| 3gd8 |
| ID: | 1408344966 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 223 (221) | ||
| Sequences: | 3164 (2089.9) | ||
| Seq/Len: | 14.317 | ||
| Nf(neff/√len): | 140.6 |
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: 14.317).
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 |
| 11_F | 97_I | 3.968 | 1.00 |
| 70_T | 84_S | 3.831 | 1.00 |
| 133_L | 212_L | 3.812 | 1.00 |
| 74_V | 81_I | 3.689 | 1.00 |
| 133_L | 208_I | 3.396 | 1.00 |
| 15_L | 101_I | 3.338 | 1.00 |
| 74_V | 84_S | 3.241 | 1.00 |
| 15_L | 98_G | 3.094 | 1.00 |
| 129_L | 205_G | 3.045 | 1.00 |
| 11_F | 93_L | 2.951 | 1.00 |
| 7_V | 90_A | 2.912 | 1.00 |
| 129_L | 133_L | 2.897 | 1.00 |
| 7_V | 86_F | 2.812 | 1.00 |
| 75_C | 211_V | 2.684 | 1.00 |
| 135_I | 173_A | 2.516 | 1.00 |
| 142_T | 165_S | 2.515 | 1.00 |
| 180_S | 186_S | 2.431 | 1.00 |
| 137_F | 213_A | 2.427 | 1.00 |
| 88_I | 207_I | 2.345 | 1.00 |
| 6_A | 83_K | 2.244 | 1.00 |
| 187_F | 191_V | 2.191 | 1.00 |
| 71_V | 207_I | 2.098 | 1.00 |
| 207_I | 211_V | 2.051 | 1.00 |
| 135_I | 181_M | 1.989 | 1.00 |
| 57_F | 65_I | 1.973 | 1.00 |
| 51_A | 163_G | 1.966 | 1.00 |
| 21_S | 46_F | 1.958 | 1.00 |
| 64_H | 87_Y | 1.882 | 1.00 |
| 53_M | 57_F | 1.703 | 1.00 |
| 13_A | 65_I | 1.696 | 1.00 |
| 199_H | 203_W | 1.677 | 1.00 |
| 187_F | 203_W | 1.656 | 1.00 |
| 71_V | 88_I | 1.604 | 1.00 |
| 170_H | 174_I | 1.566 | 1.00 |
| 186_S | 190_A | 1.566 | 1.00 |
| 209_G | 213_A | 1.542 | 1.00 |
| 69_V | 143_I | 1.537 | 1.00 |
| 196_W | 199_H | 1.535 | 1.00 |
| 81_I | 84_S | 1.482 | 1.00 |
| 47_G | 167_A | 1.473 | 1.00 |
| 79_I | 84_S | 1.467 | 1.00 |
| 19_L | 101_I | 1.452 | 1.00 |
| 132_E | 177_T | 1.452 | 1.00 |
| 96_I | 188_G | 1.444 | 1.00 |
| 137_F | 216_L | 1.416 | 1.00 |
| 77_R | 218_E | 1.403 | 0.99 |
| 72_A | 76_T | 1.400 | 0.99 |
| 40_V | 44_L | 1.399 | 0.99 |
| 140_V | 210_A | 1.382 | 0.99 |
| 100_G | 104_L | 1.356 | 0.99 |
| 70_T | 79_I | 1.350 | 0.99 |
| 100_G | 192_I | 1.347 | 0.99 |
| 70_T | 91_Q | 1.335 | 0.99 |
| 137_F | 212_L | 1.331 | 0.99 |
| 16_I | 138_Q | 1.307 | 0.99 |
| 73_M | 79_I | 1.295 | 0.99 |
| 50_I | 166_V | 1.291 | 0.99 |
| 160_L | 164_F | 1.288 | 0.99 |
| 169_G | 179_A | 1.282 | 0.99 |
