| yt4 |
| ID: | 1397683749 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 51 (51) | ||
| Sequences: | 415 (246) | ||
| Seq/Len: | 8.137 | ||
| Nf(neff/√len): | 34.4 |
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: 8.137).
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 |
| 37_H | 45_N | 1.860 | 1.00 |
| 1_E | 15_I | 1.823 | 1.00 |
| 44_F | 49_A | 1.582 | 1.00 |
| 5_Y | 26_L | 1.467 | 0.99 |
| 28_A | 49_A | 1.418 | 0.99 |
| 2_E | 16_R | 1.412 | 0.99 |
| 13_P | 47_F | 1.410 | 0.99 |
| 2_E | 14_A | 1.373 | 0.99 |
| 23_S | 35_Y | 1.357 | 0.99 |
| 29_G | 36_V | 1.350 | 0.99 |
| 9_W | 51_S | 1.288 | 0.98 |
| 33_T | 51_S | 1.280 | 0.98 |
| 2_E | 42_L | 1.277 | 0.98 |
| 36_V | 39_E | 1.263 | 0.98 |
| 8_I | 11_S | 1.261 | 0.98 |
| 14_A | 25_S | 1.219 | 0.97 |
| 5_Y | 9_W | 1.203 | 0.97 |
| 41_T | 46_F | 1.193 | 0.97 |
| 17_S | 45_N | 1.192 | 0.97 |
| 33_T | 48_L | 1.149 | 0.96 |
| 15_I | 20_Y | 1.127 | 0.95 |
| 32_S | 50_H | 1.097 | 0.94 |
| 4_S | 24_G | 1.096 | 0.94 |
| 13_P | 28_A | 1.092 | 0.94 |
| 26_L | 35_Y | 1.072 | 0.93 |
| 42_L | 46_F | 1.051 | 0.92 |
| 1_E | 16_R | 1.009 | 0.90 |
| 8_I | 34_V | 1.001 | 0.89 |
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 | |
| 2vtwA | 6 | 0.4118 | 1.4 | 0.888 | Contact Map |
| 4lx2A | 1 | 0.7059 | 1.4 | 0.889 | Contact Map |
| 2b7uA | 1 | 0.451 | 1.3 | 0.892 | Contact Map |
| 3hocA | 2 | 0.3333 | 1.2 | 0.893 | Contact Map |
| 3j4sA | 1 | 0 | 1.1 | 0.895 | Contact Map |
| 2wa7A | 1 | 0.2941 | 1.1 | 0.897 | Contact Map |
| 4ltoA | 4 | 0.7647 | 1 | 0.899 | Contact Map |
| 3zjzA | 4 | 0.7451 | 0.9 | 0.9 | Contact Map |
| 4l8tA | 1 | 1 | 0.9 | 0.903 | Contact Map |
| 4bgnA | 2 | 0.8431 | 0.8 | 0.905 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)