| 4a20A |
| ID: | 1379300283 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 80 (74) | ||
| Sequences: | 1037 (707.4) | ||
| Seq/Len: | 14.014 | ||
| Nf(neff/√len): | 82.2 |
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: 14.014).
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 |
| 29_Q | 32_Q | 2.632 | 1.00 |
| 59_L | 63_D | 2.220 | 1.00 |
| 31_K | 57_D | 2.004 | 1.00 |
| 5_L | 21_F | 1.907 | 1.00 |
| 67_T | 71_S | 1.836 | 1.00 |
| 56_H | 59_L | 1.796 | 1.00 |
| 23_P | 62_S | 1.688 | 1.00 |
| 17_I | 21_F | 1.657 | 1.00 |
| 42_H | 46_I | 1.554 | 1.00 |
| 49_L | 76_M | 1.484 | 1.00 |
| 60_F | 63_D | 1.483 | 1.00 |
| 30_I | 73_I | 1.450 | 1.00 |
| 38_E | 41_S | 1.437 | 1.00 |
| 59_L | 64_L | 1.390 | 0.99 |
| 25_D | 33_H | 1.374 | 0.99 |
| 48_L | 64_L | 1.352 | 0.99 |
| 66_V | 73_I | 1.348 | 0.99 |
| 33_H | 36_S | 1.348 | 0.99 |
| 34_L | 61_L | 1.323 | 0.99 |
| 28_L | 32_Q | 1.316 | 0.99 |
| 41_S | 46_I | 1.273 | 0.99 |
| 49_L | 54_V | 1.251 | 0.99 |
| 9_K | 13_P | 1.240 | 0.98 |
| 34_L | 46_I | 1.197 | 0.98 |
| 25_D | 29_Q | 1.176 | 0.98 |
| 35_I | 44_S | 1.166 | 0.97 |
| 31_K | 46_I | 1.160 | 0.97 |
| 28_L | 57_D | 1.149 | 0.97 |
| 32_Q | 44_S | 1.142 | 0.97 |
| 49_L | 52_G | 1.128 | 0.97 |
| 25_D | 30_I | 1.117 | 0.96 |
| 21_F | 25_D | 1.112 | 0.96 |
| 6_T | 14_K | 1.111 | 0.96 |
| 22_S | 25_D | 1.109 | 0.96 |
| 22_S | 37_E | 1.108 | 0.96 |
| 12_A | 51_K | 1.100 | 0.96 |
| 59_L | 62_S | 1.099 | 0.96 |
| 4_H | 16_S | 1.054 | 0.95 |
| 49_L | 74_T | 1.027 | 0.94 |
| 32_Q | 36_S | 1.005 | 0.93 |
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 | |
| 4k95A | 12 | 0.9125 | 99.7 | 0.153 | Contact Map |
| 1oqyA | 1 | 0.9625 | 99.7 | 0.16 | Contact Map |
| 3ai5A | 1 | 0.9125 | 99.7 | 0.17 | Contact Map |
| 1se9A | 1 | 0.95 | 99.6 | 0.18 | Contact Map |
| 3u5cf | 1 | 0 | 99.6 | 0.19 | Contact Map |
| 3v7oA | 2 | 0.9375 | 99.6 | 0.195 | Contact Map |
| 2k8hA | 1 | 0.95 | 99.6 | 0.196 | Contact Map |
| 2dafA | 1 | 0.95 | 99.6 | 0.199 | Contact Map |
| 3tixA | 2 | 0.9375 | 99.6 | 0.2 | Contact Map |
| 3u5em | 1 | 0 | 99.6 | 0.202 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)