| P49768 350-467 |
| ID: | 1416067067 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 118 (109) | ||
| Sequences: | 164 (113.6) | ||
| Seq/Len: | 1.505 | ||
| Nf(neff/√len): | 10.9 |
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: 1.505).
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 |
| 47_A | 65_I | 2.199 | 0.99 |
| 55_W | 58_T | 2.035 | 0.98 |
| 46_K | 94_L | 1.775 | 0.95 |
| 44_V | 75_L | 1.695 | 0.93 |
| 114_H | 117_Y | 1.515 | 0.87 |
| 45_G | 98_F | 1.515 | 0.87 |
| 31_K | 34_L | 1.465 | 0.84 |
| 42_V | 81_K | 1.432 | 0.83 |
| 96_F | 107_F | 1.430 | 0.82 |
| 60_A | 75_L | 1.380 | 0.79 |
| 42_V | 75_L | 1.367 | 0.78 |
| 70_C | 94_L | 1.359 | 0.78 |
| 29_G | 93_G | 1.324 | 0.75 |
| 62_F | 82_A | 1.282 | 0.72 |
| 71_L | 93_G | 1.278 | 0.71 |
| 97_Y | 101_D | 1.267 | 0.70 |
| 54_D | 98_F | 1.250 | 0.69 |
| 56_N | 98_F | 1.227 | 0.67 |
| 48_S | 104_V | 1.222 | 0.66 |
| 42_V | 69_L | 1.215 | 0.66 |
| 31_K | 42_V | 1.212 | 0.66 |
| 38_I | 44_V | 1.207 | 0.65 |
| 29_G | 55_W | 1.205 | 0.65 |
| 57_T | 60_A | 1.184 | 0.63 |
| 34_L | 76_L | 1.177 | 0.62 |
| 38_I | 95_V | 1.167 | 0.61 |
| 95_V | 103_L | 1.163 | 0.61 |
| 33_G | 40_Y | 1.158 | 0.60 |
| 32_L | 69_L | 1.151 | 0.60 |
| 47_A | 61_C | 1.149 | 0.59 |
| 54_D | 57_T | 1.148 | 0.59 |
| 57_T | 96_F | 1.144 | 0.59 |
| 41_S | 90_I | 1.144 | 0.59 |
| 113_F | 116_F | 1.137 | 0.58 |
| 75_L | 88_I | 1.135 | 0.58 |
| 71_L | 88_I | 1.122 | 0.57 |
| 44_V | 94_L | 1.106 | 0.55 |
| 32_L | 65_I | 1.105 | 0.55 |
| 38_I | 100_T | 1.105 | 0.55 |
| 64_A | 93_G | 1.104 | 0.55 |
| 9_R | 12_V | 1.101 | 0.55 |
| 82_A | 90_I | 1.098 | 0.54 |
| 105_Q | 117_Y | 1.090 | 0.53 |
| 34_L | 89_S | 1.085 | 0.53 |
| 63_V | 92_F | 1.074 | 0.52 |
| 43_L | 93_G | 1.070 | 0.51 |
| 80_K | 90_I | 1.067 | 0.51 |
| 21_A | 25_P | 1.067 | 0.51 |
| 65_I | 100_T | 1.065 | 0.51 |
| 42_V | 77_A | 1.063 | 0.51 |
| 82_A | 88_I | 1.059 | 0.50 |
| 74_L | 81_K | 1.049 | 0.49 |
| 65_I | 82_A | 1.047 | 0.49 |
| 31_K | 46_K | 1.045 | 0.49 |
| 69_L | 75_L | 1.036 | 0.48 |
| 54_D | 81_K | 1.032 | 0.47 |
| 34_L | 82_A | 1.028 | 0.47 |
| 69_L | 111_L | 1.027 | 0.47 |
| 10_A | 14_E | 1.027 | 0.47 |
| 43_L | 88_I | 1.016 | 0.46 |
| 38_I | 91_T | 1.000 | 0.44 |
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 | |
| 2kr6A | 1 | 1 | 100 | 0.117 | Contact Map |
| 4hygA | 4 | 0.6695 | 99.4 | 0.685 | Contact Map |
| 2bg9B | 1 | 0.6186 | 5 | 0.952 | Contact Map |
| 2qmwA | 2 | 0.6102 | 4.1 | 0.954 | Contact Map |
| 4k0jA | 6 | 0.8898 | 3.1 | 0.956 | Contact Map |
| 4pypA | 1 | 0.0254 | 3 | 0.957 | Contact Map |
| 2jlnA | 1 | 0.8644 | 2.7 | 0.958 | Contact Map |
| 2qmxA | 2 | 0.6525 | 2.6 | 0.958 | Contact Map |
| 4k6jA | 2 | 0.6102 | 2.1 | 0.96 | Contact Map |
| 3ne5A | 1 | 0.8898 | 2 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)