| roll 300-470 20-160 |
| ID: | 1384279060 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (141) | ||
| Sequences: | 145 (104.9) | ||
| Seq/Len: | 1.028 | ||
| Nf(neff/√len): | 8.8 |
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: 1.028).
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 |
| 18_C | 23_C | 3.037 | 1.00 |
| 5_F | 8_L | 1.930 | 0.94 |
| 102_L | 133_T | 1.894 | 0.94 |
| 49_T | 52_G | 1.845 | 0.93 |
| 131_V | 134_V | 1.782 | 0.91 |
| 91_T | 103_L | 1.687 | 0.87 |
| 101_V | 134_V | 1.642 | 0.85 |
| 116_S | 122_F | 1.585 | 0.83 |
| 22_L | 138_G | 1.428 | 0.72 |
| 73_G | 102_L | 1.423 | 0.72 |
| 122_F | 133_T | 1.420 | 0.72 |
| 128_S | 141_Y | 1.420 | 0.72 |
| 124_L | 140_L | 1.391 | 0.70 |
| 16_T | 91_T | 1.352 | 0.66 |
| 97_V | 136_L | 1.339 | 0.65 |
| 88_L | 96_Y | 1.325 | 0.64 |
| 8_L | 123_S | 1.323 | 0.64 |
| 40_A | 96_Y | 1.318 | 0.64 |
| 66_T | 110_P | 1.305 | 0.62 |
| 22_L | 71_T | 1.254 | 0.58 |
| 29_K | 34_I | 1.245 | 0.57 |
| 49_T | 53_R | 1.225 | 0.55 |
| 124_L | 127_T | 1.224 | 0.55 |
| 18_C | 133_T | 1.223 | 0.55 |
| 6_V | 10_G | 1.219 | 0.55 |
| 57_Q | 90_G | 1.217 | 0.54 |
| 51_E | 56_L | 1.196 | 0.52 |
| 19_Q | 43_A | 1.187 | 0.52 |
| 47_L | 55_Y | 1.186 | 0.52 |
| 130_P | 137_F | 1.185 | 0.51 |
| 1_D | 28_Y | 1.183 | 0.51 |
| 3_F | 58_I | 1.167 | 0.50 |
| 20_K | 78_T | 1.149 | 0.48 |
| 124_L | 134_V | 1.142 | 0.47 |
| 7_K | 60_T | 1.141 | 0.47 |
| 56_L | 76_A | 1.128 | 0.46 |
| 18_C | 83_F | 1.126 | 0.46 |
| 26_L | 141_Y | 1.123 | 0.46 |
| 23_C | 83_F | 1.111 | 0.45 |
| 80_S | 129_G | 1.110 | 0.44 |
| 126_P | 136_L | 1.105 | 0.44 |
| 4_T | 141_Y | 1.105 | 0.44 |
| 69_L | 92_F | 1.102 | 0.44 |
| 13_G | 41_L | 1.100 | 0.43 |
| 3_F | 67_T | 1.098 | 0.43 |
| 21_D | 43_A | 1.096 | 0.43 |
| 133_T | 137_F | 1.092 | 0.43 |
| 124_L | 133_T | 1.092 | 0.43 |
| 87_S | 91_T | 1.092 | 0.43 |
| 15_Y | 141_Y | 1.085 | 0.42 |
| 22_L | 63_K | 1.084 | 0.42 |
| 127_T | 137_F | 1.083 | 0.42 |
| 40_A | 48_H | 1.077 | 0.41 |
| 25_H | 86_F | 1.062 | 0.40 |
| 28_Y | 57_Q | 1.059 | 0.40 |
| 130_P | 136_L | 1.050 | 0.39 |
| 39_Y | 86_F | 1.049 | 0.39 |
| 75_S | 105_E | 1.049 | 0.39 |
| 4_T | 90_G | 1.047 | 0.39 |
| 1_D | 79_A | 1.047 | 0.39 |
| 45_D | 55_Y | 1.045 | 0.39 |
| 17_V | 45_D | 1.043 | 0.38 |
| 23_C | 133_T | 1.039 | 0.38 |
| 27_S | 125_K | 1.036 | 0.38 |
| 19_Q | 39_Y | 1.027 | 0.37 |
| 11_V | 77_E | 1.024 | 0.37 |
| 17_V | 43_A | 1.024 | 0.37 |
| 15_Y | 31_S | 1.022 | 0.37 |
| 15_Y | 74_D | 1.017 | 0.36 |
| 44_F | 88_L | 1.016 | 0.36 |
| 49_T | 106_N | 1.014 | 0.36 |
| 115_V | 121_L | 1.014 | 0.36 |
| 100_E | 133_T | 1.012 | 0.36 |
| 21_D | 108_L | 1.011 | 0.36 |
| 86_F | 107_Q | 1.007 | 0.35 |
| 134_V | 141_Y | 1.006 | 0.35 |
| 89_S | 121_L | 1.003 | 0.35 |
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 | |
| 4m70E | 4 | 0.234 | 2.7 | 0.958 | Contact Map |
| 4m70R | 1 | 0.0426 | 2.5 | 0.959 | Contact Map |
| 1v9vA | 1 | 0.4397 | 2.3 | 0.96 | Contact Map |
| 3aa0A | 1 | 0.9433 | 1.8 | 0.962 | Contact Map |
| 2dyuA | 2 | 0.4255 | 1.3 | 0.965 | Contact Map |
| 3ncxA | 2 | 0.4326 | 1.1 | 0.967 | Contact Map |
| 2r0hA | 4 | 0.4539 | 1.1 | 0.967 | Contact Map |
| 3r07C | 1 | 0.2624 | 1.1 | 0.967 | Contact Map |
| 2kaoA | 1 | 0.6241 | 1 | 0.967 | Contact Map |
| 3vpjE | 4 | 0.5035 | 1 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)