| staph nuclease |
| ID: | 1488365573 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (134) | ||
| Sequences: | 4024 (3008.8) | ||
| Seq/Len: | 30.030 | ||
| Nf(neff/√len): | 259.9 |
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: 30.030).
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 |
| 96_E | 123_S | 3.194 | 1.00 |
| 19_K | 28_T | 2.641 | 1.00 |
| 56_F | 101_Q | 2.625 | 1.00 |
| 57_T | 94_V | 2.494 | 1.00 |
| 31_L | 57_T | 2.276 | 1.00 |
| 97_A | 100_R | 2.227 | 1.00 |
| 13_I | 19_K | 2.158 | 1.00 |
| 97_A | 101_Q | 2.154 | 1.00 |
| 31_L | 95_N | 2.082 | 1.00 |
| 126_Q | 130_E | 1.999 | 1.00 |
| 32_L | 84_L | 1.982 | 1.00 |
| 96_E | 119_H | 1.965 | 1.00 |
| 56_F | 98_L | 1.945 | 1.00 |
| 100_R | 126_Q | 1.902 | 1.00 |
| 86_Y | 93_M | 1.901 | 1.00 |
| 93_M | 120_L | 1.897 | 1.00 |
| 18_V | 87_I | 1.880 | 1.00 |
| 54_S | 58_K | 1.758 | 1.00 |
| 7_A | 20_L | 1.747 | 1.00 |
| 124_E | 128_K | 1.703 | 1.00 |
| 92_K | 97_A | 1.679 | 1.00 |
| 99_V | 120_L | 1.531 | 1.00 |
| 11_K | 19_K | 1.518 | 1.00 |
| 125_A | 129_K | 1.516 | 1.00 |
| 62_E | 65_K | 1.515 | 1.00 |
| 106_V | 124_E | 1.497 | 1.00 |
| 124_E | 135_W | 1.453 | 1.00 |
| 29_F | 85_A | 1.448 | 1.00 |
| 56_F | 97_A | 1.447 | 1.00 |
| 56_F | 60_M | 1.441 | 1.00 |
| 27_M | 77_T | 1.434 | 1.00 |
| 49_Y | 103_L | 1.422 | 1.00 |
| 35_D | 38_E | 1.417 | 1.00 |
| 57_T | 98_L | 1.382 | 0.99 |
| 56_F | 59_K | 1.372 | 0.99 |
| 69_V | 85_A | 1.359 | 0.99 |
| 60_M | 97_A | 1.325 | 0.99 |
| 39_T | 54_S | 1.321 | 0.99 |
| 17_T | 28_T | 1.312 | 0.99 |
| 61_V | 94_V | 1.286 | 0.99 |
| 6_P | 68_E | 1.274 | 0.99 |
| 36_T | 104_A | 1.253 | 0.99 |
| 69_V | 87_I | 1.246 | 0.98 |
| 9_L | 67_I | 1.239 | 0.98 |
| 88_Y | 93_M | 1.228 | 0.98 |
| 51_P | 55_A | 1.218 | 0.98 |
| 96_E | 100_R | 1.207 | 0.98 |
| 14_D | 17_T | 1.205 | 0.98 |
| 9_L | 12_A | 1.198 | 0.98 |
| 126_Q | 132_L | 1.183 | 0.98 |
| 71_F | 85_A | 1.173 | 0.98 |
| 60_M | 94_V | 1.159 | 0.97 |
| 18_V | 31_L | 1.153 | 0.97 |
| 19_K | 26_P | 1.151 | 0.97 |
| 39_T | 50_G | 1.138 | 0.97 |
| 76_R | 84_L | 1.125 | 0.97 |
| 16_D | 38_E | 1.090 | 0.96 |
| 70_E | 88_Y | 1.088 | 0.96 |
| 55_A | 59_K | 1.083 | 0.96 |
| 4_K | 68_E | 1.081 | 0.95 |
| 14_D | 38_E | 1.065 | 0.95 |
| 98_L | 104_A | 1.064 | 0.95 |
| 27_M | 83_G | 1.061 | 0.95 |
| 71_F | 76_R | 1.060 | 0.95 |
| 55_A | 58_K | 1.054 | 0.95 |
| 78_D | 82_R | 1.048 | 0.94 |
| 56_F | 103_L | 1.046 | 0.94 |
| 39_T | 51_P | 1.041 | 0.94 |
| 53_A | 98_L | 1.038 | 0.94 |
| 117_E | 121_R | 1.025 | 0.93 |
| 34_V | 104_A | 1.017 | 0.93 |
| 6_P | 66_K | 1.006 | 0.93 |
| 101_Q | 132_L | 1.005 | 0.93 |
| 58_K | 63_N | 1.005 | 0.93 |
| 99_V | 106_V | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3bdlA | 1 | 0.9926 | 100 | 0.037 | Contact Map |
| 4eqpA | 1 | 0.9485 | 99.9 | 0.051 | Contact Map |
| 4qmgA | 5 | 0.9632 | 99.9 | 0.054 | Contact Map |
| 2wacA | 2 | 0.9118 | 99.7 | 0.361 | Contact Map |
| 2hqxA | 2 | 0.1985 | 99.7 | 0.371 | Contact Map |
| 4b9wA | 2 | 0.6985 | 97 | 0.737 | Contact Map |
| 4q5yA | 1 | 0.6471 | 93.7 | 0.792 | Contact Map |
| 3ntkA | 2 | 0.6397 | 91.4 | 0.807 | Contact Map |
| 4b9xA | 1 | 0.6985 | 90.8 | 0.81 | Contact Map |
| 4q5wA | 2 | 0.7279 | 66.3 | 0.853 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)