| e4b |
| ID: | 1381876777 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (100) | ||
| Sequences: | 322 (234.8) | ||
| Seq/Len: | 3.220 | ||
| Nf(neff/√len): | 23.5 |
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: 3.220).
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 |
| 43_D | 55_R | 2.864 | 1.00 |
| 32_F | 89_Q | 2.691 | 1.00 |
| 46_R | 83_V | 2.365 | 1.00 |
| 84_P | 87_K | 2.066 | 1.00 |
| 49_S | 68_D | 1.851 | 0.99 |
| 42_T | 94_M | 1.682 | 0.98 |
| 92_A | 96_E | 1.609 | 0.98 |
| 12_E | 16_A | 1.597 | 0.98 |
| 47_L | 68_D | 1.593 | 0.98 |
| 52_V | 83_V | 1.550 | 0.97 |
| 13_E | 17_K | 1.547 | 0.97 |
| 53_M | 57_I | 1.507 | 0.96 |
| 33_R | 93_W | 1.500 | 0.96 |
| 92_A | 95_R | 1.495 | 0.96 |
| 31_E | 89_Q | 1.490 | 0.96 |
| 87_K | 91_Q | 1.439 | 0.95 |
| 38_D | 93_W | 1.423 | 0.95 |
| 86_L | 90_I | 1.394 | 0.94 |
| 2_E | 6_L | 1.347 | 0.92 |
| 61_H | 72_R | 1.339 | 0.92 |
| 88_E | 92_A | 1.260 | 0.88 |
| 83_V | 89_Q | 1.252 | 0.88 |
| 57_I | 80_L | 1.245 | 0.87 |
| 34_D | 57_I | 1.232 | 0.87 |
| 36_L | 64_N | 1.230 | 0.87 |
| 6_L | 10_K | 1.219 | 0.86 |
| 77_E | 80_L | 1.212 | 0.85 |
| 12_E | 92_A | 1.194 | 0.84 |
| 11_V | 23_I | 1.171 | 0.83 |
| 47_L | 54_D | 1.164 | 0.82 |
| 59_L | 77_E | 1.163 | 0.82 |
| 36_L | 39_T | 1.156 | 0.82 |
| 59_L | 80_L | 1.142 | 0.81 |
| 4_F | 8_A | 1.134 | 0.80 |
| 7_L | 20_R | 1.123 | 0.79 |
| 71_N | 75_L | 1.119 | 0.79 |
| 95_R | 100_S | 1.118 | 0.79 |
| 30_D | 39_T | 1.107 | 0.78 |
| 6_L | 16_A | 1.073 | 0.74 |
| 2_E | 5_K | 1.041 | 0.71 |
| 15_V | 24_D | 1.030 | 0.70 |
| 9_E | 13_E | 1.028 | 0.70 |
| 6_L | 100_S | 1.027 | 0.70 |
| 32_F | 86_L | 1.021 | 0.69 |
| 53_M | 80_L | 1.019 | 0.69 |
| 38_D | 53_M | 1.018 | 0.69 |
| 8_A | 11_V | 1.017 | 0.69 |
| 30_D | 71_N | 1.016 | 0.69 |
| 32_F | 41_M | 1.012 | 0.68 |
| 39_T | 82_P | 1.001 | 0.67 |
| 48_P | 68_D | 1.001 | 0.67 |
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 | |
| 3m62A | 1 | 0.9902 | 99.9 | 0.276 | Contact Map |
| 2c2lA | 4 | 0.9902 | 99.6 | 0.538 | Contact Map |
| 2kreA | 1 | 0.9804 | 99.5 | 0.573 | Contact Map |
| 2f42A | 1 | 0.9706 | 99.4 | 0.578 | Contact Map |
| 2kr4A | 1 | 0.8333 | 99.3 | 0.602 | Contact Map |
| 1wgmA | 1 | 0.9118 | 99.3 | 0.605 | Contact Map |
| 3htkC | 1 | 1 | 99.2 | 0.617 | Contact Map |
| 2yu4A | 1 | 0.7647 | 98.8 | 0.68 | Contact Map |
| 1t1hA | 1 | 0.7549 | 98.8 | 0.681 | Contact Map |
| 2bayA | 6 | 0.5784 | 98.7 | 0.686 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)