| T0778 |
| ID: | 1400096588 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (123) | ||
| Sequences: | 350 (257.9) | ||
| Seq/Len: | 2.846 | ||
| Nf(neff/√len): | 23.3 |
Jackhmmer Results: (2014_04_16)
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: 2.846).
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 |
| 54_R | 70_D | 3.718 | 1.00 |
| 63_K | 66_E | 3.387 | 1.00 |
| 88_R | 104_D | 3.256 | 1.00 |
| 97_K | 100_E | 2.848 | 1.00 |
| 108_V | 118_A | 2.794 | 1.00 |
| 38_T | 54_R | 2.346 | 1.00 |
| 29_K | 32_R | 2.051 | 1.00 |
| 21_G | 37_Y | 2.031 | 1.00 |
| 89_G | 105_F | 1.958 | 0.99 |
| 75_I | 85_F | 1.816 | 0.99 |
| 72_T | 88_R | 1.774 | 0.99 |
| 55_A | 71_C | 1.679 | 0.98 |
| 17_E | 36_C | 1.597 | 0.97 |
| 18_K | 22_N | 1.565 | 0.96 |
| 68_E | 92_R | 1.551 | 0.96 |
| 88_R | 92_R | 1.547 | 0.96 |
| 83_K | 87_R | 1.544 | 0.96 |
| 102_K | 122_L | 1.529 | 0.96 |
| 37_Y | 53_N | 1.501 | 0.95 |
| 18_K | 87_R | 1.389 | 0.92 |
| 7_H | 105_F | 1.379 | 0.92 |
| 40_G | 50_L | 1.332 | 0.90 |
| 53_N | 87_R | 1.310 | 0.89 |
| 57_A | 61_I | 1.277 | 0.87 |
| 45_G | 79_G | 1.276 | 0.87 |
| 22_N | 83_K | 1.265 | 0.86 |
| 89_G | 101_A | 1.234 | 0.84 |
| 105_F | 121_E | 1.229 | 0.84 |
| 89_G | 108_V | 1.203 | 0.82 |
| 30_Y | 54_R | 1.193 | 0.81 |
| 65_E | 95_L | 1.174 | 0.80 |
| 21_G | 53_N | 1.173 | 0.80 |
| 21_G | 40_G | 1.171 | 0.80 |
| 18_K | 53_N | 1.148 | 0.78 |
| 31_E | 63_K | 1.142 | 0.77 |
| 76_L | 79_G | 1.135 | 0.77 |
| 25_F | 57_A | 1.122 | 0.76 |
| 73_Q | 76_L | 1.117 | 0.75 |
| 14_A | 40_G | 1.101 | 0.74 |
| 58_Y | 63_K | 1.086 | 0.72 |
| 59_L | 89_G | 1.065 | 0.70 |
| 108_V | 111_L | 1.058 | 0.69 |
| 71_C | 87_R | 1.050 | 0.69 |
| 66_E | 73_Q | 1.039 | 0.67 |
| 54_R | 61_I | 1.038 | 0.67 |
| 74_A | 84_A | 1.037 | 0.67 |
| 54_R | 88_R | 1.022 | 0.66 |
| 5_H | 65_E | 1.021 | 0.65 |
| 25_F | 30_Y | 1.013 | 0.64 |
| 45_G | 113_P | 1.007 | 0.64 |
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 | |
| 2vyiA | 2 | 0.9606 | 99.7 | 0.218 | Contact Map |
| 3iegA | 2 | 0.9134 | 99.7 | 0.219 | Contact Map |
| 1p5qA | 3 | 1 | 99.7 | 0.222 | Contact Map |
| 3fp2A | 1 | 1 | 99.7 | 0.224 | Contact Map |
| 4i2zA | 1 | 0.9213 | 99.7 | 0.224 | Contact Map |
| 2y4tA | 3 | 0.9213 | 99.7 | 0.227 | Contact Map |
| 1kt0A | 1 | 0.9685 | 99.7 | 0.238 | Contact Map |
| 1dceA | 2 | 1 | 99.7 | 0.238 | Contact Map |
| 2pl2A | 2 | 0.9055 | 99.7 | 0.238 | Contact Map |
| 3uq3A | 1 | 1 | 99.7 | 0.238 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)