| e coli ycgr |
| ID: | 1487286111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 244 (232) | ||
| Sequences: | 1374 (1102.8) | ||
| Seq/Len: | 5.922 | ||
| Nf(neff/√len): | 72.4 |
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: 5.922).
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 |
| 186_A | 211_F | 4.142 | 1.00 |
| 86_V | 102_T | 3.498 | 1.00 |
| 53_L | 102_T | 2.996 | 1.00 |
| 84_F | 105_P | 2.277 | 1.00 |
| 187_Q | 212_R | 2.268 | 1.00 |
| 189_I | 210_S | 2.169 | 1.00 |
| 152_G | 208_R | 2.025 | 1.00 |
| 231_L | 234_E | 1.950 | 1.00 |
| 73_I | 84_F | 1.949 | 1.00 |
| 117_F | 233_R | 1.868 | 1.00 |
| 115_R | 212_R | 1.841 | 1.00 |
| 116_Y | 149_G | 1.839 | 1.00 |
| 217_S | 220_V | 1.761 | 1.00 |
| 86_V | 105_P | 1.749 | 1.00 |
| 119_I | 228_I | 1.719 | 1.00 |
| 187_Q | 214_L | 1.711 | 1.00 |
| 151_M | 211_F | 1.687 | 1.00 |
| 117_F | 232_E | 1.675 | 1.00 |
| 227_I | 231_L | 1.608 | 0.99 |
| 41_S | 56_G | 1.591 | 0.99 |
| 151_M | 213_F | 1.586 | 0.99 |
| 44_L | 99_A | 1.565 | 0.99 |
| 144_Y | 152_G | 1.564 | 0.99 |
| 74_T | 113_R | 1.561 | 0.99 |
| 149_G | 213_F | 1.553 | 0.99 |
| 168_R | 187_Q | 1.549 | 0.99 |
| 233_R | 236_R | 1.536 | 0.99 |
| 188_L | 211_F | 1.502 | 0.99 |
| 86_V | 103_V | 1.501 | 0.99 |
| 148_L | 224_L | 1.497 | 0.99 |
| 189_I | 212_R | 1.476 | 0.99 |
| 164_Q | 167_M | 1.444 | 0.99 |
| 105_P | 210_S | 1.428 | 0.98 |
| 172_I | 186_A | 1.424 | 0.98 |
| 148_L | 225_Q | 1.417 | 0.98 |
| 168_R | 185_D | 1.384 | 0.98 |
| 155_L | 209_L | 1.378 | 0.98 |
| 232_E | 236_R | 1.371 | 0.98 |
| 72_T | 83_E | 1.361 | 0.98 |
| 153_A | 211_F | 1.358 | 0.98 |
| 145_D | 152_G | 1.352 | 0.98 |
| 116_Y | 148_L | 1.349 | 0.98 |
| 23_L | 75_A | 1.344 | 0.97 |
| 148_L | 228_I | 1.335 | 0.97 |
| 185_D | 215_N | 1.329 | 0.97 |
| 148_L | 221_E | 1.327 | 0.97 |
| 50_K | 101_I | 1.307 | 0.97 |
| 32_L | 73_I | 1.304 | 0.97 |
| 5_H | 9_L | 1.297 | 0.97 |
| 77_T | 210_S | 1.286 | 0.96 |
| 121_A | 143_L | 1.286 | 0.96 |
| 190_S | 210_S | 1.276 | 0.96 |
| 10_K | 19_V | 1.257 | 0.96 |
| 10_K | 14_L | 1.242 | 0.95 |
| 6_E | 12_N | 1.237 | 0.95 |
| 163_L | 188_L | 1.231 | 0.95 |
| 74_T | 83_E | 1.230 | 0.95 |
| 33_S | 72_T | 1.221 | 0.95 |
| 127_Y | 143_L | 1.218 | 0.95 |
| 105_P | 108_L | 1.214 | 0.95 |
| 74_T | 81_K | 1.195 | 0.94 |
