| RWD |
| ID: | 1512490529 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 126 (85) | ||
| Sequences: | 189 (181.7) | ||
| Seq/Len: | 2.224 | ||
| Nf(neff/√len): | 19.7 |
Jackhmmer Results: (2016_04)
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: 2.224).
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 |
| 28_S | 38_I | 2.194 | 1.00 |
| 3_E | 9_R | 2.151 | 1.00 |
| 40_Y | 116_M | 1.665 | 0.96 |
| 21_H | 41_R | 1.557 | 0.94 |
| 27_T | 120_L | 1.466 | 0.91 |
| 12_N | 16_D | 1.423 | 0.90 |
| 8_L | 52_A | 1.418 | 0.89 |
| 22_F | 107_N | 1.384 | 0.88 |
| 15_E | 54_I | 1.372 | 0.87 |
| 11_I | 38_I | 1.365 | 0.87 |
| 24_L | 108_T | 1.300 | 0.83 |
| 42_L | 113_Y | 1.263 | 0.81 |
| 7_G | 112_F | 1.247 | 0.79 |
| 111_Q | 114_T | 1.246 | 0.79 |
| 43_I | 107_N | 1.236 | 0.79 |
| 95_P | 102_L | 1.232 | 0.78 |
| 6_T | 117_N | 1.219 | 0.77 |
| 6_T | 125_K | 1.199 | 0.76 |
| 80_T | 108_T | 1.186 | 0.75 |
| 9_R | 35_E | 1.179 | 0.74 |
| 110_S | 123_G | 1.167 | 0.73 |
| 8_L | 11_I | 1.158 | 0.72 |
| 90_L | 93_L | 1.156 | 0.72 |
| 38_I | 113_Y | 1.150 | 0.71 |
| 4_L | 91_L | 1.138 | 0.70 |
| 24_L | 117_N | 1.128 | 0.69 |
| 4_L | 11_I | 1.126 | 0.69 |
| 12_N | 30_N | 1.106 | 0.67 |
| 2_L | 32_S | 1.104 | 0.67 |
| 89_M | 92_D | 1.101 | 0.66 |
| 29_T | 120_L | 1.097 | 0.66 |
| 28_S | 36_L | 1.094 | 0.66 |
| 80_T | 109_L | 1.092 | 0.66 |
| 108_T | 111_Q | 1.089 | 0.65 |
| 11_I | 113_Y | 1.084 | 0.65 |
| 26_Q | 123_G | 1.078 | 0.64 |
| 6_T | 21_H | 1.076 | 0.64 |
| 81_M | 86_N | 1.076 | 0.64 |
| 41_R | 103_T | 1.068 | 0.63 |
| 104_F | 115_K | 1.065 | 0.63 |
| 51_T | 116_M | 1.064 | 0.63 |
| 25_K | 103_T | 1.055 | 0.62 |
| 5_L | 38_I | 1.040 | 0.60 |
| 3_E | 120_L | 1.018 | 0.58 |
| 31_G | 124_A | 1.017 | 0.57 |
| 45_S | 102_L | 1.007 | 0.56 |
| 5_L | 19_K | 1.001 | 0.56 |
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 | |
| 3n4sA | 4 | 0.7778 | 99.3 | 0.464 | Contact Map |
| 4emcA | 2 | 0.7778 | 99.3 | 0.466 | Contact Map |
| 2ve7A | 2 | 0.6667 | 98.2 | 0.638 | Contact Map |
| 3vz9B | 1 | 0.6984 | 98.2 | 0.639 | Contact Map |
| 2ftxA | 1 | 0.619 | 96.7 | 0.729 | Contact Map |
| 4dzoA | 2 | 0.6508 | 93.2 | 0.782 | Contact Map |
| 2lruA | 1 | 0.6508 | 5.9 | 0.91 | Contact Map |
| 2lh0A | 2 | 0.3492 | 2.7 | 0.924 | Contact Map |
| 4nm9A | 2 | 0.6349 | 2.1 | 0.928 | Contact Map |
| 2psoA | 3 | 0.7302 | 2.1 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)