| GrpE |
| ID: | 1402261824 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 197 (189) | ||
| Sequences: | 3778 (3243) | ||
| Seq/Len: | 19.989 | ||
| Nf(neff/√len): | 235.9 |
Jackhmmer Results: (2014_04_16)
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: 19.989).
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 |
| 55_Q | 58_E | 3.265 | 1.00 |
| 141_V | 176_K | 2.998 | 1.00 |
| 143_A | 147_V | 2.678 | 1.00 |
| 140_E | 179_T | 2.594 | 1.00 |
| 47_L | 52_A | 2.537 | 1.00 |
| 94_E | 137_F | 2.533 | 1.00 |
| 60_D | 64_R | 2.446 | 1.00 |
| 101_S | 129_S | 2.362 | 1.00 |
| 175_Q | 189_M | 2.335 | 1.00 |
| 101_S | 104_R | 2.294 | 1.00 |
| 155_Q | 189_M | 2.233 | 1.00 |
| 132_D | 135_R | 2.088 | 1.00 |
| 135_R | 140_E | 2.050 | 1.00 |
| 48_E | 51_L | 1.995 | 1.00 |
| 94_E | 136_K | 1.949 | 1.00 |
| 160_V | 171_L | 1.947 | 1.00 |
| 172_G | 191_T | 1.932 | 1.00 |
| 144_E | 173_I | 1.871 | 1.00 |
| 72_L | 76_T | 1.867 | 1.00 |
| 158_A | 191_T | 1.827 | 1.00 |
| 162_S | 165_V | 1.823 | 1.00 |
| 69_M | 72_L | 1.820 | 1.00 |
| 54_A | 59_R | 1.765 | 1.00 |
| 51_L | 55_Q | 1.741 | 1.00 |
| 59_R | 63_L | 1.724 | 1.00 |
| 70_E | 73_R | 1.689 | 1.00 |
| 153_V | 179_T | 1.662 | 1.00 |
| 92_I | 139_V | 1.631 | 1.00 |
| 132_D | 136_K | 1.630 | 1.00 |
| 92_I | 185_I | 1.626 | 1.00 |
| 78_L | 82_K | 1.606 | 1.00 |
| 103_D | 176_K | 1.576 | 1.00 |
| 74_R | 78_L | 1.569 | 1.00 |
| 103_D | 127_L | 1.567 | 1.00 |
| 52_A | 56_T | 1.535 | 1.00 |
| 161_E | 194_K | 1.511 | 1.00 |
| 67_A | 71_N | 1.510 | 1.00 |
| 44_V | 47_L | 1.509 | 1.00 |
| 44_V | 48_E | 1.499 | 1.00 |
| 104_R | 107_E | 1.495 | 1.00 |
| 166_A | 169_N | 1.474 | 1.00 |
| 124_E | 128_K | 1.471 | 1.00 |
| 160_V | 191_T | 1.466 | 1.00 |
| 53_E | 57_R | 1.466 | 1.00 |
| 142_I | 184_T | 1.459 | 1.00 |
| 88_L | 91_F | 1.457 | 1.00 |
| 167_P | 195_A | 1.435 | 1.00 |
| 171_L | 193_A | 1.421 | 1.00 |
| 70_E | 74_R | 1.413 | 1.00 |
| 105_A | 123_I | 1.405 | 0.99 |
| 49_A | 52_A | 1.371 | 0.99 |
| 162_S | 193_A | 1.359 | 0.99 |
| 65_V | 69_M | 1.354 | 0.99 |
| 43_K | 48_E | 1.354 | 0.99 |
| 89_E | 183_R | 1.317 | 0.99 |
| 118_A | 121_E | 1.309 | 0.99 |
| 48_E | 52_A | 1.297 | 0.99 |
| 100_D | 186_R | 1.274 | 0.99 |
| 64_R | 67_A | 1.265 | 0.99 |
