| Tim23-Tim17 My align 3 cover 50 |
| ID: | 1488385732 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 248 (244) | ||
| Sequences: | 468 (125.9) | ||
| Seq/Len: | 1.918 | ||
| Nf(neff/√len): | 8.1 |
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: 1.918).
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 |
| 165_R | 168_V | 2.004 | 0.99 |
| 159_M | 163_K | 1.917 | 0.98 |
| 174_G | 226_C | 1.827 | 0.98 |
| 122_I | 125_D | 1.719 | 0.96 |
| 166_A | 170_G | 1.693 | 0.96 |
| 201_I | 205_F | 1.662 | 0.95 |
| 148_N | 152_G | 1.631 | 0.94 |
| 230_L | 235_G | 1.620 | 0.94 |
| 129_A | 132_M | 1.550 | 0.92 |
| 130_F | 166_A | 1.500 | 0.90 |
| 206_T | 210_L | 1.477 | 0.90 |
| 91_A | 106_S | 1.469 | 0.89 |
| 208_G | 223_S | 1.462 | 0.89 |
| 206_T | 211_A | 1.455 | 0.89 |
| 136_G | 148_N | 1.450 | 0.88 |
| 152_G | 157_G | 1.429 | 0.87 |
| 186_A | 189_A | 1.427 | 0.87 |
| 163_K | 168_V | 1.401 | 0.86 |
| 150_P | 171_G | 1.377 | 0.85 |
| 223_S | 234_E | 1.356 | 0.83 |
| 183_F | 209_A | 1.355 | 0.83 |
| 173_F | 185_C | 1.348 | 0.83 |
| 132_M | 237_G | 1.294 | 0.79 |
| 203_G | 207_G | 1.284 | 0.79 |
| 105_S | 109_V | 1.277 | 0.78 |
| 230_L | 234_E | 1.270 | 0.77 |
| 196_P | 199_A | 1.267 | 0.77 |
| 195_D | 198_N | 1.266 | 0.77 |
| 125_D | 129_A | 1.262 | 0.77 |
| 233_I | 238_L | 1.253 | 0.76 |
| 159_M | 229_L | 1.248 | 0.76 |
| 202_A | 227_A | 1.248 | 0.76 |
| 103_G | 107_A | 1.241 | 0.75 |
| 36_L | 45_I | 1.235 | 0.75 |
| 65_I | 138_V | 1.232 | 0.74 |
| 173_F | 176_W | 1.232 | 0.74 |
| 121_V | 124_N | 1.214 | 0.73 |
| 176_W | 185_C | 1.212 | 0.73 |
| 201_I | 208_G | 1.207 | 0.72 |
| 202_A | 232_V | 1.201 | 0.72 |
| 196_P | 238_L | 1.195 | 0.71 |
| 18_F | 22_M | 1.191 | 0.71 |
| 202_A | 221_N | 1.184 | 0.70 |
| 125_D | 234_E | 1.179 | 0.70 |
| 168_V | 172_N | 1.168 | 0.69 |
| 184_D | 235_G | 1.165 | 0.68 |
| 142_G | 162_I | 1.164 | 0.68 |
| 58_I | 61_L | 1.158 | 0.68 |
| 135_I | 206_T | 1.156 | 0.68 |
| 170_G | 178_G | 1.152 | 0.67 |
| 182_T | 202_A | 1.151 | 0.67 |
| 204_F | 227_A | 1.143 | 0.66 |
| 154_R | 157_G | 1.143 | 0.66 |
| 136_G | 147_R | 1.137 | 0.66 |
| 148_N | 157_G | 1.135 | 0.65 |
| 136_G | 184_D | 1.134 | 0.65 |
| 83_I | 110_A | 1.134 | 0.65 |
| 203_G | 210_L | 1.132 | 0.65 |
| 230_L | 237_G | 1.129 | 0.65 |
| 185_C | 213_R | 1.126 | 0.65 |
| 129_A | 177_G | 1.123 | 0.64 |
| 87_A | 110_A | 1.118 | 0.64 |
| 209_A | 212_V | 1.116 | 0.64 |
| 47_K | 70_I | 1.115 | 0.63 |
| 122_I | 185_C | 1.114 | 0.63 |
| 121_V | 125_D | 1.112 | 0.63 |
| 187_V | 224_I | 1.112 | 0.63 |
| 140_W | 183_F | 1.111 | 0.63 |
| 23_Q | 48_R | 1.108 | 0.63 |
| 74_R | 78_D | 1.105 | 0.62 |
| 184_D | 234_E | 1.102 | 0.62 |
| 190_V | 205_F | 1.102 | 0.62 |
