| testelo |
| ID: | 1501325049 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 279 (252) | ||
| Sequences: | 1854 (1200.1) | ||
| Seq/Len: | 7.357 | ||
| Nf(neff/√len): | 75.6 |
HHblits Results: (2016_02)
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: 7.357).
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 |
| 93_C | 225_C | 3.222 | 1.00 |
| 63_I | 183_G | 3.048 | 1.00 |
| 249_N | 253_H | 2.995 | 1.00 |
| 50_M | 132_K | 2.863 | 1.00 |
| 143_F | 242_I | 2.678 | 1.00 |
| 77_V | 173_S | 2.629 | 1.00 |
| 74_L | 176_V | 2.553 | 1.00 |
| 112_W | 116_F | 2.360 | 1.00 |
| 174_V | 204_I | 2.356 | 1.00 |
| 41_F | 126_V | 2.231 | 1.00 |
| 79_E | 106_R | 2.210 | 1.00 |
| 67_F | 183_G | 2.131 | 1.00 |
| 122_L | 149_P | 2.125 | 1.00 |
| 206_L | 248_S | 2.103 | 1.00 |
| 206_L | 244_F | 2.090 | 1.00 |
| 139_F | 143_F | 2.085 | 1.00 |
| 61_F | 127_I | 2.055 | 1.00 |
| 70_V | 180_L | 2.017 | 1.00 |
| 50_M | 53_R | 1.993 | 1.00 |
| 48_R | 51_A | 1.970 | 1.00 |
| 73_S | 121_E | 1.967 | 1.00 |
| 126_V | 130_L | 1.909 | 1.00 |
| 72_L | 117_S | 1.841 | 1.00 |
| 245_M | 249_N | 1.807 | 1.00 |
| 122_L | 126_V | 1.756 | 1.00 |
| 50_M | 56_F | 1.683 | 1.00 |
| 46_G | 129_I | 1.645 | 1.00 |
| 69_L | 121_E | 1.635 | 1.00 |
| 244_F | 248_S | 1.622 | 1.00 |
| 128_F | 137_V | 1.571 | 1.00 |
| 114_F | 117_S | 1.549 | 1.00 |
| 178_M | 202_T | 1.547 | 1.00 |
| 116_F | 120_I | 1.543 | 1.00 |
| 65_Y | 69_L | 1.523 | 0.99 |
| 19_I | 25_M | 1.510 | 0.99 |
| 250_F | 255_Y | 1.482 | 0.99 |
| 63_I | 186_A | 1.480 | 0.99 |
| 173_S | 204_I | 1.465 | 0.99 |
| 49_I | 56_F | 1.465 | 0.99 |
| 173_S | 177_I | 1.464 | 0.99 |
| 39_V | 146_S | 1.459 | 0.99 |
| 171_N | 175_H | 1.454 | 0.99 |
| 74_L | 78_Y | 1.449 | 0.99 |
| 147_V | 243_F | 1.439 | 0.99 |
| 177_I | 204_I | 1.434 | 0.99 |
| 175_H | 178_M | 1.429 | 0.99 |
| 196_W | 200_H | 1.419 | 0.99 |
| 37_T | 41_F | 1.403 | 0.99 |
| 144_H | 171_N | 1.398 | 0.99 |
| 62_M | 127_I | 1.390 | 0.99 |
| 114_F | 148_L | 1.381 | 0.99 |
| 210_V | 244_F | 1.336 | 0.98 |
| 49_I | 53_R | 1.323 | 0.98 |
| 202_T | 205_Q | 1.322 | 0.98 |
| 63_I | 187_F | 1.317 | 0.98 |
| 175_H | 205_Q | 1.315 | 0.98 |
| 197_W | 201_M | 1.302 | 0.98 |
| 171_N | 179_Y | 1.302 | 0.98 |
| 46_G | 50_M | 1.297 | 0.98 |
| 58_L | 130_L | 1.288 | 0.98 |
| 41_F | 46_G | 1.280 | 0.98 |
| 183_G | 187_F | 1.271 | 0.98 |
