| dhp-ca |
| ID: | 1383228835 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 216 (214) | ||
| Sequences: | 56355 (46090.6) | ||
| Seq/Len: | 263.341 | ||
| Nf(neff/√len): | 3150.7 |
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: 263.341).
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 |
| 156_S | 210_T | 2.869 | 1.00 |
| 200_W | 212_T | 2.677 | 1.00 |
| 77_T | 114_I | 2.641 | 1.00 |
| 189_K | 193_K | 2.518 | 1.00 |
| 150_Q | 214_V | 2.489 | 1.00 |
| 157_D | 161_G | 2.455 | 1.00 |
| 154_S | 210_T | 2.346 | 1.00 |
| 154_S | 212_T | 2.273 | 1.00 |
| 31_L | 50_S | 2.219 | 1.00 |
| 143_T | 154_S | 2.186 | 1.00 |
| 134_S | 158_Q | 2.154 | 1.00 |
| 152_I | 214_V | 2.125 | 1.00 |
| 114_I | 195_H | 2.124 | 1.00 |
| 163_P | 166_D | 2.096 | 1.00 |
| 152_I | 212_T | 2.089 | 1.00 |
| 102_I | 141_T | 2.083 | 1.00 |
| 204_E | 207_E | 2.005 | 1.00 |
| 102_I | 139_K | 1.970 | 1.00 |
| 104_D | 143_T | 1.951 | 1.00 |
| 167_L | 203_S | 1.921 | 1.00 |
| 139_K | 158_Q | 1.920 | 1.00 |
| 28_K | 55_N | 1.917 | 1.00 |
| 35_D | 51_L | 1.878 | 1.00 |
| 76_L | 113_E | 1.866 | 1.00 |
| 28_K | 54_T | 1.862 | 1.00 |
| 141_T | 156_S | 1.859 | 1.00 |
| 188_A | 199_I | 1.828 | 1.00 |
| 201_A | 211_F | 1.818 | 1.00 |
| 145_Q | 152_I | 1.811 | 1.00 |
| 122_V | 192_V | 1.801 | 1.00 |
| 143_T | 156_S | 1.763 | 1.00 |
| 167_L | 201_A | 1.734 | 1.00 |
| 78_N | 81_A | 1.727 | 1.00 |
| 202_N | 212_T | 1.725 | 1.00 |
| 192_V | 197_G | 1.706 | 1.00 |
| 202_N | 210_T | 1.703 | 1.00 |
| 164_K | 167_L | 1.692 | 1.00 |
| 85_Y | 120_T | 1.688 | 1.00 |
| 171_F | 199_I | 1.680 | 1.00 |
| 145_Q | 154_S | 1.645 | 1.00 |
| 198_F | 214_V | 1.642 | 1.00 |
| 162_I | 170_I | 1.634 | 1.00 |
| 104_D | 141_T | 1.627 | 1.00 |
| 76_L | 111_W | 1.626 | 1.00 |
| 58_M | 62_T | 1.597 | 1.00 |
| 169_L | 175_Y | 1.585 | 1.00 |
| 100_E | 139_K | 1.582 | 1.00 |
| 35_D | 48_K | 1.574 | 1.00 |
| 166_D | 169_L | 1.571 | 1.00 |
| 75_E | 116_T | 1.540 | 1.00 |
| 90_F | 124_D | 1.536 | 1.00 |
| 192_V | 213_I | 1.529 | 1.00 |
| 128_N | 132_K | 1.523 | 1.00 |
| 122_V | 188_A | 1.511 | 1.00 |
| 27_V | 54_T | 1.509 | 1.00 |
| 169_L | 172_D | 1.490 | 1.00 |
| 147_T | 152_I | 1.465 | 1.00 |
| 122_V | 191_I | 1.448 | 1.00 |
| 32_E | 51_L | 1.441 | 1.00 |