| 198_N | 203_G | 1.099 | 0.62 |
| 174_G | 187_V | 1.098 | 0.62 |
| 203_G | 235_G | 1.097 | 0.62 |
| 18_F | 34_G | 1.096 | 0.61 |
| 241_Q | 248_A | 1.092 | 0.61 |
| 170_G | 214_G | 1.092 | 0.61 |
| 136_G | 235_G | 1.091 | 0.61 |
| 149_S | 157_G | 1.087 | 0.61 |
| 4_G | 77_H | 1.084 | 0.60 |
| 146_F | 192_K | 1.083 | 0.60 |
| 12_G | 71_D | 1.083 | 0.60 |
| 9_Y | 39_N | 1.079 | 0.60 |
| 121_V | 174_G | 1.078 | 0.60 |
| 173_F | 213_R | 1.074 | 0.59 |
| 203_G | 230_L | 1.070 | 0.59 |
| 185_C | 210_L | 1.068 | 0.58 |
| 140_W | 172_N | 1.066 | 0.58 |
| 187_V | 229_L | 1.066 | 0.58 |
| 146_F | 151_L | 1.065 | 0.58 |
| 169_L | 214_G | 1.063 | 0.58 |
| 144_K | 149_S | 1.063 | 0.58 |
| 173_F | 234_E | 1.063 | 0.58 |
| 191_R | 195_D | 1.058 | 0.57 |
| 27_N | 40_T | 1.056 | 0.57 |
| 152_G | 164_A | 1.055 | 0.57 |
| 202_A | 217_R | 1.054 | 0.57 |
| 21_M | 115_V | 1.052 | 0.57 |
| 108_M | 111_A | 1.052 | 0.57 |
| 140_W | 165_R | 1.050 | 0.57 |
| 144_K | 148_N | 1.048 | 0.56 |
| 154_R | 179_L | 1.046 | 0.56 |
| 162_I | 227_A | 1.045 | 0.56 |
| 191_R | 198_N | 1.044 | 0.56 |
| 174_G | 185_C | 1.042 | 0.56 |
| 173_F | 206_T | 1.040 | 0.55 |
| 188_K | 226_C | 1.040 | 0.55 |
| 187_V | 202_A | 1.040 | 0.55 |
| 184_D | 230_L | 1.038 | 0.55 |
| 176_W | 184_D | 1.038 | 0.55 |
| 141_H | 169_L | 1.037 | 0.55 |
| 143_I | 147_R | 1.036 | 0.55 |
| 180_F | 198_N | 1.034 | 0.55 |
| 173_F | 210_L | 1.034 | 0.55 |
| 70_I | 83_I | 1.031 | 0.54 |
| 177_G | 184_D | 1.030 | 0.54 |
| 132_M | 136_G | 1.027 | 0.54 |
| 125_D | 176_W | 1.027 | 0.54 |
| 199_A | 232_V | 1.026 | 0.54 |
| 125_D | 130_F | 1.025 | 0.54 |
| 121_V | 226_C | 1.021 | 0.53 |
| 209_A | 227_A | 1.020 | 0.53 |
| 124_N | 174_G | 1.020 | 0.53 |
| 97_K | 117_C | 1.019 | 0.53 |
| 143_I | 231_G | 1.017 | 0.53 |
| 173_F | 194_E | 1.016 | 0.53 |
| 220_R | 227_A | 1.011 | 0.52 |
| 203_G | 206_T | 1.007 | 0.52 |
| 149_S | 152_G | 1.005 | 0.52 |
| 196_P | 236_V | 1.003 | 0.51 |
| 128_G | 229_L | 1.003 | 0.51 |
| 184_D | 233_I | 1.003 | 0.51 |
| 170_G | 205_F | 1.003 | 0.51 |
| 150_P | 184_D | 1.001 | 0.51 |
| 21_M | 84_G | 1.000 | 0.51 |
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 | |
| 3dl8C | 2 | 0.1411 | 3 | 0.978 | Contact Map |
| 2loqA | 1 | 0.2298 | 2.9 | 0.978 | Contact Map |
| 3dinD | 2 | 0.2258 | 2.8 | 0.978 | Contact Map |
| 3tdsE | 5 | 0.2863 | 2.1 | 0.979 | Contact Map |
| 1iijA | 1 | 0.1411 | 1.8 | 0.98 | Contact Map |
| 2ls2A | 1 | 0.1008 | 1.4 | 0.981 | Contact Map |
| 2g9pA | 1 | 0.0847 | 1.3 | 0.982 | Contact Map |
| 1zlaK | 1 | 0.0565 | 1.1 | 0.983 | Contact Map |
| 4qanA | 2 | 0.2177 | 1.1 | 0.983 | Contact Map |
| 4l7iA | 2 | 0.2097 | 1 | 0.983 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)