| yeex long -force run |
| ID: | 1499263039 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (103) | ||
| Sequences: | 58 (21.6) | ||
| Seq/Len: | 0.563 | ||
| Nf(neff/√len): | 2.1 |
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: 0.563).
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 |
| 36_F | 119_L | 2.078 | 0.90 |
| 85_G | 89_S | 1.773 | 0.78 |
| 102_I | 111_E | 1.669 | 0.72 |
| 30_F | 74_I | 1.585 | 0.66 |
| 72_D | 104_K | 1.505 | 0.60 |
| 42_R | 111_E | 1.494 | 0.59 |
| 47_Q | 82_A | 1.483 | 0.59 |
| 103_I | 112_R | 1.467 | 0.57 |
| 36_F | 40_F | 1.466 | 0.57 |
| 27_K | 68_D | 1.455 | 0.56 |
| 78_M | 82_A | 1.406 | 0.53 |
| 96_D | 117_K | 1.400 | 0.52 |
| 35_E | 120_K | 1.385 | 0.51 |
| 49_E | 122_M | 1.375 | 0.50 |
| 55_K | 111_E | 1.373 | 0.50 |
| 30_F | 65_L | 1.357 | 0.49 |
| 65_L | 74_I | 1.357 | 0.49 |
| 36_F | 96_D | 1.354 | 0.48 |
| 38_R | 89_S | 1.333 | 0.47 |
| 42_R | 104_K | 1.330 | 0.46 |
| 72_D | 75_K | 1.316 | 0.45 |
| 80_V | 83_I | 1.290 | 0.43 |
| 40_F | 47_Q | 1.285 | 0.43 |
| 50_I | 116_S | 1.252 | 0.40 |
| 53_V | 89_S | 1.246 | 0.40 |
| 80_V | 108_L | 1.236 | 0.39 |
| 80_V | 91_K | 1.212 | 0.37 |
| 49_E | 81_E | 1.212 | 0.37 |
| 104_K | 115_I | 1.199 | 0.36 |
| 46_L | 82_A | 1.195 | 0.36 |
| 49_E | 83_I | 1.182 | 0.35 |
| 42_R | 55_K | 1.176 | 0.35 |
| 36_F | 47_Q | 1.174 | 0.35 |
| 64_V | 98_V | 1.162 | 0.34 |
| 55_K | 84_Q | 1.161 | 0.34 |
| 29_S | 80_V | 1.157 | 0.33 |
| 102_I | 116_S | 1.150 | 0.33 |
| 42_R | 102_I | 1.145 | 0.33 |
| 54_E | 115_I | 1.118 | 0.31 |
| 57_I | 113_R | 1.114 | 0.30 |
| 50_I | 102_I | 1.109 | 0.30 |
| 68_D | 91_K | 1.100 | 0.29 |
| 84_Q | 102_I | 1.100 | 0.29 |
| 55_K | 82_A | 1.090 | 0.29 |
| 57_I | 101_Y | 1.086 | 0.29 |
| 39_L | 91_K | 1.075 | 0.28 |
| 53_V | 114_D | 1.071 | 0.28 |
| 71_S | 121_A | 1.064 | 0.27 |
| 33_V | 38_R | 1.062 | 0.27 |
| 45_K | 109_S | 1.055 | 0.27 |
| 61_Q | 118_K | 1.047 | 0.26 |
| 33_V | 120_K | 1.043 | 0.26 |
| 54_E | 88_A | 1.036 | 0.25 |
| 51_Q | 88_A | 1.032 | 0.25 |
| 33_V | 50_I | 1.028 | 0.25 |
| 72_D | 77_G | 1.025 | 0.25 |
| 108_L | 115_I | 1.021 | 0.25 |
| 31_Q | 78_M | 1.020 | 0.24 |
| 37_V | 95_E | 1.017 | 0.24 |
| 49_E | 71_S | 1.013 | 0.24 |
| 76_P | 92_G | 1.009 | 0.24 |
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 | |
| 2kldA | 1 | 0.5344 | 54.1 | 0.943 | Contact Map |
| 1q08A | 2 | 0.4809 | 20 | 0.955 | Contact Map |
| 1xahA | 2 | 0.5115 | 17.1 | 0.957 | Contact Map |
| 2gsvA | 2 | 0.5191 | 15.5 | 0.957 | Contact Map |
| 3gpvA | 2 | 0.7176 | 14.2 | 0.958 | Contact Map |
| 3hh0A | 4 | 0.8168 | 14 | 0.958 | Contact Map |
| 2xppA | 1 | 0.3588 | 12.7 | 0.959 | Contact Map |
| 2bnxA | 2 | 0.6718 | 11.5 | 0.96 | Contact Map |
| 2vz4A | 1 | 0.687 | 10.5 | 0.96 | Contact Map |
| 3ojaB | 1 | 0.7176 | 10.1 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)