| 203_S | 209_S | 1.438 | 1.00 |
| 94_Q | 131_I | 1.414 | 1.00 |
| 162_I | 166_D | 1.405 | 0.99 |
| 200_W | 214_V | 1.400 | 0.99 |
| 28_K | 58_M | 1.397 | 0.99 |
| 138_G | 158_Q | 1.394 | 0.99 |
| 162_I | 209_S | 1.363 | 0.99 |
| 114_I | 119_M | 1.355 | 0.99 |
| 166_D | 175_Y | 1.332 | 0.99 |
| 123_I | 153_L | 1.330 | 0.99 |
| 74_V | 113_E | 1.286 | 0.99 |
| 134_S | 138_G | 1.279 | 0.99 |
| 178_D | 181_R | 1.276 | 0.99 |
| 31_L | 51_L | 1.268 | 0.99 |
| 193_K | 198_F | 1.268 | 0.99 |
| 51_L | 55_N | 1.265 | 0.99 |
| 163_P | 205_E | 1.247 | 0.99 |
| 30_Y | 46_F | 1.241 | 0.98 |
| 28_K | 51_L | 1.229 | 0.98 |
| 80_T | 144_M | 1.202 | 0.98 |
| 118_K | 194_Q | 1.191 | 0.98 |
| 80_T | 84_N | 1.189 | 0.98 |
| 166_D | 177_V | 1.187 | 0.98 |
| 191_I | 195_H | 1.184 | 0.98 |
| 115_D | 118_K | 1.171 | 0.98 |
| 172_D | 175_Y | 1.161 | 0.97 |
| 171_F | 201_A | 1.159 | 0.97 |
| 19_E | 121_Q | 1.138 | 0.97 |
| 91_D | 95_S | 1.131 | 0.97 |
| 153_L | 213_I | 1.110 | 0.96 |
| 130_A | 140_V | 1.110 | 0.96 |
| 11_L | 15_N | 1.109 | 0.96 |
| 15_N | 173_R | 1.109 | 0.96 |
| 134_S | 140_V | 1.108 | 0.96 |
| 21_R | 62_T | 1.105 | 0.96 |
| 203_S | 207_E | 1.099 | 0.96 |
| 30_Y | 49_V | 1.088 | 0.96 |
| 118_K | 121_Q | 1.087 | 0.96 |
| 78_N | 111_W | 1.079 | 0.95 |
| 116_T | 120_T | 1.076 | 0.95 |
| 141_T | 158_Q | 1.061 | 0.95 |
| 170_I | 201_A | 1.060 | 0.95 |
| 125_N | 188_A | 1.037 | 0.94 |
| 53_E | 56_R | 1.033 | 0.94 |
| 7_R | 11_L | 1.023 | 0.93 |
| 31_L | 54_T | 1.016 | 0.93 |
| 59_R | 117_D | 1.011 | 0.93 |
| 26_S | 30_Y | 1.010 | 0.93 |
| 27_V | 50_S | 1.009 | 0.93 |
| 203_S | 206_G | 1.003 | 0.93 |
| 89_R | 120_T | 1.002 | 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 | |
| 4i5sA | 2 | 0.9722 | 100 | 0.071 | Contact Map |
| 2c2aA | 1 | 0.9907 | 100 | 0.091 | Contact Map |
| 4ew8A | 2 | 1 | 100 | 0.109 | Contact Map |
| 3a0rA | 1 | 0.9722 | 100 | 0.125 | Contact Map |
| 3d36A | 2 | 0.9676 | 100 | 0.134 | Contact Map |
| 4gczA | 2 | 1 | 100 | 0.135 | Contact Map |
| 4mpcA | 1 | 0.9676 | 100 | 0.138 | Contact Map |
| 3jz3A | 2 | 0.713 | 100 | 0.139 | Contact Map |
| 1y8oA | 1 | 0.9722 | 100 | 0.146 | Contact Map |
| 4e01A | 1 | 0.9907 | 100 | 0.146 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)