| chey_edited |
| ID: | 1504721551 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 112 (108) | ||
| Sequences: | 206863 (142446) | ||
| Seq/Len: | 1915.398 | ||
| Nf(neff/√len): | 13706.9 |
Jackhmmer Results: (2016_04)
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: 1915.398).
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 |
| 10_R | 27_E | 3.065 | 1.00 |
| 14_R | 27_E | 2.767 | 1.00 |
| 10_R | 29_E | 2.716 | 1.00 |
| 3_V | 34_A | 2.403 | 1.00 |
| 26_E | 43_Y | 2.316 | 1.00 |
| 32_V | 54_N | 2.116 | 1.00 |
| 35_L | 63_T | 2.069 | 1.00 |
| 68_G | 71_S | 2.062 | 1.00 |
| 51_N | 81_E | 2.022 | 1.00 |
| 31_G | 55_M | 2.015 | 1.00 |
| 39_Q | 67_D | 1.966 | 1.00 |
| 55_M | 63_T | 1.938 | 1.00 |
| 28_A | 37_K | 1.915 | 1.00 |
| 26_E | 37_K | 1.901 | 1.00 |
| 48_S | 60_L | 1.876 | 1.00 |
| 26_E | 41_G | 1.809 | 1.00 |
| 77_M | 95_A | 1.789 | 1.00 |
| 16_L | 105_A | 1.772 | 1.00 |
| 30_D | 54_N | 1.763 | 1.00 |
| 61_L | 75_V | 1.741 | 1.00 |
| 29_E | 33_D | 1.689 | 1.00 |
| 65_R | 96_S | 1.524 | 1.00 |
| 62_K | 93_A | 1.488 | 1.00 |
| 14_R | 18_K | 1.448 | 1.00 |
| 50_W | 58_L | 1.447 | 1.00 |
| 63_T | 67_D | 1.436 | 1.00 |
| 37_K | 41_G | 1.408 | 1.00 |
| 30_D | 33_D | 1.344 | 0.99 |
| 31_G | 60_L | 1.317 | 0.99 |
| 81_E | 86_N | 1.315 | 0.99 |
| 55_M | 59_E | 1.315 | 0.99 |
| 38_L | 64_I | 1.315 | 0.99 |
| 37_K | 40_A | 1.303 | 0.99 |
| 32_V | 55_M | 1.273 | 0.99 |
| 84_K | 88_I | 1.253 | 0.99 |
| 56_D | 59_E | 1.252 | 0.99 |
| 37_K | 43_Y | 1.245 | 0.98 |
| 46_V | 73_L | 1.196 | 0.98 |
| 63_T | 66_A | 1.188 | 0.98 |
| 35_L | 60_L | 1.175 | 0.98 |
| 58_L | 90_A | 1.175 | 0.98 |
| 88_I | 92_Q | 1.171 | 0.98 |
| 5_D | 49_D | 1.118 | 0.96 |
| 7_S | 29_E | 1.115 | 0.96 |
| 89_A | 93_A | 1.109 | 0.96 |
| 61_L | 77_M | 1.097 | 0.96 |
| 78_V | 103_F | 1.059 | 0.95 |
| 83_K | 86_N | 1.050 | 0.94 |
| 58_L | 89_A | 1.049 | 0.94 |
| 77_M | 90_A | 1.041 | 0.94 |
| 28_A | 34_A | 1.019 | 0.93 |
| 34_A | 60_L | 1.005 | 0.93 |
| 2_V | 13_V | 1.002 | 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 | |
| 4g97A | 1 | 0.9464 | 99.9 | 0.077 | Contact Map |
| 1w25A | 2 | 0.9911 | 99.8 | 0.079 | Contact Map |
| 3n0rA | 1 | 0.9464 | 99.8 | 0.084 | Contact Map |
| 3breA | 2 | 0.9911 | 99.8 | 0.088 | Contact Map |
| 3dzdA | 2 | 0.9732 | 99.8 | 0.106 | Contact Map |
| 3eq2A | 2 | 0.9732 | 99.8 | 0.114 | Contact Map |
| 4l4uA | 1 | 0.9732 | 99.8 | 0.123 | Contact Map |
| 3lufA | 2 | 0.9911 | 99.8 | 0.128 | Contact Map |
| 2ayxA | 1 | 0.9732 | 99.8 | 0.129 | Contact Map |
| 3rqiA | 1 | 0.9643 | 99.8 | 0.136 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)