| 4ipu |
| ID: | 1500382060 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 137 (136) | ||
| Sequences: | 1054 (842.2) | ||
| Seq/Len: | 7.750 | ||
| Nf(neff/√len): | 72.2 |
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: 7.750).
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 |
| 12_Q | 16_E | 3.327 | 1.00 |
| 28_E | 32_Q | 3.178 | 1.00 |
| 39_Q | 51_S | 2.950 | 1.00 |
| 41_L | 51_S | 2.870 | 1.00 |
| 25_A | 38_I | 2.764 | 1.00 |
| 28_E | 31_S | 2.728 | 1.00 |
| 24_Y | 64_L | 2.187 | 1.00 |
| 22_L | 86_L | 2.144 | 1.00 |
| 6_T | 10_E | 1.983 | 1.00 |
| 21_M | 50_L | 1.870 | 1.00 |
| 35_A | 87_T | 1.863 | 1.00 |
| 55_L | 59_S | 1.795 | 1.00 |
| 37_S | 87_T | 1.771 | 1.00 |
| 29_A | 92_G | 1.748 | 1.00 |
| 101_T | 115_V | 1.700 | 1.00 |
| 32_Q | 36_I | 1.612 | 1.00 |
| 53_G | 57_S | 1.593 | 1.00 |
| 4_P | 8_R | 1.545 | 1.00 |
| 117_S | 125_Q | 1.536 | 1.00 |
| 85_H | 100_R | 1.523 | 1.00 |
| 115_V | 127_E | 1.424 | 0.99 |
| 7_E | 107_N | 1.418 | 0.99 |
| 21_M | 67_H | 1.392 | 0.99 |
| 11_L | 106_Q | 1.333 | 0.98 |
| 21_M | 24_Y | 1.333 | 0.98 |
| 39_Q | 53_G | 1.327 | 0.98 |
| 24_Y | 52_I | 1.325 | 0.98 |
| 7_E | 10_E | 1.292 | 0.98 |
| 18_L | 38_I | 1.279 | 0.98 |
| 16_E | 23_Q | 1.262 | 0.98 |
| 15_A | 126_L | 1.262 | 0.98 |
| 21_M | 52_I | 1.251 | 0.97 |
| 105_C | 115_V | 1.233 | 0.97 |
| 19_N | 23_Q | 1.231 | 0.97 |
| 101_T | 117_S | 1.219 | 0.97 |
| 53_G | 61_A | 1.214 | 0.97 |
| 22_L | 38_I | 1.202 | 0.97 |
| 40_A | 46_W | 1.163 | 0.96 |
| 21_M | 49_G | 1.163 | 0.96 |
| 103_A | 115_V | 1.133 | 0.95 |
| 37_S | 85_H | 1.126 | 0.95 |
| 45_D | 48_K | 1.111 | 0.94 |
| 131_K | 136_C | 1.105 | 0.94 |
| 11_L | 104_I | 1.103 | 0.94 |
| 16_E | 20_A | 1.095 | 0.93 |
| 70_F | 104_I | 1.083 | 0.93 |
| 89_T | 116_L | 1.081 | 0.93 |
| 116_L | 124_I | 1.078 | 0.93 |
| 37_S | 53_G | 1.073 | 0.92 |
| 46_W | 49_G | 1.066 | 0.92 |
| 74_T | 86_L | 1.049 | 0.91 |
| 38_I | 52_I | 1.048 | 0.91 |
| 19_N | 116_L | 1.036 | 0.91 |
| 117_S | 127_E | 1.032 | 0.90 |
| 100_R | 118_I | 1.026 | 0.90 |
| 57_S | 61_A | 1.024 | 0.90 |
| 14_A | 75_L | 1.024 | 0.90 |
| 88_F | 124_I | 1.005 | 0.89 |
| 105_C | 117_S | 1.005 | 0.89 |
| 30_V | 66_K | 1.000 | 0.88 |
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 | 100 | 0.118 | Contact Map |
| 4dq9A | 2 | 0.8759 | 97.3 | 0.744 | Contact Map |
| 2knqA | 1 | 0.8832 | 82.1 | 0.845 | Contact Map |
| 2iz6A | 2 | 0.4891 | 5.8 | 0.922 | Contact Map |
| 1oqwA | 2 | 0.7883 | 4.9 | 0.925 | Contact Map |
| 1xccA | 4 | 0.562 | 4.4 | 0.926 | Contact Map |
| 1prxA | 2 | 0.5693 | 3.5 | 0.929 | Contact Map |
| 4i99C | 2 | 0.3358 | 2.1 | 0.937 | Contact Map |
| 4kf9A | 1 | 0.6277 | 2 | 0.938 | Contact Map |
| 4fczB | 2 | 0.1971 | 2 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)