| 4ryr |
| ID: | 1500381823 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (145) | ||
| Sequences: | 2559 (1975.6) | ||
| Seq/Len: | 17.648 | ||
| Nf(neff/√len): | 164.1 |
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: 17.648).
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 | 3.902 | 1.00 |
| 91_F | 104_D | 3.902 | 1.00 |
| 112_T | 137_S | 3.096 | 1.00 |
| 99_F | 148_Y | 3.033 | 1.00 |
| 43_M | 47_M | 3.000 | 1.00 |
| 38_W | 142_Y | 2.940 | 1.00 |
| 62_I | 123_S | 2.705 | 1.00 |
| 102_T | 145_W | 2.599 | 1.00 |
| 84_F | 111_T | 2.194 | 1.00 |
| 115_L | 130_L | 1.982 | 1.00 |
| 102_T | 144_S | 1.948 | 1.00 |
| 77_L | 118_F | 1.879 | 1.00 |
| 146_T | 149_S | 1.870 | 1.00 |
| 116_I | 127_A | 1.832 | 1.00 |
| 120_S | 127_A | 1.825 | 1.00 |
| 145_W | 149_S | 1.789 | 1.00 |
| 60_V | 78_F | 1.782 | 1.00 |
| 128_W | 131_I | 1.768 | 1.00 |
| 77_L | 114_L | 1.752 | 1.00 |
| 109_A | 137_S | 1.683 | 1.00 |
| 109_A | 141_T | 1.641 | 1.00 |
| 146_T | 150_I | 1.576 | 1.00 |
| 115_L | 119_S | 1.575 | 1.00 |
| 59_S | 130_L | 1.566 | 1.00 |
| 29_W | 98_L | 1.530 | 1.00 |
| 84_F | 107_L | 1.524 | 1.00 |
| 105_C | 141_T | 1.517 | 1.00 |
| 15_L | 86_Q | 1.507 | 1.00 |
| 53_F | 85_N | 1.467 | 1.00 |
| 88_F | 144_S | 1.384 | 0.99 |
| 114_L | 118_F | 1.366 | 0.99 |
| 35_K | 147_I | 1.301 | 0.99 |
| 108_V | 133_Y | 1.281 | 0.99 |
| 34_E | 150_I | 1.277 | 0.99 |
| 142_Y | 146_T | 1.275 | 0.99 |
| 29_W | 96_K | 1.264 | 0.99 |
| 60_V | 75_W | 1.264 | 0.99 |
| 91_F | 101_A | 1.261 | 0.99 |
| 84_F | 104_D | 1.237 | 0.98 |
| 63_I | 119_S | 1.212 | 0.98 |
| 44_T | 48_I | 1.204 | 0.98 |
| 74_F | 119_S | 1.182 | 0.98 |
| 120_S | 124_K | 1.181 | 0.98 |
| 109_A | 112_T | 1.170 | 0.97 |
| 81_N | 111_T | 1.166 | 0.97 |
| 105_C | 144_S | 1.152 | 0.97 |
| 35_K | 39_T | 1.144 | 0.97 |
| 97_N | 100_L | 1.128 | 0.97 |
| 9_F | 60_V | 1.128 | 0.97 |
| 62_I | 65_N | 1.127 | 0.97 |
| 101_A | 104_D | 1.117 | 0.96 |
| 38_W | 146_T | 1.109 | 0.96 |
| 116_I | 130_L | 1.103 | 0.96 |
| 59_S | 126_S | 1.080 | 0.95 |
| 83_I | 87_A | 1.075 | 0.95 |
| 76_F | 80_L | 1.059 | 0.95 |
| 120_S | 128_W | 1.056 | 0.95 |
| 102_T | 148_Y | 1.056 | 0.95 |
| 54_G | 58_L | 1.052 | 0.95 |
| 63_I | 74_F | 1.051 | 0.94 |
| 116_I | 134_F | 1.049 | 0.94 |
| 105_C | 137_S | 1.047 | 0.94 |
| 67_Y | 71_P | 1.040 | 0.94 |
| 81_N | 115_L | 1.020 | 0.93 |
| 37_S | 146_T | 1.018 | 0.93 |
| 113_L | 134_F | 1.016 | 0.93 |
| 109_A | 113_L | 1.016 | 0.93 |
| 63_I | 122_L | 1.011 | 0.93 |
| 85_N | 133_Y | 1.006 | 0.93 |
| 44_T | 139_F | 1.001 | 0.92 |
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 | Contact Map |
| 4uc1A | 3 | 0.9801 | 100 | 0.037 | Contact Map |
| 2mgyA | 1 | 1 | 100 | 0.067 | Contact Map |
| 4ev6A | 5 | 0.4106 | 6 | 0.921 | Contact Map |
| 4i0uA | 10 | 0.3974 | 4.8 | 0.924 | Contact Map |
| 1rh5B | 1 | 0.2053 | 3.2 | 0.93 | Contact Map |
| 4phzK | 3 | 0.7219 | 2.3 | 0.936 | Contact Map |
| 2rlwA | 1 | 0.2252 | 1.5 | 0.942 | Contact Map |
| 4qncA | 2 | 0.3709 | 1.4 | 0.943 | Contact Map |
| 1yewC | 3 | 0.6093 | 1.2 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)