| E coli W3110 ExbB |
| ID: | 1509882255 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 244 (220) | ||
| Sequences: | 3998 (2338.5) | ||
| Seq/Len: | 18.173 | ||
| Nf(neff/√len): | 157.7 |
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: 18.173).
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 |
| 67_S | 70_Q | 3.540 | 1.00 |
| 41_F | 194_I | 3.486 | 1.00 |
| 86_H | 122_V | 3.325 | 1.00 |
| 42_F | 46_V | 3.258 | 1.00 |
| 154_N | 176_E | 3.225 | 1.00 |
| 135_T | 193_V | 3.056 | 1.00 |
| 137_G | 192_V | 2.859 | 1.00 |
| 132_Y | 136_I | 2.515 | 1.00 |
| 37_T | 191_A | 2.438 | 1.00 |
| 44_K | 47_E | 2.408 | 1.00 |
| 123_G | 206_K | 2.114 | 1.00 |
| 185_L | 189_I | 2.082 | 1.00 |
| 26_V | 146_F | 1.979 | 1.00 |
| 91_A | 115_L | 1.857 | 1.00 |
| 135_T | 196_N | 1.813 | 1.00 |
| 155_S | 173_G | 1.808 | 1.00 |
| 40_I | 132_Y | 1.729 | 1.00 |
| 121_A | 211_D | 1.702 | 1.00 |
| 30_L | 187_A | 1.650 | 1.00 |
| 157_I | 175_A | 1.636 | 1.00 |
| 13_W | 17_Q | 1.615 | 1.00 |
| 27_M | 183_I | 1.612 | 1.00 |
| 37_T | 41_F | 1.597 | 1.00 |
| 90_E | 118_R | 1.580 | 1.00 |
| 122_V | 125_Q | 1.568 | 1.00 |
| 142_F | 152_I | 1.559 | 1.00 |
| 130_N | 202_I | 1.513 | 1.00 |
| 34_S | 38_W | 1.505 | 1.00 |
| 139_I | 193_V | 1.505 | 1.00 |
| 119_V | 123_G | 1.464 | 1.00 |
| 51_Q | 205_F | 1.423 | 1.00 |
| 48_F | 202_I | 1.418 | 1.00 |
| 62_L | 212_V | 1.383 | 0.99 |
| 197_V | 201_Q | 1.364 | 0.99 |
| 49_F | 53_R | 1.355 | 0.99 |
| 118_R | 122_V | 1.338 | 0.99 |
| 58_E | 62_L | 1.338 | 0.99 |
| 19_A | 23_V | 1.331 | 0.99 |
| 87_L | 118_R | 1.328 | 0.99 |
| 91_A | 114_R | 1.319 | 0.99 |
| 9_D | 14_G | 1.311 | 0.99 |
| 146_F | 186_V | 1.305 | 0.99 |
| 37_T | 133_L | 1.276 | 0.99 |
| 149_V | 181_T | 1.275 | 0.99 |
| 19_A | 179_L | 1.266 | 0.99 |
| 126_M | 202_I | 1.259 | 0.99 |
| 150_W | 176_E | 1.249 | 0.99 |
| 33_A | 143_V | 1.232 | 0.98 |
| 20_D | 154_N | 1.231 | 0.98 |
| 156_F | 173_G | 1.226 | 0.98 |
| 119_V | 213_A | 1.225 | 0.98 |
| 28_I | 32_L | 1.210 | 0.98 |
| 30_L | 143_V | 1.208 | 0.98 |
| 14_G | 18_H | 1.202 | 0.98 |
| 20_D | 24_K | 1.202 | 0.98 |
| 177_A | 181_T | 1.201 | 0.98 |
| 31_I | 35_V | 1.198 | 0.98 |
| 61_L | 65_A | 1.196 | 0.98 |
| 30_L | 34_S | 1.165 | 0.97 |
