| XRES |
| ID: | 1479623234 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 135 (113) | ||
| Sequences: | 708 (511.1) | ||
| Seq/Len: | 6.265 | ||
| Nf(neff/√len): | 48.1 |
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: 6.265).
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 |
| 112_C | 132_C | 3.494 | 1.00 |
| 63_K | 82_Q | 2.700 | 1.00 |
| 88_C | 98_C | 2.426 | 1.00 |
| 60_L | 86_S | 2.369 | 1.00 |
| 119_L | 124_E | 1.979 | 1.00 |
| 55_D | 85_R | 1.857 | 1.00 |
| 81_V | 114_F | 1.792 | 1.00 |
| 44_F | 127_L | 1.740 | 1.00 |
| 38_V | 67_A | 1.721 | 1.00 |
| 119_L | 122_N | 1.679 | 1.00 |
| 30_S | 66_H | 1.675 | 1.00 |
| 26_N | 70_Q | 1.573 | 0.99 |
| 62_D | 109_K | 1.569 | 0.99 |
| 30_S | 68_K | 1.561 | 0.99 |
| 68_K | 78_Q | 1.548 | 0.99 |
| 46_M | 83_I | 1.489 | 0.99 |
| 66_H | 80_D | 1.488 | 0.99 |
| 42_V | 61_V | 1.475 | 0.99 |
| 28_F | 78_Q | 1.464 | 0.99 |
| 76_E | 115_L | 1.462 | 0.99 |
| 88_C | 112_C | 1.418 | 0.99 |
| 26_N | 71_I | 1.407 | 0.98 |
| 48_E | 51_K | 1.405 | 0.98 |
| 42_V | 81_V | 1.327 | 0.98 |
| 65_L | 111_S | 1.323 | 0.97 |
| 84_S | 100_P | 1.306 | 0.97 |
| 35_N | 67_A | 1.305 | 0.97 |
| 73_D | 119_L | 1.301 | 0.97 |
| 70_Q | 74_R | 1.266 | 0.96 |
| 26_N | 74_R | 1.261 | 0.96 |
| 71_I | 75_M | 1.250 | 0.96 |
| 50_N | 90_K | 1.235 | 0.96 |
| 70_Q | 76_E | 1.221 | 0.95 |
| 53_S | 90_K | 1.211 | 0.95 |
| 116_V | 121_W | 1.202 | 0.95 |
| 73_D | 76_E | 1.184 | 0.94 |
| 62_D | 84_S | 1.182 | 0.94 |
| 69_L | 75_M | 1.173 | 0.94 |
| 74_R | 121_W | 1.158 | 0.93 |
| 26_N | 72_T | 1.145 | 0.93 |
| 65_L | 82_Q | 1.134 | 0.92 |
| 60_L | 100_P | 1.126 | 0.92 |
| 50_N | 85_R | 1.117 | 0.92 |
| 49_Y | 114_F | 1.112 | 0.91 |
| 80_D | 111_S | 1.110 | 0.91 |
| 72_T | 76_E | 1.083 | 0.90 |
| 24_A | 27_Y | 1.079 | 0.90 |
| 83_I | 110_M | 1.076 | 0.90 |
| 31_I | 69_L | 1.075 | 0.89 |
| 117_G | 124_E | 1.054 | 0.88 |
| 46_M | 50_N | 1.040 | 0.87 |
| 86_S | 112_C | 1.033 | 0.87 |
| 114_F | 127_L | 1.032 | 0.87 |
| 52_E | 130_K | 1.029 | 0.87 |
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 | |
| 3gaxA | 2 | 0.8074 | 99.9 | 0.279 | Contact Map |
| 1roaA | 1 | 0.8148 | 99.9 | 0.29 | Contact Map |
| 4it7A | 4 | 0.7926 | 99.9 | 0.291 | Contact Map |
| 1yvbI | 1 | 0.8222 | 99.9 | 0.296 | Contact Map |
| 4n6oB | 1 | 0.8074 | 99.9 | 0.296 | Contact Map |
| 2ch9A | 1 | 0.9037 | 99.9 | 0.312 | Contact Map |
| 3l0rA | 2 | 0.7852 | 99.9 | 0.326 | Contact Map |
| 3mwzA | 1 | 0.8296 | 99.9 | 0.335 | Contact Map |
| 2l4vA | 1 | 0.8148 | 99.8 | 0.437 | Contact Map |
| 3ul5A | 4 | 0.6148 | 99.8 | 0.446 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)