| 4pgrA |
| ID: | 1491921490 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (205) | ||
| Sequences: | 3303 (1978.8) | ||
| Seq/Len: | 16.112 | ||
| Nf(neff/√len): | 138.2 |
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: 16.112).
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 |
| 155_G | 197_N | 3.301 | 1.00 |
| 12_L | 167_L | 3.169 | 1.00 |
| 121_W | 165_Y | 2.739 | 1.00 |
| 107_G | 167_L | 2.606 | 1.00 |
| 18_T | 65_V | 2.245 | 1.00 |
| 98_S | 202_F | 2.227 | 1.00 |
| 42_I | 46_A | 2.219 | 1.00 |
| 12_L | 107_G | 2.179 | 1.00 |
| 44_E | 72_S | 2.109 | 1.00 |
| 166_D | 190_D | 2.087 | 1.00 |
| 135_G | 151_Y | 2.078 | 1.00 |
| 156_T | 194_L | 2.073 | 1.00 |
| 105_V | 129_L | 2.067 | 1.00 |
| 153_V | 201_F | 1.992 | 1.00 |
| 106_L | 160_S | 1.967 | 1.00 |
| 80_V | 92_V | 1.967 | 1.00 |
| 124_L | 161_L | 1.937 | 1.00 |
| 83_Y | 203_G | 1.913 | 1.00 |
| 163_I | 194_L | 1.902 | 1.00 |
| 95_A | 198_L | 1.852 | 1.00 |
| 22_A | 188_Y | 1.850 | 1.00 |
| 95_A | 201_F | 1.743 | 1.00 |
| 196_I | 200_R | 1.738 | 1.00 |
| 124_L | 165_Y | 1.726 | 1.00 |
| 189_L | 193_N | 1.721 | 1.00 |
| 154_I | 158_V | 1.712 | 1.00 |
| 16_V | 104_A | 1.707 | 1.00 |
| 131_L | 155_G | 1.704 | 1.00 |
| 108_T | 112_K | 1.686 | 1.00 |
| 107_G | 111_A | 1.681 | 1.00 |
| 153_V | 157_I | 1.646 | 1.00 |
| 23_T | 97_G | 1.634 | 1.00 |
| 146_A | 150_A | 1.622 | 1.00 |
| 50_L | 54_M | 1.613 | 1.00 |
| 125_L | 129_L | 1.605 | 1.00 |
| 166_D | 169_Q | 1.592 | 1.00 |
| 101_V | 133_V | 1.484 | 1.00 |
| 63_A | 67_T | 1.466 | 1.00 |
| 187_L | 190_D | 1.457 | 1.00 |
| 44_E | 75_T | 1.437 | 1.00 |
| 137_F | 141_S | 1.429 | 1.00 |
| 117_L | 164_L | 1.406 | 0.99 |
| 60_V | 64_F | 1.403 | 0.99 |
| 148_M | 200_R | 1.403 | 0.99 |
| 113_M | 117_L | 1.396 | 0.99 |
| 166_D | 189_L | 1.381 | 0.99 |
| 97_G | 101_V | 1.378 | 0.99 |
| 150_A | 154_I | 1.377 | 0.99 |
| 149_M | 201_F | 1.371 | 0.99 |
| 46_A | 50_L | 1.369 | 0.99 |
| 169_Q | 186_S | 1.367 | 0.99 |
| 10_R | 180_I | 1.347 | 0.99 |
| 160_S | 194_L | 1.344 | 0.99 |
| 110_G | 168_N | 1.314 | 0.99 |
| 98_S | 198_L | 1.313 | 0.99 |
| 95_A | 98_S | 1.310 | 0.99 |
| 129_L | 133_V | 1.294 | 0.99 |
| 134_V | 151_Y | 1.282 | 0.99 |
| 25_G | 70_F | 1.278 | 0.99 |
| 109_I | 113_M | 1.277 | 0.99 |
| 62_Y | 66_Y | 1.273 | 0.99 |
| 168_N | 172_H | 1.272 | 0.99 |
| 38_L | 42_I | 1.254 | 0.99 |
| 14_V | 62_Y | 1.252 | 0.99 |
| 113_M | 168_N | 1.247 | 0.99 |
| 169_Q | 190_D | 1.243 | 0.98 |
| 109_I | 115_K | 1.239 | 0.98 |
| 68_F | 72_S | 1.228 | 0.98 |
| 120_L | 124_L | 1.212 | 0.98 |
| 131_L | 158_V | 1.204 | 0.98 |
| 60_V | 63_A | 1.202 | 0.98 |
| 18_T | 69_A | 1.190 | 0.98 |
| 198_L | 202_F | 1.189 | 0.98 |
| 128_V | 132_A | 1.174 | 0.98 |
| 132_A | 136_I | 1.162 | 0.97 |
| 197_N | 200_R | 1.156 | 0.97 |
| 49_I | 53_W | 1.152 | 0.97 |
| 67_T | 71_V | 1.147 | 0.97 |
| 102_I | 106_L | 1.143 | 0.97 |
| 27_F | 31_F | 1.138 | 0.97 |
| 138_N | 141_S | 1.125 | 0.97 |
| 138_N | 144_N | 1.118 | 0.96 |
| 159_F | 193_N | 1.118 | 0.96 |
| 58_K | 62_Y | 1.114 | 0.96 |
| 3_S | 174_H | 1.102 | 0.96 |
| 128_V | 189_L | 1.096 | 0.96 |
| 157_I | 161_L | 1.095 | 0.96 |
| 159_F | 189_L | 1.092 | 0.96 |
| 50_L | 64_F | 1.089 | 0.96 |
| 152_S | 200_R | 1.086 | 0.96 |
| 170_I | 187_L | 1.085 | 0.96 |
| 21_I | 66_Y | 1.082 | 0.96 |
| 102_I | 105_V | 1.073 | 0.95 |
| 136_I | 139_I | 1.069 | 0.95 |
| 93_L | 97_G | 1.067 | 0.95 |
| 152_S | 156_T | 1.067 | 0.95 |
| 76_L | 196_I | 1.050 | 0.94 |
| 41_S | 45_V | 1.047 | 0.94 |
| 4_K | 174_H | 1.045 | 0.94 |
| 119_F | 122_S | 1.043 | 0.94 |
| 159_F | 166_D | 1.031 | 0.94 |
| 4_K | 7_I | 1.029 | 0.94 |
| 123_F | 127_A | 1.028 | 0.94 |
| 149_M | 153_V | 1.028 | 0.94 |
| 43_L | 71_V | 1.022 | 0.93 |
| 47_M | 71_V | 1.019 | 0.93 |
| 43_L | 46_A | 1.006 | 0.93 |
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 | |
| 4pgrA | 1 | 0.9903 | 100 | 0.068 | Contact Map |
| 4ev6A | 5 | 0.2899 | 7.7 | 0.941 | Contact Map |
| 4i0uA | 10 | 0.2802 | 4.2 | 0.948 | Contact Map |
| 1r8hA | 6 | 0.1401 | 2.6 | 0.953 | Contact Map |
| 3b5dA | 2 | 0.0242 | 1.6 | 0.958 | Contact Map |
| 2xq2A | 1 | 0.7729 | 1.3 | 0.96 | Contact Map |
| 3w9iA | 6 | 0.7246 | 1.2 | 0.961 | Contact Map |
| 3ne5A | 1 | 0.7246 | 1.2 | 0.961 | Contact Map |
| 4dx5A | 3 | 0.7729 | 1.2 | 0.961 | Contact Map |
| 4n7wA | 2 | 0.43 | 1 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)