| T0768 70-170 |
| ID: | 1401231088 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 101 (95) | ||
| Sequences: | 1008 (971) | ||
| Seq/Len: | 10.611 | ||
| Nf(neff/√len): | 99.6 |
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: 10.611).
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 |
| 26_V | 30_V | 3.125 | 1.00 |
| 72_I | 76_V | 2.979 | 1.00 |
| 49_L | 53_L | 2.912 | 1.00 |
| 33_I | 37_A | 2.286 | 1.00 |
| 12_G | 15_A | 2.139 | 1.00 |
| 64_C | 86_S | 2.074 | 1.00 |
| 56_I | 60_A | 1.863 | 1.00 |
| 13_E | 34_G | 1.772 | 1.00 |
| 69_E | 91_T | 1.769 | 1.00 |
| 11_I | 15_A | 1.758 | 1.00 |
| 10_V | 32_S | 1.757 | 1.00 |
| 83_F | 86_S | 1.685 | 1.00 |
| 33_I | 60_A | 1.682 | 1.00 |
| 23_G | 46_D | 1.645 | 1.00 |
| 70_I | 92_V | 1.590 | 1.00 |
| 45_S | 68_K | 1.586 | 1.00 |
| 24_V | 47_V | 1.583 | 1.00 |
| 41_C | 64_C | 1.540 | 1.00 |
| 36_L | 39_A | 1.531 | 1.00 |
| 13_E | 35_R | 1.503 | 1.00 |
| 11_I | 37_A | 1.442 | 1.00 |
| 86_S | 89_L | 1.442 | 1.00 |
| 9_T | 31_I | 1.402 | 0.99 |
| 54_I | 77_E | 1.401 | 0.99 |
| 40_Y | 85_W | 1.392 | 0.99 |
| 31_I | 54_I | 1.348 | 0.99 |
| 32_S | 55_Y | 1.318 | 0.99 |
| 22_T | 45_S | 1.280 | 0.99 |
| 19_T | 41_C | 1.278 | 0.99 |
| 33_I | 61_F | 1.253 | 0.99 |
| 34_G | 37_A | 1.221 | 0.98 |
| 14_K | 36_L | 1.221 | 0.98 |
| 17_E | 39_A | 1.183 | 0.98 |
| 68_K | 90_D | 1.179 | 0.98 |
| 35_R | 58_E | 1.177 | 0.98 |
| 66_A | 88_A | 1.170 | 0.97 |
| 37_A | 60_A | 1.145 | 0.97 |
| 40_Y | 63_S | 1.145 | 0.97 |
| 57_N | 60_A | 1.130 | 0.97 |
| 47_V | 70_I | 1.127 | 0.97 |
| 46_D | 69_E | 1.122 | 0.97 |
| 15_A | 37_A | 1.108 | 0.96 |
| 35_R | 57_N | 1.089 | 0.96 |
| 70_I | 86_S | 1.076 | 0.95 |
| 41_C | 86_S | 1.068 | 0.95 |
| 22_T | 68_K | 1.066 | 0.95 |
| 56_I | 82_P | 1.052 | 0.95 |
| 9_T | 54_I | 1.029 | 0.94 |
| 36_L | 59_L | 1.029 | 0.94 |
| 72_I | 94_M | 1.022 | 0.93 |
| 10_V | 55_Y | 1.016 | 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 | |
| 2lz0A | 1 | 0.9604 | 99.5 | 0.368 | Contact Map |
| 4gt6A | 1 | 0.9901 | 99.3 | 0.45 | Contact Map |
| 4h09A | 5 | 1 | 99.3 | 0.457 | Contact Map |
| 4fdwA | 1 | 0.9901 | 99.2 | 0.466 | Contact Map |
| 3sb4A | 2 | 0.9406 | 99.2 | 0.476 | Contact Map |
| 4fs7A | 1 | 0.9802 | 99.2 | 0.481 | Contact Map |
| 4kt1A | 1 | 1 | 98.6 | 0.577 | Contact Map |
| 3t6qA | 2 | 1 | 98.3 | 0.62 | Contact Map |
| 1ziwA | 1 | 1 | 98.2 | 0.634 | Contact Map |
| 4lxrA | 1 | 1 | 98.1 | 0.636 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)