| 4pgr |
| ID: | 1500381611 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 207 (207) | ||
| Sequences: | 4199 (2408.5) | ||
| Seq/Len: | 20.285 | ||
| Nf(neff/√len): | 167.4 |
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: 20.285).
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 | 3.126 | 1.00 |
| 12_L | 167_L | 3.097 | 1.00 |
| 107_G | 167_L | 2.425 | 1.00 |
| 121_W | 165_Y | 2.406 | 1.00 |
| 42_I | 46_A | 2.371 | 1.00 |
| 83_Y | 203_G | 2.234 | 1.00 |
| 156_T | 194_L | 2.182 | 1.00 |
| 153_V | 157_I | 2.172 | 1.00 |
| 80_V | 92_V | 2.163 | 1.00 |
| 98_S | 202_F | 2.134 | 1.00 |
| 18_T | 65_V | 2.026 | 1.00 |
| 166_D | 190_D | 2.015 | 1.00 |
| 131_L | 155_G | 1.981 | 1.00 |
| 12_L | 107_G | 1.948 | 1.00 |
| 43_L | 71_V | 1.947 | 1.00 |
| 124_L | 161_L | 1.942 | 1.00 |
| 106_L | 160_S | 1.930 | 1.00 |
| 153_V | 201_F | 1.920 | 1.00 |
| 44_E | 72_S | 1.906 | 1.00 |
| 124_L | 165_Y | 1.825 | 1.00 |
| 46_A | 50_L | 1.817 | 1.00 |
| 125_L | 129_L | 1.802 | 1.00 |
| 146_A | 150_A | 1.784 | 1.00 |
| 105_V | 129_L | 1.775 | 1.00 |
| 95_A | 198_L | 1.760 | 1.00 |
| 163_I | 194_L | 1.756 | 1.00 |
| 135_G | 151_Y | 1.733 | 1.00 |
| 150_A | 154_I | 1.700 | 1.00 |
| 129_L | 133_V | 1.629 | 1.00 |
| 128_V | 162_Y | 1.605 | 1.00 |
| 22_A | 188_Y | 1.565 | 1.00 |
| 16_V | 104_A | 1.564 | 1.00 |
| 107_G | 111_A | 1.541 | 1.00 |
| 95_A | 201_F | 1.511 | 1.00 |
| 166_D | 169_Q | 1.478 | 1.00 |
| 108_T | 112_K | 1.476 | 1.00 |
| 196_I | 200_R | 1.475 | 1.00 |
| 102_I | 198_L | 1.471 | 1.00 |
| 128_V | 132_A | 1.460 | 1.00 |
| 63_A | 67_T | 1.454 | 1.00 |
| 189_L | 193_N | 1.449 | 1.00 |
| 131_L | 158_V | 1.439 | 1.00 |
| 168_N | 172_H | 1.424 | 1.00 |
| 60_V | 64_F | 1.422 | 1.00 |
| 49_I | 53_W | 1.415 | 1.00 |
| 98_S | 198_L | 1.410 | 1.00 |
| 44_E | 75_T | 1.410 | 1.00 |
| 23_T | 97_G | 1.401 | 0.99 |
| 170_I | 187_L | 1.399 | 0.99 |
| 198_L | 202_F | 1.396 | 0.99 |
| 117_L | 164_L | 1.377 | 0.99 |
| 91_V | 202_F | 1.375 | 0.99 |
| 48_I | 52_F | 1.373 | 0.99 |
| 154_I | 158_V | 1.372 | 0.99 |
| 157_I | 161_L | 1.368 | 0.99 |
| 101_V | 133_V | 1.362 | 0.99 |
| 103_F | 191_F | 1.333 | 0.99 |
| 67_T | 71_V | 1.308 | 0.99 |
| 149_M | 201_F | 1.277 | 0.99 |
| 132_A | 136_I | 1.243 | 0.98 |
| 79_I | 196_I | 1.233 | 0.98 |
| 187_L | 190_D | 1.229 | 0.98 |
| 113_M | 117_L | 1.213 | 0.98 |
| 25_G | 70_F | 1.205 | 0.98 |
| 47_M | 71_V | 1.203 | 0.98 |
| 27_F | 31_F | 1.200 | 0.98 |
| 148_M | 200_R | 1.191 | 0.98 |
| 97_G | 101_V | 1.187 | 0.98 |
| 106_L | 164_L | 1.183 | 0.98 |
| 137_F | 141_S | 1.177 | 0.98 |
| 169_Q | 186_S | 1.175 | 0.98 |
| 68_F | 72_S | 1.173 | 0.98 |
| 197_N | 200_R | 1.164 | 0.97 |
| 120_L | 124_L | 1.164 | 0.97 |
| 149_M | 153_V | 1.162 | 0.97 |
| 109_I | 115_K | 1.158 | 0.97 |
| 79_I | 83_Y | 1.152 | 0.97 |
| 95_A | 98_S | 1.149 | 0.97 |
| 109_I | 113_M | 1.145 | 0.97 |
| 38_L | 42_I | 1.140 | 0.97 |
| 173_R | 183_M | 1.120 | 0.96 |
| 4_K | 7_I | 1.119 | 0.96 |
| 62_Y | 66_Y | 1.114 | 0.96 |
| 134_V | 151_Y | 1.109 | 0.96 |
| 102_I | 105_V | 1.101 | 0.96 |
| 84_A | 91_V | 1.091 | 0.96 |
| 159_F | 189_L | 1.089 | 0.96 |
| 166_D | 189_L | 1.083 | 0.96 |
| 10_R | 180_I | 1.080 | 0.95 |
| 51_A | 64_F | 1.075 | 0.95 |
| 94_E | 202_F | 1.072 | 0.95 |
| 169_Q | 190_D | 1.066 | 0.95 |
| 83_Y | 196_I | 1.063 | 0.95 |
| 110_G | 168_N | 1.060 | 0.95 |
| 159_F | 193_N | 1.050 | 0.94 |
| 18_T | 69_A | 1.046 | 0.94 |
| 47_M | 64_F | 1.044 | 0.94 |
| 98_S | 156_T | 1.042 | 0.94 |
| 50_L | 64_F | 1.038 | 0.94 |
| 3_S | 174_H | 1.027 | 0.94 |
| 145_S | 148_M | 1.024 | 0.93 |
| 119_F | 122_S | 1.022 | 0.93 |
| 103_F | 187_L | 1.019 | 0.93 |
| 151_Y | 155_G | 1.017 | 0.93 |
| 14_V | 62_Y | 1.017 | 0.93 |
| 43_L | 46_A | 1.006 | 0.93 |
| 7_I | 11_I | 1.005 | 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 | 0.9952 | 100 | 0.006 | Contact Map |
| 4i0uA | 10 | 0.2802 | 5.8 | 0.935 | Contact Map |
| 4ev6A | 5 | 0.2899 | 5.7 | 0.936 | Contact Map |
| 1r8hA | 6 | 0.1401 | 3 | 0.944 | Contact Map |
| 2xq2A | 1 | 0.7778 | 1.9 | 0.949 | Contact Map |
| 4b4aA | 1 | 0.6473 | 1.9 | 0.949 | Contact Map |
| 3w9iA | 6 | 0.7295 | 1.5 | 0.953 | Contact Map |
| 4k0jA | 6 | 0.6908 | 1.4 | 0.953 | Contact Map |
| 4n7wA | 2 | 0.43 | 1.2 | 0.955 | Contact Map |
| 3b5dA | 2 | 0.0193 | 1.1 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)