| 2g03 |
| ID: | 1452701000 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 194 (177) | ||
| Sequences: | 735 (531.5) | ||
| Seq/Len: | 4.153 | ||
| Nf(neff/√len): | 39.9 |
HHblits Results: (2015_06)
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: 4.153).
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 |
| 24_N | 54_G | 3.802 | 1.00 |
| 171_D | 174_N | 2.904 | 1.00 |
| 67_N | 78_A | 2.237 | 1.00 |
| 42_T | 85_L | 2.193 | 1.00 |
| 24_N | 27_R | 2.175 | 1.00 |
| 42_T | 63_I | 2.149 | 1.00 |
| 66_D | 113_L | 2.130 | 1.00 |
| 70_K | 114_E | 1.959 | 1.00 |
| 75_F | 117_G | 1.920 | 1.00 |
| 107_N | 117_G | 1.897 | 1.00 |
| 104_V | 153_S | 1.855 | 1.00 |
| 117_G | 121_R | 1.806 | 1.00 |
| 84_A | 87_K | 1.804 | 1.00 |
| 128_L | 136_V | 1.781 | 1.00 |
| 25_A | 52_L | 1.776 | 0.99 |
| 103_Y | 124_L | 1.693 | 0.99 |
| 97_E | 161_R | 1.664 | 0.99 |
| 122_I | 125_D | 1.655 | 0.99 |
| 73_F | 108_I | 1.603 | 0.99 |
| 48_I | 122_I | 1.583 | 0.99 |
| 75_F | 107_N | 1.500 | 0.98 |
| 152_R | 159_E | 1.416 | 0.96 |
| 107_N | 150_M | 1.392 | 0.96 |
| 57_Y | 60_A | 1.364 | 0.95 |
| 85_L | 109_A | 1.360 | 0.95 |
| 42_T | 89_E | 1.360 | 0.95 |
| 44_G | 126_L | 1.333 | 0.95 |
| 46_Q | 82_K | 1.327 | 0.94 |
| 103_Y | 146_Y | 1.326 | 0.94 |
| 53_F | 115_G | 1.325 | 0.94 |
| 110_H | 118_R | 1.288 | 0.93 |
| 25_A | 122_I | 1.278 | 0.93 |
| 73_F | 76_A | 1.278 | 0.93 |
| 103_Y | 164_L | 1.277 | 0.93 |
| 124_L | 164_L | 1.271 | 0.93 |
| 88_I | 109_A | 1.270 | 0.93 |
| 73_F | 154_P | 1.263 | 0.92 |
| 137_N | 140_N | 1.258 | 0.92 |
| 114_E | 118_R | 1.254 | 0.92 |
| 24_N | 44_G | 1.253 | 0.92 |
| 76_A | 84_A | 1.235 | 0.91 |
| 51_Y | 54_G | 1.233 | 0.91 |
| 59_F | 113_L | 1.221 | 0.91 |
| 21_S | 52_L | 1.209 | 0.90 |
| 101_A | 161_R | 1.196 | 0.89 |
| 184_Q | 187_Y | 1.195 | 0.89 |
| 92_P | 96_F | 1.190 | 0.89 |
| 146_Y | 150_M | 1.182 | 0.89 |
| 46_Q | 63_I | 1.181 | 0.88 |
| 41_T | 44_G | 1.178 | 0.88 |
| 17_I | 113_L | 1.173 | 0.88 |
| 93_E | 131_N | 1.172 | 0.88 |
| 121_R | 138_W | 1.159 | 0.87 |
| 145_L | 166_D | 1.146 | 0.86 |
| 17_I | 70_K | 1.142 | 0.86 |
| 163_L | 167_N | 1.141 | 0.86 |
| 107_N | 120_T | 1.131 | 0.85 |
| 180_K | 183_E | 1.123 | 0.85 |
| 117_G | 147_L | 1.119 | 0.85 |
| 27_R | 55_G | 1.113 | 0.84 |
| 43_A | 46_Q | 1.113 | 0.84 |
| 176_E | 179_F | 1.109 | 0.84 |
| 40_G | 102_K | 1.101 | 0.83 |
| 74_R | 154_P | 1.094 | 0.83 |
| 45_L | 111_P | 1.086 | 0.82 |
| 24_N | 55_G | 1.079 | 0.82 |
| 65_E | 82_K | 1.076 | 0.81 |
| 16_S | 19_E | 1.069 | 0.81 |
| 162_F | 166_D | 1.067 | 0.81 |
| 80_Y | 105_E | 1.056 | 0.80 |
| 164_L | 167_N | 1.056 | 0.80 |
| 76_A | 88_I | 1.034 | 0.78 |
| 17_I | 20_Q | 1.032 | 0.77 |
| 23_H | 26_R | 1.032 | 0.77 |
| 20_Q | 24_N | 1.029 | 0.77 |
| 142_S | 146_Y | 1.029 | 0.77 |
| 125_D | 129_K | 1.028 | 0.77 |
| 121_R | 146_Y | 1.021 | 0.76 |
| 182_I | 185_S | 1.021 | 0.76 |
| 27_R | 54_G | 1.020 | 0.76 |
| 96_F | 128_L | 1.020 | 0.76 |
| 23_H | 153_S | 1.019 | 0.76 |
| 114_E | 117_G | 1.017 | 0.76 |
| 107_N | 147_L | 1.001 | 0.74 |
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 | |
| 2jk8A | 2 | 0.9794 | 100 | 0.397 | Contact Map |
| 4npsA | 1 | 0.9639 | 100 | 0.403 | Contact Map |
| 2f6sA | 2 | 0.9227 | 100 | 0.418 | Contact Map |
| 3zc7A | 1 | 0.9021 | 100 | 0.418 | Contact Map |
| 3zlmA | 1 | 0.9124 | 100 | 0.421 | Contact Map |
| 4n67A | 1 | 0.8918 | 100 | 0.431 | Contact Map |
| 4m16A | 1 | 0.9021 | 100 | 0.433 | Contact Map |
| 4py3A | 10 | 0 | 100 | 0.436 | Contact Map |
| 3shgA | 1 | 0.866 | 100 | 0.439 | Contact Map |
| 3se5A | 4 | 0.7938 | 100 | 0.489 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)