| Tar Dna binding 90-270 |
| ID: | 1390462853 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 181 (167) | ||
| Sequences: | 7844 (5185) | ||
| Seq/Len: | 46.970 | ||
| Nf(neff/√len): | 401.2 |
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: 46.970).
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 |
| 40_E | 64_T | 3.181 | 1.00 |
| 147_D | 150_I | 2.875 | 1.00 |
| 65_E | 68_T | 2.874 | 1.00 |
| 127_D | 146_A | 2.706 | 1.00 |
| 30_D | 80_D | 2.312 | 1.00 |
| 114_T | 117_E | 2.290 | 1.00 |
| 24_W | 82_R | 2.274 | 1.00 |
| 71_K | 75_Q | 2.073 | 1.00 |
| 17_L | 73_M | 2.065 | 1.00 |
| 38_F | 75_Q | 2.044 | 1.00 |
| 32_K | 36_S | 1.979 | 1.00 |
| 19_V | 35_F | 1.922 | 1.00 |
| 119_R | 123_S | 1.895 | 1.00 |
| 71_K | 74_S | 1.870 | 1.00 |
| 27_T | 30_D | 1.839 | 1.00 |
| 79_I | 84_C | 1.796 | 1.00 |
| 106_V | 122_F | 1.757 | 1.00 |
| 115_E | 119_R | 1.746 | 1.00 |
| 118_L | 141_A | 1.736 | 1.00 |
| 70_V | 88_L | 1.735 | 1.00 |
| 129_M | 146_A | 1.729 | 1.00 |
| 111_E | 164_I | 1.710 | 1.00 |
| 31_L | 59_G | 1.701 | 1.00 |
| 49_D | 52_T | 1.661 | 1.00 |
| 117_E | 162_K | 1.659 | 1.00 |
| 64_T | 68_T | 1.646 | 1.00 |
| 78_M | 83_W | 1.636 | 1.00 |
| 42_L | 64_T | 1.617 | 1.00 |
| 122_F | 143_V | 1.575 | 1.00 |
| 35_F | 61_V | 1.561 | 1.00 |
| 153_S | 157_E | 1.552 | 1.00 |
| 25_K | 80_D | 1.551 | 1.00 |
| 104_V | 155_C | 1.500 | 1.00 |
| 66_Y | 70_V | 1.489 | 1.00 |
| 47_K | 58_F | 1.478 | 1.00 |
| 146_A | 150_I | 1.469 | 1.00 |
| 33_E | 36_S | 1.468 | 1.00 |
| 46_V | 55_S | 1.462 | 1.00 |
| 29_Q | 33_E | 1.445 | 1.00 |
| 28_E | 32_K | 1.426 | 1.00 |
| 160_I | 163_G | 1.405 | 0.99 |
| 134_P | 140_F | 1.395 | 0.99 |
| 40_E | 68_T | 1.386 | 0.99 |
| 107_G | 167_H | 1.373 | 0.99 |
| 70_V | 74_S | 1.369 | 0.99 |
| 78_M | 81_G | 1.361 | 0.99 |
| 151_A | 170_N | 1.347 | 0.99 |
| 129_M | 144_T | 1.330 | 0.99 |
| 30_D | 33_E | 1.327 | 0.99 |
| 120_E | 123_S | 1.314 | 0.99 |
| 131_V | 141_A | 1.307 | 0.99 |
| 69_Q | 88_L | 1.292 | 0.99 |
| 116_D | 120_E | 1.289 | 0.99 |
| 20_L | 107_G | 1.287 | 0.99 |
| 128_V | 143_V | 1.264 | 0.99 |
| 20_L | 85_D | 1.257 | 0.99 |
| 160_I | 165_S | 1.256 | 0.99 |
| 34_Y | 84_C | 1.248 | 0.99 |
| 161_I | 166_V | 1.245 | 0.98 |
| 103_K | 144_T | 1.241 | 0.98 |
| 125_Y | 157_E | 1.231 | 0.98 |
| 20_L | 58_F | 1.228 | 0.98 |
| 110_T | 113_M | 1.211 | 0.98 |
| 148_D | 152_Q | 1.207 | 0.98 |
| 23_P | 26_T | 1.207 | 0.98 |
| 121_F | 159_L | 1.194 | 0.98 |
| 34_Y | 77_H | 1.185 | 0.98 |
| 28_E | 44_V | 1.170 | 0.97 |
| 66_Y | 88_L | 1.169 | 0.97 |
| 67_E | 71_K | 1.168 | 0.97 |
| 102_R | 129_M | 1.164 | 0.97 |
| 44_V | 59_G | 1.155 | 0.97 |
| 105_F | 142_F | 1.147 | 0.97 |
| 42_L | 62_R | 1.146 | 0.97 |
| 127_D | 150_I | 1.141 | 0.97 |
| 117_E | 120_E | 1.127 | 0.97 |
| 152_Q | 156_G | 1.117 | 0.96 |
| 15_S | 69_Q | 1.097 | 0.96 |
| 15_S | 42_L | 1.095 | 0.96 |
| 16_D | 45_Q | 1.094 | 0.96 |
| 15_S | 66_Y | 1.081 | 0.95 |
| 102_R | 144_T | 1.079 | 0.95 |
| 34_Y | 76_R | 1.070 | 0.95 |
| 115_E | 131_V | 1.062 | 0.95 |
| 46_V | 59_G | 1.056 | 0.95 |
| 153_S | 156_G | 1.047 | 0.94 |
| 106_V | 143_V | 1.032 | 0.94 |
| 28_E | 48_K | 1.031 | 0.94 |
| 41_V | 61_V | 1.009 | 0.93 |
| 107_G | 140_F | 1.005 | 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 | |
| 4bs2A | 1 | 0.9613 | 100 | 0.172 | Contact Map |
| 4f02A | 2 | 0.9227 | 100 | 0.248 | Contact Map |
| 1l3kA | 1 | 0.8619 | 100 | 0.26 | Contact Map |
| 2cjkA | 1 | 0.8895 | 100 | 0.263 | Contact Map |
| 2qfjA | 2 | 0.9834 | 100 | 0.267 | Contact Map |
| 3smzA | 1 | 1 | 100 | 0.304 | Contact Map |
| 2adcA | 1 | 0.9337 | 100 | 0.307 | Contact Map |
| 3md3A | 1 | 0.8619 | 100 | 0.313 | Contact Map |
| 1fxlA | 1 | 0.8619 | 100 | 0.314 | Contact Map |
| 1b7fA | 2 | 0.8619 | 100 | 0.315 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)