| T0789-D2 152-277 |
| ID: | 1448557484 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 126 (126) | ||
| Sequences: | 236 (184.6) | ||
| Seq/Len: | 1.873 | ||
| Nf(neff/√len): | 16.4 |
HHblits Results: (2015_06)
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: 1.873).
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 |
| 83_D | 88_R | 3.117 | 1.00 |
| 17_R | 100_E | 2.489 | 1.00 |
| 7_A | 89_V | 2.167 | 0.99 |
| 98_D | 104_T | 1.980 | 0.99 |
| 51_S | 89_V | 1.844 | 0.98 |
| 60_V | 81_I | 1.664 | 0.95 |
| 2_A | 82_V | 1.479 | 0.89 |
| 22_A | 32_L | 1.461 | 0.88 |
| 6_P | 86_A | 1.454 | 0.88 |
| 14_L | 114_A | 1.434 | 0.87 |
| 66_C | 126_D | 1.408 | 0.86 |
| 48_V | 84_T | 1.372 | 0.84 |
| 81_I | 117_I | 1.318 | 0.80 |
| 100_E | 118_Q | 1.318 | 0.80 |
| 81_I | 108_G | 1.316 | 0.80 |
| 45_A | 112_A | 1.303 | 0.79 |
| 82_V | 91_V | 1.288 | 0.78 |
| 22_A | 125_P | 1.286 | 0.78 |
| 9_F | 107_P | 1.257 | 0.76 |
| 13_S | 94_S | 1.254 | 0.76 |
| 61_E | 116_A | 1.242 | 0.75 |
| 7_A | 60_V | 1.235 | 0.74 |
| 102_V | 112_A | 1.229 | 0.73 |
| 98_D | 101_W | 1.226 | 0.73 |
| 70_G | 106_S | 1.225 | 0.73 |
| 45_A | 72_H | 1.225 | 0.73 |
| 14_L | 86_A | 1.221 | 0.73 |
| 17_R | 84_T | 1.221 | 0.73 |
| 81_I | 109_T | 1.219 | 0.73 |
| 24_E | 45_A | 1.214 | 0.72 |
| 20_A | 115_V | 1.201 | 0.71 |
| 19_G | 46_R | 1.196 | 0.71 |
| 14_L | 110_P | 1.182 | 0.69 |
| 57_R | 91_V | 1.139 | 0.65 |
| 13_S | 25_R | 1.124 | 0.64 |
| 3_H | 122_A | 1.109 | 0.62 |
| 76_E | 123_C | 1.109 | 0.62 |
| 76_E | 85_S | 1.105 | 0.62 |
| 80_S | 97_F | 1.101 | 0.61 |
| 77_V | 123_C | 1.095 | 0.61 |
| 64_A | 70_G | 1.073 | 0.58 |
| 84_T | 100_E | 1.070 | 0.58 |
| 2_A | 5_P | 1.068 | 0.58 |
| 63_V | 75_T | 1.064 | 0.57 |
| 66_C | 125_P | 1.064 | 0.57 |
| 9_F | 59_Y | 1.062 | 0.57 |
| 16_T | 28_S | 1.061 | 0.57 |
| 61_E | 109_T | 1.060 | 0.57 |
| 15_P | 40_G | 1.058 | 0.57 |
| 1_L | 113_I | 1.055 | 0.56 |
| 12_F | 79_L | 1.054 | 0.56 |
| 9_F | 49_V | 1.054 | 0.56 |
| 55_G | 85_S | 1.053 | 0.56 |
| 6_P | 29_G | 1.051 | 0.56 |
| 42_P | 48_V | 1.039 | 0.55 |
| 19_G | 91_V | 1.038 | 0.55 |
| 68_R | 85_S | 1.037 | 0.54 |
| 50_E | 102_V | 1.030 | 0.54 |
| 12_F | 49_V | 1.026 | 0.53 |
| 5_P | 83_D | 1.024 | 0.53 |
| 32_L | 117_I | 1.021 | 0.53 |
| 23_D | 112_A | 1.016 | 0.52 |
| 1_L | 80_S | 1.012 | 0.52 |
| 63_V | 121_T | 1.012 | 0.52 |
| 3_H | 44_S | 1.007 | 0.51 |
| 18_V | 54_S | 1.004 | 0.51 |
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 | |
| 4w4iA | 1 | 1 | 99.9 | 0.161 | Contact Map |
| 4l4wA | 2 | 1 | 99.9 | 0.161 | Contact Map |
| 4w4lC | 1 | 1 | 99.9 | 0.189 | Contact Map |
| 3kfwX | 1 | 0.881 | 13.1 | 0.91 | Contact Map |
| 4goqA | 5 | 0.6667 | 9.7 | 0.915 | Contact Map |
| 3qsjA | 1 | 0.4683 | 5.7 | 0.924 | Contact Map |
| 2knrA | 1 | 0.6667 | 4.7 | 0.927 | Contact Map |
| 3nn1A | 5 | 0.3889 | 3.9 | 0.93 | Contact Map |
| 2rrkA | 1 | 0.4524 | 3.9 | 0.93 | Contact Map |
| 1ez0A | 4 | 0.4127 | 3.7 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)