| bc1 |
| ID: | 1513229301 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 149 (118) | ||
| Sequences: | 163 (67.1) | ||
| Seq/Len: | 1.381 | ||
| Nf(neff/√len): | 6.2 |
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: 1.381).
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 |
| 113_F | 118_M | 1.983 | 0.97 |
| 122_I | 126_M | 1.765 | 0.94 |
| 95_E | 104_M | 1.709 | 0.93 |
| 110_I | 149_V | 1.707 | 0.93 |
| 90_F | 94_E | 1.598 | 0.89 |
| 38_N | 41_G | 1.584 | 0.88 |
| 76_M | 139_D | 1.579 | 0.88 |
| 65_T | 68_P | 1.557 | 0.87 |
| 52_E | 149_V | 1.523 | 0.86 |
| 55_S | 62_L | 1.425 | 0.80 |
| 32_M | 68_P | 1.384 | 0.77 |
| 109_R | 137_I | 1.375 | 0.77 |
| 117_D | 124_M | 1.333 | 0.73 |
| 132_V | 135_I | 1.323 | 0.73 |
| 36_Y | 78_P | 1.318 | 0.72 |
| 88_F | 91_N | 1.301 | 0.71 |
| 107_D | 114_R | 1.283 | 0.69 |
| 79_Y | 89_D | 1.280 | 0.69 |
| 134_D | 146_N | 1.279 | 0.69 |
| 73_K | 133_I | 1.275 | 0.69 |
| 89_D | 92_I | 1.273 | 0.68 |
| 83_G | 129_E | 1.268 | 0.68 |
| 133_I | 148_C | 1.243 | 0.66 |
| 82_D | 107_D | 1.224 | 0.64 |
| 82_D | 108_S | 1.203 | 0.62 |
| 49_K | 92_I | 1.187 | 0.61 |
| 66_R | 73_K | 1.184 | 0.60 |
| 32_M | 65_T | 1.184 | 0.60 |
| 56_I | 67_S | 1.173 | 0.59 |
| 36_Y | 46_I | 1.156 | 0.58 |
| 67_S | 93_L | 1.155 | 0.57 |
| 37_N | 110_I | 1.154 | 0.57 |
| 128_H | 133_I | 1.147 | 0.57 |
| 101_L | 118_M | 1.142 | 0.56 |
| 45_R | 114_R | 1.141 | 0.56 |
| 128_H | 146_N | 1.134 | 0.55 |
| 57_L | 147_V | 1.132 | 0.55 |
| 37_N | 107_D | 1.130 | 0.55 |
| 37_N | 66_R | 1.121 | 0.54 |
| 61_E | 102_K | 1.110 | 0.53 |
| 43_E | 71_A | 1.107 | 0.53 |
| 113_F | 135_I | 1.107 | 0.53 |
| 59_L | 126_M | 1.107 | 0.53 |
| 59_L | 115_Q | 1.102 | 0.52 |
| 145_T | 148_C | 1.102 | 0.52 |
| 124_M | 149_V | 1.100 | 0.52 |
| 34_I | 78_P | 1.094 | 0.51 |
| 35_K | 43_E | 1.093 | 0.51 |
| 52_E | 57_L | 1.086 | 0.50 |
| 83_G | 130_A | 1.075 | 0.49 |
| 106_K | 148_C | 1.070 | 0.49 |
| 101_L | 104_M | 1.058 | 0.48 |
| 52_E | 107_D | 1.053 | 0.47 |
| 76_M | 115_Q | 1.053 | 0.47 |
| 99_N | 102_K | 1.050 | 0.47 |
| 110_I | 119_V | 1.031 | 0.45 |
| 79_Y | 88_F | 1.030 | 0.45 |
| 114_R | 138_A | 1.029 | 0.45 |
| 112_E | 117_D | 1.029 | 0.45 |
| 81_H | 129_E | 1.022 | 0.44 |
| 52_E | 66_R | 1.018 | 0.44 |
| 130_A | 141_Y | 1.018 | 0.44 |
| 41_G | 44_F | 1.010 | 0.43 |
| 143_V | 147_V | 1.005 | 0.42 |
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 | |
| 1vbkA | 2 | 0.8389 | 7.2 | 0.966 | Contact Map |
| 4eljA | 1 | 0.3893 | 6.7 | 0.967 | Contact Map |
| 1vb3A | 1 | 0.604 | 5.5 | 0.968 | Contact Map |
| 1dj7B | 1 | 0.3893 | 4.8 | 0.969 | Contact Map |
| 3drwA | 2 | 0.9128 | 4.6 | 0.969 | Contact Map |
| 2bptB | 1 | 0.1946 | 4 | 0.97 | Contact Map |
| 4ajyC | 1 | 0.5168 | 3.7 | 0.971 | Contact Map |
| 2l7xA | 1 | 0.3289 | 2.8 | 0.973 | Contact Map |
| 4ellA | 2 | 0.4899 | 2.7 | 0.973 | Contact Map |
| 2vpkA | 1 | 0.7383 | 2.5 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)