Map |
| 2dfsA | 2 | 0.7541 | 55.4 | 0.797 | Contact Map |
| 4cgkA | 2 | 0.9016 | 52.5 | 0.799 | Contact Map |
| 1i84S | 2 | 0 | 50.3 | 0.802 | Contact Map |
| 3ojaB | 1 | 1 | 36.1 | 0.818 | Contact Map |
| 3q0xA | 2 | 0.9672 | 34.8 | 0.82 | Contact Map |
| 3cazA | 2 | 0.541 | 33.5 | 0.822 | Contact Map |
| 4ll8A | 1 | 0.541 | 32.7 | 0.823 | Contact Map |
| 3hnwA | 2 | 0.9508 | 31.2 | 0.825 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)