| test3 |
| ID: | 1478096505 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (94) | ||
| Sequences: | 10308 (7955.2) | ||
| Seq/Len: | 109.660 | ||
| Nf(neff/√len): | 820.5 |
Jackhmmer Results: (2016_04)
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: 109.660).
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 |
| 21_M | 33_Q | 1.613 | 1.00 |
| 18_Q | 30_T | 1.515 | 1.00 |
| 67_H | 79_P | 1.475 | 1.00 |
| 27_H | 39_L | 1.447 | 1.00 |
| 64_P | 76_P | 1.433 | 1.00 |
| 33_Q | 45_Q | 1.429 | 1.00 |
| 30_T | 42_P | 1.392 | 0.99 |
| 76_P | 88_P | 1.344 | 0.99 |
| 58_Q | 70_Q | 1.336 | 0.99 |
| 73_P | 85_Q | 1.316 | 0.99 |
| 24_P | 36_Q | 1.300 | 0.99 |
| 61_Q | 73_P | 1.242 | 0.98 |
| 53_Q | 64_P | 1.223 | 0.98 |
| 27_H | 45_Q | 1.212 | 0.98 |
| 33_Q | 70_Q | 1.195 | 0.98 |
| 30_T | 36_Q | 1.191 | 0.98 |
| 15_I | 27_H | 1.189 | 0.98 |
| 53_Q | 88_P | 1.173 | 0.98 |
| 53_Q | 76_P | 1.163 | 0.97 |
| 79_P | 91_L | 1.163 | 0.97 |
| 21_M | 45_Q | 1.157 | 0.97 |
| 24_P | 42_P | 1.157 | 0.97 |
| 62_P | 74_P | 1.153 | 0.97 |
| 26_Q | 29_M | 1.139 | 0.97 |
| 55_Q | 67_H | 1.139 | 0.97 |
| 61_Q | 79_P | 1.130 | 0.97 |
| 21_M | 39_L | 1.125 | 0.97 |
| 67_H | 91_L | 1.125 | 0.97 |
| 64_P | 88_P | 1.124 | 0.97 |
| 39_L | 45_Q | 1.123 | 0.97 |
| 55_Q | 58_Q | 1.114 | 0.96 |
| 65_P | 83_P | 1.108 | 0.96 |
| 44_Q | 47_Y | 1.107 | 0.96 |
| 73_P | 79_P | 1.103 | 0.96 |
| 67_H | 73_P | 1.097 | 0.96 |
| 61_Q | 85_Q | 1.096 | 0.96 |
| 24_P | 30_T | 1.077 | 0.95 |
| 30_T | 48_Q | 1.069 | 0.95 |
| 18_Q | 24_P | 1.064 | 0.95 |
| 67_H | 85_Q | 1.059 | 0.95 |
| 70_Q | 82_F | 1.054 | 0.95 |
| 35_H | 38_N | 1.050 | 0.94 |
| 39_L | 64_P | 1.050 | 0.94 |
| 73_P | 76_P | 1.037 | 0.94 |
| 50_Q | 53_Q | 1.037 | 0.94 |
| 79_P | 82_F | 1.024 | 0.93 |
| 12_Q | 15_I | 1.018 | 0.93 |
| 90_M | 93_D | 1.014 | 0.93 |
| 78_L | 81_M | 1.010 | 0.93 |
| 9_P | 12_Q | 1.007 | 0.93 |
| 55_Q | 73_P | 1.005 | 0.93 |
| 15_I | 21_M | 1.003 | 0.93 |
| 68_P | 80_P | 1.002 | 0.92 |
| 27_H | 64_P | 1.001 | 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 | |
| 1wckA | 1 | 0.16 | 2.2 | 0.877 | Contact Map |
| 2o8lA | 1 | 0.08 | 1.8 | 0.883 | Contact Map |
| 1pwbA | 3 | 0.26 | 1 | 0.902 | Contact Map |
| 2wd6A | 2 | 0.16 | 0.6 | 0.913 | Contact Map |
| 2ptrA | 2 | 0.31 | 0.5 | 0.918 | Contact Map |
| 4p7tA | 6 | 0.1 | 0.4 | 0.923 | Contact Map |
| 2klwA | 1 | 0.3 | 0.4 | 0.924 | Contact Map |
| 4yc7B | 1 | 0 | 0.4 | 0.928 | Contact Map |
| 4nh0A | 2 | 0 | 0.3 | 0.933 | Contact Map |
| 3cnqP | 1 | 0.28 | 0.3 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)