| TVMCP 70-201 |
| ID: | 1488666131 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (126) | ||
| Sequences: | 1110 (523.6) | ||
| Seq/Len: | 8.810 | ||
| Nf(neff/√len): | 46.6 |
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: 8.810).
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 |
| 27_S | 122_A | 3.165 | 1.00 |
| 46_I | 96_G | 3.072 | 1.00 |
| 28_L | 80_A | 2.903 | 1.00 |
| 41_K | 69_D | 2.488 | 1.00 |
| 25_G | 124_L | 2.350 | 1.00 |
| 42_L | 100_V | 2.349 | 1.00 |
| 35_N | 38_S | 2.263 | 1.00 |
| 30_L | 119_L | 2.236 | 1.00 |
| 25_G | 126_D | 2.206 | 1.00 |
| 35_N | 111_A | 2.099 | 1.00 |
| 29_K | 77_E | 2.028 | 1.00 |
| 43_I | 61_T | 1.979 | 1.00 |
| 41_K | 67_I | 1.970 | 1.00 |
| 27_S | 77_E | 1.929 | 1.00 |
| 38_S | 106_L | 1.832 | 1.00 |
| 67_I | 103_Y | 1.767 | 1.00 |
| 44_A | 98_L | 1.731 | 1.00 |
| 23_S | 128_K | 1.702 | 1.00 |
| 46_I | 80_A | 1.684 | 1.00 |
| 16_F | 129_F | 1.643 | 1.00 |
| 29_K | 75_S | 1.599 | 1.00 |
| 46_I | 78_I | 1.549 | 1.00 |
| 40_G | 70_F | 1.516 | 1.00 |
| 45_A | 60_L | 1.462 | 1.00 |
| 27_S | 79_I | 1.458 | 1.00 |
| 40_G | 102_V | 1.418 | 0.99 |
| 80_A | 96_G | 1.376 | 0.99 |
| 45_A | 99_V | 1.367 | 0.99 |
| 42_L | 102_V | 1.325 | 0.99 |
| 126_D | 131_M | 1.317 | 0.99 |
| 26_F | 121_S | 1.267 | 0.98 |
| 40_G | 106_L | 1.262 | 0.98 |
| 19_Y | 23_S | 1.258 | 0.98 |
| 68_L | 78_I | 1.216 | 0.98 |
| 44_A | 100_V | 1.203 | 0.97 |
| 106_L | 115_I | 1.198 | 0.97 |
| 31_L | 120_T | 1.188 | 0.97 |
| 56_S | 59_L | 1.171 | 0.97 |
| 11_Y | 14_H | 1.167 | 0.97 |
| 47_I | 60_L | 1.166 | 0.97 |
| 44_A | 119_L | 1.164 | 0.97 |
| 78_I | 98_L | 1.161 | 0.97 |
| 34_G | 70_F | 1.155 | 0.96 |
| 123_P | 127_F | 1.146 | 0.96 |
| 84_K | 89_H | 1.143 | 0.96 |
| 47_I | 99_V | 1.104 | 0.95 |
| 70_F | 115_I | 1.074 | 0.94 |
| 100_V | 117_I | 1.068 | 0.94 |
| 102_V | 106_L | 1.062 | 0.94 |
| 33_A | 118_K | 1.060 | 0.93 |
| 60_L | 101_M | 1.047 | 0.93 |
| 42_L | 106_L | 1.044 | 0.93 |
| 35_N | 106_L | 1.040 | 0.93 |
| 75_S | 122_A | 1.032 | 0.92 |
| 27_S | 125_P | 1.012 | 0.91 |
| 37_F | 40_G | 1.007 | 0.91 |
| 46_I | 49_P | 1.002 | 0.91 |
| 21_G | 130_T | 1.002 | 0.91 |
| 14_H | 18_M | 1.000 | 0.91 |
| 32_V | 44_A | 1.000 | 0.91 |
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 | |
| 3vbhC | 1 | 1 | 100 | 0.119 | Contact Map |
| 1bev3 | 1 | 1 | 100 | 0.12 | Contact Map |
| 2ws93 | 1 | 1 | 100 | 0.122 | Contact Map |
| 4ejrA | 2 | 0.9924 | 100 | 0.122 | Contact Map |
| 1m113 | 1 | 1 | 100 | 0.125 | Contact Map |
| 4gb33 | 1 | 1 | 100 | 0.125 | Contact Map |
| 3cjiB | 1 | 1 | 100 | 0.125 | Contact Map |
| 4wm8C | 1 | 1 | 100 | 0.126 | Contact Map |
| 2mev3 | 1 | 1 | 100 | 0.127 | Contact Map |
| 1tme3 | 1 | 1 | 100 | 0.128 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)