| 1bxe |
| ID: | 1453736799 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (111) | ||
| Sequences: | 2892 (1494.7) | ||
| Seq/Len: | 26.054 | ||
| Nf(neff/√len): | 141.9 |
HHblits Results: (2015_06)
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: 26.054).
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 |
| 9_Y | 80_P | 2.714 | 1.00 |
| 7_A | 50_V | 2.701 | 1.00 |
| 21_V | 76_V | 2.688 | 1.00 |
| 72_K | 108_G | 2.615 | 1.00 |
| 7_A | 10_V | 2.531 | 1.00 |
| 37_R | 48_A | 2.339 | 1.00 |
| 29_L | 55_A | 2.331 | 1.00 |
| 48_A | 52_E | 2.159 | 1.00 |
| 54_A | 107_L | 2.059 | 1.00 |
| 88_R | 94_D | 2.015 | 1.00 |
| 33_R | 48_A | 1.979 | 1.00 |
| 85_V | 93_A | 1.926 | 1.00 |
| 33_R | 55_A | 1.903 | 1.00 |
| 27_K | 35_I | 1.903 | 1.00 |
| 21_V | 74_A | 1.885 | 1.00 |
| 59_V | 66_E | 1.884 | 1.00 |
| 27_K | 31_E | 1.876 | 1.00 |
| 22_D | 25_R | 1.743 | 1.00 |
| 68_R | 109_E | 1.726 | 1.00 |
| 78_E | 81_A | 1.668 | 1.00 |
| 28_S | 31_E | 1.598 | 1.00 |
| 42_R | 46_F | 1.547 | 1.00 |
| 73_A | 106_I | 1.513 | 1.00 |
| 86_L | 94_D | 1.493 | 1.00 |
| 70_Y | 110_K | 1.475 | 1.00 |
| 81_A | 99_R | 1.475 | 1.00 |
| 10_V | 46_F | 1.467 | 1.00 |
| 12_I | 17_V | 1.465 | 1.00 |
| 81_A | 97_K | 1.425 | 1.00 |
| 21_V | 47_V | 1.416 | 1.00 |
| 2_E | 108_G | 1.410 | 1.00 |
| 79_G | 100_T | 1.389 | 0.99 |
| 58_A | 69_L | 1.353 | 0.99 |
| 17_V | 47_V | 1.349 | 0.99 |
| 85_V | 95_I | 1.349 | 0.99 |
| 3_A | 107_L | 1.331 | 0.99 |
| 24_I | 51_L | 1.325 | 0.99 |
| 12_I | 43_G | 1.297 | 0.99 |
| 65_L | 68_R | 1.284 | 0.99 |
| 78_E | 99_R | 1.276 | 0.99 |
| 75_Y | 104_T | 1.273 | 0.99 |
| 77_D | 104_T | 1.240 | 0.98 |
| 17_V | 103_I | 1.229 | 0.98 |
| 85_V | 94_D | 1.220 | 0.98 |
| 87_P | 93_A | 1.220 | 0.98 |
| 23_L | 35_I | 1.204 | 0.98 |
| 19_L | 41_K | 1.188 | 0.98 |
| 51_L | 55_A | 1.168 | 0.97 |
| 1_M | 109_E | 1.146 | 0.97 |
| 51_L | 71_V | 1.142 | 0.97 |
| 33_R | 52_E | 1.115 | 0.96 |
| 86_L | 96_I | 1.089 | 0.96 |
| 89_A | 94_D | 1.087 | 0.96 |
| 53_S | 57_N | 1.080 | 0.95 |
| 90_R | 94_D | 1.066 | 0.95 |
| 72_K | 106_I | 1.064 | 0.95 |
| 18_R | 78_E | 1.057 | 0.95 |
| 51_L | 105_V | 1.052 | 0.95 |
| 87_P | 94_D | 1.041 | 0.94 |
| 20_V | 47_V | 1.015 | 0.93 |
| 79_G | 102_H | 1.004 | 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 | 0.9735 | 100 | -0.034 | Contact Map |
| 3j3wS | 1 | 0.9912 | 100 | -0.029 | Contact Map |
| 2zjrP | 1 | 1 | 100 | -0.025 | Contact Map |
| 3bboU | 1 | 1 | 100 | -0.019 | Contact Map |
| 3j7yT | 1 | 1 | 100 | -0.002 | Contact Map |
| 4ce4W | 1 | 0.9646 | 100 | -0.002 | Contact Map |
| 1i4jA | 2 | 0.9735 | 100 | 0.006 | Contact Map |
| 1vq8R | 1 | 0.9646 | 100 | 0.014 | Contact Map |
| 1vw4O | 1 | 0.9912 | 100 | 0.017 | Contact Map |
| 3j21S | 1 | 0.9823 | 100 | 0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)