| contact-prediction-test |
| ID: | 1506308976 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 63 (63) | ||
| Sequences: | 2100 (1325.3) | ||
| Seq/Len: | 33.333 | ||
| Nf(neff/√len): | 167.0 |
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: 33.333).
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 |
| 8_Y | 56_A | 2.803 | 1.00 |
| 16_L | 59_V | 2.241 | 1.00 |
| 12_V | 59_V | 2.228 | 1.00 |
| 9_N | 22_P | 2.221 | 1.00 |
| 9_N | 21_E | 1.965 | 1.00 |
| 10_N | 13_R | 1.956 | 1.00 |
| 9_N | 23_A | 1.767 | 1.00 |
| 13_R | 19_D | 1.740 | 1.00 |
| 7_E | 53_L | 1.511 | 1.00 |
| 38_I | 42_L | 1.493 | 1.00 |
| 32_G | 41_V | 1.394 | 0.99 |
| 2_R | 42_L | 1.377 | 0.99 |
| 16_L | 63_A | 1.321 | 0.99 |
| 58_Q | 62_K | 1.291 | 0.99 |
| 8_Y | 52_Y | 1.286 | 0.99 |
| 29_D | 42_L | 1.276 | 0.99 |
| 1_R | 54_D | 1.265 | 0.99 |
| 6_A | 10_N | 1.223 | 0.98 |
| 25_N | 55_A | 1.213 | 0.98 |
| 1_R | 7_E | 1.195 | 0.98 |
| 2_R | 29_D | 1.184 | 0.98 |
| 58_Q | 61_A | 1.162 | 0.97 |
| 27_P | 48_L | 1.156 | 0.97 |
| 51_K | 54_D | 1.137 | 0.97 |
| 4_N | 36_D | 1.121 | 0.97 |
| 44_V | 49_V | 1.121 | 0.97 |
| 32_G | 43_S | 1.095 | 0.96 |
| 47_L | 50_E | 1.082 | 0.96 |
| 57_E | 60_A | 1.079 | 0.95 |
| 25_N | 58_Q | 1.058 | 0.95 |
| 9_N | 26_F | 1.049 | 0.94 |
| 5_R | 28_S | 1.024 | 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 | |
| 2ijaA | 1 | 0.5556 | 21.9 | 0.82 | Contact Map |
| 4nv8A | 2 | 0.5714 | 10.8 | 0.843 | Contact Map |
| 3lnbA | 1 | 0.3016 | 9.1 | 0.848 | Contact Map |
| 4guzA | 4 | 0.5556 | 8.1 | 0.851 | Contact Map |
| 3pukA | 2 | 0.9841 | 8 | 0.852 | Contact Map |
| 3ayfA | 1 | 0.8889 | 7.6 | 0.853 | Contact Map |
| 4h0nA | 4 | 0.7937 | 6.9 | 0.856 | Contact Map |
| 3d9wA | 4 | 0.5714 | 6.2 | 0.859 | Contact Map |
| 1e2tA | 8 | 0.619 | 6.1 | 0.86 | Contact Map |
| 1xrsA | 1 | 0.4127 | 5.5 | 0.862 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)