| 1B6C_l |
| ID: | 1404766281 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (107) | ||
| Sequences: | 3986 (2646.7) | ||
| Seq/Len: | 37.252 | ||
| Nf(neff/√len): | 255.9 |
HHblits Results: (2013_03)
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: 37.252).
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 |
| 28_G | 36_F | 2.831 | 1.00 |
| 5_E | 73_K | 2.667 | 1.00 |
| 35_K | 41_D | 2.665 | 1.00 |
| 78_P | 94_H | 2.283 | 1.00 |
| 71_R | 102_E | 2.267 | 1.00 |
| 68_V | 105_K | 2.254 | 1.00 |
| 92_P | 95_A | 2.221 | 1.00 |
| 27_T | 35_K | 2.138 | 1.00 |
| 27_T | 40_R | 2.096 | 1.00 |
| 58_G | 76_I | 2.052 | 1.00 |
| 84_A | 94_H | 2.032 | 1.00 |
| 23_V | 47_K | 1.963 | 1.00 |
| 66_M | 72_A | 1.948 | 1.00 |
| 62_G | 74_L | 1.948 | 1.00 |
| 49_M | 54_E | 1.883 | 1.00 |
| 7_I | 73_K | 1.871 | 1.00 |
| 6_T | 70_Q | 1.844 | 1.00 |
| 71_R | 100_D | 1.801 | 1.00 |
| 67_S | 70_Q | 1.789 | 1.00 |
| 68_V | 106_L | 1.730 | 1.00 |
| 15_F | 67_S | 1.726 | 1.00 |
| 78_P | 96_T | 1.652 | 1.00 |
| 66_M | 103_L | 1.581 | 1.00 |
| 9_P | 70_Q | 1.575 | 1.00 |
| 16_P | 103_L | 1.568 | 1.00 |
| 75_T | 96_T | 1.519 | 1.00 |
| 27_T | 100_D | 1.481 | 1.00 |
| 86_G | 93_P | 1.457 | 1.00 |
| 16_P | 65_Q | 1.425 | 1.00 |
| 23_V | 105_K | 1.413 | 1.00 |
| 61_E | 80_Y | 1.379 | 0.99 |
| 86_G | 95_A | 1.341 | 0.99 |
| 25_H | 104_L | 1.307 | 0.99 |
| 53_Q | 60_E | 1.306 | 0.99 |
| 65_Q | 72_A | 1.281 | 0.99 |
| 29_M | 35_K | 1.276 | 0.99 |
| 30_L | 34_K | 1.268 | 0.99 |
| 27_T | 38_S | 1.241 | 0.98 |
| 62_G | 72_A | 1.226 | 0.98 |
| 18_R | 64_A | 1.222 | 0.98 |
| 51_G | 60_E | 1.221 | 0.98 |
| 40_R | 71_R | 1.216 | 0.98 |
| 5_E | 75_T | 1.208 | 0.98 |
| 25_H | 40_R | 1.207 | 0.98 |
| 73_K | 100_D | 1.202 | 0.98 |
| 6_T | 9_P | 1.195 | 0.98 |
| 30_L | 92_P | 1.186 | 0.98 |
| 26_Y | 37_D | 1.182 | 0.98 |
| 45_P | 104_L | 1.176 | 0.98 |
| 17_K | 20_Q | 1.160 | 0.97 |
| 9_P | 67_S | 1.142 | 0.97 |
| 21_T | 47_K | 1.134 | 0.97 |
| 6_T | 72_A | 1.122 | 0.97 |
| 77_S | 80_Y | 1.118 | 0.96 |
| 12_G | 67_S | 1.114 | 0.96 |
| 2_V | 80_Y | 1.107 | 0.96 |
| 75_T | 98_V | 1.105 | 0.96 |
| 25_H | 39_S | 1.094 | 0.96 |
| 50_L | 64_A | 1.063 | 0.95 |
| 8_S | 71_R | 1.029 | 0.94 |
| 76_I | 81_A | 1.004 | 0.93 |
| 21_T | 49_M | 1.001 | 0.92 |
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 | |
| 1fd9A | 1 | 0.972 | 99.9 | 0.053 | Contact Map |
| 3oe2A | 1 | 0.9439 | 99.9 | 0.068 | Contact Map |
| 1q6hA | 2 | 0.9626 | 99.9 | 0.069 | Contact Map |
| 3uf8A | 1 | 0.9813 | 99.9 | 0.08 | Contact Map |
| 1kt0A | 1 | 0.8131 | 99.9 | 0.082 | Contact Map |
| 4layA | 1 | 1 | 99.9 | 0.09 | Contact Map |
| 3jxvA | 1 | 0.0093 | 99.9 | 0.096 | Contact Map |
| 4driA | 1 | 1 | 99.9 | 0.097 | Contact Map |
| 2ppnA | 1 | 1 | 99.9 | 0.1 | Contact Map |
| 2y78A | 1 | 0.9813 | 99.9 | 0.106 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)