| T0842 |
| ID: | 1404411904 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (128) | ||
| Sequences: | 169 (150.8) | ||
| Seq/Len: | 1.320 | ||
| Nf(neff/√len): | 13.3 |
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: 1.320).
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 |
| 95_K | 103_E | 2.671 | 1.00 |
| 48_V | 87_A | 2.235 | 0.99 |
| 45_C | 55_L | 1.858 | 0.95 |
| 99_R | 102_A | 1.733 | 0.93 |
| 49_Y | 57_E | 1.704 | 0.92 |
| 24_I | 124_Q | 1.635 | 0.90 |
| 57_E | 96_T | 1.612 | 0.89 |
| 17_P | 137_R | 1.490 | 0.83 |
| 40_E | 92_C | 1.488 | 0.83 |
| 60_Q | 72_L | 1.458 | 0.81 |
| 44_W | 105_G | 1.431 | 0.79 |
| 120_V | 127_I | 1.425 | 0.79 |
| 62_V | 113_L | 1.422 | 0.79 |
| 35_Q | 105_G | 1.417 | 0.78 |
| 73_S | 120_V | 1.386 | 0.76 |
| 17_P | 46_K | 1.363 | 0.75 |
| 28_M | 54_V | 1.345 | 0.73 |
| 32_P | 41_V | 1.323 | 0.71 |
| 38_Q | 49_Y | 1.305 | 0.70 |
| 134_E | 137_R | 1.272 | 0.67 |
| 34_V | 73_S | 1.268 | 0.67 |
| 23_E | 131_P | 1.267 | 0.67 |
| 23_E | 127_I | 1.266 | 0.67 |
| 39_Q | 126_N | 1.265 | 0.66 |
| 111_Q | 117_T | 1.259 | 0.66 |
| 48_V | 94_L | 1.246 | 0.65 |
| 131_P | 135_A | 1.237 | 0.64 |
| 88_G | 102_A | 1.233 | 0.64 |
| 34_V | 122_Q | 1.220 | 0.62 |
| 49_Y | 76_V | 1.206 | 0.61 |
| 79_N | 83_V | 1.186 | 0.59 |
| 104_E | 122_Q | 1.174 | 0.58 |
| 61_E | 64_Q | 1.167 | 0.57 |
| 25_A | 62_V | 1.164 | 0.57 |
| 36_A | 40_E | 1.135 | 0.54 |
| 87_A | 102_A | 1.126 | 0.53 |
| 59_M | 112_A | 1.125 | 0.53 |
| 72_L | 82_S | 1.114 | 0.52 |
| 66_P | 117_T | 1.105 | 0.51 |
| 35_Q | 108_H | 1.097 | 0.50 |
| 24_I | 96_T | 1.087 | 0.49 |
| 52_S | 64_Q | 1.081 | 0.49 |
| 41_V | 44_W | 1.069 | 0.47 |
| 20_T | 74_R | 1.068 | 0.47 |
| 48_V | 93_G | 1.063 | 0.47 |
| 25_A | 85_K | 1.061 | 0.47 |
| 112_A | 141_E | 1.057 | 0.46 |
| 25_A | 34_V | 1.056 | 0.46 |
| 56_K | 130_V | 1.051 | 0.46 |
| 94_L | 106_F | 1.047 | 0.45 |
| 130_V | 141_E | 1.046 | 0.45 |
| 22_E | 76_V | 1.040 | 0.45 |
| 31_N | 139_G | 1.038 | 0.44 |
| 34_V | 38_Q | 1.033 | 0.44 |
| 88_G | 99_R | 1.030 | 0.44 |
| 23_E | 104_E | 1.024 | 0.43 |
| 86_L | 102_A | 1.021 | 0.43 |
| 72_L | 114_D | 1.017 | 0.42 |
| 38_Q | 41_V | 1.010 | 0.42 |
| 49_Y | 53_D | 1.005 | 0.41 |
| 31_N | 131_P | 1.005 | 0.41 |
| 65_K | 82_S | 1.002 | 0.41 |
| 19_L | 23_E | 1.002 | 0.41 |
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 | |
| 2lnmA | 1 | 0.4041 | 37.2 | 0.931 | Contact Map |
| 2llwA | 1 | 0.4863 | 25.8 | 0.936 | Contact Map |
| 2zbcA | 8 | 0.5274 | 22 | 0.938 | Contact Map |
| 2llvA | 1 | 0.4863 | 22 | 0.938 | Contact Map |
| 3hwsA | 6 | 0.6438 | 18.5 | 0.94 | Contact Map |
| 2djwA | 10 | 0.5205 | 13.1 | 0.944 | Contact Map |
| 3v3kB | 8 | 0.4315 | 7.9 | 0.95 | Contact Map |
| 4o4fA | 1 | 0.9452 | 7.4 | 0.95 | Contact Map |
| 1um8A | 1 | 0.6301 | 7.2 | 0.95 | Contact Map |
| 2oeqA | 4 | 0.4726 | 6.2 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)