| T0836 |
| ID: | 1404168992 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 204 (166) | ||
| Sequences: | 184 (87.9) | ||
| Seq/Len: | 1.108 | ||
| Nf(neff/√len): | 6.8 |
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: 1.108).
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 | 2.443 | 0.99 |
| 62_F | 91_F | 2.246 | 0.99 |
| 99_W | 143_T | 1.929 | 0.95 |
| 50_G | 95_A | 1.902 | 0.95 |
| 95_A | 197_A | 1.859 | 0.94 |
| 180_L | 183_R | 1.782 | 0.92 |
| 91_F | 94_A | 1.765 | 0.91 |
| 61_N | 188_L | 1.749 | 0.91 |
| 50_G | 197_A | 1.733 | 0.90 |
| 132_F | 135_I | 1.590 | 0.84 |
| 56_L | 91_F | 1.590 | 0.84 |
| 95_A | 146_F | 1.582 | 0.84 |
| 114_E | 175_A | 1.533 | 0.81 |
| 115_A | 150_W | 1.498 | 0.79 |
| 154_W | 180_L | 1.488 | 0.79 |
| 50_G | 135_I | 1.487 | 0.79 |
| 142_A | 146_F | 1.484 | 0.78 |
| 154_W | 158_K | 1.444 | 0.76 |
| 75_L | 78_A | 1.433 | 0.75 |
| 47_V | 197_A | 1.394 | 0.72 |
| 137_T | 142_A | 1.384 | 0.71 |
| 50_G | 142_A | 1.384 | 0.71 |
| 95_A | 135_I | 1.346 | 0.68 |
| 65_I | 119_G | 1.345 | 0.68 |
| 178_A | 183_R | 1.337 | 0.67 |
| 100_V | 104_L | 1.337 | 0.67 |
| 62_F | 89_F | 1.335 | 0.67 |
| 95_A | 142_A | 1.327 | 0.67 |
| 156_N | 160_A | 1.323 | 0.66 |
| 47_V | 50_G | 1.296 | 0.64 |
| 64_Q | 67_V | 1.293 | 0.64 |
| 135_I | 192_M | 1.291 | 0.63 |
| 61_N | 65_I | 1.271 | 0.62 |
| 39_Q | 137_T | 1.270 | 0.62 |
| 156_N | 177_T | 1.261 | 0.61 |
| 45_L | 118_L | 1.242 | 0.59 |
| 166_A | 173_K | 1.240 | 0.59 |
| 163_I | 168_A | 1.233 | 0.58 |
| 59_Y | 190_I | 1.212 | 0.56 |
| 62_F | 158_K | 1.205 | 0.56 |
| 50_G | 195_T | 1.198 | 0.55 |
| 112_L | 164_V | 1.192 | 0.54 |
| 179_M | 183_R | 1.190 | 0.54 |
| 47_V | 193_L | 1.179 | 0.53 |
| 49_F | 193_L | 1.157 | 0.51 |
| 61_N | 89_F | 1.152 | 0.51 |
| 84_A | 161_L | 1.152 | 0.51 |
| 72_P | 89_F | 1.146 | 0.50 |
| 78_A | 83_I | 1.139 | 0.49 |
| 45_L | 101_M | 1.133 | 0.49 |
| 51_I | 133_T | 1.130 | 0.48 |
| 114_E | 179_M | 1.102 | 0.46 |
| 82_Y | 123_G | 1.100 | 0.46 |
| 68_M | 80_S | 1.094 | 0.45 |
| 51_I | 104_L | 1.093 | 0.45 |
| 60_F | 88_L | 1.092 | 0.45 |
| 61_N | 186_T | 1.089 | 0.45 |
| 73_A | 78_A | 1.085 | 0.44 |
| 156_N | 174_A | 1.082 | 0.44 |
| 62_F | 65_I | 1.081 | 0.44 |
| 156_N | 175_A | 1.080 | 0.44 |
| 161_L | 178_A | 1.079 | 0.44 |
| 64_Q | 179_M | 1.078 | 0.43 |
| 56_L | 94_A | 1.072 | 0.43 |
| 69_P | 142_A | 1.064 | 0.42 |
| 77_P | 110_G | 1.064 | 0.42 |
| 147_F | 158_K | 1.055 | 0.41 |
| 71_I | 141_L | 1.046 | 0.41 |
| 56_L | 160_A | 1.046 | 0.41 |
| 110_G | 123_G | 1.045 | 0.40 |
| 103_V | 146_F | 1.045 | 0.40 |
| 95_A | 176_K | 1.042 | 0.40 |
| 106_A | 139_M | 1.040 | 0.40 |
| 132_F | 146_F | 1.035 | 0.40 |
| 80_S | 83_I | 1.031 | 0.39 |
| 127_G | 130_M | 1.029 | 0.39 |
| 42_F | 108_N | 1.027 | 0.39 |
| 118_L | 193_L | 1.027 | 0.39 |
| 115_A | 169_D | 1.021 | 0.38 |
| 173_K | 177_T | 1.012 | 0.37 |
| 160_A | 183_R | 1.009 | 0.37 |
| 65_I | 71_I | 1.008 | 0.37 |
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 | |
| 1kqfC | 1 | 0.8873 | 4.5 | 0.974 | Contact Map |
| 1j2rA | 4 | 0.3088 | 3.1 | 0.976 | Contact Map |
| 3hd7A | 2 | 0.152 | 2.3 | 0.978 | Contact Map |
| 2hc9A | 1 | 0.3137 | 2.1 | 0.978 | Contact Map |
| 3kzwA | 12 | 0.3137 | 1.5 | 0.98 | Contact Map |
| 1c1yB | 1 | 0.2696 | 1.3 | 0.981 | Contact Map |
| 3peiA | 1 | 0.3333 | 1.3 | 0.981 | Contact Map |
| 3kr4A | 12 | 0.3039 | 1.3 | 0.981 | Contact Map |
| 1gytA | 12 | 0.299 | 1.2 | 0.981 | Contact Map |
| 4l35A | 1 | 0.7108 | 1.1 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)