| 3j9i_A |
| ID: | 1484578441 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 224 (223) | ||
| Sequences: | 6040 (2834.6) | ||
| Seq/Len: | 27.085 | ||
| Nf(neff/√len): | 189.8 |
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: 27.085).
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 |
| 176_P | 179_E | 4.053 | 1.00 |
| 40_I | 184_G | 3.765 | 1.00 |
| 138_R | 150_E | 2.905 | 1.00 |
| 30_G | 39_L | 2.749 | 1.00 |
| 30_G | 139_L | 2.517 | 1.00 |
| 34_A | 174_N | 2.502 | 1.00 |
| 33_F | 180_A | 2.453 | 1.00 |
| 33_F | 36_G | 2.418 | 1.00 |
| 28_A | 68_V | 2.374 | 1.00 |
| 39_L | 130_A | 2.362 | 1.00 |
| 213_R | 219_E | 2.296 | 1.00 |
| 65_V | 103_L | 2.028 | 1.00 |
| 31_M | 184_G | 2.025 | 1.00 |
| 170_E | 186_K | 2.005 | 1.00 |
| 172_K | 179_E | 1.952 | 1.00 |
| 177_E | 207_T | 1.945 | 1.00 |
| 65_V | 100_I | 1.936 | 1.00 |
| 170_E | 183_L | 1.879 | 1.00 |
| 91_K | 97_L | 1.857 | 1.00 |
| 37_V | 130_A | 1.840 | 1.00 |
| 32_K | 150_E | 1.824 | 1.00 |
| 100_I | 131_G | 1.814 | 1.00 |
| 60_L | 63_D | 1.811 | 1.00 |
| 62_D | 91_K | 1.769 | 1.00 |
| 128_I | 154_T | 1.765 | 1.00 |
| 35_N | 208_V | 1.747 | 1.00 |
| 4_T | 12_L | 1.698 | 1.00 |
| 140_F | 150_E | 1.680 | 1.00 |
| 177_E | 181_V | 1.647 | 1.00 |
| 133_D | 136_G | 1.631 | 1.00 |
| 216_D | 219_E | 1.631 | 1.00 |
| 2_A | 5_V | 1.624 | 1.00 |
| 69_T | 76_A | 1.615 | 1.00 |
| 66_A | 212_Y | 1.584 | 1.00 |
| 38_L | 184_G | 1.561 | 1.00 |
| 152_K | 173_E | 1.555 | 1.00 |
| 175_L | 183_L | 1.554 | 1.00 |
| 56_E | 202_E | 1.512 | 1.00 |
| 31_M | 180_A | 1.507 | 1.00 |
| 99_N | 102_N | 1.499 | 1.00 |
| 40_I | 203_I | 1.486 | 1.00 |
| 64_Y | 97_L | 1.481 | 1.00 |
| 67_A | 129_F | 1.466 | 1.00 |
| 11_R | 16_E | 1.460 | 1.00 |
| 38_L | 181_V | 1.458 | 1.00 |
| 67_A | 80_V | 1.444 | 1.00 |
| 87_A | 103_L | 1.437 | 1.00 |
| 33_F | 177_E | 1.419 | 1.00 |
| 36_G | 180_A | 1.417 | 1.00 |
| 86_S | 106_R | 1.416 | 1.00 |
| 172_K | 175_L | 1.394 | 0.99 |
| 181_V | 203_I | 1.377 | 0.99 |
| 166_F | 170_E | 1.357 | 0.99 |
| 217_Q | 220_V | 1.356 | 0.99 |
| 61_I | 87_A | 1.351 | 0.99 |
| 112_Q | 116_Q | 1.340 | 0.99 |
| 181_V | 205_S | 1.322 | 0.99 |
| 36_G | 177_E | 1.298 | 0.99 |
| 207_T | 213_R | 1.297 | 0.99 |
| 58_I | 204_A | 1.287 | 0.99 |
| 86_S | 89_Q | 1.277 | 0.99 |
| 32_K | 152_K | 1.269 | 0.99 |
| 38_L | 205_S | 1.266 | 0.99 |
| 82_F | 86_S | 1.255 | 0.99 |
| 121_R | 124_G | 1.254 | 0.99 |
| 66_A | 204_A | 1.247 | 0.99 |
