| PhyR_Coev_2 |
| ID: | 1482819574 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 267 (141) | ||
| Sequences: | 21064 (15009.7) | ||
| Seq/Len: | 149.390 | ||
| Nf(neff/√len): | 1264.0 |
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: 149.390).
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 |
| 39_A | 67_L | 2.780 | 1.00 |
| 106_T | 116_A | 2.624 | 1.00 |
| 14_V | 57_R | 2.137 | 1.00 |
| 99_D | 137_A | 2.132 | 1.00 |
| 94_G | 141_A | 2.009 | 1.00 |
| 114_P | 124_G | 1.998 | 1.00 |
| 91_A | 141_A | 1.955 | 1.00 |
| 19_A | 64_L | 1.948 | 1.00 |
| 125_G | 128_I | 1.905 | 1.00 |
| 111_L | 119_V | 1.873 | 1.00 |
| 65_N | 69_D | 1.834 | 1.00 |
| 43_A | 46_R | 1.809 | 1.00 |
| 98_A | 130_R | 1.769 | 1.00 |
| 36_C | 64_L | 1.743 | 1.00 |
| 27_D | 30_D | 1.695 | 1.00 |
| 48_G | 53_G | 1.682 | 1.00 |
| 132_K | 136_A | 1.636 | 1.00 |
| 28_R | 71_S | 1.571 | 1.00 |
| 5_E | 9_F | 1.551 | 1.00 |
| 55_G | 58_L | 1.551 | 1.00 |
| 99_D | 130_R | 1.539 | 1.00 |
| 113_L | 124_G | 1.503 | 1.00 |
| 123_E | 126_E | 1.489 | 1.00 |
| 122_L | 130_R | 1.483 | 1.00 |
| 96_P | 99_D | 1.475 | 1.00 |
| 22_L | 68_F | 1.450 | 1.00 |
| 18_Y | 61_Y | 1.447 | 1.00 |
| 112_S | 115_Q | 1.437 | 1.00 |
| 23_T | 32_L | 1.437 | 1.00 |
| 105_L | 119_V | 1.417 | 1.00 |
| 100_R | 104_L | 1.415 | 1.00 |
| 107_A | 135_R | 1.404 | 0.99 |
| 15_L | 64_L | 1.400 | 0.99 |
| 113_L | 128_I | 1.383 | 0.99 |
| 6_C | 10_E | 1.382 | 0.99 |
| 113_L | 131_L | 1.373 | 0.99 |
| 40_A | 60_M | 1.368 | 0.99 |
| 62_A | 65_N | 1.357 | 0.99 |
| 15_L | 33_V | 1.352 | 0.99 |
| 67_L | 70_R | 1.346 | 0.99 |
| 122_L | 127_A | 1.333 | 0.99 |
| 137_A | 141_A | 1.332 | 0.99 |
| 38_E | 42_M | 1.307 | 0.99 |
| 35_R | 67_L | 1.306 | 0.99 |
| 129_R | 132_K | 1.293 | 0.99 |
| 19_A | 68_F | 1.284 | 0.99 |
| 57_R | 61_Y | 1.280 | 0.99 |
| 11_V | 37_V | 1.266 | 0.99 |
| 126_E | 130_R | 1.242 | 0.98 |
| 20_R | 26_T | 1.237 | 0.98 |
| 19_A | 32_L | 1.234 | 0.98 |
| 124_G | 128_I | 1.224 | 0.98 |
| 70_R | 73_E | 1.210 | 0.98 |
| 106_T | 113_L | 1.203 | 0.98 |
| 25_A | 28_R | 1.203 | 0.98 |
| 39_A | 43_A | 1.196 | 0.98 |
| 32_L | 71_S | 1.188 | 0.98 |
| 102_L | 131_L | 1.187 | 0.98 |
| 4_Y | 41_V | 1.185 | 0.98 |
| 8_L | 12_V | 1.179 | 0.98 |
| 129_R | 133_A | 1.177 | 0.98 |
| 114_P | 118_K | 1.173 | 0.98 |
| 16_R | 20_R | 1.154 | 0.97 |
| 105_L | 111_L | 1.136 | 0.97 |
| 14_V | 61_Y | 1.124 | 0.97 |
| 8_L | 37_V | 1.120 | 0.96 |
| 116_A | 127_A | 1.114 | 0.96 |
| 102_L | 134_A | 1.112 | 0.96 |
| 18_Y | 65_N | 1.110 | 0.96 |
| 36_C | 63_L | 1.110 | 0.96 |
| 125_G | 129_R | 1.098 | 0.96 |
| 107_A | 131_L | 1.093 | 0.96 |
| 102_L | 130_R | 1.091 | 0.96 |
| 126_E | 129_R | 1.085 | 0.96 |
| 16_R | 30_D | 1.079 | 0.95 |
| 93_A | 100_R | 1.070 | 0.95 |
| 16_R | 26_T | 1.059 | 0.95 |
| 111_L | 115_Q | 1.048 | 0.94 |
| 125_G | 132_K | 1.043 | 0.94 |
| 99_D | 102_L | 1.022 | 0.93 |
| 23_T | 68_F | 1.017 | 0.93 |
| 62_A | 66_L | 1.014 | 0.93 |
| 26_T | 30_D | 1.007 | 0.93 |
| 39_A | 70_R | 1.002 | 0.92 |
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 | |
| 4g97A | 1 | 0.8914 | 100 | 0.03 | Contact Map |
| 3n0rA | 1 | 0.9625 | 100 | 0.061 | Contact Map |
| 4qicA | 2 | 0 | 100 | 0.082 | Contact Map |
| 2lfwA | 1 | 0.5768 | 99.9 | 0.564 | Contact Map |
| 1w25A | 2 | 0.4607 | 99.8 | 0.582 | Contact Map |
| 4cxfA | 1 | 0.5206 | 99.8 | 0.582 | Contact Map |
| 3dzdA | 2 | 0.4569 | 99.8 | 0.587 | Contact Map |
| 2q1zA | 2 | 0.5243 | 99.8 | 0.589 | Contact Map |
| 1or7A | 2 | 0.5356 | 99.8 | 0.59 | Contact Map |
| 3eq2A | 2 | 0.4644 | 99.8 | 0.593 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)