| 131_G | 200_R | 1.156 | 0.97 |
| 98_S | 110_R | 1.156 | 0.97 |
| 142_F | 188_A | 1.151 | 0.97 |
| 34_S | 39_A | 1.148 | 0.97 |
| 50_N | 54_R | 1.145 | 0.97 |
| 156_F | 175_A | 1.143 | 0.97 |
| 158_G | 169_V | 1.125 | 0.97 |
| 87_L | 209_L | 1.125 | 0.97 |
| 138_A | 192_V | 1.119 | 0.96 |
| 8_T | 14_G | 1.115 | 0.96 |
| 48_F | 205_F | 1.112 | 0.96 |
| 172_P | 176_E | 1.111 | 0.96 |
| 30_L | 183_I | 1.107 | 0.96 |
| 134_A | 195_Y | 1.105 | 0.96 |
| 117_R | 211_D | 1.101 | 0.96 |
| 52_K | 201_Q | 1.097 | 0.96 |
| 70_Q | 73_D | 1.096 | 0.96 |
| 32_L | 36_V | 1.094 | 0.96 |
| 195_Y | 199_A | 1.093 | 0.96 |
| 21_I | 25_C | 1.090 | 0.96 |
| 139_I | 143_V | 1.085 | 0.96 |
| 59_Q | 63_A | 1.080 | 0.95 |
| 76_A | 89_N | 1.073 | 0.95 |
| 14_G | 17_Q | 1.073 | 0.95 |
| 35_V | 39_A | 1.070 | 0.95 |
| 45_S | 49_F | 1.069 | 0.95 |
| 124_R | 207_A | 1.064 | 0.95 |
| 145_L | 188_A | 1.063 | 0.95 |
| 146_F | 150_W | 1.063 | 0.95 |
| 83_L | 122_V | 1.053 | 0.95 |
| 110_R | 216_V | 1.052 | 0.95 |
| 70_Q | 74_I | 1.051 | 0.94 |
| 83_L | 209_L | 1.049 | 0.94 |
| 25_C | 29_G | 1.045 | 0.94 |
| 137_G | 190_P | 1.045 | 0.94 |
| 37_T | 194_I | 1.044 | 0.94 |
| 162_T | 169_V | 1.037 | 0.94 |
| 146_F | 182_A | 1.032 | 0.94 |
| 91_A | 216_V | 1.028 | 0.94 |
| 36_V | 132_Y | 1.023 | 0.93 |
| 203_G | 206_K | 1.021 | 0.93 |
| 43_S | 47_E | 1.020 | 0.93 |
| 128_R | 204_G | 1.018 | 0.93 |
| 194_I | 198_F | 1.018 | 0.93 |
| 82_S | 85_L | 1.016 | 0.93 |
| 145_L | 175_A | 1.012 | 0.93 |
| 139_I | 192_V | 1.012 | 0.93 |
| 131_G | 134_A | 1.003 | 0.93 |
| 150_W | 182_A | 1.003 | 0.93 |
| 71_A | 75_A | 1.001 | 0.92 |
| 91_A | 95_L | 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 | |
| 4tllB | 2 | 0.0123 | 10.3 | 0.958 | Contact Map |
| 4f4sA | 10 | 0.2664 | 4.2 | 0.965 | Contact Map |
| 1pi7A | 1 | 0.0779 | 4 | 0.965 | Contact Map |
| 4av3A | 2 | 0.4262 | 3.5 | 0.966 | Contact Map |
| 4i5sA | 2 | 0.8033 | 3.5 | 0.966 | Contact Map |
| 4cbkA | 13 | 0.2377 | 3.3 | 0.966 | Contact Map |
| 3hlsA | 8 | 0.2459 | 3.3 | 0.967 | Contact Map |
| 4mndA | 1 | 0.2049 | 3 | 0.967 | Contact Map |
| 2kncA | 1 | 0.2131 | 3 | 0.967 | Contact Map |
| 3b5mA | 4 | 0.2787 | 2.9 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)