| shuangxi |
| ID: | 1491913448 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (74) | ||
| Sequences: | 1502 (1260.6) | ||
| Seq/Len: | 20.297 | ||
| Nf(neff/√len): | 146.5 |
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: 20.297).
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 | 14_I | 3.021 | 1.00 |
| 34_V | 43_A | 2.928 | 1.00 |
| 43_A | 57_F | 2.439 | 1.00 |
| 10_R | 20_D | 2.391 | 1.00 |
| 13_N | 17_H | 2.180 | 1.00 |
| 4_I | 66_S | 2.120 | 1.00 |
| 36_P | 40_D | 2.095 | 1.00 |
| 4_I | 64_A | 2.088 | 1.00 |
| 23_D | 47_F | 1.912 | 1.00 |
| 26_F | 47_F | 1.803 | 1.00 |
| 34_V | 57_F | 1.585 | 1.00 |
| 13_N | 69_S | 1.568 | 1.00 |
| 14_I | 20_D | 1.552 | 1.00 |
| 2_K | 64_A | 1.551 | 1.00 |
| 23_D | 26_F | 1.518 | 1.00 |
| 51_I | 72_A | 1.510 | 1.00 |
| 12_T | 16_K | 1.482 | 1.00 |
| 50_L | 71_S | 1.447 | 1.00 |
| 6_D | 66_S | 1.411 | 1.00 |
| 10_R | 22_A | 1.333 | 0.99 |
| 9_K | 21_F | 1.332 | 0.99 |
| 34_V | 42_L | 1.311 | 0.99 |
| 47_F | 52_I | 1.305 | 0.99 |
| 11_Q | 14_I | 1.304 | 0.99 |
| 7_E | 10_R | 1.301 | 0.99 |
| 27_E | 30_L | 1.266 | 0.99 |
| 27_E | 43_A | 1.244 | 0.98 |
| 53_I | 72_A | 1.219 | 0.98 |
| 7_E | 11_Q | 1.212 | 0.98 |
| 19_L | 52_I | 1.208 | 0.98 |
| 3_I | 65_L | 1.159 | 0.97 |
| 57_F | 60_V | 1.158 | 0.97 |
| 27_E | 45_G | 1.139 | 0.97 |
| 28_F | 45_G | 1.127 | 0.97 |
| 46_E | 51_I | 1.117 | 0.96 |
| 6_D | 9_K | 1.117 | 0.96 |
| 27_E | 52_I | 1.101 | 0.96 |
| 42_L | 65_L | 1.075 | 0.95 |
| 13_N | 16_K | 1.049 | 0.94 |
| 39_A | 66_S | 1.022 | 0.93 |
| 27_E | 32_A | 1.018 | 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 | |
| 3u97A | 1 | 0.9865 | 99.8 | 0.107 | Contact Map |
| 3egaA | 1 | 0.9459 | 5.3 | 0.899 | Contact Map |
| 3nmqA | 1 | 0.9459 | 4.1 | 0.904 | Contact Map |
| 3o0iA | 1 | 0.9459 | 4.1 | 0.904 | Contact Map |
| 2cg9A | 2 | 0.9459 | 3.8 | 0.906 | Contact Map |
| 1yc1A | 1 | 0.9459 | 3.8 | 0.906 | Contact Map |
| 2iorA | 1 | 0.9459 | 3.5 | 0.907 | Contact Map |
| 3iedA | 1 | 0.9459 | 3 | 0.911 | Contact Map |
| 4ivgA | 1 | 0.9459 | 2.9 | 0.912 | Contact Map |
| 2nwvA | 1 | 0.5676 | 2.8 | 0.912 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)