| T0821 |
| ID: | 1402944438 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 275 (246) | ||
| Sequences: | 27788 (23125.3) | ||
| Seq/Len: | 112.959 | ||
| Nf(neff/√len): | 1474.4 |
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: 112.959).
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_N | 179_E | 3.177 | 1.00 |
| 142_N | 145_W | 3.165 | 1.00 |
| 244_E | 247_R | 3.139 | 1.00 |
| 108_E | 111_K | 3.138 | 1.00 |
| 210_K | 213_R | 3.104 | 1.00 |
| 74_K | 77_E | 3.100 | 1.00 |
| 37_D | 40_S | 2.948 | 1.00 |
| 62_L | 81_S | 2.294 | 1.00 |
| 201_R | 217_D | 2.169 | 1.00 |
| 133_R | 149_D | 2.151 | 1.00 |
| 100_A | 116_Y | 2.132 | 1.00 |
| 99_R | 115_D | 2.122 | 1.00 |
| 66_G | 82_Y | 2.117 | 1.00 |
| 134_G | 150_F | 2.117 | 1.00 |
| 198_Y | 217_D | 2.103 | 1.00 |
| 232_Y | 251_D | 2.078 | 1.00 |
| 202_A | 218_I | 2.045 | 1.00 |
| 235_R | 251_D | 2.036 | 1.00 |
| 65_L | 81_S | 2.033 | 1.00 |
| 130_L | 149_D | 2.009 | 1.00 |
| 167_H | 183_I | 1.985 | 1.00 |
| 45_L | 64_N | 1.969 | 1.00 |
| 96_L | 115_D | 1.961 | 1.00 |
| 164_R | 183_I | 1.950 | 1.00 |
| 219_E | 235_R | 1.927 | 1.00 |
| 117_N | 133_R | 1.923 | 1.00 |
| 151_D | 167_H | 1.913 | 1.00 |
| 46_K | 65_L | 1.896 | 1.00 |
| 185_N | 201_R | 1.881 | 1.00 |
| 168_A | 184_F | 1.864 | 1.00 |
| 83_T | 99_R | 1.844 | 1.00 |
| 236_G | 252_F | 1.763 | 1.00 |
| 29_S | 45_L | 1.699 | 1.00 |
| 28_K | 44_S | 1.645 | 1.00 |
| 82_Y | 98_N | 1.630 | 1.00 |
| 116_Y | 132_C | 1.600 | 1.00 |
| 218_I | 234_L | 1.527 | 1.00 |
| 150_F | 166_G | 1.437 | 1.00 |
| 215_M | 219_E | 1.429 | 1.00 |
| 184_F | 200_G | 1.425 | 1.00 |
| 42_E | 46_K | 1.416 | 1.00 |
| 79_L | 83_T | 1.388 | 0.99 |
| 25_L | 44_S | 1.387 | 0.99 |
| 69_Q | 81_S | 1.384 | 0.99 |
| 103_Y | 111_K | 1.380 | 0.99 |
| 137_Y | 145_W | 1.374 | 0.99 |
| 69_Q | 77_E | 1.374 | 0.99 |
| 113_L | 117_N | 1.357 | 0.99 |
| 147_E | 151_D | 1.353 | 0.99 |
| 181_E | 185_N | 1.342 | 0.99 |
| 199_E | 234_L | 1.324 | 0.99 |
| 103_Y | 115_D | 1.321 | 0.99 |
| 215_M | 238_I | 1.282 | 0.99 |
| 42_E | 69_Q | 1.280 | 0.99 |
| 99_R | 103_Y | 1.277 | 0.99 |
| 239_K | 247_R | 1.275 | 0.99 |
| 171_E | 179_E | 1.268 | 0.99 |
| 39_V | 72_Q | 1.267 | 0.99 |
| 254_K | 257_S | 1.252 | 0.99 |
| 76_Q | 106_L | 1.239 | 0.98 |
| 239_K | 244_E | 1.234 | 0.98 |
| 133_R | 137_Y | 1.231 | 0.98 |
| 32_F | 40_S | 1.226 | 0.98 |
| 152_K | 155_E | 1.220 | 0.98 |
| 42_E | 68_I | 1.216 | 0.98 |
| 201_R | 205_Y | 1.215 | 0.98 |
| 187_L | 197_L | 1.213 | 0.98 |
| 86_L | 95_I | 1.206 | 0.98 |
| 249_A | 253_K | 1.204 | 0.98 |
| 42_E | 72_Q | 1.200 | 0.98 |
| 220_K | 223_T | 1.200 | 0.98 |
| 181_E | 204_L | 1.194 | 0.98 |
| 84_S | 87_S | 1.187 | 0.98 |
| 110_E | 140_L | 1.185 | 0.98 |
