| T0808 150-418 -force run |
| ID: | 1405031266 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 269 (265) | ||
| Sequences: | 108 (93) | ||
| Seq/Len: | 0.408 | ||
| Nf(neff/√len): | 5.7 |
Jackhmmer Results: (2014_04_16)
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: 0.408).
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 |
| 77_N | 80_E | 2.329 | 0.92 |
| 71_S | 106_S | 2.203 | 0.89 |
| 126_M | 140_A | 2.074 | 0.84 |
| 90_L | 156_F | 2.012 | 0.82 |
| 24_E | 127_Q | 1.979 | 0.80 |
| 204_T | 252_C | 1.971 | 0.80 |
| 128_I | 165_Y | 1.926 | 0.78 |
| 25_W | 141_Y | 1.870 | 0.75 |
| 210_H | 246_M | 1.773 | 0.69 |
| 66_L | 109_Q | 1.771 | 0.69 |
| 41_S | 96_V | 1.712 | 0.65 |
| 188_F | 234_L | 1.710 | 0.65 |
| 120_N | 144_A | 1.665 | 0.62 |
| 214_A | 222_Y | 1.659 | 0.62 |
| 25_W | 167_R | 1.590 | 0.57 |
| 202_R | 252_C | 1.582 | 0.56 |
| 14_L | 186_V | 1.548 | 0.54 |
| 156_F | 218_V | 1.545 | 0.53 |
| 179_Q | 237_G | 1.479 | 0.49 |
| 61_T | 86_K | 1.473 | 0.48 |
| 26_F | 168_P | 1.423 | 0.45 |
| 31_T | 121_T | 1.412 | 0.44 |
| 45_A | 124_F | 1.393 | 0.42 |
| 30_I | 179_Q | 1.365 | 0.40 |
| 193_A | 257_K | 1.362 | 0.40 |
| 122_Y | 142_F | 1.353 | 0.40 |
| 40_H | 236_M | 1.352 | 0.39 |
| 5_W | 223_Q | 1.348 | 0.39 |
| 125_L | 200_W | 1.336 | 0.38 |
| 38_T | 237_G | 1.309 | 0.37 |
| 10_P | 180_G | 1.304 | 0.36 |
| 14_L | 206_A | 1.302 | 0.36 |
| 44_M | 66_L | 1.294 | 0.36 |
| 71_S | 81_I | 1.277 | 0.34 |
| 126_M | 165_Y | 1.270 | 0.34 |
| 62_E | 174_N | 1.266 | 0.34 |
| 254_P | 257_K | 1.265 | 0.34 |
| 65_I | 186_V | 1.260 | 0.33 |
| 5_W | 87_I | 1.253 | 0.33 |
| 23_T | 83_D | 1.246 | 0.32 |
| 83_D | 132_G | 1.244 | 0.32 |
| 82_P | 103_N | 1.234 | 0.32 |
| 40_H | 43_Y | 1.222 | 0.31 |
| 45_A | 65_I | 1.218 | 0.31 |
| 257_K | 262_D | 1.214 | 0.30 |
| 8_R | 224_G | 1.211 | 0.30 |
| 160_K | 237_G | 1.201 | 0.30 |
| 99_G | 103_N | 1.196 | 0.29 |
| 134_G | 263_W | 1.185 | 0.29 |
| 24_E | 129_R | 1.182 | 0.28 |
| 188_F | 243_S | 1.179 | 0.28 |
| 40_H | 76_Q | 1.177 | 0.28 |
| 25_W | 203_L | 1.176 | 0.28 |
| 30_I | 260_E | 1.174 | 0.28 |
| 260_E | 264_E | 1.173 | 0.28 |
| 27_Y | 192_W | 1.165 | 0.27 |
| 135_N | 157_L | 1.163 | 0.27 |
| 71_S | 75_T | 1.161 | 0.27 |
| 37_E | 40_H | 1.156 | 0.27 |
| 19_P | 208_F | 1.155 | 0.27 |
| 122_Y | 161_T | 1.155 | 0.27 |
| 184_R | 232_F | 1.154 | 0.27 |
| 76_Q | 166_K | 1.144 | 0.26 |
| 66_L | 111_Y | 1.143 | 0.26 |
| 16_Y | 28_N | 1.142 | 0.26 |
| 10_P | 221_D | 1.138 | 0.26 |
| 74_D | 230_N | 1.137 | 0.26 |
| 169_H | 263_W | 1.127 | 0.25 |
| 98_I | 166_K | 1.126 | 0.25 |
| 37_E | 57_Y | 1.126 | 0.25 |
| 188_F | 195_S | 1.125 | 0.25 |
| 28_N | 234_L | 1.123 | 0.25 |
| 55_M | 83_D | 1.121 | 0.25 |
| 255_T | 265_A | 1.119 | 0.25 |
| 46_A | 66_L | 1.111 | 0.24 |
