| 4ipu |
| ID: | 1501760637 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 137 (128) | ||
| Sequences: | 753 (746) | ||
| Seq/Len: | 5.883 | ||
| Nf(neff/√len): | 65.9 |
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: 5.883).
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 |
| 28_E | 32_Q | 3.326 | 1.00 |
| 117_S | 125_Q | 2.410 | 1.00 |
| 6_T | 10_E | 2.266 | 1.00 |
| 12_Q | 16_E | 2.222 | 1.00 |
| 25_A | 38_I | 2.210 | 1.00 |
| 11_L | 104_I | 2.112 | 1.00 |
| 21_M | 50_L | 2.105 | 1.00 |
| 22_L | 38_I | 2.078 | 1.00 |
| 46_W | 49_G | 1.990 | 1.00 |
| 19_N | 116_L | 1.988 | 1.00 |
| 39_Q | 51_S | 1.903 | 1.00 |
| 17_E | 21_M | 1.812 | 1.00 |
| 39_Q | 105_C | 1.740 | 1.00 |
| 28_E | 31_S | 1.739 | 1.00 |
| 22_L | 124_I | 1.734 | 1.00 |
| 101_T | 117_S | 1.689 | 1.00 |
| 39_Q | 53_G | 1.606 | 0.99 |
| 37_S | 87_T | 1.599 | 0.99 |
| 32_Q | 36_I | 1.588 | 0.99 |
| 40_A | 46_W | 1.533 | 0.99 |
| 15_A | 126_L | 1.502 | 0.99 |
| 118_I | 124_I | 1.429 | 0.98 |
| 88_F | 124_I | 1.404 | 0.98 |
| 19_N | 23_Q | 1.389 | 0.98 |
| 11_L | 106_Q | 1.303 | 0.97 |
| 119_S | 125_Q | 1.298 | 0.97 |
| 25_A | 36_I | 1.298 | 0.97 |
| 35_A | 87_T | 1.288 | 0.96 |
| 33_R | 90_A | 1.285 | 0.96 |
| 11_L | 15_A | 1.282 | 0.96 |
| 118_I | 122_G | 1.273 | 0.96 |
| 101_T | 115_V | 1.236 | 0.95 |
| 2_I | 6_T | 1.229 | 0.95 |
| 94_L | 100_R | 1.220 | 0.95 |
| 14_A | 17_E | 1.209 | 0.94 |
| 101_T | 123_R | 1.182 | 0.94 |
| 28_E | 36_I | 1.178 | 0.93 |
| 37_S | 53_G | 1.176 | 0.93 |
| 115_V | 127_E | 1.167 | 0.93 |
| 22_L | 34_R | 1.156 | 0.93 |
| 12_Q | 114_R | 1.147 | 0.92 |
| 20_A | 121_A | 1.131 | 0.91 |
| 24_Y | 52_I | 1.127 | 0.91 |
| 55_L | 59_S | 1.125 | 0.91 |
| 30_V | 92_G | 1.102 | 0.90 |
| 15_A | 116_L | 1.100 | 0.90 |
| 38_I | 82_A | 1.096 | 0.90 |
| 88_F | 116_L | 1.085 | 0.89 |
| 53_G | 59_S | 1.080 | 0.89 |
| 33_R | 123_R | 1.067 | 0.88 |
| 23_Q | 124_I | 1.056 | 0.87 |
| 117_S | 123_R | 1.051 | 0.87 |
| 5_F | 8_R | 1.044 | 0.86 |
| 37_S | 84_E | 1.041 | 0.86 |
| 23_Q | 26_R | 1.017 | 0.84 |
| 120_Q | 124_I | 1.009 | 0.84 |
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 | |
| 4ipuA | 4 | 1 | 99.8 | 0.086 | Contact Map |
| 4dq9A | 2 | 0.8686 | 98.5 | 0.536 | Contact Map |
| 2knqA | 1 | 0.9051 | 97.6 | 0.633 | Contact Map |
| 1oqwA | 2 | 0.8832 | 10.8 | 0.881 | Contact Map |
| 1s21A | 1 | 0.4088 | 2 | 0.916 | Contact Map |
| 2w87A | 2 | 0.9416 | 1.7 | 0.92 | Contact Map |
| 4wt3A | 1 | 0 | 1.6 | 0.922 | Contact Map |
| 4i4oA | 2 | 0.7445 | 1.4 | 0.923 | Contact Map |
| 3dwlE | 2 | 0.1825 | 1.3 | 0.926 | Contact Map |
| 4xesA | 1 | 0 | 1.1 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)