| T0836 |
| ID: | 1404155991 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (159) | ||
| Sequences: | 170 (83.7) | ||
| Seq/Len: | 1.069 | ||
| Nf(neff/√len): | 6.6 |
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: 1.069).
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 |
| 49_F | 97_A | 2.436 | 0.99 |
| 99_W | 143_T | 2.068 | 0.97 |
| 62_F | 91_F | 1.949 | 0.95 |
| 91_F | 94_A | 1.849 | 0.93 |
| 180_L | 183_R | 1.812 | 0.92 |
| 95_A | 197_A | 1.792 | 0.92 |
| 132_F | 135_I | 1.741 | 0.90 |
| 50_G | 95_A | 1.725 | 0.90 |
| 61_N | 188_L | 1.676 | 0.88 |
| 154_W | 158_K | 1.664 | 0.87 |
| 95_A | 146_F | 1.656 | 0.87 |
| 121_A | 132_F | 1.639 | 0.86 |
| 156_N | 160_A | 1.576 | 0.83 |
| 100_V | 104_L | 1.555 | 0.82 |
| 178_A | 183_R | 1.546 | 0.81 |
| 56_L | 91_F | 1.497 | 0.78 |
| 142_A | 146_F | 1.489 | 0.78 |
| 166_A | 173_K | 1.488 | 0.78 |
| 50_G | 135_I | 1.468 | 0.76 |
| 50_G | 197_A | 1.460 | 0.76 |
| 61_N | 65_I | 1.452 | 0.75 |
| 95_A | 135_I | 1.444 | 0.75 |
| 137_T | 142_A | 1.382 | 0.70 |
| 72_P | 89_F | 1.379 | 0.70 |
| 95_A | 142_A | 1.375 | 0.69 |
| 154_W | 180_L | 1.344 | 0.67 |
| 156_N | 177_T | 1.333 | 0.66 |
| 39_Q | 137_T | 1.312 | 0.64 |
| 47_V | 197_A | 1.306 | 0.64 |
| 64_Q | 179_M | 1.299 | 0.63 |
| 154_W | 178_A | 1.288 | 0.62 |
| 59_Y | 190_I | 1.286 | 0.62 |
| 62_F | 89_F | 1.274 | 0.61 |
| 47_V | 193_L | 1.269 | 0.60 |
| 76_K | 91_F | 1.246 | 0.58 |
| 50_G | 142_A | 1.225 | 0.56 |
| 156_N | 174_A | 1.205 | 0.54 |
| 118_L | 193_L | 1.189 | 0.53 |
| 50_G | 195_T | 1.185 | 0.53 |
| 115_A | 150_W | 1.181 | 0.52 |
| 37_Y | 44_W | 1.180 | 0.52 |
| 114_E | 175_A | 1.174 | 0.52 |
| 173_K | 177_T | 1.160 | 0.50 |
| 160_A | 183_R | 1.154 | 0.50 |
| 163_I | 168_A | 1.153 | 0.50 |
| 84_A | 161_L | 1.147 | 0.49 |
| 118_L | 195_T | 1.134 | 0.48 |
| 62_F | 65_I | 1.133 | 0.48 |
| 56_L | 94_A | 1.126 | 0.47 |
| 51_I | 133_T | 1.117 | 0.46 |
| 50_G | 101_M | 1.115 | 0.46 |
| 65_I | 119_G | 1.113 | 0.46 |
| 45_L | 151_V | 1.108 | 0.45 |
| 39_Q | 159_I | 1.105 | 0.45 |
| 75_L | 78_A | 1.094 | 0.44 |
| 74_E | 92_R | 1.084 | 0.43 |
| 49_F | 193_L | 1.084 | 0.43 |
| 47_V | 50_G | 1.079 | 0.43 |
| 141_L | 146_F | 1.078 | 0.43 |
| 47_V | 79_V | 1.068 | 0.42 |
| 61_N | 186_T | 1.065 | 0.41 |
| 97_A | 142_A | 1.052 | 0.40 |
| 79_V | 193_L | 1.044 | 0.39 |
| 60_F | 88_L | 1.040 | 0.39 |
| 79_V | 144_V | 1.038 | 0.39 |
| 44_W | 172_A | 1.030 | 0.38 |
| 51_I | 91_F | 1.028 | 0.38 |
| 71_I | 141_L | 1.026 | 0.38 |
| 116_F | 178_A | 1.026 | 0.38 |
| 160_A | 174_A | 1.026 | 0.38 |
| 64_Q | 103_V | 1.024 | 0.38 |
| 174_A | 188_L | 1.023 | 0.38 |
| 156_N | 175_A | 1.023 | 0.38 |
| 75_L | 80_S | 1.018 | 0.37 |
| 114_E | 179_M | 1.017 | 0.37 |
| 64_Q | 183_R | 1.014 | 0.37 |
| 135_I | 142_A | 1.005 | 0.36 |
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 | |
| 2hc9A | 1 | 0.2941 | 2.8 | 0.977 | Contact Map |
| 1kqfC | 1 | 0.8873 | 2.5 | 0.977 | Contact Map |
| 3hd7A | 2 | 0.152 | 2.3 | 0.977 | Contact Map |
| 1j2rA | 4 | 0.3088 | 2 | 0.978 | Contact Map |
| 3kzwA | 12 | 0.3137 | 1.7 | 0.979 | Contact Map |
| 3peiA | 1 | 0.3333 | 1.6 | 0.979 | Contact Map |
| 1c1yB | 1 | 0.2598 | 1.3 | 0.98 | Contact Map |
| 3j01B | 1 | 0.5686 | 1.3 | 0.98 | Contact Map |
| 2kluA | 1 | 0.3137 | 1.3 | 0.981 | Contact Map |
| 1ji6A | 1 | 0.402 | 1.3 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)