| 3OUF |
| ID: | 1448278226 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 156 (134) | ||
| Sequences: | 676 (494.3) | ||
| Seq/Len: | 5.045 | ||
| Nf(neff/√len): | 42.7 |
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: 5.045).
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 |
| 67_L | 83_G | 2.876 | 1.00 |
| 15_G | 60_F | 2.724 | 1.00 |
| 70_A | 121_L | 2.347 | 1.00 |
| 104_R | 107_P | 2.286 | 1.00 |
| 63_F | 67_L | 2.112 | 1.00 |
| 22_F | 94_F | 2.056 | 1.00 |
| 11_V | 80_A | 1.999 | 1.00 |
| 12_T | 68_W | 1.730 | 1.00 |
| 21_Y | 95_Q | 1.714 | 1.00 |
| 11_V | 87_L | 1.648 | 0.99 |
| 8_L | 76_E | 1.626 | 0.99 |
| 78_A | 121_L | 1.615 | 0.99 |
| 85_V | 114_A | 1.551 | 0.99 |
| 22_F | 56_C | 1.528 | 0.99 |
| 63_F | 83_G | 1.508 | 0.99 |
| 29_A | 49_V | 1.503 | 0.99 |
| 100_S | 103_L | 1.503 | 0.99 |
| 26_V | 57_S | 1.491 | 0.98 |
| 29_A | 33_F | 1.448 | 0.98 |
| 18_L | 86_Y | 1.443 | 0.98 |
| 78_A | 81_L | 1.424 | 0.98 |
| 8_L | 71_G | 1.421 | 0.98 |
| 80_A | 84_L | 1.416 | 0.98 |
| 33_F | 49_V | 1.403 | 0.97 |
| 94_F | 98_A | 1.384 | 0.97 |
| 30_R | 38_P | 1.367 | 0.97 |
| 16_V | 62_L | 1.357 | 0.97 |
| 89_A | 114_A | 1.348 | 0.97 |
| 89_A | 111_S | 1.343 | 0.96 |
| 49_V | 98_A | 1.324 | 0.96 |
| 55_N | 93_Y | 1.304 | 0.96 |
| 47_E | 50_Y | 1.303 | 0.96 |
| 27_I | 32_A | 1.267 | 0.95 |
| 18_L | 22_F | 1.243 | 0.94 |
| 129_H | 132_P | 1.235 | 0.94 |
| 128_A | 132_P | 1.214 | 0.93 |
| 18_L | 91_L | 1.213 | 0.93 |
| 82_C | 117_L | 1.207 | 0.93 |
| 71_G | 79_A | 1.199 | 0.92 |
| 129_H | 133_A | 1.170 | 0.91 |
| 64_L | 67_L | 1.160 | 0.91 |
| 66_T | 119_V | 1.159 | 0.91 |
| 130_F | 133_A | 1.128 | 0.89 |
| 37_P | 96_G | 1.127 | 0.89 |
| 22_F | 86_Y | 1.119 | 0.88 |
| 82_C | 114_A | 1.118 | 0.88 |
| 15_G | 86_Y | 1.117 | 0.88 |
| 93_Y | 97_Y | 1.116 | 0.88 |
| 26_V | 54_V | 1.115 | 0.88 |
| 25_Q | 98_A | 1.107 | 0.88 |
| 46_F | 93_Y | 1.101 | 0.87 |
| 10_A | 126_L | 1.088 | 0.86 |
| 86_Y | 94_F | 1.086 | 0.86 |
| 123_A | 127_L | 1.077 | 0.86 |
| 89_A | 110_A | 1.076 | 0.86 |
| 129_H | 134_A | 1.075 | 0.85 |
| 91_L | 95_Q | 1.066 | 0.85 |
| 46_F | 97_Y | 1.063 | 0.85 |
| 70_A | 122_A | 1.063 | 0.85 |
| 70_A | 75_H | 1.040 | 0.83 |
| 11_V | 83_G | 1.039 | 0.83 |
| 50_Y | 53_Q | 1.032 | 0.82 |
| 12_T | 65_A | 1.031 | 0.82 |
| 30_R | 51_R | 1.031 | 0.82 |
| 2_K | 5_V | 1.023 | 0.81 |
| 40_T | 54_V | 1.010 | 0.80 |
| 9_A | 108_L | 1.006 | 0.80 |
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 | |
| 2q7rA | 6 | 0.9295 | 100 | 0.216 | Contact Map |
| 3pcvA | 1 | 0.9359 | 100 | 0.229 | Contact Map |
| 4bpmA | 1 | 0.9231 | 99.9 | 0.421 | Contact Map |
| 2h8aA | 1 | 0.75 | 99.8 | 0.484 | Contact Map |
| 4al0A | 1 | 0.8333 | 99.8 | 0.492 | Contact Map |
| 3rkoJ | 2 | 0.2308 | 3.5 | 0.949 | Contact Map |
| 2l6wA | 2 | 0.2308 | 3.4 | 0.949 | Contact Map |
| 2m3dA | 1 | 0.3974 | 1.6 | 0.957 | Contact Map |
| 4c48C | 1 | 0.2756 | 1.5 | 0.958 | Contact Map |
| 2z34C | 2 | 0.1474 | 1.5 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)