| cd59 |
| ID: | 1504435975 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (124) | ||
| Sequences: | 151 (110) | ||
| Seq/Len: | 1.218 | ||
| Nf(neff/√len): | 9.9 |
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: 1.218).
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 |
| 41_A | 45_S | 1.608 | 0.87 |
| 26_L | 38_C | 1.594 | 0.87 |
| 38_C | 44_C | 1.578 | 0.86 |
| 26_L | 120_L | 1.520 | 0.83 |
| 31_C | 38_C | 1.482 | 0.81 |
| 76_T | 86_Y | 1.464 | 0.79 |
| 29_Y | 93_L | 1.413 | 0.76 |
| 3_I | 128_P | 1.396 | 0.75 |
| 26_L | 44_C | 1.381 | 0.74 |
| 39_K | 73_N | 1.367 | 0.73 |
| 2_G | 62_N | 1.360 | 0.72 |
| 79_L | 84_L | 1.356 | 0.72 |
| 49_D | 52_L | 1.346 | 0.71 |
| 38_C | 49_D | 1.326 | 0.69 |
| 6_G | 111_T | 1.301 | 0.67 |
| 6_G | 14_L | 1.260 | 0.64 |
| 104_G | 127_H | 1.256 | 0.63 |
| 97_N | 124_W | 1.235 | 0.61 |
| 123_A | 128_P | 1.234 | 0.61 |
| 16_L | 41_A | 1.230 | 0.61 |
| 9_L | 111_T | 1.227 | 0.60 |
| 18_V | 73_N | 1.224 | 0.60 |
| 23_G | 39_K | 1.213 | 0.59 |
| 26_L | 31_C | 1.205 | 0.58 |
| 55_K | 124_W | 1.202 | 0.58 |
| 4_Q | 128_P | 1.198 | 0.58 |
| 92_D | 115_L | 1.197 | 0.58 |
| 26_L | 86_Y | 1.162 | 0.54 |
| 54_T | 77_T | 1.158 | 0.54 |
| 54_T | 78_R | 1.157 | 0.54 |
| 21_H | 108_S | 1.138 | 0.52 |
| 3_I | 127_H | 1.137 | 0.52 |
| 16_L | 114_L | 1.134 | 0.52 |
| 27_Q | 83_E | 1.134 | 0.52 |
| 125_S | 128_P | 1.126 | 0.51 |
| 35_T | 116_V | 1.125 | 0.51 |
| 9_L | 20_C | 1.120 | 0.50 |
| 86_Y | 122_A | 1.115 | 0.50 |
| 110_K | 121_A | 1.111 | 0.49 |
| 74_D | 87_Y | 1.107 | 0.49 |
| 64_C | 70_C | 1.106 | 0.49 |
| 20_C | 29_Y | 1.103 | 0.49 |
| 8_V | 117_T | 1.103 | 0.49 |
| 15_V | 116_V | 1.091 | 0.47 |
| 106_S | 109_E | 1.086 | 0.47 |
| 31_C | 89_C | 1.084 | 0.47 |
| 86_Y | 120_L | 1.076 | 0.46 |
| 38_C | 75_V | 1.071 | 0.45 |
| 13_L | 122_A | 1.070 | 0.45 |
| 46_S | 71_N | 1.069 | 0.45 |
| 30_N | 85_T | 1.068 | 0.45 |
| 16_L | 29_Y | 1.066 | 0.45 |
| 59_Q | 66_K | 1.064 | 0.45 |
| 10_F | 45_S | 1.060 | 0.44 |
| 63_K | 80_R | 1.057 | 0.44 |
| 76_T | 123_A | 1.056 | 0.44 |
| 90_K | 126_L | 1.055 | 0.44 |
| 26_L | 90_K | 1.052 | 0.44 |
| 40_T | 66_K | 1.049 | 0.43 |
| 90_K | 98_E | 1.044 | 0.43 |
| 30_N | 73_N | 1.042 | 0.43 |
| 33_N | 63_K | 1.036 | 0.42 |
| 18_V | 112_V | 1.036 | 0.42 |
| 65_W | 75_V | 1.021 | 0.41 |
| 79_L | 122_A | 1.020 | 0.41 |
| 104_G | 128_P | 1.019 | 0.40 |
| 55_K | 83_E | 1.017 | 0.40 |
| 22_S | 112_V | 1.017 | 0.40 |
| 64_C | 89_C | 1.014 | 0.40 |
| 22_S | 119_F | 1.011 | 0.40 |
| 115_L | 119_F | 1.011 | 0.40 |
| 70_C | 89_C | 1.006 | 0.39 |
| 98_E | 110_K | 1.000 | 0.39 |
| 31_C | 64_C | 1.000 | 0.39 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2j8bA | 1 | 0.6094 | 99.6 | 0.546 | Contact Map |
| 1ywhA | 8 | 0.7812 | 99.3 | 0.62 | Contact Map |
| 2fd6U | 1 | 0.7891 | 99.1 | 0.649 | Contact Map |
| 2l03A | 1 | 0.5391 | 99 | 0.658 | Contact Map |
| 3laqU | 2 | 0.7891 | 98.8 | 0.687 | Contact Map |
| 2h7zB | 1 | 0.5469 | 98.5 | 0.719 | Contact Map |
| 1hc9A | 1 | 0.5156 | 98.5 | 0.723 | Contact Map |
| 3neqA | 2 | 0.4766 | 98.4 | 0.727 | Contact Map |
| 4iyeA | 1 | 0.4766 | 98.4 | 0.728 | Contact Map |
| 1jgkA | 1 | 0.4844 | 98.3 | 0.732 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)