| hellp |
| ID: | 1444311276 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (115) | ||
| Sequences: | 473 (407.5) | ||
| Seq/Len: | 4.113 | ||
| Nf(neff/√len): | 38.0 |
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: 4.113).
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 |
| 3_E | 6_G | 6.913 | 1.00 |
| 4_A | 8_A | 2.429 | 1.00 |
| 16_A | 20_H | 2.182 | 1.00 |
| 5_L | 9_G | 1.915 | 1.00 |
| 5_L | 10_S | 1.820 | 1.00 |
| 39_L | 79_I | 1.634 | 0.99 |
| 13_G | 16_A | 1.618 | 0.99 |
| 5_L | 14_I | 1.569 | 0.98 |
| 13_G | 20_H | 1.531 | 0.98 |
| 2_A | 6_G | 1.460 | 0.97 |
| 5_L | 13_G | 1.435 | 0.97 |
| 53_L | 82_C | 1.429 | 0.97 |
| 49_A | 110_R | 1.388 | 0.96 |
| 45_D | 52_A | 1.332 | 0.94 |
| 3_E | 7_V | 1.322 | 0.94 |
| 21_V | 46_L | 1.316 | 0.94 |
| 17_T | 83_S | 1.254 | 0.92 |
| 8_A | 14_I | 1.249 | 0.92 |
| 12_V | 17_T | 1.217 | 0.90 |
| 61_E | 91_A | 1.216 | 0.90 |
| 101_T | 106_S | 1.199 | 0.89 |
| 7_V | 10_S | 1.197 | 0.89 |
| 8_A | 111_G | 1.183 | 0.88 |
| 46_L | 86_C | 1.166 | 0.87 |
| 90_G | 94_K | 1.165 | 0.87 |
| 84_E | 87_N | 1.158 | 0.87 |
| 20_H | 28_D | 1.151 | 0.87 |
| 9_G | 12_V | 1.149 | 0.86 |
| 6_G | 10_S | 1.134 | 0.85 |
| 102_D | 105_L | 1.132 | 0.85 |
| 13_G | 83_S | 1.128 | 0.85 |
| 36_P | 55_S | 1.123 | 0.85 |
| 107_W | 110_R | 1.123 | 0.85 |
| 46_L | 59_I | 1.120 | 0.84 |
| 86_C | 89_F | 1.111 | 0.84 |
| 9_G | 13_G | 1.111 | 0.84 |
| 31_N | 51_R | 1.080 | 0.81 |
| 15_V | 18_A | 1.069 | 0.80 |
| 29_V | 46_L | 1.055 | 0.79 |
| 20_H | 67_L | 1.032 | 0.77 |
| 58_D | 83_S | 1.028 | 0.77 |
| 105_L | 109_D | 1.023 | 0.76 |
| 44_S | 81_S | 1.023 | 0.76 |
| 55_S | 89_F | 1.021 | 0.76 |
| 11_I | 15_V | 1.019 | 0.76 |
| 21_V | 86_C | 1.016 | 0.76 |
| 29_V | 50_D | 1.012 | 0.75 |
| 32_I | 46_L | 1.011 | 0.75 |
| 93_L | 96_W | 1.011 | 0.75 |
| 86_C | 109_D | 1.010 | 0.75 |
| 104_K | 112_N | 1.009 | 0.75 |
| 24_K | 36_P | 1.007 | 0.75 |
| 1_M | 6_G | 1.004 | 0.74 |
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 | |
| 4btfA | 1 | 0.7203 | 94.1 | 0.772 | Contact Map |
| 2msvA | 1 | 0.8559 | 74.2 | 0.833 | Contact Map |
| 3qflA | 1 | 0.8475 | 53.7 | 0.854 | Contact Map |
| 4q4gX | 1 | 0 | 45.2 | 0.861 | Contact Map |
| 3ghgA | 4 | 0.9068 | 41.8 | 0.864 | Contact Map |
| 4w8jA | 1 | 0.8559 | 34.6 | 0.87 | Contact Map |
| 4cgkA | 2 | 0.6271 | 30.3 | 0.874 | Contact Map |
| 2ljbA | 4 | 0.2542 | 28.8 | 0.875 | Contact Map |
| 1dlcA | 1 | 0.8898 | 26.7 | 0.877 | Contact Map |
| 4j2cA | 2 | 0.7881 | 25.5 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)