| AlkB |
| ID: | 1485182229 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 216 (205) | ||
| Sequences: | 3706 (2255.6) | ||
| Seq/Len: | 18.078 | ||
| Nf(neff/√len): | 157.5 |
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: 18.078).
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 |
| 30_A | 102_R | 3.245 | 1.00 |
| 31_E | 172_H | 3.094 | 1.00 |
| 145_S | 206_N | 2.976 | 1.00 |
| 21_I | 171_E | 2.792 | 1.00 |
| 121_R | 203_C | 2.765 | 1.00 |
| 27_F | 30_A | 2.516 | 1.00 |
| 155_Q | 167_R | 2.438 | 1.00 |
| 26_A | 148_L | 2.402 | 1.00 |
| 117_C | 207_L | 2.352 | 1.00 |
| 100_C | 104_A | 2.328 | 1.00 |
| 36_D | 95_S | 2.224 | 1.00 |
| 38_N | 203_C | 2.182 | 1.00 |
| 130_L | 188_G | 2.167 | 1.00 |
| 150_L | 195_G | 2.127 | 1.00 |
| 50_V | 56_T | 2.104 | 1.00 |
| 33_L | 148_L | 2.066 | 1.00 |
| 153_I | 167_R | 2.001 | 1.00 |
| 151_P | 169_L | 1.968 | 1.00 |
| 155_Q | 190_Q | 1.967 | 1.00 |
| 171_E | 174_D | 1.932 | 1.00 |
| 127_K | 191_P | 1.920 | 1.00 |
| 28_N | 31_E | 1.917 | 1.00 |
| 151_P | 171_E | 1.864 | 1.00 |
| 67_L | 213_G | 1.862 | 1.00 |
| 41_A | 62_T | 1.858 | 1.00 |
| 132_Q | 159_L | 1.858 | 1.00 |
| 41_A | 46_F | 1.845 | 1.00 |
| 19_A | 182_S | 1.802 | 1.00 |
| 192_L | 201_I | 1.782 | 1.00 |
| 155_Q | 188_G | 1.768 | 1.00 |
| 153_I | 169_L | 1.721 | 1.00 |
| 138_D | 141_A | 1.701 | 1.00 |
| 130_L | 157_G | 1.659 | 1.00 |
| 146_V | 175_V | 1.655 | 1.00 |
| 18_G | 182_S | 1.642 | 1.00 |
| 21_I | 174_D | 1.634 | 1.00 |
| 34_I | 205_Y | 1.612 | 1.00 |
| 38_N | 121_R | 1.603 | 1.00 |
| 44_S | 119_I | 1.576 | 1.00 |
| 115_D | 212_A | 1.542 | 1.00 |
| 204_R | 210_R | 1.535 | 1.00 |
| 101_Q | 113_Q | 1.529 | 1.00 |
| 23_R | 171_E | 1.522 | 1.00 |
| 153_I | 192_L | 1.521 | 1.00 |
| 145_S | 154_F | 1.500 | 1.00 |
| 145_S | 176_V | 1.498 | 1.00 |
| 16_A | 182_S | 1.427 | 1.00 |
| 17_A | 181_E | 1.411 | 1.00 |
| 94_Q | 98_N | 1.399 | 0.99 |
| 63_N | 116_A | 1.392 | 0.99 |
| 77_L | 82_D | 1.392 | 0.99 |
| 19_A | 176_V | 1.379 | 0.99 |
| 181_E | 185_F | 1.376 | 0.99 |
| 97_H | 101_Q | 1.375 | 0.99 |
| 144_V | 175_V | 1.365 | 0.99 |
| 158_G | 161_R | 1.358 | 0.99 |
| 154_F | 206_N | 1.318 | 0.99 |
| 37_I | 205_Y | 1.311 | 0.99 |
| 151_P | 172_H | 1.298 | 0.99 |
| 20_V | 179_G | 1.294 | 0.99 |
| 101_Q | 105_T | 1.292 | 0.99 |
| 98_N | 102_R | 1.278 | 0.99 |
| 97_H | 100_C | 1.272 | 0.99 |
| 26_A | 99_L | 1.253 | 0.99 |
| 140_R | 184_L | 1.242 | 0.98 |
| 155_Q | 165_L | 1.232 | 0.98 |
| 182_S | 185_F | 1.207 | 0.98 |
| 26_A | 146_V | 1.202 | 0.98 |
| 115_D | 211_Q | 1.202 | 0.98 |
| 24_R | 174_D | 1.196 | 0.98 |
| 151_P | 174_D | 1.194 | 0.98 |
| 25_F | 175_V | 1.186 | 0.98 |
| 34_I | 149_G | 1.181 | 0.98 |
| 50_V | 58_S | 1.158 | 0.97 |
| 32_Q | 36_D | 1.138 | 0.97 |
| 204_R | 208_T | 1.136 | 0.97 |
| 103_A | 107_A | 1.125 | 0.97 |
| 139_L | 184_L | 1.122 | 0.97 |
| 26_A | 173_G | 1.121 | 0.97 |
| 18_G | 181_E | 1.114 | 0.96 |
| 31_E | 35_R | 1.110 | 0.96 |
| 22_L | 177_V | 1.098 | 0.96 |
| 123_A | 126_A | 1.085 | 0.96 |
| 75_G | 82_D | 1.083 | 0.96 |
| 206_N | 210_R | 1.072 | 0.95 |
| 156_F | 176_V | 1.063 | 0.95 |
| 96_F | 117_C | 1.062 | 0.95 |
| 25_F | 106_A | 1.054 | 0.95 |
| 46_F | 119_I | 1.037 | 0.94 |
| 36_D | 39_D | 1.028 | 0.94 |
| 195_G | 201_I | 1.016 | 0.93 |
| 138_D | 142_P | 1.011 | 0.93 |
| 156_F | 182_S | 1.005 | 0.93 |
| 134_K | 138_D | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4jhtA | 1 | 0.9306 | 100 | 0.202 | Contact Map |
| 2iuwA | 1 | 0.8657 | 100 | 0.329 | Contact Map |
| 3thtA | 4 | 0.8426 | 100 | 0.345 | Contact Map |
| 3s57A | 1 | 0.8657 | 100 | 0.351 | Contact Map |
| 4nj4A | 2 | 0.8981 | 100 | 0.371 | Contact Map |
| 4qkdA | 3 | 0.8426 | 100 | 0.373 | Contact Map |
| 4nplA | 2 | 0.8935 | 100 | 0.376 | Contact Map |
| 4ie5A | 1 | 0.8889 | 100 | 0.489 | Contact Map |
| 4bqyA | 1 | 0.8889 | 97.3 | 0.852 | Contact Map |
| 4j25A | 8 | 0.8333 | 97.1 | 0.855 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)