| lppn 61-175 |
| ID: | 1442996949 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (110) | ||
| Sequences: | 636 (517.4) | ||
| Seq/Len: | 5.782 | ||
| Nf(neff/√len): | 49.3 |
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: 5.782).
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 |
| 40_L | 61_G | 3.276 | 1.00 |
| 38_V | 100_L | 2.692 | 1.00 |
| 39_Y | 62_F | 2.676 | 1.00 |
| 87_R | 95_S | 2.597 | 1.00 |
| 86_D | 94_P | 2.510 | 1.00 |
| 37_E | 65_Y | 2.436 | 1.00 |
| 42_A | 97_V | 1.880 | 1.00 |
| 29_D | 32_T | 1.879 | 1.00 |
| 46_V | 49_A | 1.816 | 1.00 |
| 7_Q | 10_D | 1.718 | 1.00 |
| 67_G | 73_S | 1.709 | 1.00 |
| 87_R | 93_T | 1.595 | 0.99 |
| 36_A | 100_L | 1.574 | 0.99 |
| 54_A | 97_V | 1.436 | 0.98 |
| 12_L | 38_V | 1.381 | 0.98 |
| 35_S | 108_L | 1.334 | 0.97 |
| 32_T | 114_R | 1.328 | 0.97 |
| 65_Y | 114_R | 1.324 | 0.97 |
| 37_E | 112_S | 1.313 | 0.97 |
| 15_L | 101_L | 1.310 | 0.97 |
| 62_F | 70_V | 1.236 | 0.95 |
| 82_D | 94_P | 1.196 | 0.94 |
| 45_A | 87_R | 1.187 | 0.94 |
| 39_Y | 77_V | 1.181 | 0.93 |
| 70_V | 73_S | 1.168 | 0.93 |
| 6_L | 38_V | 1.135 | 0.91 |
| 34_H | 37_E | 1.125 | 0.91 |
| 54_A | 79_Y | 1.122 | 0.91 |
| 33_A | 110_T | 1.118 | 0.91 |
| 8_V | 73_S | 1.109 | 0.90 |
| 6_L | 98_I | 1.103 | 0.90 |
| 45_A | 115_R | 1.095 | 0.89 |
| 36_A | 71_D | 1.094 | 0.89 |
| 87_R | 94_P | 1.088 | 0.89 |
| 63_A | 84_H | 1.084 | 0.89 |
| 5_N | 27_I | 1.081 | 0.88 |
| 15_L | 26_T | 1.043 | 0.86 |
| 13_A | 28_V | 1.042 | 0.86 |
| 109_L | 113_A | 1.041 | 0.86 |
| 75_Y | 113_A | 1.039 | 0.86 |
| 82_D | 95_S | 1.025 | 0.85 |
| 15_L | 18_A | 1.023 | 0.84 |
| 45_A | 95_S | 1.007 | 0.83 |
| 51_V | 79_Y | 1.001 | 0.83 |
| 14_D | 53_M | 1.001 | 0.83 |
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 | |
| 2mpoA | 1 | 0.6609 | 4.9 | 0.917 | Contact Map |
| 2gpiA | 1 | 0.3304 | 3.1 | 0.925 | Contact Map |
| 4b29A | 1 | 0.4174 | 3 | 0.926 | Contact Map |
| 3c9zA | 1 | 0.3739 | 2.9 | 0.926 | Contact Map |
| 1at0A | 1 | 0.4957 | 2.7 | 0.928 | Contact Map |
| 2oqjC | 4 | 0.1391 | 2.1 | 0.932 | Contact Map |
| 2pytA | 2 | 0.3478 | 1.8 | 0.934 | Contact Map |
| 1o4tA | 2 | 0.3391 | 1.8 | 0.934 | Contact Map |
| 4aivA | 1 | 0.3391 | 1.7 | 0.935 | Contact Map |
| 1vclA | 2 | 0.8957 | 1.6 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)