| T0814 360-424 |
| ID: | 1404852228 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 65 (60) | ||
| Sequences: | 216 (187.9) | ||
| Seq/Len: | 3.600 | ||
| Nf(neff/√len): | 24.3 |
Jackhmmer Results: (2014_04_16)
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: 3.600).
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 |
| 43_R | 50_D | 3.562 | 1.00 |
| 37_S | 55_V | 3.003 | 1.00 |
| 39_Y | 52_L | 2.331 | 1.00 |
| 44_P | 47_A | 2.302 | 1.00 |
| 1_L | 6_Y | 2.161 | 1.00 |
| 3_Q | 50_D | 1.681 | 0.99 |
| 5_S | 25_I | 1.534 | 0.97 |
| 48_R | 52_L | 1.494 | 0.97 |
| 37_S | 49_Y | 1.425 | 0.96 |
| 7_N | 25_I | 1.412 | 0.95 |
| 26_E | 56_T | 1.382 | 0.95 |
| 46_G | 49_Y | 1.380 | 0.94 |
| 6_Y | 46_G | 1.256 | 0.90 |
| 5_S | 39_Y | 1.241 | 0.89 |
| 23_G | 28_N | 1.165 | 0.85 |
| 18_S | 59_R | 1.116 | 0.81 |
| 44_P | 51_R | 1.090 | 0.79 |
| 26_E | 52_L | 1.078 | 0.78 |
| 33_Q | 39_Y | 1.069 | 0.77 |
| 17_S | 31_Q | 1.057 | 0.76 |
| 5_S | 49_Y | 1.051 | 0.75 |
| 44_P | 49_Y | 1.041 | 0.74 |
| 14_P | 17_S | 1.036 | 0.74 |
| 17_S | 20_G | 1.030 | 0.73 |
| 14_P | 18_S | 1.027 | 0.73 |
| 35_E | 38_I | 1.003 | 0.70 |
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 | |
| 3ce2A | 1 | 0.7846 | 5.7 | 0.919 | Contact Map |
| 2qr4A | 2 | 0.7846 | 4.1 | 0.924 | Contact Map |
| 3hl6A | 2 | 0.2308 | 3.7 | 0.926 | Contact Map |
| 1jg7A | 1 | 0.4769 | 3.2 | 0.928 | Contact Map |
| 3n2oA | 4 | 0.2 | 2.7 | 0.931 | Contact Map |
| 2gzqA | 1 | 0.4769 | 2.6 | 0.932 | Contact Map |
| 2e8gA | 2 | 0.5692 | 2.5 | 0.932 | Contact Map |
| 1gcyA | 1 | 0 | 2.4 | 0.933 | Contact Map |
| 2licA | 1 | 0.4923 | 2.3 | 0.933 | Contact Map |
| 3qwnA | 12 | 0.9538 | 2.1 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)