| 76_I | 117_S | 1.270 | 0.97 |
| 68_S | 120_I | 1.267 | 0.97 |
| 197_W | 200_H | 1.260 | 0.97 |
| 138_T | 142_V | 1.250 | 0.97 |
| 62_M | 131_R | 1.246 | 0.97 |
| 76_I | 172_S | 1.242 | 0.97 |
| 144_H | 175_H | 1.234 | 0.97 |
| 35_L | 146_S | 1.228 | 0.97 |
| 34_I | 122_L | 1.228 | 0.97 |
| 252_Y | 256_T | 1.227 | 0.97 |
| 171_N | 202_T | 1.215 | 0.96 |
| 50_M | 55_P | 1.215 | 0.96 |
| 35_L | 39_V | 1.214 | 0.96 |
| 21_G | 26_G | 1.212 | 0.96 |
| 115_L | 119_F | 1.201 | 0.96 |
| 90_T | 94_D | 1.199 | 0.96 |
| 129_I | 132_K | 1.196 | 0.96 |
| 175_H | 202_T | 1.195 | 0.96 |
| 53_R | 132_K | 1.194 | 0.96 |
| 171_N | 205_Q | 1.157 | 0.95 |
| 242_I | 245_M | 1.155 | 0.95 |
| 202_T | 208_Q | 1.151 | 0.95 |
| 248_S | 252_Y | 1.151 | 0.95 |
| 166_F | 211_L | 1.150 | 0.95 |
| 184_L | 191_A | 1.147 | 0.95 |
| 253_H | 257_K | 1.147 | 0.95 |
| 40_Y | 45_L | 1.140 | 0.94 |
| 73_S | 76_I | 1.140 | 0.94 |
| 251_W | 255_Y | 1.135 | 0.94 |
| 247_F | 255_Y | 1.114 | 0.94 |
| 205_Q | 208_Q | 1.105 | 0.93 |
| 134_D | 137_V | 1.098 | 0.93 |
| 145_H | 171_N | 1.083 | 0.92 |
| 45_L | 49_I | 1.082 | 0.92 |
| 175_H | 179_Y | 1.080 | 0.92 |
| 27_S | 30_L | 1.078 | 0.92 |
| 111_A | 168_A | 1.076 | 0.92 |
| 199_K | 209_F | 1.070 | 0.92 |
| 171_N | 178_M | 1.066 | 0.91 |
| 59_R | 63_I | 1.061 | 0.91 |
| 178_M | 205_Q | 1.058 | 0.91 |
| 101_S | 104_A | 1.057 | 0.91 |
| 22_Y | 112_W | 1.056 | 0.91 |
| 241_T | 245_M | 1.055 | 0.91 |
| 141_H | 144_H | 1.055 | 0.91 |
| 113_L | 116_F | 1.050 | 0.91 |
| 252_Y | 257_K | 1.034 | 0.90 |
| 70_V | 121_E | 1.024 | 0.89 |
| 179_Y | 205_Q | 1.021 | 0.89 |
| 239_Y | 243_F | 1.019 | 0.89 |
| 141_H | 145_H | 1.014 | 0.88 |
| 58_L | 61_F | 1.013 | 0.88 |
| 55_P | 132_K | 1.007 | 0.88 |
| 53_R | 56_F | 1.000 | 0.88 |
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 | |
| 3ze3A | 6 | 0.1685 | 4.4 | 0.972 | Contact Map |
| 2ks1B | 1 | 0.1398 | 4.2 | 0.972 | Contact Map |
| 2wwbC | 1 | 0.129 | 2 | 0.976 | Contact Map |
| 2jwaA | 2 | 0.1326 | 1.5 | 0.978 | Contact Map |
| 2ww9C | 1 | 0.0753 | 1.5 | 0.978 | Contact Map |
| 4x5mA | 3 | 0.3226 | 1.4 | 0.978 | Contact Map |
| 4hkcB | 1 | 0.0251 | 1.4 | 0.978 | Contact Map |
| 3he5B | 3 | 0.1111 | 1.4 | 0.978 | Contact Map |
| 2rddB | 1 | 0.1326 | 1.3 | 0.979 | Contact Map |
| 2losA | 1 | 0.2366 | 1.2 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)