| d4nasb1 |
| ID: | 1448378080 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 113 (112) | ||
| Sequences: | 791 (388.8) | ||
| Seq/Len: | 7.062 | ||
| Nf(neff/√len): | 36.7 |
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: 7.062).
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 |
| 5_A | 100_L | 3.265 | 1.00 |
| 2_A | 71_A | 2.493 | 1.00 |
| 52_G | 69_D | 2.248 | 1.00 |
| 16_L | 66_A | 1.902 | 1.00 |
| 84_L | 109_L | 1.868 | 1.00 |
| 4_V | 69_D | 1.800 | 1.00 |
| 1_D | 108_E | 1.787 | 1.00 |
| 26_G | 91_K | 1.770 | 1.00 |
| 84_L | 105_M | 1.707 | 1.00 |
| 4_V | 71_A | 1.666 | 1.00 |
| 30_G | 73_P | 1.611 | 1.00 |
| 16_L | 68_I | 1.584 | 1.00 |
| 51_E | 71_A | 1.579 | 1.00 |
| 34_D | 43_V | 1.554 | 1.00 |
| 6_T | 104_Q | 1.498 | 0.99 |
| 3_V | 77_L | 1.483 | 0.99 |
| 34_D | 40_K | 1.431 | 0.99 |
| 80_T | 83_S | 1.393 | 0.99 |
| 40_K | 43_V | 1.363 | 0.98 |
| 19_R | 26_G | 1.351 | 0.98 |
| 10_R | 65_V | 1.318 | 0.98 |
| 51_E | 72_Y | 1.315 | 0.98 |
| 74_V | 106_P | 1.304 | 0.98 |
| 13_K | 45_K | 1.249 | 0.97 |
| 4_V | 104_Q | 1.230 | 0.97 |
| 28_T | 48_G | 1.219 | 0.96 |
| 24_A | 31_T | 1.218 | 0.96 |
| 25_V | 37_A | 1.200 | 0.96 |
| 35_L | 72_Y | 1.186 | 0.95 |
| 25_V | 28_T | 1.129 | 0.94 |
| 83_S | 86_V | 1.128 | 0.94 |
| 105_M | 110_V | 1.128 | 0.94 |
| 88_V | 103_L | 1.126 | 0.94 |
| 54_R | 67_E | 1.123 | 0.93 |
| 92_L | 95_D | 1.122 | 0.93 |
| 29_I | 47_C | 1.113 | 0.93 |
| 83_S | 91_K | 1.109 | 0.93 |
| 86_V | 89_F | 1.089 | 0.92 |
| 17_E | 21_E | 1.086 | 0.92 |
| 69_D | 104_Q | 1.085 | 0.92 |
| 89_F | 93_S | 1.077 | 0.91 |
| 55_V | 64_V | 1.072 | 0.91 |
| 80_T | 91_K | 1.072 | 0.91 |
| 107_D | 111_R | 1.070 | 0.91 |
| 84_L | 88_V | 1.058 | 0.90 |
| 77_L | 105_M | 1.051 | 0.90 |
| 54_R | 69_D | 1.036 | 0.89 |
| 88_V | 100_L | 1.024 | 0.88 |
| 16_L | 53_I | 1.024 | 0.88 |
| 59_R | 111_R | 1.021 | 0.88 |
| 3_V | 6_T | 1.020 | 0.88 |
| 74_V | 111_R | 1.019 | 0.88 |
| 2_A | 51_E | 1.018 | 0.88 |
| 23_I | 98_I | 1.017 | 0.88 |
| 23_I | 70_I | 1.004 | 0.87 |
| 49_R | 102_R | 1.001 | 0.87 |
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 | |
| 4nasA | 4 | 1 | 100 | 0.087 | Contact Map |
| 2zviA | 4 | 0.9823 | 100 | 0.089 | Contact Map |
| 3fk4A | 2 | 0.9558 | 100 | 0.092 | Contact Map |
| 2oemA | 2 | 0.9912 | 100 | 0.101 | Contact Map |
| 3nwrA | 1 | 0.8761 | 100 | 0.107 | Contact Map |
| 2qygA | 4 | 0.9823 | 100 | 0.129 | Contact Map |
| 1ykwA | 2 | 0.885 | 100 | 0.132 | Contact Map |
| 3qfwA | 2 | 0.885 | 100 | 0.133 | Contact Map |
| 1wddA | 2 | 0.9735 | 100 | 0.149 | Contact Map |
| 3kdnA | 10 | 0.9558 | 100 | 0.152 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)