| 83_A | 107_V | 1.237 | 0.98 |
| 215_Y | 220_V | 1.235 | 0.98 |
| 155_A | 167_L | 1.231 | 0.98 |
| 129_F | 142_C | 1.213 | 0.98 |
| 128_I | 156_I | 1.204 | 0.98 |
| 89_Q | 93_T | 1.203 | 0.98 |
| 59_Q | 69_T | 1.201 | 0.98 |
| 62_D | 97_L | 1.197 | 0.98 |
| 106_R | 110_Q | 1.188 | 0.98 |
| 70_S | 156_I | 1.184 | 0.98 |
| 39_L | 68_V | 1.181 | 0.98 |
| 27_T | 159_G | 1.176 | 0.98 |
| 14_Q | 17_Y | 1.169 | 0.97 |
| 153_A | 167_L | 1.166 | 0.97 |
| 82_F | 110_Q | 1.160 | 0.97 |
| 12_L | 15_V | 1.156 | 0.97 |
| 171_Y | 175_L | 1.146 | 0.97 |
| 218_E | 222_K | 1.144 | 0.97 |
| 40_I | 188_L | 1.142 | 0.97 |
| 182_T | 186_K | 1.134 | 0.97 |
| 58_I | 68_V | 1.129 | 0.97 |
| 62_D | 65_V | 1.125 | 0.97 |
| 166_F | 187_A | 1.124 | 0.97 |
| 7_S | 13_F | 1.124 | 0.97 |
| 218_E | 221_K | 1.123 | 0.97 |
| 43_K | 202_E | 1.116 | 0.96 |
| 33_F | 207_T | 1.116 | 0.96 |
| 171_Y | 174_N | 1.116 | 0.96 |
| 66_A | 206_I | 1.111 | 0.96 |
| 8_P | 13_F | 1.111 | 0.96 |
| 59_Q | 80_V | 1.108 | 0.96 |
| 80_V | 84_R | 1.108 | 0.96 |
| 28_A | 41_S | 1.104 | 0.96 |
| 132_I | 208_V | 1.099 | 0.96 |
| 34_A | 176_P | 1.098 | 0.96 |
| 90_E | 94_Y | 1.095 | 0.96 |
| 10_G | 14_Q | 1.089 | 0.96 |
| 27_T | 163_V | 1.078 | 0.95 |
| 143_D | 147_T | 1.076 | 0.95 |
| 104_V | 148_I | 1.062 | 0.95 |
| 26_S | 42_D | 1.052 | 0.95 |
| 20_E | 23_K | 1.048 | 0.94 |
| 133_D | 138_R | 1.042 | 0.94 |
| 178_K | 182_T | 1.041 | 0.94 |
| 41_S | 58_I | 1.032 | 0.94 |
| 217_Q | 221_K | 1.031 | 0.94 |
| 39_L | 66_A | 1.029 | 0.94 |
| 17_Y | 20_E | 1.027 | 0.94 |
| 141_D | 154_T | 1.027 | 0.94 |
| 79_L | 125_V | 1.024 | 0.93 |
| 186_K | 189_K | 1.022 | 0.93 |
| 146_G | 157_G | 1.020 | 0.93 |
| 29_L | 184_G | 1.017 | 0.93 |
| 61_I | 67_A | 1.015 | 0.93 |
| 85_I | 89_Q | 1.014 | 0.93 |
| 35_N | 177_E | 1.011 | 0.93 |
| 166_F | 183_L | 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 | |
| 1yarA | 7 | 0.9866 | 100 | 0.031 | Contact Map |
| 1rypE | 2 | 1 | 100 | 0.04 | Contact Map |
| 4r3oE | 2 | 1 | 100 | 0.04 | Contact Map |
| 1rypB | 2 | 1 | 100 | 0.041 | Contact Map |
| 4r3oB | 2 | 0.9955 | 100 | 0.041 | Contact Map |
| 1rypF | 2 | 0.9911 | 100 | 0.043 | Contact Map |
| 1rypC | 2 | 1 | 100 | 0.047 | Contact Map |
| 3h4pA | 14 | 0.9866 | 100 | 0.049 | Contact Map |
| 4r3oF | 2 | 0.9911 | 100 | 0.051 | Contact Map |
| 1j2pA | 7 | 0.9955 | 100 | 0.051 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)