| T0830 400-575 -force run |
| ID: | 1405373923 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (170) | ||
| Sequences: | 76 (60.2) | ||
| Seq/Len: | 0.447 | ||
| Nf(neff/√len): | 4.6 |
Jackhmmer Results: (2014_04_16)
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: 0.447).
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 |
| 71_I | 165_V | 1.956 | 0.81 |
| 72_A | 112_A | 1.801 | 0.73 |
| 160_D | 163_R | 1.799 | 0.73 |
| 77_P | 151_T | 1.682 | 0.66 |
| 20_L | 68_A | 1.648 | 0.64 |
| 115_E | 118_R | 1.642 | 0.63 |
| 54_G | 154_M | 1.605 | 0.61 |
| 137_M | 156_V | 1.584 | 0.59 |
| 4_Y | 10_W | 1.560 | 0.57 |
| 23_A | 157_V | 1.556 | 0.57 |
| 41_A | 97_H | 1.489 | 0.52 |
| 117_Q | 120_V | 1.487 | 0.52 |
| 54_G | 117_Q | 1.470 | 0.51 |
| 24_V | 124_D | 1.455 | 0.50 |
| 99_L | 104_Q | 1.443 | 0.49 |
| 40_Y | 89_H | 1.441 | 0.48 |
| 124_D | 128_K | 1.430 | 0.48 |
| 37_V | 167_A | 1.423 | 0.47 |
| 69_P | 73_Q | 1.414 | 0.46 |
| 148_L | 157_V | 1.391 | 0.45 |
| 97_H | 158_A | 1.363 | 0.43 |
| 40_Y | 87_L | 1.323 | 0.40 |
| 127_T | 152_L | 1.306 | 0.39 |
| 107_E | 110_F | 1.299 | 0.38 |
| 11_V | 27_L | 1.293 | 0.38 |
| 92_P | 119_V | 1.279 | 0.37 |
| 29_L | 43_G | 1.272 | 0.36 |
| 55_H | 115_E | 1.268 | 0.36 |
| 88_D | 108_L | 1.267 | 0.36 |
| 5_R | 15_F | 1.253 | 0.35 |
| 41_A | 95_L | 1.245 | 0.34 |
| 119_V | 157_V | 1.237 | 0.34 |
| 6_A | 157_V | 1.233 | 0.34 |
| 105_A | 112_A | 1.233 | 0.34 |
| 18_M | 42_M | 1.230 | 0.33 |
| 106_D | 160_D | 1.214 | 0.32 |
| 140_M | 167_A | 1.214 | 0.32 |
| 84_V | 116_P | 1.205 | 0.32 |
| 51_A | 117_Q | 1.204 | 0.32 |
| 64_G | 160_D | 1.196 | 0.31 |
| 110_F | 119_V | 1.189 | 0.31 |
| 124_D | 167_A | 1.188 | 0.31 |
| 47_G | 139_V | 1.188 | 0.31 |
| 6_A | 77_P | 1.184 | 0.30 |
| 105_A | 109_T | 1.176 | 0.30 |
| 131_K | 165_V | 1.174 | 0.30 |
| 76_T | 126_F | 1.159 | 0.29 |
| 37_V | 144_T | 1.159 | 0.29 |
| 21_G | 43_G | 1.156 | 0.29 |
| 87_L | 108_L | 1.146 | 0.28 |
| 89_H | 107_E | 1.145 | 0.28 |
| 56_E | 152_L | 1.145 | 0.28 |
| 82_Y | 116_P | 1.144 | 0.28 |
| 2_S | 109_T | 1.143 | 0.28 |
| 62_A | 99_L | 1.140 | 0.28 |
| 17_V | 149_A | 1.134 | 0.27 |
| 95_L | 126_F | 1.133 | 0.27 |
| 55_H | 106_D | 1.133 | 0.27 |
| 11_V | 72_A | 1.130 | 0.27 |
| 101_M | 146_L | 1.124 | 0.27 |
| 141_S | 157_V | 1.121 | 0.27 |
| 37_V | 120_V | 1.120 | 0.26 |
| 77_P | 155_Y | 1.113 | 0.26 |
| 123_V | 132_N | 1.113 | 0.26 |
| 103_G | 108_L | 1.110 | 0.26 |
| 136_A | 154_M | 1.099 | 0.25 |
| 89_H | 101_M | 1.096 | 0.25 |
| 63_S | 88_D | 1.087 | 0.25 |
| 73_Q | 152_L | 1.082 | 0.24 |
| 72_A | 86_M | 1.082 | 0.24 |
| 51_A | 87_L | 1.079 | 0.24 |
| 15_F | 89_H | 1.077 | 0.24 |
| 2_S | 93_F | 1.070 | 0.24 |
| 27_L | 164_V | 1.067 | 0.23 |
| 133_G | 169_V | 1.057 | 0.23 |
| 28_L | 37_V | 1.052 | 0.23 |
| 88_D | 107_E | 1.044 | 0.22 |
| 140_M | 166_V | 1.043 | 0.22 |
| 67_I | 145_Y | 1.040 | 0.22 |
| 38_A | 104_Q | 1.031 | 0.22 |
| 6_A | 30_R | 1.030 | 0.22 |
| 64_G | 163_R | 1.030 | 0.22 |
| 75_L | 78_E | 1.028 | 0.21 |
| 82_Y | 122_D | 1.027 | 0.21 |
| 86_M | 112_A | 1.025 | 0.21 |
| 13_V | 150_P | 1.019 | 0.21 |
| 81_L | 159_R | 1.016 | 0.21 |
| 38_A | 122_D | 1.015 | 0.21 |
| 75_L | 137_M | 1.009 | 0.21 |
| 15_F | 87_L | 1.008 | 0.20 |
| 59_G | 110_F | 1.003 | 0.20 |
| 56_E | 160_D | 1.001 | 0.20 |
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 | |
| 2l5bA | 1 | 0.1705 | 17.1 | 0.96 | Contact Map |
| 3mxtA | 1 | 0.3466 | 9.3 | 0.964 | Contact Map |
| 4z0nA | 1 | 0.5398 | 6.9 | 0.966 | Contact Map |
| 2fx5A | 1 | 0.733 | 5.3 | 0.968 | Contact Map |
| 1cz3A | 2 | 0.4091 | 5 | 0.968 | Contact Map |
| 2aznA | 6 | 0.4545 | 4.6 | 0.969 | Contact Map |
| 4nfuA | 1 | 0.892 | 3.9 | 0.97 | Contact Map |
| 4b19A | 1 | 0.1705 | 3.9 | 0.97 | Contact Map |
| 1kmvA | 1 | 0.4318 | 3.7 | 0.97 | Contact Map |
| 1hdgO | 2 | 0.6534 | 3.2 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)