| 1pv6 1-190 |
| ID: | 1496696427 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 190 (177) | ||
| Sequences: | 79102 (48816.5) | ||
| Seq/Len: | 446.904 | ||
| Nf(neff/√len): | 3669.3 |
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: 446.904).
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 |
| 102_N | 106_G | 2.980 | 1.00 |
| 63_F | 120_A | 2.866 | 1.00 |
| 91_F | 171_W | 2.747 | 1.00 |
| 82_G | 117_C | 2.709 | 1.00 |
| 72_L | 131_K | 2.698 | 1.00 |
| 89_P | 110_G | 2.661 | 1.00 |
| 55_F | 112_I | 2.544 | 1.00 |
| 133_S | 139_E | 2.454 | 1.00 |
| 103_I | 106_G | 2.111 | 1.00 |
| 86_M | 110_G | 2.086 | 1.00 |
| 79_I | 120_A | 2.020 | 1.00 |
| 59_F | 116_F | 2.015 | 1.00 |
| 73_R | 77_L | 2.014 | 1.00 |
| 44_D | 104_L | 1.975 | 1.00 |
| 71_G | 74_K | 1.956 | 1.00 |
| 84_L | 177_A | 1.905 | 1.00 |
| 105_V | 109_V | 1.868 | 1.00 |
| 67_S | 124_A | 1.835 | 1.00 |
| 135_R | 138_F | 1.834 | 1.00 |
| 86_M | 113_Y | 1.816 | 1.00 |
| 104_L | 108_I | 1.748 | 1.00 |
| 13_G | 146_F | 1.740 | 1.00 |
| 41_S | 44_D | 1.708 | 1.00 |
| 65_L | 69_K | 1.681 | 1.00 |
| 86_M | 117_C | 1.659 | 1.00 |
| 77_L | 185_F | 1.641 | 1.00 |
| 64_G | 68_D | 1.640 | 1.00 |
| 40_I | 104_L | 1.639 | 1.00 |
| 17_F | 150_G | 1.639 | 1.00 |
| 20_F | 147_G | 1.589 | 1.00 |
| 74_K | 78_W | 1.568 | 1.00 |
| 51_A | 112_I | 1.566 | 1.00 |
| 62_L | 65_L | 1.551 | 1.00 |
| 105_V | 108_I | 1.534 | 1.00 |
| 25_A | 158_V | 1.514 | 1.00 |
| 77_L | 181_A | 1.511 | 1.00 |
| 72_L | 127_A | 1.498 | 1.00 |
| 106_G | 110_G | 1.482 | 1.00 |
| 21_F | 154_G | 1.476 | 1.00 |
| 182_V | 186_F | 1.467 | 1.00 |
| 90_F | 110_G | 1.452 | 1.00 |
| 81_T | 181_A | 1.448 | 1.00 |
| 91_F | 174_S | 1.443 | 1.00 |
| 66_L | 70_L | 1.427 | 1.00 |
| 88_A | 174_S | 1.418 | 1.00 |
| 7_T | 11_M | 1.385 | 0.99 |
| 101_Y | 106_G | 1.371 | 0.99 |
| 11_M | 186_F | 1.355 | 0.99 |
| 40_I | 44_D | 1.354 | 0.99 |
| 84_L | 174_S | 1.349 | 0.99 |
| 84_L | 181_A | 1.342 | 0.99 |
| 70_L | 74_K | 1.326 | 0.99 |
| 86_M | 114_L | 1.313 | 0.99 |
| 130_E | 136_S | 1.269 | 0.99 |
| 70_L | 75_Y | 1.261 | 0.99 |
| 51_A | 108_I | 1.242 | 0.98 |
| 168_F | 171_W | 1.234 | 0.98 |
| 52_I | 115_G | 1.226 | 0.98 |
| 55_F | 59_F | 1.220 | 0.98 |
| 32_I | 35_H | 1.220 | 0.98 |
| 84_L | 178_L | 1.219 | 0.98 |
| 171_W | 175_G | 1.212 | 0.98 |
| 47_I | 51_A | 1.202 | 0.98 |
| 44_D | 108_I | 1.162 | 0.97 |
| 71_G | 75_Y | 1.162 | 0.97 |
| 138_F | 142_R | 1.159 | 0.97 |
| 74_K | 77_L | 1.152 | 0.97 |
| 34_L | 40_I | 1.148 | 0.97 |
| 130_E | 140_F | 1.138 | 0.97 |
| 59_F | 62_L | 1.125 | 0.97 |
| 48_I | 107_S | 1.115 | 0.96 |
| 175_G | 179_I | 1.113 | 0.96 |
| 34_L | 45_T | 1.106 | 0.96 |
| 78_W | 82_G | 1.090 | 0.96 |
| 90_F | 107_S | 1.083 | 0.96 |
| 43_S | 47_I | 1.080 | 0.95 |
| 29_F | 162_F | 1.064 | 0.95 |
| 129_I | 143_A | 1.063 | 0.95 |
| 59_F | 119_N | 1.061 | 0.95 |
| 101_Y | 110_G | 1.051 | 0.94 |
| 80_I | 180_L | 1.051 | 0.94 |
| 167_Q | 171_W | 1.043 | 0.94 |
| 126_E | 140_F | 1.038 | 0.94 |
| 83_M | 177_A | 1.032 | 0.94 |
| 165_N | 168_F | 1.029 | 0.94 |
| 156_S | 160_I | 1.029 | 0.94 |
| 89_P | 106_G | 1.022 | 0.93 |
| 16_F | 147_G | 1.018 | 0.93 |
| 67_S | 72_L | 1.018 | 0.93 |
| 19_Y | 121_G | 1.015 | 0.93 |
| 58_L | 62_L | 1.014 | 0.93 |
| 55_F | 115_G | 1.011 | 0.93 |
| 91_F | 100_Q | 1.007 | 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 | |
| 2cfqA | 1 | 1 | 99.8 | 0.049 | Contact Map |
| 3wdoA | 1 | 0.9474 | 99.8 | 0.101 | Contact Map |
| 4q65A | 1 | 0.9474 | 99.7 | 0.104 | Contact Map |
| 4tphA | 2 | 0.9474 | 99.7 | 0.106 | Contact Map |
| 4j05A | 2 | 0.9053 | 99.7 | 0.112 | Contact Map |
| 4oh3A | 2 | 1 | 99.7 | 0.117 | Contact Map |
| 2gfpA | 2 | 0.9158 | 99.7 | 0.122 | Contact Map |
| 4xnjA | 1 | 0 | 99.7 | 0.125 | Contact Map |
| 4uvmA | 1 | 0.9474 | 99.7 | 0.125 | Contact Map |
| 1pw4A | 1 | 0.9474 | 99.7 | 0.142 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)