| FYRN-FYRC |
| ID: | 1434572861 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (136) | ||
| Sequences: | 243 (178.7) | ||
| Seq/Len: | 1.787 | ||
| Nf(neff/√len): | 15.3 |
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: 1.787).
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 |
| 6_I | 114_V | 2.569 | 1.00 |
| 119_E | 130_Y | 2.551 | 1.00 |
| 60_I | 80_L | 2.387 | 1.00 |
| 22_L | 118_I | 2.087 | 0.99 |
| 49_I | 109_I | 1.978 | 0.99 |
| 60_I | 106_M | 1.962 | 0.98 |
| 7_D | 30_S | 1.803 | 0.97 |
| 8_C | 23_F | 1.622 | 0.93 |
| 31_R | 123_G | 1.607 | 0.93 |
| 33_Y | 42_R | 1.599 | 0.93 |
| 77_W | 121_L | 1.582 | 0.92 |
| 77_W | 80_L | 1.519 | 0.90 |
| 49_I | 124_A | 1.487 | 0.89 |
| 48_K | 59_E | 1.459 | 0.88 |
| 33_Y | 45_Y | 1.457 | 0.87 |
| 23_F | 121_L | 1.434 | 0.86 |
| 47_C | 100_G | 1.373 | 0.83 |
| 17_D | 122_S | 1.307 | 0.78 |
| 22_L | 130_Y | 1.299 | 0.78 |
| 127_C | 130_Y | 1.297 | 0.78 |
| 60_I | 77_W | 1.278 | 0.76 |
| 35_S | 45_Y | 1.267 | 0.75 |
| 70_A | 73_I | 1.264 | 0.75 |
| 31_R | 122_S | 1.262 | 0.75 |
| 74_E | 104_L | 1.228 | 0.72 |
| 21_K | 74_E | 1.212 | 0.71 |
| 23_F | 75_D | 1.211 | 0.71 |
| 18_C | 90_N | 1.209 | 0.70 |
| 54_K | 104_L | 1.209 | 0.70 |
| 21_K | 104_L | 1.207 | 0.70 |
| 74_E | 105_R | 1.201 | 0.70 |
| 39_A | 110_L | 1.196 | 0.69 |
| 28_Q | 48_K | 1.196 | 0.69 |
| 48_K | 57_V | 1.161 | 0.66 |
| 21_K | 43_C | 1.158 | 0.66 |
| 119_E | 124_A | 1.155 | 0.65 |
| 61_S | 67_Q | 1.146 | 0.64 |
| 22_L | 30_S | 1.146 | 0.64 |
| 70_A | 75_D | 1.135 | 0.63 |
| 27_Y | 36_T | 1.134 | 0.63 |
| 68_I | 73_I | 1.120 | 0.62 |
| 17_D | 22_L | 1.117 | 0.61 |
| 29_C | 107_L | 1.106 | 0.60 |
| 81_T | 112_D | 1.106 | 0.60 |
| 12_L | 15_L | 1.099 | 0.60 |
| 8_C | 84_V | 1.090 | 0.59 |
| 18_C | 22_L | 1.072 | 0.57 |
| 111_H | 117_L | 1.070 | 0.57 |
| 116_F | 121_L | 1.068 | 0.56 |
| 41_K | 66_F | 1.060 | 0.55 |
| 14_D | 64_D | 1.058 | 0.55 |
| 15_L | 101_V | 1.049 | 0.54 |
| 62_S | 73_I | 1.044 | 0.54 |
| 29_C | 72_S | 1.043 | 0.54 |
| 28_Q | 46_T | 1.042 | 0.54 |
| 91_A | 112_D | 1.039 | 0.53 |
| 4_M | 108_G | 1.025 | 0.52 |
| 80_L | 89_S | 1.019 | 0.51 |
| 49_I | 58_F | 1.018 | 0.51 |
| 88_R | 108_G | 1.016 | 0.51 |
| 90_N | 109_I | 1.014 | 0.51 |
| 12_L | 127_C | 1.005 | 0.50 |
| 75_D | 107_L | 1.002 | 0.49 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2wzoA | 1 | 0.9568 | 100 | 0.223 | Contact Map |
| 2b6cA | 2 | 0.4101 | 19.5 | 0.94 | Contact Map |
| 2wteA | 2 | 0.7122 | 17.2 | 0.941 | Contact Map |
| 2od4A | 2 | 0.4388 | 12.1 | 0.945 | Contact Map |
| 4k7hA | 5 | 0.9065 | 8.7 | 0.949 | Contact Map |
| 3qq6A | 2 | 0.4317 | 7.8 | 0.95 | Contact Map |
| 3k2zA | 2 | 0.4676 | 7.6 | 0.95 | Contact Map |
| 2x1lA | 3 | 0.5612 | 6.9 | 0.951 | Contact Map |
| 1l1oC | 2 | 0.7986 | 5.8 | 0.953 | Contact Map |
| 3jxyA | 1 | 0.4892 | 5.4 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)