| 2WIE |
| ID: | 1448230319 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (76) | ||
| Sequences: | 1719 (834.5) | ||
| Seq/Len: | 22.618 | ||
| Nf(neff/√len): | 95.7 |
HHblits Results: (2015_06)
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: 22.618).
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 |
| 35_Q | 38_E | 3.871 | 1.00 |
| 33_A | 57_S | 3.447 | 1.00 |
| 29_Q | 63_A | 2.432 | 1.00 |
| 47_E | 51_R | 2.395 | 1.00 |
| 46_A | 50_I | 1.841 | 1.00 |
| 36_A | 50_I | 1.822 | 1.00 |
| 29_Q | 61_M | 1.635 | 1.00 |
| 16_L | 20_I | 1.600 | 1.00 |
| 40_I | 53_T | 1.546 | 1.00 |
| 21_G | 68_G | 1.472 | 1.00 |
| 18_V | 68_G | 1.420 | 1.00 |
| 29_Q | 64_L | 1.405 | 0.99 |
| 29_Q | 58_L | 1.383 | 0.99 |
| 25_P | 65_T | 1.342 | 0.99 |
| 40_I | 47_E | 1.326 | 0.99 |
| 24_G | 28_G | 1.319 | 0.99 |
| 73_L | 77_F | 1.314 | 0.99 |
| 31_Q | 34_G | 1.288 | 0.99 |
| 25_P | 29_Q | 1.271 | 0.99 |
| 33_A | 58_L | 1.266 | 0.99 |
| 14_A | 76_L | 1.242 | 0.98 |
| 54_L | 58_L | 1.231 | 0.98 |
| 31_Q | 35_Q | 1.225 | 0.98 |
| 5_L | 8_A | 1.182 | 0.98 |
| 9_A | 12_I | 1.158 | 0.97 |
| 27_L | 31_Q | 1.156 | 0.97 |
| 58_L | 64_L | 1.142 | 0.97 |
| 32_A | 61_M | 1.119 | 0.96 |
| 19_G | 22_S | 1.083 | 0.96 |
| 5_L | 9_A | 1.068 | 0.95 |
| 36_A | 63_A | 1.057 | 0.95 |
| 17_A | 72_A | 1.057 | 0.95 |
| 29_Q | 60_F | 1.045 | 0.94 |
| 36_A | 54_L | 1.035 | 0.94 |
| 37_V | 50_I | 1.022 | 0.93 |
| 51_R | 55_L | 1.018 | 0.93 |
| 32_A | 58_L | 1.006 | 0.93 |
| 70_V | 73_L | 1.005 | 0.93 |
| 60_F | 63_A | 1.002 | 0.92 |
| 40_I | 46_A | 1.002 | 0.92 |
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 | |
| 2xquA | 5 | 0.9878 | 99.8 | 0.061 | Contact Map |
| 4v1gA | 3 | 0 | 99.8 | 0.08 | Contact Map |
| 1a91A | 1 | 0.9634 | 99.7 | 0.096 | Contact Map |
| 3zk1A | 22 | 0.9878 | 99.7 | 0.132 | Contact Map |
| 4bemA | 9 | 0.9756 | 99.7 | 0.134 | Contact Map |
| 4bemJ | 1 | 0.9878 | 99.7 | 0.139 | Contact Map |
| 1wu0A | 1 | 0.878 | 99.6 | 0.187 | Contact Map |
| 4cbkA | 13 | 0.8293 | 99.6 | 0.196 | Contact Map |
| 4f4sA | 10 | 0.9024 | 99.6 | 0.21 | Contact Map |
| 2xndJ | 8 | 0.878 | 99.5 | 0.227 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)