| 200_W | 204_V | 1.276 | 0.99 |
| 81_I | 85_V | 1.260 | 0.99 |
| 25_T | 42_I | 1.252 | 0.99 |
| 90_A | 94_G | 1.251 | 0.99 |
| 137_F | 141_F | 1.236 | 0.98 |
| 119_V | 128_G | 1.235 | 0.98 |
| 148_D | 217_Y | 1.188 | 0.98 |
| 84_S | 88_I | 1.185 | 0.98 |
| 14_M | 95_A | 1.184 | 0.98 |
| 99_A | 189_P | 1.181 | 0.98 |
| 92_C | 203_W | 1.177 | 0.98 |
| 64_H | 70_T | 1.177 | 0.98 |
| 95_A | 99_A | 1.174 | 0.98 |
| 57_F | 63_G | 1.166 | 0.97 |
| 187_F | 199_H | 1.156 | 0.97 |
| 74_V | 79_I | 1.148 | 0.97 |
| 133_L | 205_G | 1.141 | 0.97 |
| 131_V | 177_T | 1.134 | 0.97 |
| 105_V | 131_V | 1.123 | 0.97 |
| 68_A | 183_P | 1.122 | 0.97 |
| 70_T | 88_I | 1.122 | 0.97 |
| 54_V | 159_A | 1.118 | 0.96 |
| 96_I | 192_I | 1.112 | 0.96 |
| 27_N | 34_P | 1.111 | 0.96 |
| 128_G | 177_T | 1.110 | 0.96 |
| 15_L | 97_I | 1.106 | 0.96 |
| 133_L | 209_G | 1.102 | 0.96 |
| 129_L | 204_V | 1.101 | 0.96 |
| 116_V | 119_V | 1.094 | 0.96 |
| 61_S | 87_Y | 1.088 | 0.96 |
| 185_R | 189_P | 1.084 | 0.96 |
| 68_A | 210_A | 1.071 | 0.95 |
| 18_V | 22_L | 1.068 | 0.95 |
| 158_I | 162_I | 1.065 | 0.95 |
| 136_T | 210_A | 1.057 | 0.95 |
| 139_L | 166_V | 1.055 | 0.95 |
| 56_C | 142_T | 1.049 | 0.94 |
| 131_V | 135_I | 1.043 | 0.94 |
| 166_V | 181_M | 1.041 | 0.94 |
| 67_P | 184_A | 1.041 | 0.94 |
| 129_L | 201_I | 1.029 | 0.94 |
| 25_T | 29_G | 1.028 | 0.94 |
| 173_A | 179_A | 1.024 | 0.93 |
| 30_G | 35_L | 1.017 | 0.93 |
| 85_V | 89_A | 1.017 | 0.93 |
| 101_I | 134_I | 1.013 | 0.93 |
| 9_A | 60_I | 1.010 | 0.93 |
| 126_G | 130_L | 1.009 | 0.93 |
| 17_F | 50_I | 1.005 | 0.93 |
| 55_Q | 159_A | 1.003 | 0.93 |
| 22_L | 102_L | 1.001 | 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 | |
| 3gd8A | 1 | 1 | 100 | 0.016 | Contact Map |
| 2zz9A | 1 | 0.991 | 100 | 0.02 | Contact Map |
| 3iyzA | 1 | 0.991 | 100 | 0.02 | Contact Map |
| 1j4nA | 1 | 1 | 100 | 0.047 | Contact Map |
| 4oj2X | 1 | 0.9821 | 100 | 0.05 | Contact Map |
| 4nefA | 4 | 0.9821 | 100 | 0.055 | Contact Map |
| 2b6oA | 1 | 0.9821 | 100 | 0.056 | Contact Map |
| 3d9sA | 4 | 0.9821 | 100 | 0.063 | Contact Map |
| 3cn5A | 1 | 1 | 100 | 0.078 | Contact Map |
| 1ldfA | 1 | 0.9865 | 100 | 0.085 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)