| 49_D | 169_F | 1.193 | 0.94 |
| 221_E | 225_Q | 1.185 | 0.94 |
| 44_L | 52_V | 1.182 | 0.94 |
| 234_E | 237_E | 1.181 | 0.94 |
| 128_F | 140_R | 1.179 | 0.93 |
| 48_P | 104_P | 1.167 | 0.93 |
| 84_F | 108_L | 1.166 | 0.93 |
| 169_F | 211_F | 1.160 | 0.93 |
| 96_Q | 113_R | 1.156 | 0.93 |
| 32_L | 39_L | 1.154 | 0.93 |
| 15_A | 18_G | 1.151 | 0.92 |
| 188_L | 209_L | 1.149 | 0.92 |
| 73_I | 86_V | 1.142 | 0.92 |
| 7_Q | 10_K | 1.138 | 0.92 |
| 120_S | 145_D | 1.135 | 0.92 |
| 51_L | 165_E | 1.131 | 0.92 |
| 29_P | 40_I | 1.128 | 0.91 |
| 178_Q | 230_S | 1.120 | 0.91 |
| 42_K | 54_D | 1.119 | 0.91 |
| 41_S | 55_F | 1.112 | 0.91 |
| 16_V | 21_R | 1.110 | 0.90 |
| 5_H | 8_F | 1.110 | 0.90 |
| 169_F | 188_L | 1.110 | 0.90 |
| 173_E | 181_V | 1.109 | 0.90 |
| 18_G | 21_R | 1.097 | 0.90 |
| 122_P | 142_R | 1.095 | 0.90 |
| 70_H | 85_T | 1.091 | 0.89 |
| 39_L | 56_G | 1.083 | 0.89 |
| 75_A | 82_V | 1.079 | 0.89 |
| 8_F | 11_Q | 1.077 | 0.89 |
| 6_E | 9_L | 1.076 | 0.89 |
| 32_L | 41_S | 1.075 | 0.89 |
| 70_H | 87_E | 1.073 | 0.88 |
| 218_P | 221_E | 1.067 | 0.88 |
| 84_F | 209_L | 1.062 | 0.88 |
| 14_L | 17_L | 1.058 | 0.87 |
| 143_L | 151_M | 1.056 | 0.87 |
| 9_L | 14_L | 1.056 | 0.87 |
| 127_Y | 141_F | 1.051 | 0.87 |
| 43_L | 46_I | 1.049 | 0.87 |
| 45_A | 96_Q | 1.046 | 0.87 |
| 139_L | 190_S | 1.045 | 0.87 |
| 231_L | 235_A | 1.043 | 0.86 |
| 11_Q | 14_L | 1.036 | 0.86 |
| 9_L | 19_V | 1.020 | 0.85 |
| 67_K | 164_Q | 1.016 | 0.84 |
| 47_T | 228_I | 1.015 | 0.84 |
| 16_V | 20_L | 1.015 | 0.84 |
| 5_H | 12_N | 1.013 | 0.84 |
| 108_L | 112_Q | 1.009 | 0.84 |
| 19_V | 22_D | 1.004 | 0.83 |
| 46_I | 113_R | 1.002 | 0.83 |
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 | |
| 3kyfA | 1 | 0.9139 | 100 | 0.252 | Contact Map |
| 2rdeA | 2 | 0.8607 | 99.9 | 0.37 | Contact Map |
| 4rt1A | 3 | 0.4344 | 99.5 | 0.628 | Contact Map |
| 4i86A | 2 | 0.4139 | 99.4 | 0.65 | Contact Map |
| 1ywuA | 1 | 0.4836 | 99.2 | 0.681 | Contact Map |
| 2l74A | 1 | 0.4754 | 99.1 | 0.687 | Contact Map |
| 4p02A | 1 | 0.9016 | 99.1 | 0.689 | Contact Map |
| 3ph1A | 4 | 0.7254 | 98.5 | 0.75 | Contact Map |
| 3cnrA | 2 | 0.3689 | 98.3 | 0.763 | Contact Map |
| 2l1tA | 1 | 0.418 | 95.5 | 0.845 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)