| rhodo monomer |
| ID: | 1517760685 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (144) | ||
| Sequences: | 1852 (1210.6) | ||
| Seq/Len: | 12.861 | ||
| Nf(neff/√len): | 100.9 |
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: 12.861).
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 |
| 70_W | 105_S | 3.575 | 1.00 |
| 58_L | 112_A | 2.728 | 1.00 |
| 34_E | 127_G | 2.678 | 1.00 |
| 12_I | 149_T | 2.539 | 1.00 |
| 146_L | 150_T | 2.469 | 1.00 |
| 68_L | 72_F | 2.357 | 1.00 |
| 51_R | 121_G | 2.346 | 1.00 |
| 21_G | 62_L | 2.300 | 1.00 |
| 32_D | 54_Q | 2.204 | 1.00 |
| 96_A | 147_S | 2.181 | 1.00 |
| 113_A | 117_K | 2.102 | 1.00 |
| 15_V | 69_A | 2.082 | 1.00 |
| 140_L | 144_M | 2.032 | 1.00 |
| 105_S | 109_G | 2.024 | 1.00 |
| 46_M | 49_L | 2.021 | 1.00 |
| 10_L | 72_F | 2.011 | 1.00 |
| 100_G | 147_S | 1.926 | 1.00 |
| 95_V | 99_A | 1.922 | 1.00 |
| 118_I | 123_S | 1.892 | 1.00 |
| 14_A | 68_L | 1.848 | 1.00 |
| 100_G | 143_V | 1.810 | 1.00 |
| 117_K | 122_T | 1.763 | 1.00 |
| 17_A | 65_A | 1.747 | 1.00 |
| 41_P | 46_M | 1.721 | 1.00 |
| 128_K | 132_M | 1.714 | 1.00 |
| 16_I | 141_A | 1.646 | 1.00 |
| 14_A | 72_F | 1.581 | 1.00 |
| 74_L | 78_H | 1.559 | 1.00 |
| 13_L | 142_I | 1.552 | 1.00 |
| 110_F | 114_Q | 1.520 | 1.00 |
| 94_M | 98_L | 1.505 | 1.00 |
| 5_D | 8_R | 1.482 | 1.00 |
| 47_Q | 121_G | 1.468 | 1.00 |
| 52_L | 56_R | 1.383 | 0.99 |
| 7_A | 75_W | 1.354 | 0.99 |
| 47_Q | 51_R | 1.354 | 0.99 |
| 13_L | 145_V | 1.313 | 0.99 |
| 100_G | 144_M | 1.301 | 0.99 |
| 111_L | 133_T | 1.294 | 0.99 |
| 31_Y | 52_L | 1.289 | 0.99 |
| 24_F | 53_W | 1.270 | 0.99 |
| 115_R | 119_A | 1.228 | 0.98 |
| 106_G | 109_G | 1.222 | 0.98 |
| 114_Q | 129_F | 1.217 | 0.98 |
| 93_W | 148_V | 1.217 | 0.98 |
| 55_T | 60_I | 1.210 | 0.98 |
| 9_G | 150_T | 1.197 | 0.98 |
| 92_P | 95_V | 1.177 | 0.98 |
| 123_S | 130_W | 1.164 | 0.97 |
| 9_G | 146_L | 1.162 | 0.97 |
| 30_A | 33_A | 1.139 | 0.97 |
| 81_V | 86_A | 1.120 | 0.96 |
| 109_G | 112_A | 1.115 | 0.96 |
| 78_H | 81_V | 1.094 | 0.96 |
| 98_L | 102_F | 1.084 | 0.96 |
| 23_L | 107_W | 1.080 | 0.95 |
| 81_V | 85_G | 1.071 | 0.95 |
| 107_W | 111_L | 1.058 | 0.95 |
| 6_L | 146_L | 1.057 | 0.95 |
| 117_K | 124_K | 1.056 | 0.95 |
| 34_E | 56_R | 1.049 | 0.94 |
| 114_Q | 130_W | 1.039 | 0.94 |
| 92_P | 96_A | 1.038 | 0.94 |
| 3_T | 7_A | 1.037 | 0.94 |
| 80_D | 85_G | 1.033 | 0.94 |
| 56_R | 60_I | 1.033 | 0.94 |
| 27_R | 134_N | 1.032 | 0.94 |
| 63_T | 108_H | 1.020 | 0.93 |
| 7_A | 150_T | 1.016 | 0.93 |
| 80_D | 86_A | 1.011 | 0.93 |
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 | |
| 2wdqC | 3 | 0.7516 | 2.8 | 0.95 | Contact Map |
| 2kncB | 1 | 0.2288 | 1.3 | 0.959 | Contact Map |
| 2wdqD | 3 | 0.6667 | 1.2 | 0.959 | Contact Map |
| 2lp1A | 1 | 0.2549 | 1.2 | 0.96 | Contact Map |
| 2llmA | 1 | 0.2745 | 1.2 | 0.96 | Contact Map |
| 3zuxA | 1 | 0.5882 | 1 | 0.962 | Contact Map |
| 3s8fA | 1 | 0.7255 | 0.9 | 0.962 | Contact Map |
| 2lzrA | 1 | 0.1373 | 0.9 | 0.963 | Contact Map |
| 3w9iA | 6 | 0.2484 | 0.9 | 0.963 | Contact Map |
| 3x29A | 2 | 0.4706 | 0.9 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)