| 3dhw |
| ID: | 1408398921 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 203 (195) | ||
| Sequences: | 45516 (30132) | ||
| Seq/Len: | 233.415 | ||
| Nf(neff/√len): | 2157.8 |
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: 233.415).
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 |
| 124_T | 127_Q | 3.461 | 1.00 |
| 127_Q | 131_K | 3.439 | 1.00 |
| 126_M | 130_R | 3.066 | 1.00 |
| 21_F | 92_T | 2.677 | 1.00 |
| 119_R | 128_I | 2.641 | 1.00 |
| 9_W | 13_A | 2.609 | 1.00 |
| 115_I | 133_L | 2.300 | 1.00 |
| 118_S | 128_I | 2.272 | 1.00 |
| 17_V | 88_I | 2.203 | 1.00 |
| 119_R | 125_P | 2.184 | 1.00 |
| 115_I | 128_I | 2.179 | 1.00 |
| 125_P | 128_I | 2.124 | 1.00 |
| 30_G | 103_V | 2.009 | 1.00 |
| 34_Y | 107_L | 1.938 | 1.00 |
| 24_V | 28_P | 1.925 | 1.00 |
| 114_L | 136_E | 1.903 | 1.00 |
| 118_S | 132_V | 1.855 | 1.00 |
| 127_Q | 130_R | 1.832 | 1.00 |
| 113_G | 116_E | 1.802 | 1.00 |
| 26_G | 99_I | 1.801 | 1.00 |
| 30_G | 34_Y | 1.785 | 1.00 |
| 19_G | 145_A | 1.783 | 1.00 |
| 180_N | 183_V | 1.769 | 1.00 |
| 104_E | 108_L | 1.696 | 1.00 |
| 29_V | 100_A | 1.688 | 1.00 |
| 27_L | 103_V | 1.653 | 1.00 |
| 48_Y | 104_E | 1.625 | 1.00 |
| 61_I | 66_L | 1.622 | 1.00 |
| 103_V | 141_L | 1.613 | 1.00 |
| 6_R | 9_W | 1.613 | 1.00 |
| 10_E | 13_A | 1.612 | 1.00 |
| 123_A | 127_Q | 1.611 | 1.00 |
| 107_L | 133_L | 1.598 | 1.00 |
| 106_A | 140_G | 1.593 | 1.00 |
| 13_A | 17_V | 1.588 | 1.00 |
| 5_V | 9_W | 1.580 | 1.00 |
| 35_V | 115_I | 1.572 | 1.00 |
| 115_I | 119_R | 1.562 | 1.00 |
| 99_I | 148_T | 1.561 | 1.00 |
| 23_F | 145_A | 1.546 | 1.00 |
| 118_S | 123_A | 1.493 | 1.00 |
| 107_L | 137_A | 1.492 | 1.00 |
| 87_A | 159_G | 1.477 | 1.00 |
| 156_S | 166_G | 1.474 | 1.00 |
| 124_T | 128_I | 1.435 | 1.00 |
| 34_Y | 108_L | 1.429 | 1.00 |
| 22_G | 95_A | 1.429 | 1.00 |
| 33_L | 100_A | 1.405 | 0.99 |
| 45_A | 48_Y | 1.398 | 0.99 |
| 31_V | 107_L | 1.390 | 0.99 |
| 85_Q | 89_V | 1.372 | 0.99 |
| 117_A | 121_M | 1.347 | 0.99 |
| 13_A | 84_L | 1.343 | 0.99 |
| 96_A | 100_A | 1.338 | 0.99 |
| 84_L | 88_I | 1.337 | 0.99 |
| 25_I | 28_P | 1.329 | 0.99 |
| 10_E | 164_A | 1.328 | 0.99 |
| 48_Y | 108_L | 1.326 | 0.99 |
| 46_K | 50_T | 1.300 | 0.99 |
| 50_T | 54_I | 1.291 | 0.99 |
| 6_R | 10_E | 1.287 | 0.99 |
| 25_I | 96_A | 1.284 | 0.99 |
| 55_V | 100_A | 1.276 | 0.99 |
| 15_T | 149_L | 1.271 | 0.99 |
| 34_Y | 104_E | 1.265 | 0.99 |
| 25_I | 92_T | 1.243 | 0.98 |
| 88_I | 92_T | 1.238 | 0.98 |
| 14_M | 84_L | 1.224 | 0.98 |
| 125_P | 129_V | 1.214 | 0.98 |
| 29_V | 96_A | 1.212 | 0.98 |
| 102_M | 144_A | 1.210 | 0.98 |
| 16_F | 20_F | 1.201 | 0.98 |
| 30_G | 107_L | 1.199 | 0.98 |
| 8_V | 167_L | 1.198 | 0.98 |
| 129_V | 134_L | 1.197 | 0.98 |
| 31_V | 129_V | 1.194 | 0.98 |
| 28_P | 32_L | 1.177 | 0.98 |
| 26_G | 103_V | 1.157 | 0.97 |
| 110_I | 137_A | 1.142 | 0.97 |
| 143_N | 147_I | 1.138 | 0.97 |
| 91_L | 152_L | 1.134 | 0.97 |
| 27_L | 137_A | 1.128 | 0.97 |
| 44_N | 48_Y | 1.127 | 0.97 |
| 99_I | 103_V | 1.125 | 0.97 |
| 18_S | 22_G | 1.123 | 0.97 |
| 46_K | 49_R | 1.119 | 0.96 |
| 110_I | 136_E | 1.107 | 0.96 |
| 12_L | 16_F | 1.104 | 0.96 |
| 36_T | 125_P | 1.087 | 0.96 |
| 70_M | 90_P | 1.087 | 0.96 |
| 21_F | 88_I | 1.086 | 0.96 |
| 146_T | 202_G | 1.084 | 0.96 |
| 19_G | 149_L | 1.057 | 0.95 |
| 171_G | 187_V | 1.054 | 0.95 |
| 18_S | 91_L | 1.054 | 0.95 |
| 17_V | 20_F | 1.051 | 0.94 |
| 83_G | 86_A | 1.043 | 0.94 |
| 106_A | 137_A | 1.036 | 0.94 |
| 20_F | 24_V | 1.021 | 0.93 |
| 77_I | 80_T | 1.013 | 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 | |
| 3tuiA | 4 | 1 | 99.9 | 0.199 | Contact Map |
| 2onkC | 4 | 0.9606 | 99.9 | 0.227 | Contact Map |
| 3d31C | 2 | 0.9606 | 99.9 | 0.228 | Contact Map |
| 3rlfF | 1 | 0.9507 | 99.9 | 0.24 | Contact Map |
| 3rlfG | 1 | 0.9557 | 99.9 | 0.301 | Contact Map |
| 4fc4A | 10 | 0.4039 | 2.9 | 0.938 | Contact Map |
| 4humA | 1 | 0.8966 | 1.8 | 0.945 | Contact Map |
| 3tdsE | 5 | 0.4187 | 1.4 | 0.947 | Contact Map |
| 4lz6A | 1 | 0.4187 | 1.3 | 0.949 | Contact Map |
| 1iijA | 1 | 0.1724 | 1.3 | 0.949 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)