| T0790 136-265 |
| ID: | 1417687792 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (130) | ||
| Sequences: | 436 (384.9) | ||
| Seq/Len: | 3.354 | ||
| Nf(neff/√len): | 33.8 |
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: 3.354).
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 |
| 7_A | 89_I | 4.169 | 1.00 |
| 83_D | 88_R | 3.247 | 1.00 |
| 60_V | 81_I | 2.503 | 1.00 |
| 9_F | 89_I | 2.179 | 1.00 |
| 81_I | 89_I | 1.987 | 1.00 |
| 7_A | 116_A | 1.749 | 0.99 |
| 109_S | 112_A | 1.515 | 0.97 |
| 98_D | 104_T | 1.478 | 0.96 |
| 17_A | 117_V | 1.463 | 0.96 |
| 60_V | 64_A | 1.455 | 0.96 |
| 55_G | 85_P | 1.407 | 0.94 |
| 8_R | 112_A | 1.336 | 0.92 |
| 64_A | 70_G | 1.325 | 0.92 |
| 109_S | 116_A | 1.305 | 0.91 |
| 89_I | 108_G | 1.294 | 0.91 |
| 60_V | 83_D | 1.288 | 0.90 |
| 37_E | 43_P | 1.277 | 0.90 |
| 98_D | 101_W | 1.265 | 0.89 |
| 6_P | 110_A | 1.262 | 0.89 |
| 49_V | 82_I | 1.259 | 0.89 |
| 9_F | 107_P | 1.249 | 0.88 |
| 9_F | 108_G | 1.241 | 0.88 |
| 102_I | 112_A | 1.234 | 0.88 |
| 59_Y | 90_L | 1.232 | 0.87 |
| 17_A | 100_E | 1.218 | 0.87 |
| 32_L | 38_F | 1.199 | 0.85 |
| 108_G | 112_A | 1.197 | 0.85 |
| 61_E | 120_L | 1.186 | 0.85 |
| 22_A | 32_L | 1.178 | 0.84 |
| 22_A | 40_G | 1.165 | 0.83 |
| 6_P | 58_T | 1.155 | 0.82 |
| 13_A | 102_I | 1.151 | 0.82 |
| 28_N | 31_P | 1.148 | 0.82 |
| 67_H | 71_H | 1.140 | 0.81 |
| 17_A | 21_R | 1.138 | 0.81 |
| 5_K | 88_R | 1.135 | 0.81 |
| 3_G | 49_V | 1.131 | 0.81 |
| 53_F | 103_S | 1.130 | 0.81 |
| 52_V | 116_A | 1.109 | 0.79 |
| 20_A | 69_D | 1.108 | 0.79 |
| 2_S | 60_V | 1.107 | 0.79 |
| 89_I | 109_S | 1.105 | 0.78 |
| 63_V | 119_R | 1.100 | 0.78 |
| 51_S | 86_H | 1.099 | 0.78 |
| 61_E | 65_G | 1.098 | 0.78 |
| 15_P | 105_F | 1.096 | 0.78 |
| 60_V | 67_H | 1.088 | 0.77 |
| 73_V | 108_G | 1.078 | 0.76 |
| 6_P | 29_G | 1.078 | 0.76 |
| 19_G | 105_F | 1.077 | 0.76 |
| 29_G | 32_L | 1.071 | 0.75 |
| 81_I | 108_G | 1.068 | 0.75 |
| 9_F | 70_G | 1.064 | 0.75 |
| 59_Y | 95_K | 1.062 | 0.74 |
| 14_L | 19_G | 1.055 | 0.74 |
| 125_P | 129_W | 1.053 | 0.74 |
| 52_V | 56_R | 1.052 | 0.74 |
| 78_G | 105_F | 1.047 | 0.73 |
| 13_A | 105_F | 1.042 | 0.72 |
| 2_S | 97_F | 1.036 | 0.72 |
| 54_D | 113_I | 1.024 | 0.71 |
| 52_V | 62_I | 1.023 | 0.71 |
| 5_K | 85_P | 1.022 | 0.70 |
| 12_F | 105_F | 1.008 | 0.69 |
| 31_P | 113_I | 1.001 | 0.68 |
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 | |
| 4l4wA | 2 | 1 | 99.9 | 0.11 | Contact Map |
| 4kxrC | 1 | 0.9615 | 99.9 | 0.115 | Contact Map |
| 3omdA | 2 | 0.6923 | 6.1 | 0.913 | Contact Map |
| 1ez0A | 4 | 0.3231 | 3.8 | 0.921 | Contact Map |
| 3a3dA | 2 | 0.4923 | 3.8 | 0.921 | Contact Map |
| 3v39A | 1 | 0.4154 | 3.5 | 0.923 | Contact Map |
| 3sb1A | 2 | 0.8692 | 3.2 | 0.924 | Contact Map |
| 3b4wA | 1 | 0.4769 | 2.8 | 0.927 | Contact Map |
| 3c3dA | 4 | 0.4846 | 2.4 | 0.929 | Contact Map |
| 3proC | 2 | 0.7154 | 2.4 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)