| T0765 - R0046 -force run |
| ID: | 1401143864 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (127) | ||
| Sequences: | 51 (35.8) | ||
| Seq/Len: | 0.402 | ||
| Nf(neff/√len): | 3.2 |
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: 0.402).
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 |
| 58_H | 67_F | 1.852 | 0.73 |
| 57_W | 67_F | 1.781 | 0.69 |
| 62_A | 81_F | 1.735 | 0.66 |
| 38_T | 78_L | 1.674 | 0.62 |
| 37_A | 49_G | 1.592 | 0.56 |
| 48_I | 87_G | 1.549 | 0.53 |
| 74_K | 80_K | 1.544 | 0.53 |
| 62_A | 79_I | 1.534 | 0.52 |
| 81_F | 119_R | 1.494 | 0.49 |
| 78_L | 85_A | 1.420 | 0.44 |
| 65_I | 68_K | 1.409 | 0.43 |
| 20_L | 34_Q | 1.353 | 0.39 |
| 31_A | 79_I | 1.340 | 0.38 |
| 46_Q | 65_I | 1.332 | 0.38 |
| 5_K | 47_G | 1.331 | 0.38 |
| 81_F | 89_A | 1.329 | 0.38 |
| 104_I | 113_P | 1.328 | 0.37 |
| 26_F | 48_I | 1.320 | 0.37 |
| 47_G | 82_D | 1.314 | 0.37 |
| 68_K | 99_P | 1.304 | 0.36 |
| 79_I | 119_R | 1.286 | 0.35 |
| 56_V | 82_D | 1.281 | 0.34 |
| 67_F | 78_L | 1.279 | 0.34 |
| 58_H | 78_L | 1.279 | 0.34 |
| 50_M | 55_S | 1.279 | 0.34 |
| 34_Q | 50_M | 1.274 | 0.34 |
| 62_A | 119_R | 1.265 | 0.33 |
| 16_L | 24_A | 1.264 | 0.33 |
| 81_F | 87_G | 1.263 | 0.33 |
| 87_G | 107_L | 1.255 | 0.33 |
| 57_W | 84_T | 1.247 | 0.32 |
| 23_G | 43_P | 1.243 | 0.32 |
| 12_F | 43_P | 1.236 | 0.31 |
| 73_Q | 76_G | 1.235 | 0.31 |
| 87_G | 95_G | 1.193 | 0.29 |
| 20_L | 100_H | 1.170 | 0.27 |
| 15_L | 75_D | 1.169 | 0.27 |
| 57_W | 78_L | 1.157 | 0.27 |
| 65_I | 83_S | 1.154 | 0.27 |
| 40_A | 127_L | 1.152 | 0.26 |
| 61_D | 66_R | 1.144 | 0.26 |
| 59_H | 117_L | 1.139 | 0.26 |
| 43_P | 82_D | 1.134 | 0.25 |
| 2_M | 101_G | 1.131 | 0.25 |
| 9_L | 56_V | 1.130 | 0.25 |
| 14_W | 32_V | 1.120 | 0.25 |
| 56_V | 113_P | 1.109 | 0.24 |
| 28_L | 103_I | 1.107 | 0.24 |
| 56_V | 114_T | 1.103 | 0.24 |
| 39_L | 65_I | 1.092 | 0.23 |
| 37_A | 83_S | 1.090 | 0.23 |
| 43_P | 56_V | 1.078 | 0.22 |
| 68_K | 75_D | 1.057 | 0.21 |
| 59_H | 121_R | 1.053 | 0.21 |
| 32_V | 119_R | 1.051 | 0.21 |
| 37_A | 91_K | 1.049 | 0.21 |
| 82_D | 111_N | 1.048 | 0.21 |
| 56_V | 111_N | 1.037 | 0.20 |
| 65_I | 75_D | 1.036 | 0.20 |
| 38_T | 46_Q | 1.033 | 0.20 |
| 48_I | 113_P | 1.031 | 0.20 |
| 24_A | 73_Q | 1.030 | 0.20 |
| 5_K | 115_A | 1.029 | 0.20 |
| 37_A | 66_R | 1.016 | 0.19 |
| 24_A | 80_K | 1.010 | 0.19 |
| 50_M | 67_F | 1.009 | 0.19 |
| 50_M | 58_H | 1.009 | 0.19 |
| 42_R | 62_A | 1.006 | 0.19 |
| 18_G | 28_L | 1.001 | 0.19 |
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 | |
| 4pwuA | 4 | 0.6172 | 100 | 0.537 | Contact Map |
| 2p4eP | 2 | 0.2969 | 48.1 | 0.937 | Contact Map |
| 4m1bA | 2 | 0.4844 | 30.4 | 0.943 | Contact Map |
| 3lqvP | 2 | 0.2812 | 27.1 | 0.945 | Contact Map |
| 2vrnA | 2 | 0.7344 | 17.1 | 0.95 | Contact Map |
| 2y9jY | 24 | 0.6562 | 15.3 | 0.951 | Contact Map |
| 1uv7A | 2 | 0.3906 | 12.5 | 0.953 | Contact Map |
| 3ucpA | 1 | 0.5859 | 11.9 | 0.953 | Contact Map |
| 2gqcA | 1 | 0.5469 | 8.5 | 0.956 | Contact Map |
| 3mgkA | 2 | 0.7188 | 8.3 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)