| T0999_CASP12_TEST |
| ID: | 1462058629 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (61) | ||
| Sequences: | 143 (121) | ||
| Seq/Len: | 2.344 | ||
| Nf(neff/√len): | 15.5 |
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: 2.344).
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 |
| 29_V | 37_Y | 4.398 | 1.00 |
| 8_F | 12_V | 2.353 | 1.00 |
| 12_V | 52_L | 2.061 | 0.99 |
| 37_Y | 59_V | 1.924 | 0.99 |
| 49_L | 59_V | 1.778 | 0.98 |
| 5_Y | 45_D | 1.533 | 0.94 |
| 8_F | 52_L | 1.419 | 0.90 |
| 7_T | 62_E | 1.404 | 0.90 |
| 5_Y | 25_R | 1.373 | 0.88 |
| 27_I | 37_Y | 1.331 | 0.86 |
| 4_D | 25_R | 1.303 | 0.85 |
| 18_R | 50_D | 1.283 | 0.83 |
| 57_V | 61_G | 1.229 | 0.79 |
| 17_V | 40_Y | 1.229 | 0.79 |
| 45_D | 49_L | 1.205 | 0.78 |
| 4_D | 40_Y | 1.203 | 0.77 |
| 47_K | 51_N | 1.180 | 0.75 |
| 29_V | 48_L | 1.173 | 0.75 |
| 24_G | 42_P | 1.171 | 0.75 |
| 23_N | 40_Y | 1.162 | 0.74 |
| 22_I | 59_V | 1.156 | 0.73 |
| 11_E | 16_Q | 1.128 | 0.71 |
| 21_R | 26_E | 1.087 | 0.67 |
| 6_S | 46_P | 1.086 | 0.67 |
| 18_R | 30_T | 1.070 | 0.65 |
| 17_V | 22_I | 1.061 | 0.64 |
| 10_Q | 16_Q | 1.032 | 0.61 |
| 14_N | 28_N | 1.021 | 0.59 |
| 17_V | 26_E | 1.020 | 0.59 |
| 51_N | 55_K | 1.016 | 0.59 |
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 | |
| 2muyA | 1 | 1 | 99.3 | 0.139 | Contact Map |
| 4m8aA | 3 | 1 | 99.2 | 0.2 | Contact Map |
| 2lnaA | 1 | 0.9839 | 68.6 | 0.745 | Contact Map |
| 2l48A | 2 | 0.7581 | 19.2 | 0.817 | Contact Map |
| 3vdpA | 4 | 0.8226 | 16.7 | 0.822 | Contact Map |
| 1m2oA | 2 | 0.2903 | 12.6 | 0.832 | Contact Map |
| 2oa9A | 2 | 0.8387 | 12.5 | 0.832 | Contact Map |
| 2nutA | 1 | 0.3065 | 12.4 | 0.832 | Contact Map |
| 4narA | 1 | 0.9516 | 12.3 | 0.832 | Contact Map |
| 4l1gA | 4 | 0.8387 | 10.3 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)