| hellf |
| ID: | 1428591593 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (198) | ||
| Sequences: | 2020 (1813.8) | ||
| Seq/Len: | 10.202 | ||
| Nf(neff/√len): | 128.9 |
Jackhmmer Results: (2015_01_07)
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: 10.202).
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 |
| 2_D | 5_S | 4.462 | 1.00 |
| 15_T | 19_Q | 2.847 | 1.00 |
| 3_P | 7_T | 2.492 | 1.00 |
| 27_L | 116_Y | 2.322 | 1.00 |
| 12_A | 15_T | 2.219 | 1.00 |
| 4_L | 8_A | 2.017 | 1.00 |
| 183_S | 186_D | 1.848 | 1.00 |
| 187_D | 190_I | 1.717 | 1.00 |
| 130_A | 133_Q | 1.686 | 1.00 |
| 189_G | 193_G | 1.676 | 1.00 |
| 48_T | 84_T | 1.669 | 1.00 |
| 37_S | 119_D | 1.616 | 1.00 |
| 133_Q | 138_M | 1.615 | 1.00 |
| 6_V | 9_S | 1.612 | 1.00 |
| 56_A | 60_E | 1.610 | 1.00 |
| 3_P | 6_V | 1.607 | 1.00 |
| 4_L | 9_S | 1.607 | 1.00 |
| 24_L | 27_L | 1.602 | 1.00 |
| 9_S | 12_A | 1.560 | 1.00 |
| 130_A | 134_R | 1.558 | 1.00 |
| 44_L | 126_N | 1.534 | 1.00 |
| 182_E | 185_A | 1.489 | 1.00 |
| 186_D | 189_G | 1.462 | 1.00 |
| 5_S | 12_A | 1.449 | 1.00 |
| 2_D | 6_V | 1.448 | 1.00 |
| 85_K | 89_Q | 1.444 | 1.00 |
| 151_T | 155_I | 1.441 | 1.00 |
| 6_V | 10_A | 1.425 | 1.00 |
| 5_S | 8_A | 1.409 | 1.00 |
| 155_I | 159_Q | 1.398 | 0.99 |
| 123_N | 127_R | 1.339 | 0.99 |
| 92_T | 96_T | 1.336 | 0.99 |
| 25_H | 29_D | 1.331 | 0.99 |
| 188_D | 191_A | 1.325 | 0.99 |
| 37_S | 115_V | 1.314 | 0.99 |
| 194_D | 197_A | 1.294 | 0.99 |
| 193_G | 196_S | 1.290 | 0.99 |
| 22_K | 26_D | 1.278 | 0.99 |
| 8_A | 11_V | 1.277 | 0.99 |
| 170_A | 174_A | 1.268 | 0.99 |
| 180_E | 186_D | 1.262 | 0.99 |
| 177_S | 181_P | 1.256 | 0.99 |
| 171_N | 174_A | 1.246 | 0.98 |
| 112_R | 115_V | 1.239 | 0.98 |
| 8_A | 12_A | 1.231 | 0.98 |
| 190_I | 197_A | 1.231 | 0.98 |
| 182_E | 186_D | 1.224 | 0.98 |
| 190_I | 195_S | 1.211 | 0.98 |
| 187_D | 191_A | 1.210 | 0.98 |
| 94_A | 121_K | 1.207 | 0.98 |
| 9_S | 13_L | 1.189 | 0.98 |
| 192_E | 195_S | 1.189 | 0.98 |
| 91_F | 98_V | 1.188 | 0.98 |
| 179_R | 184_Q | 1.187 | 0.98 |
| 27_L | 31_L | 1.177 | 0.98 |
| 190_I | 193_G | 1.176 | 0.98 |
| 5_S | 9_S | 1.174 | 0.98 |
| 193_G | 197_A | 1.173 | 0.98 |
| 185_A | 191_A | 1.157 | 0.97 |
| 189_G | 196_S | 1.157 | 0.97 |
| 14_A | 17_A | 1.135 | 0.97 |
| 147_V | 152_S | 1.135 | 0.97 |
| 173_S | 176_L | 1.134 | 0.97 |
| 191_A | 197_A | 1.131 | 0.97 |
| 185_A | 188_D | 1.129 | 0.97 |
| 184_Q | 194_D | 1.119 | 0.96 |
| 11_V | 15_T | 1.113 | 0.96 |
| 21_A | 24_L | 1.107 | 0.96 |
| 180_E | 187_D | 1.107 | 0.96 |
| 188_D | 194_D | 1.106 | 0.96 |
| 81_L | 88_C | 1.105 | 0.96 |
| 175_Q | 178_I | 1.094 | 0.96 |
| 119_D | 123_N | 1.088 | 0.96 |
| 171_N | 187_D | 1.085 | 0.96 |
| 181_P | 187_D | 1.085 | 0.96 |
| 158_L | 166_E | 1.083 | 0.96 |
| 49_Q | 53_G | 1.072 | 0.95 |
| 192_E | 197_A | 1.066 | 0.95 |
| 180_E | 183_S | 1.062 | 0.95 |
| 7_T | 13_L | 1.059 | 0.95 |
| 178_I | 182_E | 1.059 | 0.95 |
| 148_S | 151_T | 1.059 | 0.95 |
| 182_E | 190_I | 1.049 | 0.94 |
| 175_Q | 180_E | 1.045 | 0.94 |
| 175_Q | 183_S | 1.042 | 0.94 |
| 177_S | 182_E | 1.039 | 0.94 |
| 51_T | 138_M | 1.036 | 0.94 |
| 186_D | 191_A | 1.030 | 0.94 |
| 166_E | 169_L | 1.028 | 0.94 |
| 18_L | 22_K | 1.026 | 0.94 |
| 178_I | 184_Q | 1.019 | 0.93 |
| 191_A | 194_D | 1.016 | 0.93 |
| 154_N | 159_Q | 1.012 | 0.93 |
| 164_T | 167_K | 1.012 | 0.93 |
| 184_Q | 189_G | 1.006 | 0.93 |
| 184_Q | 190_I | 1.005 | 0.93 |
| 159_Q | 163_A | 1.003 | 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 | |
| 2wvqA | 2 | 0.8599 | 96.4 | 0.756 | Contact Map |
| 2msvA | 1 | 0.7391 | 95.2 | 0.779 | Contact Map |
| 4btfA | 1 | 0.715 | 95.1 | 0.78 | Contact Map |
| 4q4gX | 1 | 0 | 89.4 | 0.817 | Contact Map |
| 4cgkA | 2 | 0.7536 | 89.4 | 0.817 | Contact Map |
| 1i84S | 2 | 0.4589 | 69.2 | 0.852 | Contact Map |
| 3ojaB | 1 | 0.6377 | 63.3 | 0.857 | Contact Map |
| 3qflA | 1 | 0.5024 | 41.5 | 0.875 | Contact Map |
| 4b8cD | 4 | 0.2415 | 40.1 | 0.876 | Contact Map |
| 3wuqA | 1 | 0.4251 | 37.6 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)