| met -force run |
| ID: | 1486977125 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 270 (266) | ||
| Sequences: | 125 (90.9) | ||
| Seq/Len: | 0.470 | ||
| Nf(neff/√len): | 5.6 |
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: 0.470).
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 |
| 7_C | 11_G | 3.206 | 1.00 |
| 5_E | 11_G | 2.963 | 0.99 |
| 5_E | 9_W | 2.944 | 0.99 |
| 150_P | 155_E | 2.004 | 0.85 |
| 4_E | 7_C | 1.818 | 0.76 |
| 151_C | 161_C | 1.813 | 0.75 |
| 24_L | 27_A | 1.803 | 0.75 |
| 153_D | 157_L | 1.782 | 0.74 |
| 7_C | 12_S | 1.704 | 0.69 |
| 161_C | 164_D | 1.666 | 0.66 |
| 69_A | 74_E | 1.593 | 0.61 |
| 150_P | 163_S | 1.545 | 0.58 |
| 8_S | 11_G | 1.506 | 0.55 |
| 174_V | 228_F | 1.503 | 0.55 |
| 151_C | 164_D | 1.498 | 0.54 |
| 150_P | 164_D | 1.494 | 0.54 |
| 46_L | 155_E | 1.479 | 0.53 |
| 222_H | 258_R | 1.459 | 0.51 |
| 19_G | 44_L | 1.459 | 0.51 |
| 229_L | 254_Y | 1.444 | 0.50 |
| 195_Q | 200_F | 1.441 | 0.50 |
| 232_G | 257_A | 1.413 | 0.48 |
| 224_G | 228_F | 1.413 | 0.48 |
| 6_R | 9_W | 1.397 | 0.47 |
| 86_E | 258_R | 1.393 | 0.46 |
| 107_F | 264_P | 1.374 | 0.45 |
| 213_I | 248_Q | 1.371 | 0.45 |
| 232_G | 239_A | 1.355 | 0.43 |
| 187_V | 213_I | 1.351 | 0.43 |
| 151_C | 155_E | 1.341 | 0.42 |
| 4_E | 9_W | 1.336 | 0.42 |
| 174_V | 224_G | 1.333 | 0.42 |
| 75_R | 105_A | 1.316 | 0.41 |
| 5_E | 8_S | 1.308 | 0.40 |
| 226_G | 245_P | 1.306 | 0.40 |
| 150_P | 161_C | 1.303 | 0.40 |
| 195_Q | 239_A | 1.294 | 0.39 |
| 149_R | 155_E | 1.291 | 0.39 |
| 171_I | 230_F | 1.289 | 0.39 |
| 106_L | 122_A | 1.268 | 0.37 |
| 191_R | 223_P | 1.264 | 0.37 |
| 149_R | 228_F | 1.247 | 0.36 |
| 16_Q | 20_S | 1.242 | 0.35 |
| 66_F | 121_A | 1.232 | 0.35 |
| 226_G | 230_F | 1.227 | 0.34 |
| 188_V | 255_E | 1.227 | 0.34 |
| 232_G | 263_H | 1.220 | 0.34 |
| 26_L | 37_Y | 1.219 | 0.34 |
| 22_G | 196_T | 1.214 | 0.33 |
| 176_H | 183_S | 1.211 | 0.33 |
| 161_C | 165_F | 1.204 | 0.33 |
| 60_L | 173_G | 1.203 | 0.33 |
| 46_L | 164_D | 1.201 | 0.32 |
| 178_V | 270_H | 1.200 | 0.32 |
| 174_V | 221_V | 1.196 | 0.32 |
| 73_A | 96_V | 1.190 | 0.32 |
| 211_T | 229_L | 1.180 | 0.31 |
| 215_T | 221_V | 1.177 | 0.31 |
| 88_P | 222_H | 1.177 | 0.31 |
| 123_F | 230_F | 1.176 | 0.31 |
| 24_L | 227_T | 1.173 | 0.31 |
| 136_P | 139_A | 1.167 | 0.30 |
| 151_C | 163_S | 1.165 | 0.30 |
| 231_M | 249_E | 1.165 | 0.30 |
| 149_R | 226_G | 1.158 | 0.30 |
| 187_V | 230_F | 1.153 | 0.29 |
| 137_P | 270_H | 1.148 | 0.29 |
| 5_E | 12_S | 1.146 | 0.29 |
| 9_W | 12_S | 1.145 | 0.29 |
| 221_V | 231_M | 1.144 | 0.29 |
| 155_E | 163_S | 1.143 | 0.29 |
| 179_E | 182_E | 1.136 | 0.28 |
| 30_E | 167_I | 1.134 | 0.28 |
| 171_I | 187_V | 1.133 | 0.28 |
| 239_A | 254_Y | 1.131 | 0.28 |
| 25_A | 109_Q | 1.130 | 0.28 |
