| 1ubq |
| ID: | 1473193176 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (76) | ||
| Sequences: | 5369 (3693.3) | ||
| Seq/Len: | 70.645 | ||
| Nf(neff/√len): | 423.7 |
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: 70.645).
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 |
| 27_K | 52_D | 3.534 | 1.00 |
| 21_D | 29_K | 2.819 | 1.00 |
| 54_R | 58_D | 2.620 | 1.00 |
| 24_E | 28_A | 2.565 | 1.00 |
| 55_T | 58_D | 2.249 | 1.00 |
| 62_Q | 65_S | 1.991 | 1.00 |
| 51_E | 54_R | 1.922 | 1.00 |
| 21_D | 25_N | 1.855 | 1.00 |
| 54_R | 59_Y | 1.851 | 1.00 |
| 4_F | 12_T | 1.786 | 1.00 |
| 29_K | 33_K | 1.620 | 1.00 |
| 13_I | 34_E | 1.530 | 1.00 |
| 31_Q | 38_P | 1.517 | 1.00 |
| 44_I | 70_V | 1.485 | 1.00 |
| 43_L | 67_L | 1.450 | 1.00 |
| 45_F | 65_S | 1.428 | 1.00 |
| 25_N | 29_K | 1.422 | 1.00 |
| 19_P | 57_S | 1.416 | 1.00 |
| 36_I | 41_Q | 1.407 | 0.99 |
| 30_I | 43_L | 1.397 | 0.99 |
| 41_Q | 69_L | 1.372 | 0.99 |
| 56_L | 61_I | 1.357 | 0.99 |
| 2_Q | 14_T | 1.345 | 0.99 |
| 25_N | 28_A | 1.341 | 0.99 |
| 61_I | 67_L | 1.302 | 0.99 |
| 24_E | 52_D | 1.236 | 0.98 |
| 28_A | 31_Q | 1.223 | 0.98 |
| 21_D | 26_V | 1.211 | 0.98 |
| 18_E | 21_D | 1.208 | 0.98 |
| 2_Q | 16_E | 1.186 | 0.98 |
| 38_P | 41_Q | 1.146 | 0.97 |
| 17_V | 21_D | 1.128 | 0.97 |
| 24_E | 53_G | 1.101 | 0.96 |
| 44_I | 49_Q | 1.097 | 0.96 |
| 36_I | 40_Q | 1.092 | 0.96 |
| 37_P | 41_Q | 1.087 | 0.96 |
| 73_L | 76_G | 1.081 | 0.95 |
| 26_V | 56_L | 1.072 | 0.95 |
| 6_K | 12_T | 1.066 | 0.95 |
| 4_F | 14_T | 1.038 | 0.94 |
| 4_F | 66_T | 1.034 | 0.94 |
| 5_V | 15_L | 1.025 | 0.93 |
| 22_T | 25_N | 1.024 | 0.93 |
| 31_Q | 41_Q | 1.020 | 0.93 |
| 26_V | 67_L | 1.016 | 0.93 |
| 2_Q | 63_K | 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 | |
| 5c1zA | 2 | 0 | 99.3 | -0.07 | Contact Map |
| 3u5cf | 1 | 0 | 99.3 | -0.067 | Contact Map |
| 3u5em | 1 | 0 | 99.3 | -0.061 | Contact Map |
| 4k95A | 12 | 0.9605 | 99.2 | -0.052 | Contact Map |
| 4npnA | 1 | 0.9211 | 99.2 | -0.046 | Contact Map |
| 2io1B | 3 | 1 | 99.2 | -0.043 | Contact Map |
| 3l0wB | 1 | 0.9868 | 99.2 | -0.041 | Contact Map |
| 1yx5B | 1 | 1 | 99.2 | -0.04 | Contact Map |
| 1wywB | 1 | 1 | 99.2 | -0.04 | Contact Map |
| 2d07B | 1 | 0.9605 | 99.2 | -0.038 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)