| Ecoli DHFR |
| ID: | 1695297770 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 165 (140) | ||
| Sequences: | 4162 (2885.7) | ||
| Seq/Len: | 29.729 | ||
| Nf(neff/√len): | 243.9 |
HHblits Results: (2016_02)
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 |
| 44_R | 48_E | 4.287 | 1.00 |
| 13_V | 121_G | 3.472 | 1.00 |
| 10_V | 116_D | 2.923 | 1.00 |
| 3_S | 90_E | 2.764 | 1.00 |
| 4_L | 107_A | 2.549 | 1.00 |
| 62_L | 99_V | 2.355 | 1.00 |
| 4_L | 100_Y | 2.239 | 1.00 |
| 104_L | 110_L | 2.230 | 1.00 |
| 36_L | 56_G | 2.106 | 1.00 |
| 39_P | 58_K | 2.098 | 1.00 |
| 98_R | 102_Q | 2.043 | 1.00 |
| 123_T | 126_P | 1.987 | 1.00 |
| 30_W | 34_N | 1.936 | 1.00 |
| 58_K | 73_T | 1.922 | 1.00 |
| 29_A | 33_R | 1.861 | 1.00 |
| 9_A | 119_V | 1.797 | 1.00 |
| 9_A | 13_V | 1.784 | 1.00 |
| 3_S | 109_K | 1.775 | 1.00 |
| 11_D | 120_E | 1.755 | 1.00 |
| 6_A | 112_L | 1.673 | 1.00 |
| 64_S | 98_R | 1.665 | 1.00 |
| 8_L | 12_R | 1.572 | 1.00 |
| 39_P | 60_I | 1.567 | 1.00 |
| 97_G | 101_E | 1.519 | 1.00 |
| 77_S | 80_E | 1.515 | 1.00 |
| 30_W | 111_Y | 1.497 | 1.00 |
| 45_H | 48_E | 1.484 | 1.00 |
| 11_D | 118_E | 1.468 | 1.00 |
| 3_S | 111_Y | 1.466 | 1.00 |
| 6_A | 14_I | 1.435 | 1.00 |
| 35_T | 57_R | 1.422 | 1.00 |
| 135_S | 138_S | 1.412 | 1.00 |
| 16_M | 120_E | 1.410 | 1.00 |
| 32_K | 36_L | 1.392 | 0.99 |
| 8_L | 114_H | 1.385 | 0.99 |
| 7_A | 115_I | 1.375 | 0.99 |
| 10_V | 118_E | 1.366 | 0.99 |
| 46_T | 95_G | 1.286 | 0.99 |
| 78_V | 103_F | 1.282 | 0.99 |
| 81_A | 84_A | 1.241 | 0.98 |
| 107_A | 110_L | 1.239 | 0.98 |
| 38_K | 92_M | 1.224 | 0.98 |
| 50_I | 59_N | 1.221 | 0.98 |
| 13_V | 124_H | 1.181 | 0.98 |
| 33_R | 36_L | 1.179 | 0.98 |
| 14_I | 97_G | 1.172 | 0.98 |
| 54_L | 57_R | 1.144 | 0.97 |
| 93_V | 103_F | 1.139 | 0.97 |
| 31_F | 35_T | 1.117 | 0.96 |
| 59_N | 94_I | 1.116 | 0.96 |
| 45_H | 98_R | 1.115 | 0.96 |
| 98_R | 101_E | 1.110 | 0.96 |
| 76_K | 80_E | 1.069 | 0.95 |
| 42_M | 50_I | 1.056 | 0.95 |
| 15_G | 122_D | 1.055 | 0.95 |
| 99_V | 102_Q | 1.055 | 0.95 |
| 42_M | 54_L | 1.052 | 0.95 |
| 62_L | 81_A | 1.045 | 0.94 |
| 41_I | 91_I | 1.026 | 0.94 |
| 80_E | 84_A | 1.025 | 0.93 |
| 101_E | 105_P | 1.018 | 0.93 |
| 40_V | 59_N | 1.008 | 0.93 |
| 38_K | 90_E | 1.004 | 0.93 |
| 34_N | 111_Y | 1.001 | 0.92 |
| 81_A | 103_F | 1.000 | 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 | |
| 3tq8A | 1 | 0.9879 | 100 | 0.175 | Contact Map |
| 4pssA | 1 | 0.703 | 100 | 0.177 | Contact Map |
| 3ia4A | 4 | 0.9636 | 100 | 0.184 | Contact Map |
| 2w9hA | 1 | 0.9455 | 100 | 0.184 | Contact Map |
| 1zdrA | 2 | 0.9636 | 100 | 0.193 | Contact Map |
| 1juvA | 1 | 0.9394 | 100 | 0.198 | Contact Map |
| 4klxA | 2 | 0.9212 | 100 | 0.201 | Contact Map |
| 4m7uA | 1 | 0.9636 | 100 | 0.211 | Contact Map |
| 1j3kA | 2 | 0.9697 | 100 | 0.213 | Contact Map |
| 4eilA | 8 | 0.9576 | 100 | 0.217 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)