| T0789-D2 152-277 8 iterations |
| ID: | 1448565718 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 126 (126) | ||
| Sequences: | 310 (252.4) | ||
| Seq/Len: | 2.460 | ||
| Nf(neff/√len): | 22.5 |
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: 2.460).
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 | 3.588 | 1.00 |
| 7_A | 89_V | 2.380 | 1.00 |
| 60_V | 81_I | 2.293 | 1.00 |
| 17_R | 100_E | 2.052 | 1.00 |
| 55_G | 85_S | 1.688 | 0.97 |
| 81_I | 89_V | 1.683 | 0.97 |
| 98_D | 104_T | 1.606 | 0.96 |
| 52_V | 56_P | 1.483 | 0.93 |
| 102_V | 112_A | 1.470 | 0.93 |
| 82_V | 91_V | 1.465 | 0.93 |
| 19_G | 22_A | 1.461 | 0.93 |
| 51_S | 89_V | 1.390 | 0.90 |
| 57_R | 91_V | 1.374 | 0.89 |
| 66_C | 126_D | 1.357 | 0.88 |
| 81_I | 109_T | 1.352 | 0.88 |
| 85_S | 108_G | 1.335 | 0.87 |
| 9_F | 107_P | 1.300 | 0.85 |
| 64_A | 114_A | 1.288 | 0.85 |
| 17_R | 84_T | 1.268 | 0.83 |
| 60_V | 89_V | 1.257 | 0.83 |
| 3_H | 122_A | 1.248 | 0.82 |
| 100_E | 118_Q | 1.228 | 0.81 |
| 7_A | 60_V | 1.216 | 0.80 |
| 48_V | 84_T | 1.200 | 0.78 |
| 65_G | 83_D | 1.199 | 0.78 |
| 14_L | 41_I | 1.196 | 0.78 |
| 22_A | 125_P | 1.195 | 0.78 |
| 32_L | 81_I | 1.192 | 0.78 |
| 80_S | 97_F | 1.180 | 0.77 |
| 18_V | 42_P | 1.172 | 0.76 |
| 8_R | 49_V | 1.170 | 0.76 |
| 45_A | 72_H | 1.165 | 0.75 |
| 53_F | 115_V | 1.162 | 0.75 |
| 98_D | 101_W | 1.146 | 0.74 |
| 52_V | 116_A | 1.133 | 0.73 |
| 4_R | 118_Q | 1.132 | 0.73 |
| 52_V | 105_F | 1.130 | 0.72 |
| 8_R | 85_S | 1.120 | 0.71 |
| 2_A | 82_V | 1.110 | 0.70 |
| 19_G | 46_R | 1.110 | 0.70 |
| 3_H | 44_S | 1.105 | 0.70 |
| 40_G | 61_E | 1.096 | 0.69 |
| 49_V | 82_V | 1.085 | 0.68 |
| 48_V | 52_V | 1.085 | 0.68 |
| 3_H | 110_P | 1.084 | 0.68 |
| 64_A | 70_G | 1.084 | 0.68 |
| 45_A | 121_T | 1.083 | 0.68 |
| 17_R | 38_Y | 1.071 | 0.66 |
| 60_V | 108_G | 1.067 | 0.66 |
| 9_F | 60_V | 1.062 | 0.65 |
| 61_E | 116_A | 1.060 | 0.65 |
| 45_A | 112_A | 1.052 | 0.64 |
| 42_P | 48_V | 1.052 | 0.64 |
| 2_A | 72_H | 1.048 | 0.64 |
| 109_T | 116_A | 1.047 | 0.64 |
| 1_L | 59_Y | 1.047 | 0.64 |
| 83_D | 107_P | 1.041 | 0.63 |
| 9_F | 89_V | 1.040 | 0.63 |
| 109_T | 112_A | 1.032 | 0.62 |
| 96_A | 119_T | 1.030 | 0.62 |
| 2_A | 41_I | 1.026 | 0.62 |
| 62_I | 112_A | 1.025 | 0.61 |
| 63_V | 75_T | 1.025 | 0.61 |
| 81_I | 108_G | 1.024 | 0.61 |
| 5_P | 83_D | 1.023 | 0.61 |
| 61_E | 93_P | 1.013 | 0.60 |
| 9_F | 58_S | 1.006 | 0.59 |
| 12_F | 119_T | 1.005 | 0.59 |
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 | 0.108 | Contact Map |
| 4w4iA | 1 | 1 | 99.9 | 0.116 | Contact Map |
| 4w4lC | 1 | 1 | 99.9 | 0.134 | Contact Map |
| 3kfwX | 1 | 0.881 | 7.4 | 0.912 | Contact Map |
| 3nn1A | 5 | 0.3889 | 5.2 | 0.918 | Contact Map |
| 4goqA | 5 | 0.6667 | 4.2 | 0.922 | Contact Map |
| 1t0tV | 5 | 0.3492 | 3.9 | 0.923 | Contact Map |
| 1ez0A | 4 | 0.4127 | 3.6 | 0.924 | Contact Map |
| 3sb1A | 2 | 0.9048 | 3.5 | 0.924 | Contact Map |
| 4wwsA | 5 | 0.3571 | 3.4 | 0.925 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)