| 4ryrA |
| ID: | 1491921563 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (135) | ||
| Sequences: | 2093 (1617.9) | ||
| Seq/Len: | 15.504 | ||
| Nf(neff/√len): | 139.2 |
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: 15.504).
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 |
| 109_A | 138_A | 4.046 | 1.00 |
| 91_F | 104_D | 3.734 | 1.00 |
| 112_T | 137_S | 2.997 | 1.00 |
| 38_W | 142_Y | 2.969 | 1.00 |
| 43_M | 47_M | 2.897 | 1.00 |
| 62_I | 123_S | 2.756 | 1.00 |
| 99_F | 148_Y | 2.398 | 1.00 |
| 84_F | 111_T | 2.162 | 1.00 |
| 115_L | 130_L | 2.131 | 1.00 |
| 102_T | 145_W | 2.118 | 1.00 |
| 120_S | 127_A | 1.887 | 1.00 |
| 102_T | 144_S | 1.877 | 1.00 |
| 145_W | 149_S | 1.781 | 1.00 |
| 116_I | 127_A | 1.774 | 1.00 |
| 77_L | 118_F | 1.768 | 1.00 |
| 115_L | 119_S | 1.737 | 1.00 |
| 29_W | 98_L | 1.724 | 1.00 |
| 128_W | 131_I | 1.696 | 1.00 |
| 59_S | 130_L | 1.693 | 1.00 |
| 146_T | 150_I | 1.684 | 1.00 |
| 146_T | 149_S | 1.675 | 1.00 |
| 60_V | 78_F | 1.675 | 1.00 |
| 109_A | 141_T | 1.651 | 1.00 |
| 109_A | 137_S | 1.571 | 1.00 |
| 77_L | 114_L | 1.541 | 1.00 |
| 60_V | 75_W | 1.447 | 1.00 |
| 105_C | 141_T | 1.432 | 1.00 |
| 35_K | 39_T | 1.411 | 1.00 |
| 142_Y | 146_T | 1.343 | 0.99 |
| 34_E | 150_I | 1.324 | 0.99 |
| 53_F | 85_N | 1.312 | 0.99 |
| 38_W | 146_T | 1.287 | 0.99 |
| 29_W | 96_K | 1.267 | 0.99 |
| 35_K | 147_I | 1.262 | 0.99 |
| 120_S | 124_K | 1.253 | 0.99 |
| 120_S | 128_W | 1.225 | 0.98 |
| 91_F | 101_A | 1.215 | 0.98 |
| 63_I | 119_S | 1.210 | 0.98 |
| 83_I | 87_A | 1.194 | 0.98 |
| 74_F | 119_S | 1.191 | 0.98 |
| 116_I | 130_L | 1.186 | 0.98 |
| 114_L | 118_F | 1.182 | 0.98 |
| 105_C | 144_S | 1.173 | 0.98 |
| 56_I | 60_V | 1.167 | 0.97 |
| 108_V | 133_Y | 1.166 | 0.97 |
| 60_V | 64_Y | 1.161 | 0.97 |
| 57_A | 61_A | 1.157 | 0.97 |
| 109_A | 112_T | 1.152 | 0.97 |
| 101_A | 104_D | 1.137 | 0.97 |
| 62_I | 65_N | 1.135 | 0.97 |
| 97_N | 100_L | 1.132 | 0.97 |
| 19_S | 22_L | 1.119 | 0.96 |
| 59_S | 115_L | 1.100 | 0.96 |
| 37_S | 146_T | 1.083 | 0.96 |
| 84_F | 107_L | 1.080 | 0.95 |
| 88_F | 144_S | 1.071 | 0.95 |
| 76_F | 80_L | 1.059 | 0.95 |
| 63_I | 74_F | 1.045 | 0.94 |
| 81_N | 115_L | 1.043 | 0.94 |
| 88_F | 92_Q | 1.043 | 0.94 |
| 116_I | 134_F | 1.028 | 0.94 |
| 29_W | 39_T | 1.028 | 0.94 |
| 63_I | 122_L | 1.017 | 0.93 |
| 44_T | 48_I | 1.012 | 0.93 |
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 | |
| 4ryoA | 1 | 0 | 100 | 0.085 | Contact Map |
| 4uc1A | 3 | 0.9801 | 100 | 0.103 | Contact Map |
| 2mgyA | 1 | 1 | 100 | 0.173 | Contact Map |
| 4phzK | 3 | 0.755 | 9.1 | 0.935 | Contact Map |
| 1yewC | 3 | 0.5695 | 9.1 | 0.936 | Contact Map |
| 4i0uA | 10 | 0.3907 | 5.3 | 0.942 | Contact Map |
| 4ev6A | 5 | 0.404 | 3.7 | 0.946 | Contact Map |
| 4p79A | 1 | 0.4106 | 2.4 | 0.951 | Contact Map |
| 3x29A | 2 | 0.4238 | 1.4 | 0.958 | Contact Map |
| 4cadC | 4 | 0.7748 | 1.3 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)