| ECOLI_YQFA |
| ID: | 1505325490 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 219 (213) | ||
| Sequences: | 3858 (2503.4) | ||
| Seq/Len: | 18.113 | ||
| Nf(neff/√len): | 171.5 |
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: 18.113).
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 |
| 65_F | 205_S | 3.730 | 1.00 |
| 177_V | 207_C | 3.225 | 1.00 |
| 26_G | 202_L | 2.697 | 1.00 |
| 60_S | 97_G | 2.678 | 1.00 |
| 150_W | 179_S | 2.632 | 1.00 |
| 146_L | 179_S | 2.626 | 1.00 |
| 102_F | 211_A | 2.564 | 1.00 |
| 34_L | 58_G | 2.502 | 1.00 |
| 177_V | 203_G | 2.467 | 1.00 |
| 27_L | 62_I | 2.434 | 1.00 |
| 27_L | 66_L | 2.398 | 1.00 |
| 177_V | 204_G | 2.297 | 1.00 |
| 117_I | 121_S | 2.246 | 1.00 |
| 16_E | 19_N | 2.173 | 1.00 |
| 48_A | 52_T | 2.090 | 1.00 |
| 55_S | 59_G | 2.075 | 1.00 |
| 20_S | 73_A | 2.074 | 1.00 |
| 113_R | 117_I | 1.976 | 1.00 |
| 199_G | 203_G | 1.928 | 1.00 |
| 146_L | 182_V | 1.870 | 1.00 |
| 100_T | 120_W | 1.865 | 1.00 |
| 169_T | 173_V | 1.821 | 1.00 |
| 110_P | 114_G | 1.752 | 1.00 |
| 165_A | 169_T | 1.735 | 1.00 |
| 130_K | 141_S | 1.731 | 1.00 |
| 190_I | 193_N | 1.729 | 1.00 |
| 187_C | 190_I | 1.708 | 1.00 |
| 22_S | 199_G | 1.695 | 1.00 |
| 206_V | 210_L | 1.668 | 1.00 |
| 71_Y | 84_K | 1.667 | 1.00 |
| 93_L | 127_I | 1.655 | 1.00 |
| 114_G | 118_V | 1.622 | 1.00 |
| 60_S | 93_L | 1.612 | 1.00 |
| 82_W | 86_F | 1.596 | 1.00 |
| 19_N | 22_S | 1.590 | 1.00 |
| 35_V | 39_V | 1.588 | 1.00 |
| 170_L | 210_L | 1.580 | 1.00 |
| 18_A | 195_A | 1.566 | 1.00 |
| 113_R | 116_M | 1.546 | 1.00 |
| 12_S | 15_E | 1.538 | 1.00 |
| 185_Y | 188_K | 1.532 | 1.00 |
| 61_M | 205_S | 1.520 | 1.00 |
| 67_A | 86_F | 1.496 | 1.00 |
| 194_H | 198_H | 1.480 | 1.00 |
| 155_V | 158_E | 1.479 | 1.00 |
| 170_L | 207_C | 1.469 | 1.00 |
| 51_I | 55_S | 1.457 | 1.00 |
| 182_V | 197_W | 1.417 | 1.00 |
| 14_A | 192_Y | 1.401 | 0.99 |
| 13_L | 17_I | 1.396 | 0.99 |
| 168_V | 172_A | 1.392 | 0.99 |
| 61_M | 94_L | 1.371 | 0.99 |
| 96_A | 123_A | 1.369 | 0.99 |
| 14_A | 17_I | 1.358 | 0.99 |
| 173_V | 177_V | 1.349 | 0.99 |
| 167_S | 215_Y | 1.341 | 0.99 |
| 105_V | 216_I | 1.335 | 0.99 |
| 96_A | 120_W | 1.329 | 0.99 |
| 114_G | 117_I | 1.308 | 0.99 |
| 66_L | 70_L | 1.287 | 0.99 |
| 34_L | 62_I | 1.269 | 0.99 |
| 24_G | 69_T | 1.265 | 0.99 |
| 122_L | 148_M | 1.253 | 0.99 |
| 33_G | 209_F | 1.245 | 0.98 |
| 108_D | 112_A | 1.243 | 0.98 |
| 22_S | 195_A | 1.242 | 0.98 |
| 60_S | 94_L | 1.238 | 0.98 |
| 203_G | 207_C | 1.232 | 0.98 |
| 50_A | 105_V | 1.231 | 0.98 |
| 173_V | 207_C | 1.199 | 0.98 |
| 157_Y | 161_V | 1.195 | 0.98 |
| 62_I | 66_L | 1.180 | 0.98 |
| 172_A | 176_V | 1.175 | 0.98 |
| 67_A | 90_A | 1.174 | 0.98 |
| 209_F | 213_Y | 1.170 | 0.97 |
| 178_Y | 205_S | 1.166 | 0.97 |
| 103_L | 107_L | 1.151 | 0.97 |
| 40_Q | 213_Y | 1.138 | 0.97 |
| 92_Y | 126_G | 1.137 | 0.97 |
| 111_L | 158_E | 1.133 | 0.97 |
| 33_G | 37_L | 1.132 | 0.97 |
| 109_S | 112_A | 1.129 | 0.97 |
| 119_I | 148_M | 1.128 | 0.97 |
| 52_T | 55_S | 1.119 | 0.96 |
| 16_E | 22_S | 1.119 | 0.96 |
| 30_G | 61_M | 1.113 | 0.96 |
| 17_I | 21_V | 1.110 | 0.96 |
| 115_L | 155_V | 1.100 | 0.96 |
| 57_Y | 61_M | 1.097 | 0.96 |
| 128_L | 132_T | 1.091 | 0.96 |
| 138_K | 188_K | 1.082 | 0.96 |
| 49_T | 108_D | 1.080 | 0.95 |
| 38_L | 55_S | 1.078 | 0.95 |
| 21_V | 24_G | 1.071 | 0.95 |
| 53_S | 104_L | 1.070 | 0.95 |
| 95_I | 178_Y | 1.047 | 0.94 |
| 64_L | 94_L | 1.041 | 0.94 |
| 18_A | 22_S | 1.039 | 0.94 |
| 149_G | 175_G | 1.034 | 0.94 |
| 111_L | 114_G | 1.020 | 0.93 |
| 205_S | 208_H | 1.018 | 0.93 |
| 14_A | 18_A | 1.007 | 0.93 |
| 126_G | 144_T | 1.003 | 0.93 |
| 103_L | 115_L | 1.002 | 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 | |
| 3wxwA | 1 | 0.9817 | 100 | 0.188 | Contact Map |
| 4fbzA | 1 | 0.274 | 1.5 | 0.965 | Contact Map |
| 2auvA | 1 | 0.1324 | 1.2 | 0.967 | Contact Map |
| 2lifA | 1 | 0.1233 | 0.9 | 0.97 | Contact Map |
| 2ls2A | 1 | 0.1142 | 0.9 | 0.97 | Contact Map |
| 3pjzA | 2 | 0.4018 | 0.8 | 0.971 | Contact Map |
| 2losA | 1 | 0.4977 | 0.8 | 0.971 | Contact Map |
| 2nlkA | 1 | 0.0913 | 0.8 | 0.972 | Contact Map |
| 3dwlE | 2 | 0.1142 | 0.8 | 0.972 | Contact Map |
| 2mmuA | 1 | 0.2146 | 0.7 | 0.972 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)