| 3ze3A |
| ID: | 1491911939 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (114) | ||
| Sequences: | 2512 (1808.7) | ||
| Seq/Len: | 22.035 | ||
| Nf(neff/√len): | 169.4 |
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: 22.035).
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 |
| 74_V | 85_S | 3.333 | 1.00 |
| 14_K | 86_G | 3.046 | 1.00 |
| 19_A | 65_L | 2.889 | 1.00 |
| 20_W | 30_G | 2.884 | 1.00 |
| 63_V | 66_L | 2.485 | 1.00 |
| 58_M | 102_D | 2.256 | 1.00 |
| 33_V | 57_V | 2.240 | 1.00 |
| 17_R | 21_I | 2.170 | 1.00 |
| 76_R | 85_S | 1.962 | 1.00 |
| 16_L | 94_A | 1.895 | 1.00 |
| 40_A | 50_R | 1.810 | 1.00 |
| 62_I | 99_A | 1.793 | 1.00 |
| 63_V | 99_A | 1.792 | 1.00 |
| 73_V | 88_A | 1.780 | 1.00 |
| 72_A | 87_R | 1.762 | 1.00 |
| 20_W | 31_V | 1.575 | 1.00 |
| 108_A | 112_W | 1.565 | 1.00 |
| 46_D | 49_T | 1.554 | 1.00 |
| 60_V | 96_V | 1.553 | 1.00 |
| 68_S | 91_L | 1.519 | 1.00 |
| 59_L | 99_A | 1.495 | 1.00 |
| 18_A | 87_R | 1.455 | 1.00 |
| 26_F | 61_M | 1.441 | 1.00 |
| 44_D | 50_R | 1.430 | 1.00 |
| 48_V | 52_L | 1.423 | 1.00 |
| 65_L | 91_L | 1.397 | 0.99 |
| 45_V | 110_L | 1.382 | 0.99 |
| 22_N | 87_R | 1.359 | 0.99 |
| 65_L | 94_A | 1.334 | 0.99 |
| 73_V | 77_I | 1.325 | 0.99 |
| 19_A | 26_F | 1.323 | 0.99 |
| 26_F | 29_E | 1.320 | 0.99 |
| 19_A | 91_L | 1.306 | 0.99 |
| 52_L | 56_S | 1.284 | 0.99 |
| 63_V | 95_A | 1.282 | 0.99 |
| 11_Y | 14_K | 1.272 | 0.99 |
| 37_V | 57_V | 1.237 | 0.98 |
| 49_T | 114_H | 1.235 | 0.98 |
| 49_T | 110_L | 1.235 | 0.98 |
| 84_L | 88_A | 1.223 | 0.98 |
| 12_S | 93_S | 1.196 | 0.98 |
| 107_W | 111_L | 1.184 | 0.98 |
| 7_K | 10_G | 1.170 | 0.97 |
| 65_L | 98_I | 1.162 | 0.97 |
| 5_I | 24_A | 1.142 | 0.97 |
| 54_I | 102_D | 1.132 | 0.97 |
| 5_I | 9_A | 1.126 | 0.97 |
| 55_S | 102_D | 1.114 | 0.96 |
| 5_I | 28_Q | 1.102 | 0.96 |
| 45_V | 53_L | 1.095 | 0.96 |
| 38_V | 42_W | 1.085 | 0.96 |
| 23_E | 72_A | 1.079 | 0.95 |
| 60_V | 103_A | 1.064 | 0.95 |
| 29_E | 96_V | 1.059 | 0.95 |
| 112_W | 115_F | 1.030 | 0.94 |
| 47_A | 51_V | 1.010 | 0.93 |
| 25_A | 29_E | 1.003 | 0.93 |
| 77_I | 85_S | 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 | |
| 3ze3A | 6 | 1 | 100 | 0.012 | Contact Map |
| 4w252 | 1 | 0.4138 | 7.1 | 0.932 | Contact Map |
| 1rh5B | 1 | 0.3362 | 6.5 | 0.933 | Contact Map |
| 4b03D | 3 | 0.5603 | 4.4 | 0.938 | Contact Map |
| 3b8cA | 2 | 0.931 | 3.7 | 0.941 | Contact Map |
| 2lzrA | 1 | 0.3276 | 2.4 | 0.946 | Contact Map |
| 3mp7B | 1 | 0.3707 | 2.2 | 0.948 | Contact Map |
| 1pi7A | 1 | 0.1638 | 2 | 0.949 | Contact Map |
| 3nd0A | 2 | 0.2328 | 1.9 | 0.949 | Contact Map |
| 4od4A | 6 | 0.7845 | 1.9 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)