| TEst |
| ID: | 1401835975 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 0% gaps before running GREMLIN. |
| Length: | 210 (172) | ||
| Sequences: | 1862 (1230.6) | ||
| Seq/Len: | 10.826 | ||
| Nf(neff/√len): | 93.8 |
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: 10.826).
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 |
| 107_A | 118_Q | 4.313 | 1.00 |
| 57_E | 105_K | 3.580 | 1.00 |
| 62_T | 178_V | 2.966 | 1.00 |
| 48_C | 193_L | 2.957 | 1.00 |
| 45_R | 197_T | 2.777 | 1.00 |
| 60_T | 97_H | 2.622 | 1.00 |
| 52_I | 193_L | 2.586 | 1.00 |
| 178_V | 185_K | 2.346 | 1.00 |
| 64_G | 98_T | 2.327 | 1.00 |
| 103_E | 122_K | 2.274 | 1.00 |
| 184_L | 187_H | 2.080 | 1.00 |
| 70_F | 167_N | 1.873 | 1.00 |
| 120_F | 190_L | 1.789 | 1.00 |
| 171_T | 174_D | 1.761 | 1.00 |
| 177_M | 181_Q | 1.733 | 1.00 |
| 71_L | 75_Q | 1.731 | 1.00 |
| 48_C | 192_E | 1.673 | 1.00 |
| 51_E | 181_Q | 1.638 | 1.00 |
| 133_Y | 179_P | 1.622 | 1.00 |
| 51_E | 56_E | 1.612 | 1.00 |
| 55_T | 182_R | 1.611 | 1.00 |
| 181_Q | 188_L | 1.578 | 1.00 |
| 60_T | 94_L | 1.548 | 1.00 |
| 117_Y | 202_E | 1.539 | 1.00 |
| 199_E | 203_K | 1.527 | 1.00 |
| 51_E | 55_T | 1.493 | 1.00 |
| 64_G | 94_L | 1.477 | 1.00 |
| 73_P | 157_K | 1.474 | 1.00 |
| 181_Q | 184_L | 1.440 | 1.00 |
| 107_A | 119_V | 1.422 | 1.00 |
| 194_V | 206_L | 1.418 | 1.00 |
| 56_E | 59_Y | 1.418 | 1.00 |
| 59_Y | 63_L | 1.413 | 1.00 |
| 137_V | 180_M | 1.381 | 0.99 |
| 185_K | 188_L | 1.380 | 0.99 |
| 79_K | 82_D | 1.366 | 0.99 |
| 71_L | 91_E | 1.362 | 0.99 |
| 82_D | 147_V | 1.361 | 0.99 |
| 134_C | 185_K | 1.352 | 0.99 |
| 59_Y | 130_Y | 1.347 | 0.99 |
| 62_T | 168_G | 1.334 | 0.99 |
| 134_C | 187_H | 1.323 | 0.99 |
| 192_E | 195_K | 1.315 | 0.99 |
| 103_E | 123_Y | 1.292 | 0.99 |
| 187_H | 191_Q | 1.286 | 0.99 |
| 51_E | 188_L | 1.284 | 0.99 |
| 205_N | 208_L | 1.255 | 0.99 |
| 154_V | 158_L | 1.249 | 0.99 |
| 158_L | 172_L | 1.247 | 0.99 |
| 174_D | 177_M | 1.240 | 0.98 |
| 67_Q | 94_L | 1.220 | 0.98 |
| 137_V | 141_S | 1.212 | 0.98 |
| 103_E | 106_E | 1.201 | 0.98 |
| 55_T | 181_Q | 1.200 | 0.98 |
| 115_N | 205_N | 1.200 | 0.98 |
| 182_R | 186_Y | 1.191 | 0.98 |
| 66_I | 93_L | 1.190 | 0.98 |
| 47_C | 50_R | 1.189 | 0.98 |
| 101_L | 105_K | 1.184 | 0.98 |
| 177_M | 180_M | 1.182 | 0.98 |
| 66_I | 90_I | 1.180 | 0.98 |
| 144_L | 154_V | 1.176 | 0.98 |
| 58_K | 62_T | 1.174 | 0.98 |
| 180_M | 184_L | 1.168 | 0.97 |
| 197_T | 202_E | 1.166 | 0.97 |
| 181_Q | 189_L | 1.139 | 0.97 |
| 65_S | 70_F | 1.136 | 0.97 |
| 60_T | 101_L | 1.133 | 0.97 |
| 58_K | 175_L | 1.132 | 0.97 |
| 52_I | 120_F | 1.131 | 0.97 |
| 56_E | 63_L | 1.127 | 0.97 |
| 203_K | 207_R | 1.121 | 0.97 |
| 157_K | 161_C | 1.098 | 0.96 |
| 190_L | 206_L | 1.087 | 0.96 |
| 68_Q | 72_K | 1.085 | 0.96 |
| 94_L | 98_T | 1.082 | 0.96 |
| 88_I | 133_Y | 1.076 | 0.95 |
| 102_K | 106_E | 1.068 | 0.95 |
| 134_C | 180_M | 1.052 | 0.95 |
| 46_C | 50_R | 1.052 | 0.95 |
| 137_V | 184_L | 1.045 | 0.94 |
| 49_L | 53_Q | 1.044 | 0.94 |
| 197_T | 206_L | 1.025 | 0.93 |
| 70_F | 162_S | 1.025 | 0.93 |
| 51_E | 189_L | 1.025 | 0.93 |
| 147_V | 154_V | 1.020 | 0.93 |
| 134_C | 184_L | 1.019 | 0.93 |
| 194_V | 203_K | 1.014 | 0.93 |
| 87_F | 117_Y | 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 | |
| 3ky9A | 2 | 0.9381 | 100 | 0.211 | Contact Map |
| 2vrwB | 1 | 0.8143 | 100 | 0.251 | Contact Map |
| 3odwA | 2 | 0.8143 | 100 | 0.309 | Contact Map |
| 3p6aA | 2 | 0.8143 | 100 | 0.312 | Contact Map |
| 1txdA | 1 | 0.8952 | 100 | 0.316 | Contact Map |
| 3t06A | 2 | 0.8905 | 100 | 0.317 | Contact Map |
| 4d0nB | 1 | 0.9286 | 100 | 0.319 | Contact Map |
| 3jzyA | 1 | 0 | 100 | 0.321 | Contact Map |
| 4gzuA | 2 | 0.8048 | 100 | 0.323 | Contact Map |
| 3mpxA | 1 | 0.7667 | 100 | 0.325 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)