| Wei_EF |
| ID: | 1495517630 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (100) | ||
| Sequences: | 422 (307.8) | ||
| Seq/Len: | 4.220 | ||
| Nf(neff/√len): | 30.8 |
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: 4.220).
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 |
| 52_R | 56_E | 3.590 | 1.00 |
| 55_L | 59_I | 2.508 | 1.00 |
| 79_V | 86_T | 2.412 | 1.00 |
| 38_D | 52_R | 2.254 | 1.00 |
| 8_G | 12_A | 1.995 | 1.00 |
| 38_D | 56_E | 1.665 | 0.99 |
| 74_P | 82_G | 1.537 | 0.98 |
| 90_I | 100_C | 1.526 | 0.98 |
| 83_G | 86_T | 1.517 | 0.98 |
| 72_K | 75_I | 1.464 | 0.97 |
| 8_G | 11_P | 1.431 | 0.97 |
| 51_L | 56_E | 1.394 | 0.96 |
| 24_L | 29_S | 1.372 | 0.96 |
| 34_F | 46_G | 1.370 | 0.96 |
| 83_G | 89_T | 1.313 | 0.94 |
| 1_E | 13_E | 1.311 | 0.94 |
| 74_P | 99_P | 1.291 | 0.93 |
| 79_V | 85_G | 1.284 | 0.93 |
| 50_P | 54_R | 1.251 | 0.92 |
| 85_G | 89_T | 1.246 | 0.92 |
| 27_L | 34_F | 1.231 | 0.91 |
| 89_T | 98_T | 1.220 | 0.91 |
| 31_H | 38_D | 1.196 | 0.90 |
| 57_K | 60_S | 1.190 | 0.89 |
| 51_L | 55_L | 1.173 | 0.88 |
| 13_E | 17_D | 1.169 | 0.88 |
| 39_D | 60_S | 1.166 | 0.88 |
| 88_H | 98_T | 1.143 | 0.87 |
| 24_L | 51_L | 1.130 | 0.86 |
| 15_I | 18_E | 1.120 | 0.85 |
| 63_T | 66_R | 1.109 | 0.84 |
| 93_A | 100_C | 1.107 | 0.84 |
| 1_E | 6_P | 1.106 | 0.84 |
| 71_I | 84_P | 1.084 | 0.82 |
| 72_K | 87_L | 1.083 | 0.82 |
| 90_I | 94_T | 1.080 | 0.82 |
| 76_V | 83_G | 1.076 | 0.82 |
| 6_P | 9_S | 1.067 | 0.81 |
| 40_G | 52_R | 1.065 | 0.81 |
| 20_G | 23_N | 1.054 | 0.80 |
| 4_I | 18_E | 1.050 | 0.79 |
| 92_N | 96_N | 1.044 | 0.79 |
| 34_F | 41_T | 1.038 | 0.78 |
| 14_Y | 17_D | 1.032 | 0.78 |
| 87_L | 96_N | 1.030 | 0.78 |
| 6_P | 12_A | 1.030 | 0.78 |
| 39_D | 56_E | 1.028 | 0.77 |
| 72_K | 79_V | 1.028 | 0.77 |
| 49_I | 89_T | 1.022 | 0.77 |
| 26_C | 29_S | 1.016 | 0.76 |
| 72_K | 90_I | 1.003 | 0.75 |
| 47_V | 51_L | 1.001 | 0.75 |
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 | |
| 1yt5A | 4 | 0.67 | 38.4 | 0.863 | Contact Map |
| 2i2cA | 1 | 0.61 | 20.6 | 0.881 | Contact Map |
| 4v24A | 2 | 0.77 | 8.7 | 0.899 | Contact Map |
| 3a2kA | 2 | 0.45 | 6.7 | 0.904 | Contact Map |
| 4h5yA | 1 | 0.4 | 6.7 | 0.904 | Contact Map |
| 1vbiA | 1 | 0.91 | 6.3 | 0.905 | Contact Map |
| 1wy5A | 2 | 0.51 | 6 | 0.906 | Contact Map |
| 4h8aA | 2 | 0.91 | 5.9 | 0.907 | Contact Map |
| 1wtjA | 2 | 0.83 | 5.7 | 0.907 | Contact Map |
| 3p52A | 2 | 0.51 | 5.6 | 0.908 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)