| 1sbp from pdb 103-209 |
| ID: | 1513800683 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (107) | ||
| Sequences: | 1085 (452.5) | ||
| Seq/Len: | 10.140 | ||
| Nf(neff/√len): | 43.7 |
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: 10.140).
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 |
| 14_I | 60_L | 3.136 | 1.00 |
| 22_T | 34_N | 2.295 | 1.00 |
| 59_A | 63_N | 2.237 | 1.00 |
| 11_N | 45_H | 2.235 | 1.00 |
| 43_L | 53_A | 2.216 | 1.00 |
| 55_D | 59_A | 2.190 | 1.00 |
| 53_A | 57_V | 2.189 | 1.00 |
| 19_S | 65_E | 2.091 | 1.00 |
| 21_I | 65_E | 2.049 | 1.00 |
| 41_Y | 56_F | 2.008 | 1.00 |
| 20_V | 65_E | 1.868 | 1.00 |
| 58_K | 62_K | 1.852 | 1.00 |
| 43_L | 50_Q | 1.753 | 1.00 |
| 20_V | 60_L | 1.734 | 1.00 |
| 46_N | 53_A | 1.677 | 1.00 |
| 71_A | 90_W | 1.671 | 1.00 |
| 11_N | 41_Y | 1.663 | 1.00 |
| 46_N | 52_K | 1.636 | 1.00 |
| 30_G | 71_A | 1.611 | 1.00 |
| 19_S | 63_N | 1.570 | 1.00 |
| 95_L | 100_E | 1.563 | 1.00 |
| 39_W | 57_V | 1.490 | 1.00 |
| 77_T | 83_I | 1.480 | 1.00 |
| 39_W | 43_L | 1.445 | 1.00 |
| 30_G | 34_N | 1.403 | 0.99 |
| 1_K | 107_E | 1.388 | 0.99 |
| 30_G | 33_W | 1.366 | 0.99 |
| 21_I | 83_I | 1.348 | 0.99 |
| 61_F | 67_L | 1.312 | 0.99 |
| 79_V | 101_L | 1.298 | 0.99 |
| 75_T | 87_L | 1.245 | 0.98 |
| 24_N | 32_R | 1.206 | 0.98 |
| 33_W | 90_W | 1.203 | 0.98 |
| 23_P | 34_N | 1.180 | 0.98 |
| 31_A | 34_N | 1.173 | 0.98 |
| 38_A | 60_L | 1.168 | 0.97 |
| 30_G | 74_S | 1.167 | 0.97 |
| 23_P | 68_D | 1.162 | 0.97 |
| 30_G | 90_W | 1.160 | 0.97 |
| 8_H | 16_P | 1.149 | 0.97 |
| 39_W | 53_A | 1.148 | 0.97 |
| 17_G | 63_N | 1.124 | 0.97 |
| 52_K | 55_D | 1.105 | 0.96 |
| 5_K | 85_D | 1.102 | 0.96 |
| 49_D | 52_K | 1.099 | 0.96 |
| 22_T | 33_W | 1.083 | 0.96 |
| 15_K | 18_V | 1.082 | 0.96 |
| 98_T | 104_D | 1.082 | 0.96 |
| 16_P | 105_K | 1.077 | 0.95 |
| 68_D | 77_T | 1.049 | 0.94 |
| 21_I | 77_T | 1.049 | 0.94 |
| 13_L | 64_V | 1.034 | 0.94 |
| 43_L | 48_N | 1.013 | 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 | |
| 1sbpA | 1 | 1 | 99.6 | 0.649 | Contact Map |
| 4jb7A | 1 | 0.8692 | 98.7 | 0.769 | Contact Map |
| 2hxwA | 2 | 0.9252 | 97.9 | 0.816 | Contact Map |
| 3cg1A | 2 | 0.9252 | 96.1 | 0.861 | Contact Map |
| 3cfzA | 1 | 0.9626 | 95.9 | 0.863 | Contact Map |
| 4rxlA | 1 | 0.8411 | 95.3 | 0.868 | Contact Map |
| 3pu5A | 1 | 0.972 | 94.8 | 0.872 | Contact Map |
| 4g68A | 1 | 0.9813 | 94.5 | 0.874 | Contact Map |
| 2qryA | 4 | 0.9159 | 94.3 | 0.875 | Contact Map |
| 3rpwA | 1 | 0.9252 | 94 | 0.877 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)