| Roll |
| ID: | 1390931498 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (120) | ||
| Sequences: | 516 (340.5) | ||
| Seq/Len: | 4.300 | ||
| Nf(neff/√len): | 31.1 |
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: 4.300).
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 |
| 83_S | 86_Q | 3.331 | 1.00 |
| 78_L | 109_D | 2.349 | 1.00 |
| 59_H | 94_L | 2.187 | 1.00 |
| 36_E | 68_K | 2.184 | 1.00 |
| 58_H | 62_A | 1.968 | 1.00 |
| 39_L | 94_L | 1.956 | 1.00 |
| 81_F | 84_T | 1.671 | 0.99 |
| 59_H | 97_A | 1.652 | 0.99 |
| 36_E | 80_K | 1.594 | 0.99 |
| 9_L | 13_S | 1.521 | 0.98 |
| 54_F | 57_W | 1.506 | 0.98 |
| 91_K | 95_G | 1.485 | 0.98 |
| 56_V | 79_I | 1.461 | 0.97 |
| 36_E | 109_D | 1.461 | 0.97 |
| 115_A | 119_R | 1.434 | 0.97 |
| 9_L | 12_F | 1.409 | 0.97 |
| 53_G | 77_L | 1.406 | 0.97 |
| 27_W | 122_D | 1.384 | 0.96 |
| 106_L | 112_S | 1.369 | 0.96 |
| 93_V | 97_A | 1.331 | 0.95 |
| 11_Q | 14_W | 1.286 | 0.94 |
| 109_D | 113_P | 1.259 | 0.93 |
| 43_P | 126_R | 1.249 | 0.92 |
| 61_D | 64_G | 1.241 | 0.92 |
| 86_Q | 120_L | 1.239 | 0.92 |
| 90_A | 93_V | 1.221 | 0.91 |
| 40_A | 107_L | 1.218 | 0.91 |
| 104_I | 123_A | 1.215 | 0.91 |
| 62_A | 66_R | 1.197 | 0.90 |
| 26_F | 47_G | 1.193 | 0.90 |
| 64_G | 67_F | 1.182 | 0.89 |
| 17_G | 93_V | 1.173 | 0.89 |
| 67_F | 70_I | 1.171 | 0.89 |
| 75_D | 79_I | 1.166 | 0.88 |
| 41_I | 98_L | 1.164 | 0.88 |
| 14_W | 87_G | 1.159 | 0.88 |
| 54_F | 58_H | 1.146 | 0.87 |
| 65_I | 90_A | 1.144 | 0.87 |
| 61_D | 66_R | 1.139 | 0.87 |
| 36_E | 78_L | 1.137 | 0.86 |
| 63_N | 93_V | 1.126 | 0.86 |
| 42_R | 102_Y | 1.121 | 0.85 |
| 28_L | 32_V | 1.095 | 0.84 |
| 66_R | 82_D | 1.083 | 0.83 |
| 77_L | 94_L | 1.078 | 0.82 |
| 74_K | 89_A | 1.072 | 0.82 |
| 61_D | 67_F | 1.067 | 0.81 |
| 114_T | 124_P | 1.064 | 0.81 |
| 114_T | 127_L | 1.057 | 0.81 |
| 80_K | 105_A | 1.053 | 0.80 |
| 42_R | 53_G | 1.051 | 0.80 |
| 94_L | 104_I | 1.042 | 0.79 |
| 34_Q | 112_S | 1.036 | 0.79 |
| 64_G | 99_P | 1.031 | 0.78 |
| 23_G | 66_R | 1.028 | 0.78 |
| 39_L | 104_I | 1.022 | 0.77 |
| 16_L | 20_L | 1.022 | 0.77 |
| 100_H | 126_R | 1.021 | 0.77 |
| 94_L | 97_A | 1.018 | 0.77 |
| 28_L | 78_L | 1.016 | 0.77 |
| 57_W | 61_D | 1.001 | 0.75 |
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 | |
| 3aqpA | 2 | 0.9297 | 85.8 | 0.887 | Contact Map |
| 2gqcA | 1 | 0.5469 | 38.5 | 0.92 | Contact Map |
| 3w9iA | 6 | 0.9844 | 33.2 | 0.922 | Contact Map |
| 4dx5A | 3 | 0.9844 | 32.3 | 0.923 | Contact Map |
| 4k0jA | 6 | 0.9297 | 26.4 | 0.926 | Contact Map |
| 1jmtA | 1 | 0.6172 | 19 | 0.931 | Contact Map |
| 1xmxA | 1 | 0.7188 | 15.7 | 0.934 | Contact Map |
| 4c91A | 2 | 0.5703 | 15.3 | 0.934 | Contact Map |
| 2y9jY | 24 | 0.5781 | 13.6 | 0.935 | Contact Map |
| 2lepA | 1 | 0.4922 | 12.1 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)