| 108_L | 189_A | 1.128 | 0.28 |
| 214_R | 260_A | 1.125 | 0.28 |
| 73_A | 109_Q | 1.120 | 0.27 |
| 221_V | 245_P | 1.118 | 0.27 |
| 47_G | 197_P | 1.116 | 0.27 |
| 23_Q | 250_F | 1.110 | 0.27 |
| 150_P | 157_L | 1.109 | 0.27 |
| 27_A | 110_A | 1.109 | 0.27 |
| 155_E | 161_C | 1.105 | 0.26 |
| 107_F | 116_I | 1.099 | 0.26 |
| 157_L | 164_D | 1.093 | 0.26 |
| 118_R | 246_R | 1.092 | 0.26 |
| 240_R | 247_F | 1.090 | 0.26 |
| 169_G | 230_F | 1.087 | 0.25 |
| 110_A | 127_L | 1.086 | 0.25 |
| 10_R | 70_Q | 1.085 | 0.25 |
| 216_P | 253_A | 1.085 | 0.25 |
| 228_F | 245_P | 1.083 | 0.25 |
| 23_Q | 254_Y | 1.082 | 0.25 |
| 229_L | 250_F | 1.081 | 0.25 |
| 53_A | 202_A | 1.079 | 0.25 |
| 34_E | 116_I | 1.079 | 0.25 |
| 57_I | 108_L | 1.079 | 0.25 |
| 117_S | 123_F | 1.074 | 0.25 |
| 60_L | 183_S | 1.072 | 0.25 |
| 229_L | 232_G | 1.072 | 0.25 |
| 64_R | 71_V | 1.071 | 0.24 |
| 23_Q | 236_F | 1.069 | 0.24 |
| 42_L | 217_L | 1.067 | 0.24 |
| 95_C | 125_F | 1.066 | 0.24 |
| 45_T | 104_R | 1.064 | 0.24 |
| 37_Y | 224_G | 1.064 | 0.24 |
| 155_E | 164_D | 1.064 | 0.24 |
| 168_H | 171_I | 1.057 | 0.24 |
| 49_P | 209_G | 1.056 | 0.24 |
| 80_L | 226_G | 1.053 | 0.23 |
| 250_F | 254_Y | 1.052 | 0.23 |
| 239_A | 250_F | 1.049 | 0.23 |
| 211_T | 250_F | 1.046 | 0.23 |
| 258_R | 270_H | 1.045 | 0.23 |
| 88_P | 108_L | 1.044 | 0.23 |
| 151_C | 165_F | 1.043 | 0.23 |
| 22_G | 249_E | 1.041 | 0.23 |
| 97_R | 158_L | 1.040 | 0.23 |
| 12_S | 123_F | 1.033 | 0.22 |
| 42_L | 226_G | 1.032 | 0.22 |
| 191_R | 232_G | 1.028 | 0.22 |
| 82_L | 236_F | 1.028 | 0.22 |
| 60_L | 93_G | 1.026 | 0.22 |
| 88_P | 162_T | 1.024 | 0.22 |
| 60_L | 206_G | 1.022 | 0.22 |
| 176_H | 217_L | 1.019 | 0.22 |
| 4_E | 11_G | 1.019 | 0.22 |
| 108_L | 192_V | 1.019 | 0.22 |
| 181_Q | 217_L | 1.018 | 0.22 |
| 19_G | 262_L | 1.015 | 0.21 |
| 33_V | 106_L | 1.014 | 0.21 |
| 34_E | 115_D | 1.012 | 0.21 |
| 224_G | 245_P | 1.011 | 0.21 |
| 215_T | 231_M | 1.009 | 0.21 |
| 63_V | 183_S | 1.008 | 0.21 |
| 229_L | 257_A | 1.007 | 0.21 |
| 173_G | 189_A | 1.005 | 0.21 |
| 18_P | 160_A | 1.004 | 0.21 |
| 240_R | 250_F | 1.002 | 0.21 |
| 70_Q | 107_F | 1.001 | 0.21 |
| 81_E | 222_H | 1.000 | 0.21 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3ckiB | 1 | 0.4037 | 99.7 | 0.834 | Contact Map |
| 2e2dC | 1 | 0.4148 | 98.9 | 0.89 | Contact Map |
| 3v96A | 1 | 0.3815 | 98.9 | 0.893 | Contact Map |
| 1uapA | 1 | 0.4444 | 98 | 0.918 | Contact Map |
| 2hr0B | 1 | 0.8963 | 61 | 0.964 | Contact Map |
| 3prxB | 2 | 0.9 | 31.3 | 0.97 | Contact Map |
| 3hrzC | 1 | 0.8222 | 26.7 | 0.971 | Contact Map |
| 2b39A | 2 | 0.9111 | 23.3 | 0.972 | Contact Map |
| 1jb3A | 1 | 0.4037 | 18.6 | 0.973 | Contact Map |
| 4fxkC | 1 | 0.8556 | 17.6 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)