| 1BXEA |
| ID: | 1411601143 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (109) | ||
| Sequences: | 1852 (1038.7) | ||
| Seq/Len: | 16.991 | ||
| Nf(neff/√len): | 99.5 |
HHblits Results: (2013_03)
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: 16.991).
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 |
| 8_Y | 79_P | 2.759 | 1.00 |
| 6_A | 49_V | 2.704 | 1.00 |
| 20_V | 75_V | 2.655 | 1.00 |
| 71_K | 107_G | 2.521 | 1.00 |
| 6_A | 9_V | 2.450 | 1.00 |
| 28_L | 54_A | 2.262 | 1.00 |
| 47_A | 51_E | 2.055 | 1.00 |
| 26_K | 34_I | 2.001 | 1.00 |
| 87_R | 93_D | 1.911 | 1.00 |
| 23_I | 50_L | 1.863 | 1.00 |
| 36_R | 47_A | 1.839 | 1.00 |
| 21_D | 24_R | 1.825 | 1.00 |
| 77_E | 80_A | 1.788 | 1.00 |
| 41_R | 45_F | 1.734 | 1.00 |
| 53_A | 106_L | 1.718 | 1.00 |
| 67_R | 108_E | 1.712 | 1.00 |
| 80_A | 98_R | 1.678 | 1.00 |
| 77_E | 98_R | 1.671 | 1.00 |
| 20_V | 73_A | 1.605 | 1.00 |
| 84_V | 92_A | 1.571 | 1.00 |
| 26_K | 30_E | 1.567 | 1.00 |
| 32_R | 47_A | 1.560 | 1.00 |
| 20_V | 46_V | 1.560 | 1.00 |
| 84_V | 94_I | 1.502 | 1.00 |
| 85_L | 93_D | 1.478 | 1.00 |
| 58_V | 65_E | 1.477 | 1.00 |
| 9_V | 45_F | 1.463 | 1.00 |
| 27_S | 30_E | 1.432 | 1.00 |
| 50_L | 54_A | 1.426 | 1.00 |
| 50_L | 104_V | 1.423 | 1.00 |
| 76_D | 103_T | 1.415 | 1.00 |
| 11_I | 16_V | 1.410 | 1.00 |
| 18_L | 40_K | 1.365 | 0.99 |
| 52_S | 56_N | 1.350 | 0.99 |
| 84_V | 93_D | 1.349 | 0.99 |
| 50_L | 70_V | 1.343 | 0.99 |
| 86_P | 92_A | 1.311 | 0.99 |
| 78_G | 99_T | 1.296 | 0.99 |
| 32_R | 54_A | 1.290 | 0.99 |
| 14_R | 18_L | 1.267 | 0.99 |
| 16_V | 46_V | 1.245 | 0.98 |
| 17_R | 76_D | 1.218 | 0.98 |
| 2_A | 106_L | 1.217 | 0.98 |
| 46_V | 73_A | 1.200 | 0.98 |
| 11_I | 42_G | 1.191 | 0.98 |
| 74_Y | 103_T | 1.182 | 0.98 |
| 16_V | 102_I | 1.177 | 0.98 |
| 57_A | 68_L | 1.172 | 0.98 |
| 71_K | 105_I | 1.164 | 0.97 |
| 49_V | 102_I | 1.153 | 0.97 |
| 86_P | 93_D | 1.148 | 0.97 |
| 88_A | 93_D | 1.143 | 0.97 |
| 64_L | 67_R | 1.142 | 0.97 |
| 80_A | 96_K | 1.135 | 0.97 |
| 70_V | 73_A | 1.078 | 0.95 |
| 16_V | 100_S | 1.054 | 0.95 |
| 2_A | 61_H | 1.047 | 0.94 |
| 73_A | 104_V | 1.044 | 0.94 |
| 89_R | 93_D | 1.015 | 0.93 |
| 12_S | 41_R | 1.003 | 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 | |
| 4tp9S | 1 | 1 | 100 | -0.026 | Contact Map |
| 3j3wS | 1 | 1 | 100 | -0.023 | Contact Map |
| 2zjrP | 1 | 1 | 100 | -0.021 | Contact Map |
| 3bboU | 1 | 1 | 100 | -0.016 | Contact Map |
| 4ce4W | 1 | 1 | 100 | -0.004 | Contact Map |
| 1vw4O | 1 | 0.9908 | 100 | 0.006 | Contact Map |
| 1i4jA | 2 | 0.9725 | 100 | 0.024 | Contact Map |
| 1vq8R | 1 | 0.9908 | 100 | 0.041 | Contact Map |
| 3j21S | 1 | 0.9908 | 100 | 0.042 | Contact Map |
| 1vx7W | 1 | 0.9908 | 100 | 0.043 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)