| 56_T | 60_D | 1.252 | 0.99 |
| 150_D | 153_V | 1.251 | 0.99 |
| 145_T | 173_I | 1.241 | 0.98 |
| 148_P | 169_N | 1.239 | 0.98 |
| 179_T | 182_G | 1.239 | 0.98 |
| 91_F | 137_F | 1.233 | 0.98 |
| 140_E | 182_G | 1.227 | 0.98 |
| 50_Q | 54_A | 1.227 | 0.98 |
| 47_L | 50_Q | 1.224 | 0.98 |
| 159_M | 168_G | 1.217 | 0.98 |
| 46_N | 50_Q | 1.216 | 0.98 |
| 57_R | 61_G | 1.207 | 0.98 |
| 81_E | 85_K | 1.202 | 0.98 |
| 98_V | 133_V | 1.200 | 0.98 |
| 165_V | 193_A | 1.195 | 0.98 |
| 144_E | 147_V | 1.188 | 0.98 |
| 62_I | 66_K | 1.176 | 0.98 |
| 62_I | 65_V | 1.176 | 0.98 |
| 174_M | 191_T | 1.167 | 0.97 |
| 61_G | 66_K | 1.151 | 0.97 |
| 114_P | 117_S | 1.145 | 0.97 |
| 77_E | 81_E | 1.141 | 0.97 |
| 165_V | 169_N | 1.136 | 0.97 |
| 160_V | 172_G | 1.118 | 0.96 |
| 121_E | 124_E | 1.111 | 0.96 |
| 139_V | 180_L | 1.110 | 0.96 |
| 76_T | 80_I | 1.108 | 0.96 |
| 80_I | 83_A | 1.106 | 0.96 |
| 165_V | 171_L | 1.106 | 0.96 |
| 99_I | 178_Y | 1.095 | 0.96 |
| 58_E | 62_I | 1.083 | 0.96 |
| 134_V | 139_V | 1.079 | 0.95 |
| 42_E | 46_N | 1.077 | 0.95 |
| 141_V | 173_I | 1.072 | 0.95 |
| 85_K | 181_N | 1.070 | 0.95 |
| 157_I | 189_M | 1.061 | 0.95 |
| 154_H | 170_V | 1.055 | 0.95 |
| 102_L | 127_L | 1.052 | 0.95 |
| 102_L | 126_T | 1.049 | 0.94 |
| 86_F | 183_R | 1.040 | 0.94 |
| 15_E | 18_I | 1.039 | 0.94 |
| 80_I | 84_H | 1.038 | 0.94 |
| 159_M | 194_K | 1.034 | 0.94 |
| 173_I | 188_A | 1.028 | 0.94 |
| 54_A | 57_R | 1.027 | 0.94 |
| 128_K | 132_D | 1.018 | 0.93 |
| 144_E | 188_A | 1.017 | 0.93 |
| 149_L | 156_A | 1.016 | 0.93 |
| 65_V | 72_L | 1.015 | 0.93 |
| 86_F | 181_N | 1.001 | 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 | |
| 1dkgA | 2 | 0.802 | 100 | 0.057 | Contact Map |
| 4aniA | 4 | 0.7919 | 100 | 0.1 | Contact Map |
| 3a6mA | 2 | 0.8528 | 100 | 0.153 | Contact Map |
| 2dfsA | 2 | 0.6091 | 45.5 | 0.92 | Contact Map |
| 2ve7A | 2 | 0.6447 | 39.7 | 0.923 | Contact Map |
| 3vkgA | 2 | 0.9137 | 33.2 | 0.926 | Contact Map |
| 2r80A | 2 | 0.6701 | 26 | 0.93 | Contact Map |
| 2w72C | 1 | 0.6701 | 23.8 | 0.931 | Contact Map |
| 3swyA | 3 | 0.2335 | 23.6 | 0.931 | Contact Map |
| 1gcvB | 2 | 0.6701 | 22.9 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)