| CDOM_F |
| ID: | 1498552128 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (139) | ||
| Sequences: | 309 (236) | ||
| Seq/Len: | 2.223 | ||
| Nf(neff/√len): | 20.0 |
Jackhmmer Results: (2016_04)
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: 2.223).
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 |
| 120_L | 124_R | 2.248 | 1.00 |
| 68_R | 88_D | 1.927 | 0.99 |
| 73_I | 126_V | 1.792 | 0.98 |
| 80_V | 116_N | 1.688 | 0.97 |
| 124_R | 128_D | 1.489 | 0.92 |
| 69_V | 99_A | 1.485 | 0.92 |
| 78_N | 81_L | 1.481 | 0.92 |
| 32_P | 35_Q | 1.406 | 0.89 |
| 20_A | 76_L | 1.384 | 0.88 |
| 34_S | 37_T | 1.316 | 0.84 |
| 68_R | 114_E | 1.314 | 0.84 |
| 64_D | 78_N | 1.308 | 0.84 |
| 48_R | 51_L | 1.297 | 0.83 |
| 8_I | 54_A | 1.294 | 0.83 |
| 80_V | 87_T | 1.274 | 0.81 |
| 71_E | 113_M | 1.263 | 0.81 |
| 83_K | 87_T | 1.259 | 0.80 |
| 106_F | 127_I | 1.252 | 0.80 |
| 109_V | 118_Y | 1.250 | 0.80 |
| 7_C | 21_W | 1.238 | 0.79 |
| 113_M | 137_Q | 1.227 | 0.78 |
| 121_G | 124_R | 1.216 | 0.77 |
| 39_Q | 44_P | 1.202 | 0.76 |
| 111_S | 114_E | 1.200 | 0.76 |
| 86_L | 90_Q | 1.196 | 0.75 |
| 16_L | 113_M | 1.195 | 0.75 |
| 124_R | 129_L | 1.193 | 0.75 |
| 36_R | 44_P | 1.191 | 0.75 |
| 83_K | 90_Q | 1.187 | 0.75 |
| 88_D | 106_F | 1.186 | 0.75 |
| 132_K | 135_M | 1.184 | 0.74 |
| 17_S | 24_K | 1.168 | 0.73 |
| 30_T | 34_S | 1.168 | 0.73 |
| 75_D | 85_A | 1.165 | 0.73 |
| 40_E | 44_P | 1.157 | 0.72 |
| 96_K | 135_M | 1.155 | 0.72 |
| 7_C | 69_V | 1.142 | 0.71 |
| 73_I | 139_V | 1.140 | 0.70 |
| 8_I | 92_L | 1.130 | 0.69 |
| 85_A | 121_G | 1.127 | 0.69 |
| 67_R | 93_R | 1.126 | 0.69 |
| 93_R | 120_L | 1.124 | 0.69 |
| 16_L | 80_V | 1.118 | 0.68 |
| 35_Q | 43_P | 1.117 | 0.68 |
| 90_Q | 128_D | 1.115 | 0.68 |
| 45_R | 48_R | 1.107 | 0.67 |
| 16_L | 117_H | 1.104 | 0.67 |
| 11_D | 103_T | 1.097 | 0.66 |
| 72_L | 117_H | 1.097 | 0.66 |
| 100_F | 130_F | 1.096 | 0.66 |
| 78_N | 86_L | 1.094 | 0.66 |
| 68_R | 71_E | 1.080 | 0.64 |
| 113_M | 116_N | 1.077 | 0.64 |
| 118_Y | 130_F | 1.076 | 0.64 |
| 75_D | 126_V | 1.073 | 0.64 |
| 46_A | 49_P | 1.056 | 0.62 |
| 35_Q | 42_P | 1.055 | 0.62 |
| 83_K | 117_H | 1.053 | 0.61 |
| 25_T | 103_T | 1.050 | 0.61 |
| 96_K | 99_A | 1.044 | 0.60 |
| 3_S | 107_K | 1.042 | 0.60 |
| 3_S | 136_R | 1.041 | 0.60 |
| 47_A | 51_L | 1.038 | 0.60 |
| 40_E | 43_P | 1.037 | 0.60 |
| 89_L | 130_F | 1.037 | 0.60 |
| 67_R | 71_E | 1.036 | 0.60 |
| 67_R | 128_D | 1.034 | 0.59 |
| 92_L | 118_Y | 1.031 | 0.59 |
| 84_K | 106_F | 1.029 | 0.59 |
| 4_L | 8_I | 1.028 | 0.59 |
| 8_I | 79_M | 1.026 | 0.58 |
| 49_P | 52_E | 1.016 | 0.57 |
| 82_Y | 121_G | 1.016 | 0.57 |
| 32_P | 38_A | 1.015 | 0.57 |
| 94_A | 110_M | 1.011 | 0.57 |
| 77_G | 116_N | 1.008 | 0.56 |
| 25_T | 28_S | 1.006 | 0.56 |
| 11_D | 59_L | 1.006 | 0.56 |
| 4_L | 107_K | 1.006 | 0.56 |
| 79_M | 93_R | 1.006 | 0.56 |
| 67_R | 87_T | 1.005 | 0.56 |
| 90_Q | 125_M | 1.001 | 0.56 |
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 | |
| 4imiA | 2 | 0.5612 | 17.6 | 0.927 | Contact Map |
| 3o2tA | 1 | 0.5252 | 16.9 | 0.927 | Contact Map |
| 3axjB | 1 | 0.6978 | 12.7 | 0.931 | Contact Map |
| 3ldzA | 4 | 0.6547 | 10.4 | 0.934 | Contact Map |
| 3hw5A | 4 | 0.5252 | 9.2 | 0.935 | Contact Map |
| 1vbgA | 1 | 0.3381 | 8.7 | 0.936 | Contact Map |
| 2dy0A | 2 | 0.3957 | 7.9 | 0.937 | Contact Map |
| 2f9yB | 1 | 0.3381 | 7.2 | 0.938 | Contact Map |
| 2gx1A | 1 | 0.0719 | 6.8 | 0.939 | Contact Map |
| 3ml6A | 6 | 0.4964 | 6 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)