| ubiquitin precursor |
| ID: | 1488313521 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (89) | ||
| Sequences: | 258 (141.4) | ||
| Seq/Len: | 2.899 | ||
| Nf(neff/√len): | 15.0 |
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: 2.899).
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 |
| 82_L | 86_K | 1.869 | 0.99 |
| 79_T | 83_R | 1.748 | 0.99 |
| 38_I | 42_S | 1.727 | 0.98 |
| 60_C | 63_R | 1.664 | 0.98 |
| 4_L | 11_L | 1.489 | 0.95 |
| 1_Q | 15_R | 1.388 | 0.92 |
| 80_N | 83_R | 1.372 | 0.92 |
| 60_C | 72_R | 1.346 | 0.91 |
| 44_R | 48_Q | 1.339 | 0.90 |
| 68_A | 71_C | 1.299 | 0.88 |
| 3_R | 10_Q | 1.287 | 0.88 |
| 60_C | 68_A | 1.281 | 0.87 |
| 1_Q | 5_I | 1.262 | 0.86 |
| 22_I | 29_H | 1.259 | 0.86 |
| 1_Q | 23_Q | 1.253 | 0.86 |
| 75_K | 78_H | 1.229 | 0.84 |
| 40_E | 43_L | 1.220 | 0.84 |
| 57_C | 71_C | 1.210 | 0.83 |
| 28_L | 31_V | 1.176 | 0.81 |
| 62_A | 71_C | 1.167 | 0.80 |
| 5_I | 12_E | 1.162 | 0.80 |
| 30_L | 34_L | 1.155 | 0.79 |
| 83_R | 86_K | 1.153 | 0.79 |
| 34_L | 37_G | 1.142 | 0.78 |
| 18_S | 25_E | 1.140 | 0.78 |
| 52_C | 66_P | 1.139 | 0.78 |
| 26_S | 31_V | 1.139 | 0.78 |
| 10_Q | 14_G | 1.132 | 0.77 |
| 19_D | 30_L | 1.128 | 0.77 |
| 49_K | 54_K | 1.124 | 0.76 |
| 72_R | 83_R | 1.119 | 0.76 |
| 5_I | 10_Q | 1.117 | 0.76 |
| 63_R | 72_R | 1.115 | 0.75 |
| 63_R | 71_C | 1.109 | 0.75 |
| 83_R | 88_V | 1.108 | 0.75 |
| 60_C | 70_N | 1.104 | 0.74 |
| 11_L | 16_T | 1.096 | 0.74 |
| 3_R | 7_A | 1.094 | 0.74 |
| 86_K | 89_K | 1.093 | 0.73 |
| 30_L | 33_R | 1.086 | 0.73 |
| 58_R | 72_R | 1.084 | 0.73 |
| 1_Q | 9_K | 1.083 | 0.72 |
| 58_R | 83_R | 1.073 | 0.71 |
| 15_R | 24_K | 1.070 | 0.71 |
| 2_Q | 13_D | 1.068 | 0.71 |
| 58_R | 63_R | 1.062 | 0.70 |
| 15_R | 18_S | 1.051 | 0.69 |
| 84_P | 89_K | 1.038 | 0.68 |
| 19_D | 22_I | 1.031 | 0.67 |
| 82_L | 85_K | 1.030 | 0.67 |
| 73_K | 76_C | 1.029 | 0.67 |
| 16_T | 19_D | 1.019 | 0.66 |
| 75_K | 80_N | 1.016 | 0.65 |
| 68_A | 72_R | 1.013 | 0.65 |
| 26_S | 29_H | 1.001 | 0.64 |
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 | |
| 3u5em | 1 | 0.5843 | 99.9 | 0.246 | Contact Map |
| 3v7oA | 2 | 0.9775 | 99.5 | 0.522 | Contact Map |
| 3tixA | 2 | 0.9888 | 99.3 | 0.572 | Contact Map |
| 2xzm9 | 1 | 0.5281 | 99.1 | 0.599 | Contact Map |
| 2ekeC | 2 | 0.382 | 99.1 | 0.604 | Contact Map |
| 4ujrZ | 1 | 0.5843 | 99.1 | 0.608 | Contact Map |
| 4npnA | 1 | 0.3483 | 99 | 0.624 | Contact Map |
| 1se9A | 1 | 0.4607 | 99 | 0.627 | Contact Map |
| 1wz0A | 1 | 0.4607 | 98.9 | 0.63 | Contact Map |
| 4bkgA | 1 | 0 | 98.9 | 0.631 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)