| 65_I | 212_A | 1.109 | 0.24 |
| 50_E | 163_T | 1.102 | 0.24 |
| 183_S | 235_K | 1.101 | 0.24 |
| 66_L | 154_A | 1.100 | 0.24 |
| 131_D | 134_G | 1.100 | 0.24 |
| 33_P | 37_E | 1.100 | 0.24 |
| 6_G | 71_S | 1.099 | 0.24 |
| 84_D | 88_K | 1.096 | 0.24 |
| 21_G | 167_R | 1.094 | 0.23 |
| 253_K | 258_E | 1.093 | 0.23 |
| 55_M | 65_I | 1.091 | 0.23 |
| 204_T | 256_G | 1.088 | 0.23 |
| 77_N | 143_Y | 1.087 | 0.23 |
| 178_E | 250_F | 1.086 | 0.23 |
| 137_T | 160_K | 1.086 | 0.23 |
| 24_E | 186_V | 1.085 | 0.23 |
| 35_E | 148_K | 1.082 | 0.23 |
| 47_G | 67_F | 1.081 | 0.23 |
| 185_E | 228_K | 1.081 | 0.23 |
| 83_D | 260_E | 1.080 | 0.23 |
| 14_L | 103_N | 1.080 | 0.23 |
| 28_N | 188_F | 1.076 | 0.23 |
| 213_T | 250_F | 1.073 | 0.22 |
| 29_E | 219_R | 1.071 | 0.22 |
| 248_T | 254_P | 1.070 | 0.22 |
| 71_S | 78_P | 1.068 | 0.22 |
| 53_F | 206_A | 1.068 | 0.22 |
| 117_K | 264_E | 1.066 | 0.22 |
| 262_D | 265_A | 1.065 | 0.22 |
| 205_D | 251_Y | 1.064 | 0.22 |
| 39_M | 246_M | 1.062 | 0.22 |
| 128_I | 135_N | 1.058 | 0.22 |
| 103_N | 152_L | 1.057 | 0.22 |
| 17_A | 258_E | 1.055 | 0.22 |
| 255_T | 264_E | 1.053 | 0.21 |
| 170_S | 206_A | 1.045 | 0.21 |
| 108_G | 119_G | 1.045 | 0.21 |
| 164_W | 213_T | 1.042 | 0.21 |
| 207_T | 215_S | 1.038 | 0.21 |
| 14_L | 53_F | 1.037 | 0.21 |
| 141_Y | 167_R | 1.037 | 0.21 |
| 103_N | 106_S | 1.036 | 0.21 |
| 21_G | 195_S | 1.036 | 0.21 |
| 189_G | 262_D | 1.036 | 0.21 |
| 260_E | 265_A | 1.035 | 0.21 |
| 90_L | 167_R | 1.035 | 0.21 |
| 3_D | 202_R | 1.034 | 0.20 |
| 71_S | 100_E | 1.032 | 0.20 |
| 81_I | 106_S | 1.032 | 0.20 |
| 194_R | 258_E | 1.032 | 0.20 |
| 183_S | 205_D | 1.032 | 0.20 |
| 30_I | 247_G | 1.030 | 0.20 |
| 58_N | 64_R | 1.026 | 0.20 |
| 165_Y | 168_P | 1.024 | 0.20 |
| 4_Y | 161_T | 1.024 | 0.20 |
| 30_I | 197_E | 1.023 | 0.20 |
| 134_G | 234_L | 1.021 | 0.20 |
| 43_Y | 193_A | 1.020 | 0.20 |
| 180_G | 221_D | 1.020 | 0.20 |
| 172_L | 237_G | 1.014 | 0.20 |
| 40_H | 211_D | 1.013 | 0.20 |
| 131_D | 216_A | 1.013 | 0.20 |
| 39_M | 264_E | 1.012 | 0.19 |
| 112_L | 153_I | 1.010 | 0.19 |
| 4_Y | 250_F | 1.009 | 0.19 |
| 192_W | 200_W | 1.009 | 0.19 |
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 | |
| 2ww6A | 3 | 0.0929 | 11.1 | 0.975 | Contact Map |
| 4h62V | 1 | 0.0297 | 6.1 | 0.978 | Contact Map |
| 3ii7A | 1 | 0.4684 | 5.5 | 0.978 | Contact Map |
| 4ascA | 1 | 0.5688 | 5.5 | 0.978 | Contact Map |
| 1yo8A | 1 | 0.513 | 3.2 | 0.981 | Contact Map |
| 3owtC | 1 | 0.0409 | 3.1 | 0.981 | Contact Map |
| 1zg2A | 1 | 0.3234 | 2.8 | 0.981 | Contact Map |
| 3uzeC | 2 | 0.0409 | 2.6 | 0.982 | Contact Map |
| 3l3fX | 1 | 0.1524 | 2.5 | 0.982 | Contact Map |
| 3obaA | 4 | 0.4498 | 2.5 | 0.982 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)