| segaB |
| ID: | 1471685424 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (101) | ||
| Sequences: | 4546 (2151.7) | ||
| Seq/Len: | 45.010 | ||
| Nf(neff/√len): | 214.1 |
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: 45.010).
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 |
| 58_C | 70_S | 3.570 | 1.00 |
| 25_K | 76_N | 3.521 | 1.00 |
| 28_Y | 73_K | 2.665 | 1.00 |
| 69_V | 96_I | 2.651 | 1.00 |
| 22_V | 104_V | 2.632 | 1.00 |
| 35_S | 47_T | 2.458 | 1.00 |
| 31_F | 94_F | 2.286 | 1.00 |
| 35_S | 48_E | 2.169 | 1.00 |
| 15_H | 103_F | 2.160 | 1.00 |
| 26_C | 74_C | 2.064 | 1.00 |
| 59_P | 65_E | 2.016 | 1.00 |
| 24_A | 76_N | 1.958 | 1.00 |
| 29_E | 50_I | 1.907 | 1.00 |
| 47_T | 89_R | 1.823 | 1.00 |
| 108_K | 111_A | 1.760 | 1.00 |
| 11_V | 98_S | 1.755 | 1.00 |
| 61_K | 65_E | 1.730 | 1.00 |
| 71_C | 74_C | 1.708 | 1.00 |
| 22_V | 27_S | 1.696 | 1.00 |
| 57_K | 92_S | 1.691 | 1.00 |
| 28_Y | 72_G | 1.684 | 1.00 |
| 12_F | 15_H | 1.666 | 1.00 |
| 70_S | 75_G | 1.648 | 1.00 |
| 17_E | 105_P | 1.580 | 1.00 |
| 84_N | 92_S | 1.559 | 1.00 |
| 56_T | 70_S | 1.549 | 1.00 |
| 16_F | 39_H | 1.547 | 1.00 |
| 27_S | 102_K | 1.518 | 1.00 |
| 18_P | 106_K | 1.446 | 1.00 |
| 12_F | 98_S | 1.411 | 1.00 |
| 15_H | 21_Y | 1.319 | 0.99 |
| 47_T | 90_G | 1.317 | 0.99 |
| 33_S | 36_K | 1.314 | 0.99 |
| 13_Q | 16_F | 1.305 | 0.99 |
| 20_V | 29_E | 1.303 | 0.99 |
| 28_Y | 54_S | 1.299 | 0.99 |
| 102_K | 112_A | 1.295 | 0.99 |
| 11_V | 102_K | 1.271 | 0.99 |
| 23_C | 26_C | 1.197 | 0.98 |
| 23_C | 71_C | 1.191 | 0.98 |
| 22_V | 102_K | 1.190 | 0.98 |
| 20_V | 50_I | 1.187 | 0.98 |
| 60_E | 66_A | 1.185 | 0.98 |
| 57_K | 67_L | 1.181 | 0.98 |
| 62_N | 65_E | 1.166 | 0.97 |
| 32_S | 106_K | 1.155 | 0.97 |
| 56_T | 72_G | 1.153 | 0.97 |
| 23_C | 74_C | 1.109 | 0.96 |
| 78_L | 96_I | 1.105 | 0.96 |
| 16_F | 38_A | 1.077 | 0.95 |
| 37_Y | 41_S | 1.077 | 0.95 |
| 51_H | 54_S | 1.069 | 0.95 |
| 56_T | 75_G | 1.056 | 0.95 |
| 108_K | 112_A | 1.023 | 0.93 |
| 69_V | 78_L | 1.020 | 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 | |
| 2kv1A | 1 | 1 | 100 | 0.006 | Contact Map |
| 3e0mA | 4 | 0.9483 | 100 | 0.043 | Contact Map |
| 3hcgA | 4 | 0.9483 | 100 | 0.056 | Contact Map |
| 3e0oA | 6 | 0.9397 | 100 | 0.056 | Contact Map |
| 3cxkA | 2 | 0.8707 | 100 | 0.075 | Contact Map |
| 3hcjA | 2 | 0.9483 | 100 | 0.076 | Contact Map |
| 2l1uA | 1 | 0.9483 | 100 | 0.079 | Contact Map |
| 2k8dA | 1 | 0.8966 | 100 | 0.08 | Contact Map |
| 3maoA | 1 | 0.9052 | 100 | 0.088 | Contact Map |
| 5amhA | 1 | 0 | 79.1 | 0.902 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)