| T0768 70-170 |
| ID: | 1401229131 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (95) | ||
| Sequences: | 256 (249) | ||
| Seq/Len: | 2.695 | ||
| Nf(neff/√len): | 25.5 |
Jackhmmer Results: (2014_04_16)
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: 2.695).
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 |
| 49_L | 53_L | 4.293 | 1.00 |
| 26_V | 30_V | 4.281 | 1.00 |
| 33_I | 37_A | 3.388 | 1.00 |
| 72_I | 76_V | 3.239 | 1.00 |
| 33_I | 60_A | 2.335 | 1.00 |
| 83_F | 86_S | 2.185 | 1.00 |
| 41_C | 64_C | 2.164 | 1.00 |
| 64_C | 86_S | 2.074 | 1.00 |
| 11_I | 15_A | 1.848 | 0.99 |
| 69_E | 91_T | 1.790 | 0.99 |
| 47_V | 50_S | 1.768 | 0.98 |
| 10_V | 32_S | 1.701 | 0.98 |
| 41_C | 44_L | 1.619 | 0.97 |
| 37_A | 60_A | 1.586 | 0.96 |
| 72_I | 94_M | 1.584 | 0.96 |
| 56_I | 60_A | 1.534 | 0.95 |
| 12_G | 15_A | 1.460 | 0.94 |
| 23_G | 46_D | 1.426 | 0.93 |
| 31_I | 54_I | 1.425 | 0.93 |
| 46_D | 69_E | 1.355 | 0.90 |
| 73_P | 76_V | 1.292 | 0.87 |
| 56_I | 82_P | 1.290 | 0.87 |
| 54_I | 77_E | 1.275 | 0.86 |
| 72_I | 91_T | 1.206 | 0.81 |
| 33_I | 56_I | 1.203 | 0.81 |
| 32_S | 55_Y | 1.172 | 0.78 |
| 86_S | 89_L | 1.153 | 0.77 |
| 57_N | 92_V | 1.148 | 0.76 |
| 31_I | 52_N | 1.133 | 0.75 |
| 11_I | 37_A | 1.122 | 0.74 |
| 22_T | 45_S | 1.118 | 0.74 |
| 8_V | 12_G | 1.101 | 0.72 |
| 24_V | 47_V | 1.093 | 0.71 |
| 41_C | 86_S | 1.083 | 0.70 |
| 19_T | 24_V | 1.071 | 0.69 |
| 52_N | 75_S | 1.062 | 0.68 |
| 9_T | 31_I | 1.062 | 0.68 |
| 7_P | 60_A | 1.050 | 0.67 |
| 73_P | 79_M | 1.020 | 0.64 |
| 56_I | 79_M | 1.018 | 0.63 |
| 14_K | 17_E | 1.017 | 0.63 |
| 41_C | 47_V | 1.011 | 0.63 |
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 | |
| 2lz0A | 1 | 0.9604 | 99.6 | 0.403 | Contact Map |
| 4gt6A | 1 | 1 | 99.3 | 0.515 | Contact Map |
| 4h09A | 5 | 1 | 99.2 | 0.524 | Contact Map |
| 4fdwA | 1 | 0.9802 | 99.2 | 0.541 | Contact Map |
| 3sb4A | 2 | 0.9406 | 99.1 | 0.544 | Contact Map |
| 4fs7A | 1 | 0.9802 | 99.1 | 0.551 | Contact Map |
| 4kt1A | 1 | 1 | 98.3 | 0.658 | Contact Map |
| 3t6qA | 2 | 1 | 97.8 | 0.702 | Contact Map |
| 1ziwA | 1 | 1 | 97.6 | 0.712 | Contact Map |
| 4lxrA | 1 | 1 | 97.6 | 0.713 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)