| SYNTH low coverage |
| ID: | 1452592411 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 131 (130) | ||
| Sequences: | 1256 (626.8) | ||
| Seq/Len: | 9.662 | ||
| Nf(neff/√len): | 55.0 |
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: 9.662).
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 |
| 56_D | 113_E | 3.537 | 1.00 |
| 54_I | 113_E | 2.939 | 1.00 |
| 57_S | 60_D | 2.910 | 1.00 |
| 11_R | 14_S | 2.783 | 1.00 |
| 8_I | 68_V | 2.613 | 1.00 |
| 22_F | 116_D | 2.578 | 1.00 |
| 18_P | 56_D | 2.515 | 1.00 |
| 40_I | 45_M | 2.445 | 1.00 |
| 20_R | 113_E | 2.387 | 1.00 |
| 1_V | 23_G | 2.271 | 1.00 |
| 68_V | 98_V | 2.108 | 1.00 |
| 3_L | 102_R | 2.077 | 1.00 |
| 55_V | 64_A | 1.853 | 1.00 |
| 33_R | 37_R | 1.787 | 1.00 |
| 59_E | 63_R | 1.765 | 1.00 |
| 4_V | 106_I | 1.639 | 1.00 |
| 11_R | 71_A | 1.619 | 1.00 |
| 48_I | 84_S | 1.612 | 1.00 |
| 9_A | 13_E | 1.588 | 1.00 |
| 10_A | 14_S | 1.571 | 1.00 |
| 60_D | 63_R | 1.503 | 1.00 |
| 113_E | 117_R | 1.465 | 1.00 |
| 74_S | 84_S | 1.448 | 1.00 |
| 69_H | 96_T | 1.418 | 0.99 |
| 92_R | 118_V | 1.395 | 0.99 |
| 56_D | 60_D | 1.393 | 0.99 |
| 65_L | 69_H | 1.386 | 0.99 |
| 35_L | 82_F | 1.359 | 0.99 |
| 117_R | 121_E | 1.343 | 0.99 |
| 58_E | 70_R | 1.317 | 0.99 |
| 64_A | 67_V | 1.310 | 0.99 |
| 53_V | 64_A | 1.307 | 0.99 |
| 2_A | 5_S | 1.306 | 0.99 |
| 78_R | 97_T | 1.285 | 0.99 |
| 80_K | 97_T | 1.281 | 0.99 |
| 62_Y | 69_H | 1.255 | 0.98 |
| 15_S | 67_V | 1.253 | 0.98 |
| 55_V | 60_D | 1.233 | 0.98 |
| 4_V | 51_F | 1.213 | 0.98 |
| 12_L | 64_A | 1.181 | 0.97 |
| 2_A | 6_Q | 1.159 | 0.97 |
| 116_D | 120_E | 1.149 | 0.97 |
| 69_H | 79_F | 1.138 | 0.97 |
| 8_I | 108_M | 1.131 | 0.97 |
| 4_V | 72_W | 1.128 | 0.96 |
| 9_A | 20_R | 1.117 | 0.96 |
| 5_S | 9_A | 1.116 | 0.96 |
| 12_L | 19_A | 1.116 | 0.96 |
| 65_L | 87_K | 1.107 | 0.96 |
| 20_R | 35_L | 1.102 | 0.96 |
| 5_S | 51_F | 1.100 | 0.96 |
| 99_V | 103_G | 1.077 | 0.95 |
| 57_S | 114_A | 1.052 | 0.94 |
| 62_Y | 65_L | 1.050 | 0.94 |
| 25_E | 42_F | 1.048 | 0.94 |
| 94_L | 103_G | 1.047 | 0.94 |
| 19_A | 64_A | 1.035 | 0.94 |
| 13_E | 19_A | 1.020 | 0.93 |
| 49_Y | 106_I | 1.016 | 0.93 |
| 13_E | 18_P | 1.005 | 0.92 |
| 40_I | 51_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 | |
| 1vj7A | 2 | 0.9466 | 100 | 0.235 | Contact Map |
| 3l9dA | 2 | 0.9847 | 100 | 0.364 | Contact Map |
| 2be3A | 2 | 0.9924 | 100 | 0.397 | Contact Map |
| 1elkA | 2 | 0.3359 | 26.3 | 0.951 | Contact Map |
| 3u65B | 2 | 0.8321 | 17.8 | 0.954 | Contact Map |
| 1nthA | 1 | 0.4962 | 12.2 | 0.958 | Contact Map |
| 4ovtA | 2 | 0.8473 | 9.1 | 0.96 | Contact Map |
| 3fxbA | 2 | 0.8397 | 8.9 | 0.96 | Contact Map |
| 2vpnA | 2 | 0.8397 | 8 | 0.961 | Contact Map |
| 4xeqA | 4 | 0.8397 | 7.3 | 0.962 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)