| testMSA_representSequence |
| ID: | 1506153679 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (103) | ||
| Sequences: | 1496 (684.9) | ||
| Seq/Len: | 14.524 | ||
| Nf(neff/√len): | 67.5 |
HHblits Results: (2016_02)
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: 14.524).
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 |
| 46_E | 100_K | 2.646 | 1.00 |
| 11_E | 14_K | 2.056 | 1.00 |
| 73_Q | 76_T | 2.023 | 1.00 |
| 12_E | 54_V | 1.997 | 1.00 |
| 34_D | 37_G | 1.960 | 1.00 |
| 10_Q | 14_K | 1.945 | 1.00 |
| 71_V | 75_R | 1.916 | 1.00 |
| 69_M | 73_Q | 1.831 | 1.00 |
| 90_E | 93_N | 1.718 | 1.00 |
| 15_R | 47_E | 1.715 | 1.00 |
| 53_R | 90_E | 1.713 | 1.00 |
| 37_G | 40_M | 1.703 | 1.00 |
| 74_L | 78_L | 1.685 | 1.00 |
| 20_Y | 24_M | 1.662 | 1.00 |
| 66_Q | 69_M | 1.657 | 1.00 |
| 22_Q | 44_T | 1.552 | 1.00 |
| 72_E | 75_R | 1.548 | 1.00 |
| 35_R | 39_K | 1.542 | 1.00 |
| 72_E | 76_T | 1.480 | 1.00 |
| 88_M | 92_M | 1.479 | 1.00 |
| 68_K | 72_E | 1.373 | 0.99 |
| 53_R | 93_N | 1.367 | 0.99 |
| 16_L | 48_L | 1.361 | 0.99 |
| 47_E | 51_R | 1.358 | 0.99 |
| 92_M | 96_L | 1.357 | 0.99 |
| 35_R | 38_K | 1.351 | 0.99 |
| 98_R | 101_S | 1.336 | 0.99 |
| 77_Q | 80_Q | 1.329 | 0.99 |
| 42_I | 103_L | 1.317 | 0.99 |
| 12_E | 15_R | 1.314 | 0.99 |
| 90_E | 94_Q | 1.313 | 0.99 |
| 94_Q | 98_R | 1.309 | 0.99 |
| 50_E | 53_R | 1.302 | 0.99 |
| 68_K | 71_V | 1.253 | 0.99 |
| 71_V | 74_L | 1.214 | 0.98 |
| 50_E | 54_V | 1.200 | 0.98 |
| 97_S | 101_S | 1.194 | 0.98 |
| 11_E | 15_R | 1.185 | 0.98 |
| 69_M | 72_E | 1.162 | 0.97 |
| 29_E | 32_K | 1.154 | 0.97 |
| 6_S | 61_L | 1.152 | 0.97 |
| 8_I | 12_E | 1.127 | 0.97 |
| 67_A | 70_T | 1.104 | 0.96 |
| 88_M | 95_T | 1.100 | 0.96 |
| 25_Q | 37_G | 1.096 | 0.96 |
| 91_Q | 94_Q | 1.091 | 0.96 |
| 96_L | 99_M | 1.087 | 0.96 |
| 95_T | 98_R | 1.070 | 0.95 |
| 75_R | 79_G | 1.064 | 0.95 |
| 11_E | 18_N | 1.055 | 0.95 |
| 9_V | 55_F | 1.031 | 0.94 |
| 48_L | 52_Y | 1.005 | 0.93 |
| 16_L | 59_F | 1.004 | 0.93 |
| 33_F | 41_F | 1.000 | 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 | |
| 3onjA | 1 | 0.7864 | 41 | 0.896 | Contact Map |
| 1vcsA | 1 | 0.7767 | 25.1 | 0.907 | Contact Map |
| 2qywA | 1 | 0.7864 | 21.5 | 0.91 | Contact Map |
| 1v2zA | 1 | 0.699 | 17.7 | 0.913 | Contact Map |
| 3zg1A | 4 | 0.5243 | 17.5 | 0.913 | Contact Map |
| 2o8xA | 3 | 0.5922 | 16.2 | 0.915 | Contact Map |
| 1r5qA | 1 | 0.5825 | 15.3 | 0.916 | Contact Map |
| 1l9zH | 1 | 0.9223 | 12.8 | 0.919 | Contact Map |
| 2a6hF | 2 | 0.9029 | 12.8 | 0.919 | Contact Map |
| 2xxaA | 2 | 0.7864 | 10.5 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)