| FLIL_ECOLI |
| ID: | 1424817452 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 154 (152) | ||
| Sequences: | 1411 (1138.7) | ||
| Seq/Len: | 9.283 | ||
| Nf(neff/√len): | 92.4 |
Jackhmmer Results: (2015_01_07)
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: 9.283).
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 |
| 29_S | 33_S | 3.069 | 1.00 |
| 32_Y | 36_H | 2.936 | 1.00 |
| 108_Q | 125_E | 2.779 | 1.00 |
| 28_A | 32_Y | 2.319 | 1.00 |
| 30_A | 34_Y | 2.270 | 1.00 |
| 25_A | 29_S | 2.057 | 1.00 |
| 84_E | 88_S | 2.012 | 1.00 |
| 15_W | 19_L | 2.007 | 1.00 |
| 22_I | 25_A | 1.976 | 1.00 |
| 109_D | 112_V | 1.949 | 1.00 |
| 106_S | 119_K | 1.947 | 1.00 |
| 74_Y | 150_A | 1.904 | 1.00 |
| 88_S | 91_S | 1.901 | 1.00 |
| 80_R | 96_E | 1.861 | 1.00 |
| 99_S | 123_I | 1.811 | 1.00 |
| 57_Y | 81_L | 1.799 | 1.00 |
| 27_C | 31_G | 1.763 | 1.00 |
| 108_Q | 112_V | 1.728 | 1.00 |
| 26_A | 30_A | 1.721 | 1.00 |
| 23_T | 26_A | 1.705 | 1.00 |
| 101_L | 126_I | 1.692 | 1.00 |
| 79_L | 130_L | 1.637 | 1.00 |
| 29_S | 32_Y | 1.636 | 1.00 |
| 64_V | 73_L | 1.570 | 1.00 |
| 85_A | 88_S | 1.559 | 1.00 |
| 131_S | 141_Q | 1.520 | 1.00 |
| 31_G | 35_W | 1.491 | 1.00 |
| 87_R | 91_S | 1.452 | 1.00 |
| 11_K | 14_L | 1.439 | 1.00 |
| 14_L | 18_I | 1.412 | 0.99 |
| 59_L | 98_R | 1.410 | 0.99 |
| 24_L | 27_C | 1.409 | 0.99 |
| 93_Y | 96_E | 1.354 | 0.99 |
| 9_K | 13_S | 1.350 | 0.99 |
| 22_I | 26_A | 1.343 | 0.99 |
| 129_T | 132_T | 1.342 | 0.99 |
| 11_K | 15_W | 1.340 | 0.99 |
| 104_L | 126_I | 1.297 | 0.99 |
| 105_F | 126_I | 1.268 | 0.98 |
| 12_R | 16_I | 1.266 | 0.98 |
| 62_F | 98_R | 1.259 | 0.98 |
| 16_I | 20_V | 1.258 | 0.98 |
| 127_K | 146_V | 1.254 | 0.98 |
| 34_Y | 38_H | 1.252 | 0.98 |
| 60_D | 98_R | 1.246 | 0.98 |
| 101_L | 105_F | 1.226 | 0.98 |
| 18_I | 25_A | 1.223 | 0.98 |
| 68_D | 71_R | 1.208 | 0.98 |
| 89_R | 141_Q | 1.205 | 0.98 |
| 27_C | 30_A | 1.173 | 0.97 |
| 66_L | 99_S | 1.171 | 0.97 |
| 148_Y | 151_F | 1.167 | 0.97 |
| 134_L | 141_Q | 1.156 | 0.97 |
| 33_S | 37_S | 1.155 | 0.97 |
| 10_S | 13_S | 1.148 | 0.97 |
| 59_L | 97_V | 1.145 | 0.97 |
| 30_A | 33_S | 1.139 | 0.96 |
| 77_I | 126_I | 1.113 | 0.96 |
| 84_E | 87_R | 1.102 | 0.95 |
| 88_S | 92_E | 1.081 | 0.95 |
| 58_A | 78_T | 1.070 | 0.94 |
| 73_L | 105_F | 1.069 | 0.94 |
| 77_I | 148_Y | 1.069 | 0.94 |
| 12_R | 19_L | 1.067 | 0.94 |
| 13_S | 18_I | 1.067 | 0.94 |
| 13_S | 16_I | 1.065 | 0.94 |
| 6_I | 19_L | 1.065 | 0.94 |
| 20_V | 27_C | 1.059 | 0.94 |
| 131_S | 134_L | 1.053 | 0.94 |
| 63_T | 74_Y | 1.051 | 0.94 |
| 99_S | 103_L | 1.049 | 0.94 |
| 113_L | 153_L | 1.049 | 0.94 |
| 17_P | 20_V | 1.028 | 0.93 |
| 7_S | 10_S | 1.015 | 0.92 |
| 10_S | 15_W | 1.013 | 0.92 |
| 64_V | 105_F | 1.010 | 0.92 |
| 98_R | 102_L | 1.010 | 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 | |
| 3ne5B | 2 | 0.4091 | 57 | 0.909 | Contact Map |
| 3j6da | 24 | 0 | 45 | 0.915 | Contact Map |
| 2mfrA | 1 | 0.3377 | 34.2 | 0.92 | Contact Map |
| 2m8rA | 1 | 0.2403 | 28.4 | 0.924 | Contact Map |
| 4fvgA | 1 | 0.6688 | 21.2 | 0.928 | Contact Map |
| 3vmtA | 2 | 0.8117 | 17.8 | 0.93 | Contact Map |
| 3owqA | 4 | 0.487 | 12.6 | 0.935 | Contact Map |
| 3ayfA | 1 | 0.8442 | 12.5 | 0.935 | Contact Map |
| 1winA | 1 | 0.6623 | 12.4 | 0.935 | Contact Map |
| 4dvyP | 1 | 0.461 | 11.3 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)