| CHEY_ECOLI |
| ID: | 1430407794 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 114 (114) | ||
| Sequences: | 73909 (58136.9) | ||
| Seq/Len: | 648.325 | ||
| Nf(neff/√len): | 5445.0 |
HHblits Results: (2013_03)
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: 648.325).
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 |
| 11_R | 28_E | 3.064 | 1.00 |
| 15_R | 28_E | 2.719 | 1.00 |
| 11_R | 30_E | 2.680 | 1.00 |
| 4_V | 35_A | 2.498 | 1.00 |
| 27_E | 44_Y | 2.272 | 1.00 |
| 33_V | 55_N | 2.096 | 1.00 |
| 52_N | 82_E | 2.058 | 1.00 |
| 32_G | 56_M | 2.013 | 1.00 |
| 49_S | 61_L | 1.972 | 1.00 |
| 36_L | 64_T | 1.962 | 1.00 |
| 56_M | 64_T | 1.875 | 1.00 |
| 40_Q | 68_D | 1.868 | 1.00 |
| 78_M | 96_A | 1.862 | 1.00 |
| 29_A | 38_K | 1.829 | 1.00 |
| 31_D | 55_N | 1.827 | 1.00 |
| 69_G | 72_S | 1.809 | 1.00 |
| 98_G | 112_K | 1.789 | 1.00 |
| 21_L | 110_E | 1.763 | 1.00 |
| 27_E | 38_K | 1.759 | 1.00 |
| 30_E | 34_D | 1.738 | 1.00 |
| 17_L | 106_A | 1.723 | 1.00 |
| 27_E | 42_G | 1.662 | 1.00 |
| 2_L | 29_A | 1.628 | 1.00 |
| 62_L | 76_V | 1.581 | 1.00 |
| 66_R | 97_S | 1.528 | 1.00 |
| 15_R | 19_K | 1.390 | 0.99 |
| 56_M | 60_E | 1.386 | 0.99 |
| 63_K | 94_A | 1.369 | 0.99 |
| 38_K | 42_G | 1.343 | 0.99 |
| 64_T | 68_D | 1.341 | 0.99 |
| 51_W | 59_L | 1.341 | 0.99 |
| 82_E | 87_N | 1.330 | 0.99 |
| 31_D | 34_D | 1.319 | 0.99 |
| 32_G | 61_L | 1.274 | 0.99 |
| 38_K | 41_A | 1.264 | 0.99 |
| 33_V | 56_M | 1.221 | 0.98 |
| 38_K | 44_Y | 1.205 | 0.98 |
| 47_V | 74_L | 1.205 | 0.98 |
| 39_L | 65_I | 1.179 | 0.98 |
| 89_I | 93_Q | 1.177 | 0.98 |
| 85_K | 89_I | 1.168 | 0.97 |
| 36_L | 61_L | 1.164 | 0.97 |
| 6_D | 50_D | 1.147 | 0.97 |
| 57_D | 60_E | 1.146 | 0.97 |
| 78_M | 91_A | 1.110 | 0.96 |
| 79_V | 104_F | 1.096 | 0.96 |
| 84_K | 87_N | 1.089 | 0.96 |
| 64_T | 67_A | 1.089 | 0.96 |
| 62_L | 78_M | 1.085 | 0.96 |
| 108_T | 112_K | 1.072 | 0.95 |
| 59_L | 91_A | 1.059 | 0.95 |
| 2_L | 35_A | 1.040 | 0.94 |
| 29_A | 35_A | 1.030 | 0.94 |
| 90_A | 94_A | 1.020 | 0.93 |
| 8_S | 30_E | 1.016 | 0.93 |
| 59_L | 90_A | 1.013 | 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 | |
| 3cg4A | 1 | 0.9912 | 99.7 | -0.218 | Contact Map |
| 2zayA | 2 | 0.9912 | 99.7 | -0.215 | Contact Map |
| 4nicA | 4 | 0.9649 | 99.7 | -0.213 | Contact Map |
| 2qzjA | 6 | 0.9649 | 99.7 | -0.213 | Contact Map |
| 3c3mA | 1 | 0.9912 | 99.7 | -0.212 | Contact Map |
| 3crnA | 2 | 0.9649 | 99.7 | -0.211 | Contact Map |
| 3cfyA | 1 | 0.9737 | 99.7 | -0.209 | Contact Map |
| 3breA | 2 | 0.9912 | 99.7 | -0.208 | Contact Map |
| 2qxyA | 2 | 0.9649 | 99.6 | -0.184 | Contact Map |
| 2rjnA | 1 | 0.9737 | 99.6 | -0.182 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)