| Rv3587c |
| ID: | 1446714989 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 138 (134) | ||
| Sequences: | 341 (293.3) | ||
| Seq/Len: | 2.545 | ||
| Nf(neff/√len): | 25.3 |
HHblits Results: (2015_06)
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: 2.545).
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 |
| 22_A | 29_D | 3.036 | 1.00 |
| 64_K | 99_G | 2.506 | 1.00 |
| 25_Y | 31_P | 2.493 | 1.00 |
| 71_D | 100_S | 2.427 | 1.00 |
| 31_P | 97_G | 2.332 | 1.00 |
| 31_P | 134_L | 2.216 | 1.00 |
| 97_G | 134_L | 2.175 | 1.00 |
| 18_G | 118_L | 2.169 | 1.00 |
| 48_D | 78_T | 2.021 | 0.99 |
| 65_R | 71_D | 1.844 | 0.99 |
| 84_S | 87_E | 1.791 | 0.98 |
| 18_G | 33_F | 1.781 | 0.98 |
| 10_P | 13_T | 1.667 | 0.97 |
| 49_V | 113_P | 1.579 | 0.96 |
| 67_W | 100_S | 1.576 | 0.96 |
| 38_T | 88_Q | 1.518 | 0.95 |
| 98_M | 110_A | 1.509 | 0.94 |
| 21_N | 25_Y | 1.489 | 0.94 |
| 32_K | 94_T | 1.448 | 0.93 |
| 31_P | 71_D | 1.427 | 0.92 |
| 55_A | 121_Q | 1.423 | 0.92 |
| 65_R | 68_S | 1.326 | 0.87 |
| 27_V | 97_G | 1.272 | 0.84 |
| 11_D | 47_R | 1.265 | 0.84 |
| 71_D | 102_P | 1.247 | 0.83 |
| 20_T | 25_Y | 1.228 | 0.81 |
| 49_V | 107_P | 1.213 | 0.80 |
| 74_P | 103_R | 1.212 | 0.80 |
| 62_D | 66_L | 1.200 | 0.79 |
| 37_V | 111_I | 1.191 | 0.79 |
| 96_T | 124_N | 1.175 | 0.77 |
| 25_Y | 97_G | 1.173 | 0.77 |
| 111_I | 131_P | 1.152 | 0.75 |
| 49_V | 79_L | 1.145 | 0.75 |
| 41_G | 69_N | 1.136 | 0.74 |
| 98_M | 108_R | 1.131 | 0.73 |
| 20_T | 130_V | 1.130 | 0.73 |
| 28_G | 48_D | 1.124 | 0.73 |
| 39_N | 97_G | 1.119 | 0.72 |
| 60_S | 66_L | 1.118 | 0.72 |
| 25_Y | 50_G | 1.094 | 0.70 |
| 68_S | 77_E | 1.079 | 0.68 |
| 43_V | 80_V | 1.076 | 0.68 |
| 26_Y | 101_A | 1.071 | 0.67 |
| 115_T | 131_P | 1.064 | 0.67 |
| 47_R | 97_G | 1.058 | 0.66 |
| 25_Y | 134_L | 1.050 | 0.65 |
| 17_K | 38_T | 1.035 | 0.64 |
| 78_T | 118_L | 1.035 | 0.64 |
| 69_N | 113_P | 1.030 | 0.63 |
| 24_Q | 133_I | 1.023 | 0.62 |
| 33_F | 78_T | 1.018 | 0.62 |
| 68_S | 71_D | 1.014 | 0.61 |
| 28_G | 118_L | 1.010 | 0.61 |
| 39_N | 83_F | 1.010 | 0.61 |
| 63_N | 75_S | 1.009 | 0.61 |
| 59_Y | 117_N | 1.007 | 0.60 |
| 103_R | 114_G | 1.003 | 0.60 |
| 66_L | 111_I | 1.003 | 0.60 |
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 | |
| 3isyA | 1 | 0.7826 | 99.3 | 0.631 | Contact Map |
| 3iduA | 2 | 0.7464 | 91.9 | 0.856 | Contact Map |
| 2kutA | 1 | 0.7464 | 91.8 | 0.856 | Contact Map |
| 3u48A | 2 | 0.913 | 91.1 | 0.859 | Contact Map |
| 3wnoA | 2 | 0.7319 | 89.4 | 0.864 | Contact Map |
| 2l0dA | 1 | 0.7246 | 89.2 | 0.864 | Contact Map |
| 2x41A | 1 | 0.8768 | 83.4 | 0.875 | Contact Map |
| 3vmnA | 1 | 0.7536 | 81.5 | 0.878 | Contact Map |
| 4i3gA | 2 | 0.8478 | 81.2 | 0.878 | Contact Map |
| 2pn5A | 1 | 0.8116 | 81.1 | 0.878 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)