| pglB_aln |
| ID: | 1420734554 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 200 (185) | ||
| Sequences: | 3899 (3014.8) | ||
| Seq/Len: | 21.076 | ||
| Nf(neff/√len): | 221.7 |
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: 21.076).
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 |
| 7_R | 11_I | 3.693 | 1.00 |
| 28_L | 91_L | 3.205 | 1.00 |
| 45_E | 53_P | 3.133 | 1.00 |
| 43_I | 55_K | 2.927 | 1.00 |
| 158_W | 162_N | 2.914 | 1.00 |
| 35_N | 81_P | 2.888 | 1.00 |
| 31_L | 82_F | 2.827 | 1.00 |
| 45_E | 55_K | 2.760 | 1.00 |
| 100_V | 135_I | 2.742 | 1.00 |
| 85_K | 89_A | 2.572 | 1.00 |
| 61_S | 86_L | 2.515 | 1.00 |
| 127_R | 161_D | 2.232 | 1.00 |
| 138_W | 142_N | 2.180 | 1.00 |
| 18_L | 98_W | 2.110 | 1.00 |
| 170_K | 174_L | 2.020 | 1.00 |
| 33_R | 38_S | 1.993 | 1.00 |
| 108_V | 136_T | 1.964 | 1.00 |
| 151_E | 154_S | 1.957 | 1.00 |
| 138_W | 158_W | 1.916 | 1.00 |
| 48_G | 133_P | 1.916 | 1.00 |
| 29_I | 40_V | 1.879 | 1.00 |
| 9_I | 13_A | 1.860 | 1.00 |
| 15_A | 101_L | 1.765 | 1.00 |
| 57_V | 99_N | 1.733 | 1.00 |
| 28_L | 86_L | 1.705 | 1.00 |
| 28_L | 59_F | 1.666 | 1.00 |
| 10_D | 106_S | 1.662 | 1.00 |
| 14_S | 18_L | 1.657 | 1.00 |
| 43_I | 57_V | 1.655 | 1.00 |
| 41_F | 57_V | 1.655 | 1.00 |
| 33_R | 40_V | 1.649 | 1.00 |
| 114_L | 117_Y | 1.629 | 1.00 |
| 174_L | 178_K | 1.559 | 1.00 |
| 108_V | 172_L | 1.536 | 1.00 |
| 177_K | 181_I | 1.509 | 1.00 |
| 113_L | 117_Y | 1.507 | 1.00 |
| 39_P | 64_D | 1.499 | 1.00 |
| 25_F | 59_F | 1.494 | 1.00 |
| 32_I | 35_N | 1.482 | 1.00 |
| 131_M | 160_T | 1.482 | 1.00 |
| 53_P | 115_M | 1.467 | 1.00 |
| 6_K | 168_D | 1.439 | 1.00 |
| 98_W | 102_K | 1.438 | 1.00 |
| 137_G | 140_Q | 1.424 | 1.00 |
| 13_A | 107_L | 1.423 | 1.00 |
| 82_F | 86_L | 1.420 | 1.00 |
| 32_I | 36_L | 1.418 | 1.00 |
| 158_W | 167_L | 1.404 | 0.99 |
| 127_R | 130_E | 1.394 | 0.99 |
| 90_S | 144_R | 1.393 | 0.99 |
| 27_V | 31_L | 1.389 | 0.99 |
| 21_L | 25_F | 1.387 | 0.99 |
| 47_P | 53_P | 1.371 | 0.99 |
| 6_K | 10_D | 1.354 | 0.99 |
| 143_G | 147_L | 1.352 | 0.99 |
| 17_G | 21_L | 1.329 | 0.99 |
| 49_K | 132_K | 1.315 | 0.99 |
| 11_I | 15_A | 1.268 | 0.99 |
| 14_S | 101_L | 1.264 | 0.99 |
| 19_I | 22_S | 1.240 | 0.98 |
| 17_G | 97_L | 1.239 | 0.98 |
| 17_G | 107_L | 1.235 | 0.98 |
| 88_T | 182_K | 1.234 | 0.98 |
| 137_G | 152_K | 1.213 | 0.98 |
| 159_Y | 168_D | 1.189 | 0.98 |
| 39_P | 60_R | 1.184 | 0.98 |
| 138_W | 171_I | 1.183 | 0.98 |
| 179_V | 184_G | 1.161 | 0.97 |
| 97_L | 107_L | 1.143 | 0.97 |
| 44_R | 56_M | 1.142 | 0.97 |
| 11_I | 14_S | 1.130 | 0.97 |
| 30_Y | 34_K | 1.127 | 0.97 |
| 117_Y | 121_Y | 1.126 | 0.97 |
| 107_L | 172_L | 1.123 | 0.97 |
| 113_L | 118_L | 1.118 | 0.96 |
| 128_R | 156_D | 1.113 | 0.96 |
| 138_W | 167_L | 1.112 | 0.96 |
| 63_R | 66_L | 1.108 | 0.96 |
| 142_N | 174_L | 1.103 | 0.96 |
| 139_A | 152_K | 1.099 | 0.96 |
| 11_I | 101_L | 1.086 | 0.96 |
| 18_L | 22_S | 1.072 | 0.95 |
| 23_P | 26_L | 1.069 | 0.95 |
| 172_L | 176_V | 1.064 | 0.95 |
| 115_M | 119_P | 1.059 | 0.95 |
| 113_L | 149_W | 1.044 | 0.94 |
| 7_R | 14_S | 1.043 | 0.94 |
| 33_R | 36_L | 1.039 | 0.94 |
| 94_L | 97_L | 1.038 | 0.94 |
| 165_F | 169_M | 1.038 | 0.94 |
| 15_A | 19_I | 1.030 | 0.94 |
| 138_W | 155_C | 1.028 | 0.94 |
| 148_S | 151_E | 1.010 | 0.93 |
| 99_N | 104_E | 1.009 | 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 | |
| 3hinA | 2 | 0.365 | 7.4 | 0.967 | Contact Map |
| 3wguG | 2 | 0.175 | 3.2 | 0.972 | Contact Map |
| 4k84A | 2 | 0.42 | 2.6 | 0.973 | Contact Map |
| 2k44A | 1 | 0.135 | 2 | 0.975 | Contact Map |
| 2lk9A | 1 | 0.12 | 1.9 | 0.975 | Contact Map |
| 1ul1X | 3 | 0.325 | 1.8 | 0.976 | Contact Map |
| 2bzwB | 1 | 0.135 | 1.8 | 0.976 | Contact Map |
| 8tfvA | 1 | 0.105 | 1.7 | 0.976 | Contact Map |
| 1hywA | 1 | 0.24 | 1.6 | 0.976 | Contact Map |
| 1xqoA | 1 | 0.52 | 1.6 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)