| CHEY_2qv0 |
| ID: | 1450346313 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (125) | ||
| Sequences: | 95006 (70777.9) | ||
| Seq/Len: | 760.048 | ||
| Nf(neff/√len): | 6330.6 |
HHblits Results: (2015_06)
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: 760.048).
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 |
| 22_Q | 40_S | 3.068 | 1.00 |
| 26_S | 40_S | 2.736 | 1.00 |
| 22_Q | 42_D | 2.706 | 1.00 |
| 15_V | 47_V | 2.398 | 1.00 |
| 39_G | 56_V | 2.222 | 1.00 |
| 64_N | 92_W | 2.159 | 1.00 |
| 45_L | 67_S | 2.051 | 1.00 |
| 61_L | 73_L | 2.022 | 1.00 |
| 48_L | 76_N | 1.988 | 1.00 |
| 106_D | 120_M | 1.958 | 1.00 |
| 11_K | 39_G | 1.940 | 1.00 |
| 44_G | 68_L | 1.936 | 1.00 |
| 41_F | 50_F | 1.894 | 1.00 |
| 88_F | 104_A | 1.887 | 1.00 |
| 68_L | 76_N | 1.872 | 1.00 |
| 74_A | 86_I | 1.793 | 1.00 |
| 43_D | 67_S | 1.786 | 1.00 |
| 42_D | 46_D | 1.763 | 1.00 |
| 39_G | 50_F | 1.723 | 1.00 |
| 52_Q | 80_F | 1.673 | 1.00 |
| 13_I | 41_F | 1.611 | 1.00 |
| 78_S | 105_F | 1.563 | 1.00 |
| 11_K | 36_E | 1.490 | 1.00 |
| 63_I | 71_V | 1.426 | 1.00 |
| 39_G | 54_N | 1.401 | 0.99 |
| 32_H | 118_I | 1.400 | 0.99 |
| 43_D | 46_D | 1.384 | 0.99 |
| 44_G | 73_L | 1.368 | 0.99 |
| 76_N | 80_F | 1.355 | 0.99 |
| 75_Q | 102_L | 1.327 | 0.99 |
| 11_K | 57_D | 1.326 | 0.99 |
| 50_F | 56_V | 1.324 | 0.99 |
| 28_L | 114_E | 1.283 | 0.99 |
| 69_D | 72_L | 1.273 | 0.99 |
| 68_L | 72_L | 1.269 | 0.99 |
| 106_D | 123_K | 1.255 | 0.99 |
| 76_N | 79_Q | 1.229 | 0.98 |
| 10_M | 125_T | 1.228 | 0.98 |
| 51_L | 77_I | 1.220 | 0.98 |
| 97_V | 101_E | 1.214 | 0.98 |
| 120_M | 123_K | 1.213 | 0.98 |
| 59_I | 84_P | 1.210 | 0.98 |
| 48_L | 73_L | 1.190 | 0.98 |
| 45_L | 68_L | 1.175 | 0.98 |
| 11_K | 54_N | 1.162 | 0.97 |
| 116_R | 120_M | 1.160 | 0.97 |
| 74_A | 88_F | 1.159 | 0.97 |
| 89_I | 112_Y | 1.153 | 0.97 |
| 17_D | 62_D | 1.148 | 0.97 |
| 13_I | 47_V | 1.134 | 0.97 |
| 98_E | 102_L | 1.114 | 0.96 |
| 71_V | 99_A | 1.098 | 0.96 |
| 88_F | 99_A | 1.088 | 0.96 |
| 47_V | 73_L | 1.083 | 0.96 |
| 118_I | 122_Q | 1.073 | 0.95 |
| 92_W | 95_H | 1.067 | 0.95 |
| 23_Q | 26_S | 1.064 | 0.95 |
| 13_I | 56_V | 1.060 | 0.95 |
| 41_F | 47_V | 1.050 | 0.94 |
| 11_K | 37_I | 1.045 | 0.94 |
| 14_I | 25_L | 1.034 | 0.94 |
| 50_F | 54_N | 1.031 | 0.94 |
| 74_A | 104_A | 1.022 | 0.93 |
| 19_F | 42_D | 1.009 | 0.93 |
| 50_F | 53_H | 1.008 | 0.93 |
| 71_V | 98_E | 1.000 | 0.92 |
| 72_L | 75_Q | 1.000 | 0.92 |
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 | |
| 4g97A | 1 | 0.951 | 99.7 | -0.074 | Contact Map |
| 3n0rA | 1 | 0.8951 | 99.7 | -0.07 | Contact Map |
| 3eq2A | 2 | 0.9371 | 99.6 | -0.02 | Contact Map |
| 2qv0A | 2 | 0.8462 | 99.6 | -0.015 | Contact Map |
| 4l4uA | 1 | 0.979 | 99.6 | -0.014 | Contact Map |
| 1yioA | 1 | 0.9371 | 99.6 | -0.011 | Contact Map |
| 1kgsA | 1 | 0.9301 | 99.6 | -0.006 | Contact Map |
| 2ayxA | 1 | 0.9231 | 99.6 | -0.006 | Contact Map |
| 2vycA | 10 | 0.9231 | 99.6 | -0.005 | Contact Map |
| 3dzdA | 2 | 0.9231 | 99.6 | -0.005 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)