| Ubiquitin |
| ID: | 1434018168 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (68) | ||
| Sequences: | 4836 (3553.6) | ||
| Seq/Len: | 71.118 | ||
| Nf(neff/√len): | 430.9 |
HHblits Results: (2013_03)
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: 71.118).
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 |
| 22_K | 47_D | 4.880 | 1.00 |
| 16_D | 24_K | 2.693 | 1.00 |
| 49_R | 53_D | 2.296 | 1.00 |
| 50_T | 53_D | 2.262 | 1.00 |
| 16_D | 20_N | 2.208 | 1.00 |
| 49_R | 54_Y | 2.167 | 1.00 |
| 46_E | 49_R | 2.027 | 1.00 |
| 25_I | 38_L | 1.899 | 1.00 |
| 24_K | 28_K | 1.856 | 1.00 |
| 19_E | 23_A | 1.796 | 1.00 |
| 57_Q | 60_S | 1.751 | 1.00 |
| 36_Q | 64_L | 1.747 | 1.00 |
| 19_E | 47_D | 1.720 | 1.00 |
| 8_I | 29_E | 1.638 | 1.00 |
| 20_N | 23_A | 1.527 | 1.00 |
| 39_I | 65_V | 1.500 | 1.00 |
| 31_I | 36_Q | 1.471 | 1.00 |
| 26_Q | 36_Q | 1.423 | 1.00 |
| 13_E | 16_D | 1.415 | 1.00 |
| 33_P | 36_Q | 1.290 | 0.99 |
| 24_K | 27_D | 1.281 | 0.99 |
| 26_Q | 33_P | 1.271 | 0.99 |
| 12_V | 16_D | 1.268 | 0.99 |
| 37_R | 44_Q | 1.239 | 0.98 |
| 20_N | 24_K | 1.217 | 0.98 |
| 56_I | 62_L | 1.208 | 0.98 |
| 38_L | 62_L | 1.135 | 0.97 |
| 14_P | 52_S | 1.130 | 0.97 |
| 19_E | 48_G | 1.072 | 0.95 |
| 25_I | 36_Q | 1.072 | 0.95 |
| 17_T | 20_N | 1.061 | 0.95 |
| 39_I | 63_H | 1.046 | 0.94 |
| 18_I | 45_L | 1.043 | 0.94 |
| 15_S | 50_T | 1.036 | 0.94 |
| 39_I | 44_Q | 1.023 | 0.93 |
| 16_D | 21_V | 1.007 | 0.93 |
| 50_T | 54_Y | 1.006 | 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 | |
| 3ai5A | 1 | 0.9565 | 99.6 | -0.019 | Contact Map |
| 3b1lX | 1 | 1 | 99.6 | -0.01 | Contact Map |
| 3a9jA | 1 | 1 | 99.6 | 0.012 | Contact Map |
| 4k95A | 12 | 0.9855 | 99.5 | 0.074 | Contact Map |
| 4pyuA | 6 | 0.971 | 99.5 | 0.086 | Contact Map |
| 2wyqA | 1 | 0.9565 | 99.5 | 0.094 | Contact Map |
| 3q3fA | 1 | 1 | 99.5 | 0.097 | Contact Map |
| 2kdiA | 1 | 1 | 99.5 | 0.098 | Contact Map |
| 3j80f | 1 | 0 | 99.5 | 0.099 | Contact Map |
| 4adx5 | 1 | 0 | 99.4 | 0.1 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)