| UPF0093 consensus |
| ID: | 1504388561 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 147 (145) | ||
| Sequences: | 1468 (904.7) | ||
| Seq/Len: | 10.124 | ||
| Nf(neff/√len): | 75.1 |
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: 10.124).
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 |
| 67_W | 99_V | 3.623 | 1.00 |
| 35_E | 121_A | 2.810 | 1.00 |
| 55_Y | 106_G | 2.758 | 1.00 |
| 48_A | 115_G | 2.734 | 1.00 |
| 13_I | 143_V | 2.596 | 1.00 |
| 140_I | 144_V | 2.569 | 1.00 |
| 22_G | 59_M | 2.455 | 1.00 |
| 33_H | 51_E | 2.291 | 1.00 |
| 107_R | 111_R | 2.157 | 1.00 |
| 90_V | 141_L | 2.157 | 1.00 |
| 112_L | 117_N | 2.080 | 1.00 |
| 65_L | 69_S | 2.073 | 1.00 |
| 99_V | 103_G | 2.024 | 1.00 |
| 11_L | 69_S | 2.006 | 1.00 |
| 134_L | 138_I | 1.995 | 1.00 |
| 94_L | 141_L | 1.948 | 1.00 |
| 16_V | 66_T | 1.932 | 1.00 |
| 15_A | 65_L | 1.915 | 1.00 |
| 94_L | 137_A | 1.831 | 1.00 |
| 89_H | 93_V | 1.811 | 1.00 |
| 17_I | 135_L | 1.795 | 1.00 |
| 18_S | 62_A | 1.774 | 1.00 |
| 111_R | 116_E | 1.683 | 1.00 |
| 15_A | 69_S | 1.621 | 1.00 |
| 6_L | 9_K | 1.595 | 1.00 |
| 88_L | 92_L | 1.593 | 1.00 |
| 43_F | 46_R | 1.590 | 1.00 |
| 8_L | 72_L | 1.575 | 1.00 |
| 122_K | 126_I | 1.574 | 1.00 |
| 44_Y | 115_G | 1.500 | 1.00 |
| 104_W | 108_Y | 1.446 | 1.00 |
| 105_C | 127_F | 1.432 | 1.00 |
| 14_I | 139_V | 1.403 | 0.99 |
| 14_I | 136_I | 1.377 | 0.99 |
| 100_A | 103_G | 1.358 | 0.99 |
| 87_W | 142_V | 1.339 | 0.99 |
| 49_I | 53_R | 1.336 | 0.99 |
| 71_L | 75_F | 1.306 | 0.99 |
| 32_Y | 49_I | 1.305 | 0.99 |
| 108_Y | 123_F | 1.298 | 0.99 |
| 45_E | 48_A | 1.293 | 0.99 |
| 24_F | 101_Y | 1.291 | 0.99 |
| 25_Y | 50_M | 1.291 | 0.99 |
| 52_R | 57_I | 1.281 | 0.99 |
| 117_N | 124_F | 1.210 | 0.98 |
| 86_P | 147_F | 1.203 | 0.98 |
| 103_G | 106_G | 1.189 | 0.98 |
| 109_L | 113_A | 1.187 | 0.98 |
| 94_L | 138_I | 1.179 | 0.98 |
| 74_L | 88_L | 1.176 | 0.98 |
| 10_A | 144_V | 1.173 | 0.98 |
| 7_W | 140_I | 1.166 | 0.97 |
| 82_W | 85_S | 1.146 | 0.97 |
| 141_L | 146_P | 1.134 | 0.97 |
| 23_L | 59_M | 1.120 | 0.96 |
| 108_Y | 124_F | 1.120 | 0.96 |
| 86_P | 89_H | 1.117 | 0.96 |
| 28_R | 128_N | 1.117 | 0.96 |
| 4_Y | 8_L | 1.112 | 0.96 |
| 44_Y | 48_A | 1.103 | 0.96 |
| 10_A | 140_I | 1.101 | 0.96 |
| 58_I | 62_A | 1.092 | 0.96 |
| 60_T | 102_H | 1.087 | 0.96 |
| 101_Y | 105_C | 1.079 | 0.95 |
| 104_W | 127_F | 1.073 | 0.95 |
| 47_L | 50_M | 1.070 | 0.95 |
| 31_V | 34_A | 1.063 | 0.95 |
| 8_L | 144_V | 1.052 | 0.95 |
| 31_V | 124_F | 1.010 | 0.93 |
| 36_A | 43_F | 1.010 | 0.93 |
| 3_N | 6_L | 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 | |
| 3wajA | 1 | 0.8776 | 1.7 | 0.959 | Contact Map |
| 4rp9A | 1 | 0.2857 | 1.6 | 0.959 | Contact Map |
| 3zuxA | 1 | 0.6054 | 1.6 | 0.959 | Contact Map |
| 2ls2A | 1 | 0.0612 | 1.3 | 0.961 | Contact Map |
| 1wyoA | 1 | 0.3333 | 1.2 | 0.962 | Contact Map |
| 3x29A | 2 | 0.4898 | 1 | 0.964 | Contact Map |
| 2kncB | 1 | 0.2381 | 1 | 0.964 | Contact Map |
| 4gd3A | 2 | 0.2449 | 0.9 | 0.964 | Contact Map |
| 1oedA | 2 | 0.2381 | 0.9 | 0.965 | Contact Map |
| 4qq0A | 1 | 0 | 0.9 | 0.965 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)