| SubsetMark |
| ID: | 1478289371 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 92 (92) | ||
| Sequences: | 499 (499) | ||
| Seq/Len: | 5.424 | ||
| Nf(neff/√len): | 52.0 |
HHblits Results: (2016_02)
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: 5.424).
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 |
| 62_I | 79_H | 1.661 | 1.00 |
| 29_L | 33_Q | 1.465 | 0.98 |
| 23_P | 50_A | 1.419 | 0.98 |
| 5_F | 49_Q | 1.342 | 0.97 |
| 2_L | 47_S | 1.338 | 0.97 |
| 27_T | 92_P | 1.263 | 0.95 |
| 33_Q | 43_Y | 1.253 | 0.95 |
| 60_H | 63_A | 1.250 | 0.95 |
| 31_I | 69_W | 1.237 | 0.94 |
| 43_Y | 61_F | 1.224 | 0.94 |
| 8_L | 57_Y | 1.218 | 0.94 |
| 58_R | 81_F | 1.211 | 0.94 |
| 14_K | 70_F | 1.211 | 0.94 |
| 17_F | 42_G | 1.200 | 0.93 |
| 38_F | 44_N | 1.198 | 0.93 |
| 11_N | 91_Q | 1.198 | 0.93 |
| 2_L | 49_Q | 1.177 | 0.92 |
| 5_F | 70_F | 1.170 | 0.92 |
| 15_H | 79_H | 1.168 | 0.92 |
| 19_M | 79_H | 1.168 | 0.92 |
| 61_F | 87_T | 1.165 | 0.92 |
| 47_S | 76_T | 1.160 | 0.92 |
| 1_N | 34_L | 1.148 | 0.91 |
| 23_P | 67_S | 1.144 | 0.91 |
| 47_S | 75_D | 1.143 | 0.91 |
| 51_K | 65_V | 1.135 | 0.90 |
| 18_D | 86_V | 1.134 | 0.90 |
| 50_A | 78_G | 1.123 | 0.90 |
| 53_R | 89_G | 1.119 | 0.90 |
| 77_I | 80_V | 1.114 | 0.89 |
| 36_E | 81_F | 1.114 | 0.89 |
| 47_S | 90_V | 1.112 | 0.89 |
| 16_D | 64_L | 1.104 | 0.89 |
| 28_R | 92_P | 1.100 | 0.88 |
| 66_A | 82_W | 1.093 | 0.88 |
| 12_G | 86_V | 1.084 | 0.88 |
| 78_G | 84_E | 1.081 | 0.87 |
| 15_H | 45_S | 1.080 | 0.87 |
| 4_I | 62_I | 1.077 | 0.87 |
| 39_T | 47_S | 1.072 | 0.87 |
| 38_F | 82_W | 1.071 | 0.87 |
| 27_T | 39_T | 1.070 | 0.87 |
| 57_Y | 91_Q | 1.061 | 0.86 |
| 74_L | 92_P | 1.061 | 0.86 |
| 35_F | 62_I | 1.060 | 0.86 |
| 7_H | 82_W | 1.057 | 0.86 |
| 56_N | 84_E | 1.056 | 0.86 |
| 2_L | 38_F | 1.052 | 0.85 |
| 39_T | 57_Y | 1.051 | 0.85 |
| 4_I | 85_K | 1.040 | 0.84 |
| 60_H | 92_P | 1.039 | 0.84 |
| 16_D | 38_F | 1.038 | 0.84 |
| 49_Q | 73_E | 1.033 | 0.84 |
| 41_N | 46_M | 1.027 | 0.83 |
| 40_E | 48_A | 1.027 | 0.83 |
| 44_N | 67_S | 1.024 | 0.83 |
| 33_Q | 67_S | 1.024 | 0.83 |
| 22_A | 56_N | 1.018 | 0.83 |
| 52_L | 82_W | 1.018 | 0.83 |
| 56_N | 87_T | 1.008 | 0.82 |
| 30_V | 54_P | 1.006 | 0.82 |
| 10_K | 71_S | 1.006 | 0.82 |
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 | |
| 1qysA | 1 | 1 | 99.7 | 0.486 | Contact Map |
| 4kyzA | 4 | 1 | 99.2 | 0.613 | Contact Map |
| 2gjhA | 2 | 0.5326 | 98.1 | 0.737 | Contact Map |
| 2mblA | 1 | 1 | 96.1 | 0.81 | Contact Map |
| 2jvfA | 1 | 1 | 42.9 | 0.898 | Contact Map |
| 2cy7A | 1 | 0.7609 | 8.6 | 0.927 | Contact Map |
| 1q1uA | 1 | 0.6196 | 6.8 | 0.931 | Contact Map |
| 1y5oA | 1 | 0.4565 | 6.1 | 0.932 | Contact Map |
| 2p82A | 4 | 0.5978 | 4.7 | 0.935 | Contact Map |
| 3axyA | 4 | 0.6848 | 4.4 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)