| 1DQZA |
| ID: | 1411754461 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 280 (258) | ||
| Sequences: | 12256 (8669.7) | ||
| Seq/Len: | 47.504 | ||
| Nf(neff/√len): | 539.8 |
HHblits Results: (2013_03)
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: 47.504).
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 |
| 117_A | 141_Y | 4.091 | 1.00 |
| 234_Q | 252_F | 3.410 | 1.00 |
| 132_A | 142_A | 3.269 | 1.00 |
| 144_S | 147_G | 2.986 | 1.00 |
| 209_N | 254_P | 2.879 | 1.00 |
| 112_S | 115_G | 2.742 | 1.00 |
| 10_Q | 19_D | 2.645 | 1.00 |
| 237_R | 248_G | 2.599 | 1.00 |
| 31_A | 63_S | 2.423 | 1.00 |
| 32_V | 119_V | 2.389 | 1.00 |
| 12_P | 19_D | 2.326 | 1.00 |
| 117_A | 274_I | 2.224 | 1.00 |
| 104_W | 108_N | 2.176 | 1.00 |
| 29_P | 63_S | 2.121 | 1.00 |
| 253_P | 269_A | 2.110 | 1.00 |
| 251_N | 269_A | 2.059 | 1.00 |
| 31_A | 111_V | 2.048 | 1.00 |
| 62_L | 275_Q | 2.024 | 1.00 |
| 31_A | 65_I | 2.018 | 1.00 |
| 32_V | 62_L | 1.981 | 1.00 |
| 24_F | 65_I | 1.914 | 1.00 |
| 239_T | 243_D | 1.910 | 1.00 |
| 237_R | 250_F | 1.906 | 1.00 |
| 9_L | 22_V | 1.892 | 1.00 |
| 128_A | 142_A | 1.875 | 1.00 |
| 117_A | 278_L | 1.874 | 1.00 |
| 237_R | 241_A | 1.862 | 1.00 |
| 230_L | 234_Q | 1.837 | 1.00 |
| 37_G | 122_S | 1.820 | 1.00 |
| 209_N | 252_F | 1.818 | 1.00 |
| 249_V | 276_H | 1.813 | 1.00 |
| 122_S | 258_H | 1.807 | 1.00 |
| 63_S | 111_V | 1.786 | 1.00 |
| 209_N | 255_N | 1.777 | 1.00 |
| 230_L | 252_F | 1.772 | 1.00 |
| 240_Y | 245_G | 1.752 | 1.00 |
| 129_L | 144_S | 1.748 | 1.00 |
| 60_S | 271_K | 1.748 | 1.00 |
| 143_A | 274_I | 1.746 | 1.00 |
| 268_V | 272_A | 1.701 | 1.00 |
| 16_M | 70_G | 1.651 | 1.00 |
| 142_A | 203_I | 1.632 | 1.00 |
| 238_D | 242_A | 1.630 | 1.00 |
| 121_L | 146_S | 1.629 | 1.00 |
| 119_V | 143_A | 1.627 | 1.00 |
| 100_E | 104_W | 1.622 | 1.00 |
| 11_V | 22_V | 1.622 | 1.00 |
| 211_T | 227_G | 1.618 | 1.00 |
| 24_F | 63_S | 1.618 | 1.00 |
| 205_V | 237_R | 1.608 | 1.00 |
| 205_V | 233_N | 1.568 | 1.00 |
| 143_A | 270_M | 1.555 | 1.00 |
| 7_E | 26_G | 1.554 | 1.00 |
| 207_C | 233_N | 1.539 | 1.00 |
| 234_Q | 238_D | 1.512 | 1.00 |
| 205_V | 236_F | 1.492 | 1.00 |
| 34_L | 119_V | 1.487 | 1.00 |
| 144_S | 205_V | 1.469 | 1.00 |
| 118_A | 128_A | 1.464 | 1.00 |
| 207_C | 230_L | 1.452 | 1.00 |
| 22_V | 65_I | 1.413 | 1.00 |
| 60_S | 275_Q | 1.404 | 0.99 |
| 234_Q | 250_F | 1.395 | 0.99 |
| 203_I | 240_Y | 1.385 | 0.99 |
| 188_D | 191_V | 1.384 | 0.99 |
| 101_M | 104_W | 1.373 | 0.99 |
| 26_G | 63_S | 1.371 | 0.99 |
| 104_W | 107_A | 1.370 | 0.99 |
| 210_G | 255_N | 1.344 | 0.99 |
| 149_L | 236_F | 1.339 | 0.99 |
| 235_T | 238_D | 1.315 | 0.99 |
| 13_S | 16_M | 1.304 | 0.99 |
| 56_E | 60_S | 1.294 | 0.99 |
| 55_E | 59_Q | 1.292 | 0.99 |
