| shuangxi |
| ID: | 1491912326 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (74) | ||
| Sequences: | 3505 (2164.4) | ||
| Seq/Len: | 47.365 | ||
| Nf(neff/√len): | 251.6 |
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: 47.365).
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 |
| 7_K | 11_E | 3.271 | 1.00 |
| 41_Q | 49_L | 3.056 | 1.00 |
| 41_Q | 45_T | 2.611 | 1.00 |
| 9_W | 57_H | 2.264 | 1.00 |
| 36_P | 39_E | 2.098 | 1.00 |
| 8_Q | 12_T | 1.947 | 1.00 |
| 39_E | 72_D | 1.901 | 1.00 |
| 32_V | 67_K | 1.810 | 1.00 |
| 58_Q | 61_I | 1.746 | 1.00 |
| 46_R | 73_E | 1.713 | 1.00 |
| 32_V | 69_Y | 1.655 | 1.00 |
| 13_G | 53_A | 1.610 | 1.00 |
| 42_T | 45_T | 1.598 | 1.00 |
| 33_V | 68_T | 1.547 | 1.00 |
| 20_I | 32_V | 1.523 | 1.00 |
| 5_D | 9_W | 1.475 | 1.00 |
| 36_P | 71_P | 1.429 | 1.00 |
| 45_T | 48_R | 1.424 | 1.00 |
| 4_H | 7_K | 1.420 | 1.00 |
| 14_L | 49_L | 1.411 | 1.00 |
| 37_T | 41_Q | 1.377 | 0.99 |
| 48_R | 52_N | 1.345 | 0.99 |
| 16_E | 19_V | 1.336 | 0.99 |
| 30_E | 67_K | 1.311 | 0.99 |
| 15_S | 37_T | 1.295 | 0.99 |
| 51_Y | 58_Q | 1.273 | 0.99 |
| 30_E | 65_S | 1.243 | 0.98 |
| 3_T | 7_K | 1.216 | 0.98 |
| 57_H | 60_D | 1.212 | 0.98 |
| 4_H | 8_Q | 1.169 | 0.97 |
| 44_L | 48_R | 1.158 | 0.97 |
| 54_L | 64_L | 1.146 | 0.97 |
| 14_L | 33_V | 1.097 | 0.96 |
| 70_T | 73_E | 1.093 | 0.96 |
| 52_N | 55_G | 1.085 | 0.96 |
| 46_R | 68_T | 1.074 | 0.95 |
| 31_A | 64_L | 1.044 | 0.94 |
| 17_S | 36_P | 1.041 | 0.94 |
| 69_Y | 74_Y | 1.041 | 0.94 |
| 44_L | 51_Y | 1.039 | 0.94 |
| 14_L | 53_A | 1.023 | 0.93 |
| 18_R | 32_V | 1.014 | 0.93 |
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 | |
| 1ny8A | 1 | 0.9865 | 99.9 | 0.052 | Contact Map |
| 2kdnA | 1 | 1 | 99.9 | 0.065 | Contact Map |
| 3o2eA | 1 | 1 | 99.9 | 0.068 | Contact Map |
| 3tr3A | 2 | 1 | 99.9 | 0.069 | Contact Map |
| 2mm9A | 1 | 1 | 99.9 | 0.069 | Contact Map |
| 1v9jA | 1 | 1 | 99.9 | 0.072 | Contact Map |
| 1xs3A | 1 | 1 | 99.9 | 0.078 | Contact Map |
| 2dhmA | 1 | 1 | 99.9 | 0.085 | Contact Map |
| 1v60A | 1 | 1 | 99.9 | 0.095 | Contact Map |
| 2mcqA | 1 | 0.973 | 99.9 | 0.1 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)