| 79_L | 102_L | 1.185 | 0.98 |
| 92_N | 95_I | 1.183 | 0.98 |
| 205_Y | 213_R | 1.180 | 0.98 |
| 221_V | 231_L | 1.180 | 0.98 |
| 63_T | 98_N | 1.162 | 0.97 |
| 65_L | 69_Q | 1.157 | 0.97 |
| 147_E | 170_L | 1.156 | 0.97 |
| 32_F | 37_D | 1.152 | 0.97 |
| 205_Y | 210_K | 1.152 | 0.97 |
| 153_I | 163_A | 1.151 | 0.97 |
| 194_D | 197_L | 1.144 | 0.97 |
| 137_Y | 149_D | 1.136 | 0.97 |
| 171_E | 183_I | 1.136 | 0.97 |
| 212_A | 242_Q | 1.135 | 0.97 |
| 167_H | 171_E | 1.128 | 0.97 |
| 118_T | 121_I | 1.127 | 0.97 |
| 171_E | 176_N | 1.123 | 0.97 |
| 144_M | 174_R | 1.122 | 0.97 |
| 235_R | 239_K | 1.120 | 0.96 |
| 113_L | 136_L | 1.115 | 0.96 |
| 181_E | 205_Y | 1.113 | 0.96 |
| 49_M | 61_L | 1.112 | 0.96 |
| 178_D | 208_M | 1.106 | 0.96 |
| 206_F | 218_I | 1.106 | 0.96 |
| 69_Q | 74_K | 1.104 | 0.96 |
| 188_I | 197_L | 1.104 | 0.96 |
| 32_F | 44_S | 1.103 | 0.96 |
| 28_K | 32_F | 1.101 | 0.96 |
| 239_K | 251_D | 1.098 | 0.96 |
| 97_E | 132_C | 1.098 | 0.96 |
| 181_E | 208_M | 1.089 | 0.96 |
| 147_E | 174_R | 1.085 | 0.96 |
| 152_K | 156_V | 1.082 | 0.96 |
| 113_L | 133_R | 1.079 | 0.95 |
| 127_Q | 153_I | 1.075 | 0.95 |
| 131_Y | 166_G | 1.075 | 0.95 |
| 77_E | 80_I | 1.071 | 0.95 |
| 165_L | 200_G | 1.071 | 0.95 |
| 203_D | 234_L | 1.070 | 0.95 |
| 42_E | 65_L | 1.064 | 0.95 |
| 186_Y | 189_S | 1.063 | 0.95 |
| 79_L | 106_L | 1.063 | 0.95 |
| 31_D | 35_K | 1.062 | 0.95 |
| 48_A | 61_L | 1.060 | 0.95 |
| 228_T | 231_L | 1.057 | 0.95 |
| 29_S | 48_A | 1.050 | 0.94 |
| 236_G | 255_A | 1.049 | 0.94 |
| 191_M | 194_D | 1.048 | 0.94 |
| 205_Y | 217_D | 1.047 | 0.94 |
| 179_E | 182_R | 1.043 | 0.94 |
| 225_S | 228_T | 1.043 | 0.94 |
| 213_R | 216_A | 1.039 | 0.94 |
| 111_K | 114_N | 1.033 | 0.94 |
| 120_L | 129_A | 1.033 | 0.94 |
| 79_L | 99_R | 1.030 | 0.94 |
| 126_H | 129_A | 1.027 | 0.94 |
| 130_L | 152_K | 1.016 | 0.93 |
| 247_R | 250_L | 1.014 | 0.93 |
| 137_Y | 142_N | 1.013 | 0.93 |
| 215_M | 239_K | 1.008 | 0.93 |
| 215_M | 242_Q | 1.006 | 0.93 |
| 169_I | 200_G | 1.005 | 0.93 |
| 100_A | 119_L | 1.003 | 0.93 |
| 198_Y | 220_K | 1.001 | 0.92 |
| 172_K | 184_F | 1.000 | 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 | |
| 3iegA | 2 | 0.92 | 100 | 0.219 | Contact Map |
| 2y4tA | 3 | 0.9891 | 100 | 0.237 | Contact Map |
| 4eqfA | 1 | 0.9236 | 100 | 0.251 | Contact Map |
| 4kvmA | 4 | 0.9455 | 100 | 0.259 | Contact Map |
| 2xpiA | 2 | 0.9855 | 100 | 0.26 | Contact Map |
| 3hymB | 6 | 0.9891 | 100 | 0.261 | Contact Map |
| 1w3bA | 2 | 0.9891 | 100 | 0.261 | Contact Map |
| 4l9pA | 1 | 0.9855 | 100 | 0.262 | Contact Map |
| 3uq3A | 1 | 0.8909 | 100 | 0.263 | Contact Map |
| 1fchA | 2 | 0.96 | 100 | 0.264 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)