| 143_A | 204_W | 1.285 | 0.99 |
| 121_L | 145_L | 1.269 | 0.99 |
| 10_Q | 21_K | 1.264 | 0.99 |
| 114_T | 140_P | 1.257 | 0.99 |
| 106_Q | 116_N | 1.235 | 0.98 |
| 129_L | 236_F | 1.233 | 0.98 |
| 95_T | 100_E | 1.233 | 0.98 |
| 245_G | 248_G | 1.229 | 0.98 |
| 118_A | 142_A | 1.213 | 0.98 |
| 204_W | 251_N | 1.210 | 0.98 |
| 69_G | 123_M | 1.194 | 0.98 |
| 125_G | 147_G | 1.190 | 0.98 |
| 119_V | 145_L | 1.187 | 0.98 |
| 56_E | 59_Q | 1.173 | 0.98 |
| 40_A | 126_G | 1.169 | 0.97 |
| 207_C | 250_F | 1.161 | 0.97 |
| 249_V | 269_A | 1.156 | 0.97 |
| 241_A | 248_G | 1.156 | 0.97 |
| 207_C | 252_F | 1.149 | 0.97 |
| 231_R | 234_Q | 1.145 | 0.97 |
| 273_D | 277_V | 1.142 | 0.97 |
| 30_H | 115_G | 1.141 | 0.97 |
| 106_Q | 138_Q | 1.137 | 0.97 |
| 92_K | 95_T | 1.129 | 0.97 |
| 35_L | 118_A | 1.126 | 0.97 |
| 118_A | 131_L | 1.121 | 0.97 |
| 120_G | 125_G | 1.120 | 0.96 |
| 185_K | 191_V | 1.114 | 0.96 |
| 102_P | 139_F | 1.110 | 0.96 |
| 8_Y | 21_K | 1.109 | 0.96 |
| 115_G | 140_P | 1.096 | 0.96 |
| 35_L | 67_P | 1.096 | 0.96 |
| 130_I | 134_Y | 1.095 | 0.96 |
| 70_G | 95_T | 1.086 | 0.96 |
| 240_Y | 248_G | 1.078 | 0.95 |
| 145_L | 270_M | 1.077 | 0.95 |
| 13_S | 18_R | 1.068 | 0.95 |
| 30_H | 112_S | 1.067 | 0.95 |
| 94_E | 134_Y | 1.065 | 0.95 |
| 100_E | 105_L | 1.064 | 0.95 |
| 272_A | 276_H | 1.062 | 0.95 |
| 25_Q | 66_M | 1.056 | 0.95 |
| 183_A | 186_R | 1.055 | 0.95 |
| 182_P | 185_K | 1.054 | 0.95 |
| 100_E | 103_A | 1.054 | 0.95 |
| 141_Y | 202_R | 1.051 | 0.94 |
| 146_S | 260_W | 1.050 | 0.94 |
| 8_Y | 23_Q | 1.050 | 0.94 |
| 150_N | 188_D | 1.045 | 0.94 |
| 23_Q | 44_Y | 1.041 | 0.94 |
| 265_E | 269_A | 1.038 | 0.94 |
| 133_A | 236_F | 1.035 | 0.94 |
| 32_V | 57_Y | 1.034 | 0.94 |
| 99_R | 103_A | 1.032 | 0.94 |
| 146_S | 259_S | 1.028 | 0.94 |
| 32_V | 64_V | 1.027 | 0.94 |
| 125_G | 144_S | 1.025 | 0.93 |
| 65_I | 105_L | 1.024 | 0.93 |
| 32_V | 117_A | 1.021 | 0.93 |
| 31_A | 116_N | 1.020 | 0.93 |
| 158_T | 162_L | 1.014 | 0.93 |
| 235_T | 239_T | 1.013 | 0.93 |
| 11_V | 101_M | 1.012 | 0.93 |
| 9_L | 24_F | 1.010 | 0.93 |
| 150_N | 235_T | 1.007 | 0.93 |
| 33_Y | 116_N | 1.005 | 0.93 |
| 192_Q | 195_R | 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 | |
| 1sfrA | 3 | 1 | 100 | 0.306 | Contact Map |
| 4mqlA | 1 | 0.9964 | 100 | 0.307 | Contact Map |
| 1r88A | 2 | 0.9071 | 100 | 0.362 | Contact Map |
| 4h18A | 4 | 0.9036 | 100 | 0.384 | Contact Map |
| 4hvtA | 1 | 0.8821 | 100 | 0.389 | Contact Map |
| 3iujA | 1 | 0.8536 | 100 | 0.417 | Contact Map |
| 2ecfA | 1 | 0.875 | 100 | 0.418 | Contact Map |
| 4a5sA | 2 | 0.8714 | 100 | 0.419 | Contact Map |
| 3o4hA | 4 | 0.8679 | 100 | 0.419 | Contact Map |
| 1xfdA | 4 | 0.8714 | 100 | 0.423 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)