| 3OUF |
| ID: | 1448276623 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 97 (89) | ||
| Sequences: | 3973 (2644.2) | ||
| Seq/Len: | 44.640 | ||
| Nf(neff/√len): | 280.3 |
HHblits Results: (2015_06)
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: 44.640).
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 |
| 56_T | 59_G | 2.980 | 1.00 |
| 32_R | 35_D | 2.553 | 1.00 |
| 42_V | 67_I | 2.209 | 1.00 |
| 35_D | 60_K | 2.065 | 1.00 |
| 45_T | 67_I | 2.047 | 1.00 |
| 38_Y | 51_D | 1.978 | 1.00 |
| 34_I | 64_I | 1.894 | 1.00 |
| 39_F | 63_T | 1.847 | 1.00 |
| 26_S | 33_P | 1.764 | 1.00 |
| 23_I | 27_T | 1.694 | 1.00 |
| 47_V | 67_I | 1.578 | 1.00 |
| 43_T | 49_Y | 1.548 | 1.00 |
| 35_D | 52_F | 1.521 | 1.00 |
| 22_T | 33_P | 1.513 | 1.00 |
| 43_T | 67_I | 1.446 | 1.00 |
| 61_I | 65_L | 1.438 | 1.00 |
| 80_K | 84_N | 1.421 | 1.00 |
| 77_F | 80_K | 1.406 | 0.99 |
| 67_I | 71_I | 1.388 | 0.99 |
| 34_I | 60_K | 1.387 | 0.99 |
| 18_L | 22_T | 1.371 | 0.99 |
| 78_I | 83_V | 1.320 | 0.99 |
| 22_T | 26_S | 1.310 | 0.99 |
| 79_H | 82_A | 1.309 | 0.99 |
| 82_A | 86_Q | 1.280 | 0.99 |
| 38_Y | 42_V | 1.262 | 0.99 |
| 21_G | 66_Y | 1.238 | 0.98 |
| 17_T | 66_Y | 1.206 | 0.98 |
| 38_Y | 63_T | 1.204 | 0.98 |
| 74_V | 78_I | 1.180 | 0.98 |
| 28_V | 62_F | 1.174 | 0.98 |
| 28_V | 58_F | 1.166 | 0.97 |
| 43_T | 48_G | 1.160 | 0.97 |
| 57_D | 61_I | 1.159 | 0.97 |
| 8_Q | 11_F | 1.148 | 0.97 |
| 43_T | 47_V | 1.106 | 0.96 |
| 28_V | 59_G | 1.106 | 0.96 |
| 25_Y | 28_V | 1.094 | 0.96 |
| 63_T | 67_I | 1.093 | 0.96 |
| 42_V | 51_D | 1.091 | 0.96 |
| 25_Y | 63_T | 1.081 | 0.95 |
| 39_F | 51_D | 1.070 | 0.95 |
| 4_D | 7_F | 1.066 | 0.95 |
| 37_L | 64_I | 1.066 | 0.95 |
| 24_F | 62_F | 1.064 | 0.95 |
| 24_F | 28_V | 1.059 | 0.95 |
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 | |
| 3oufA | 2 | 0.9897 | 99.6 | 0.181 | Contact Map |
| 2q67A | 2 | 0.8969 | 99.6 | 0.19 | Contact Map |
| 3pjsK | 4 | 1 | 99.6 | 0.207 | Contact Map |
| 2k1eA | 4 | 0.9794 | 99.6 | 0.222 | Contact Map |
| 4bw5A | 4 | 0.9381 | 99.6 | 0.224 | Contact Map |
| 1lnqA | 8 | 0.7938 | 99.6 | 0.226 | Contact Map |
| 3vouA | 2 | 0.9897 | 99.5 | 0.229 | Contact Map |
| 2a9hA | 4 | 0.9278 | 99.5 | 0.231 | Contact Map |
| 4h33A | 1 | 0.9175 | 99.5 | 0.233 | Contact Map |
| 4wfeA | 2 | 0.9072 | 99.5 | 0.24 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)