| T0789 |
| ID: | 1400779648 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 295 (267) | ||
| Sequences: | 433 (372.1) | ||
| Seq/Len: | 1.622 | ||
| Nf(neff/√len): | 22.8 |
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: 1.622).
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 |
| 158_A | 240_V | 3.436 | 1.00 |
| 234_D | 239_R | 2.995 | 1.00 |
| 30_V | 232_I | 2.274 | 0.99 |
| 77_V | 124_A | 2.208 | 0.99 |
| 14_N | 53_E | 2.111 | 0.99 |
| 16_W | 43_R | 2.012 | 0.98 |
| 212_E | 218_N | 1.940 | 0.98 |
| 24_A | 74_I | 1.930 | 0.98 |
| 14_N | 57_M | 1.921 | 0.98 |
| 160_F | 240_V | 1.848 | 0.97 |
| 10_L | 144_L | 1.848 | 0.97 |
| 15_A | 19_A | 1.818 | 0.96 |
| 128_A | 131_V | 1.691 | 0.94 |
| 28_P | 85_D | 1.672 | 0.94 |
| 30_V | 87_R | 1.630 | 0.92 |
| 88_Y | 153_A | 1.567 | 0.90 |
| 21_T | 51_R | 1.546 | 0.90 |
| 28_P | 148_L | 1.546 | 0.90 |
| 16_W | 35_M | 1.545 | 0.90 |
| 77_V | 133_F | 1.531 | 0.89 |
| 158_A | 267_A | 1.485 | 0.87 |
| 15_A | 27_F | 1.450 | 0.85 |
| 173_A | 191_G | 1.449 | 0.85 |
| 18_I | 70_V | 1.447 | 0.85 |
| 212_E | 219_R | 1.434 | 0.84 |
| 46_F | 50_Q | 1.409 | 0.83 |
| 211_V | 218_N | 1.401 | 0.82 |
| 37_Y | 43_R | 1.395 | 0.82 |
| 16_W | 37_Y | 1.330 | 0.78 |
| 49_R | 53_E | 1.327 | 0.77 |
| 11_T | 14_N | 1.320 | 0.77 |
| 216_G | 219_R | 1.318 | 0.77 |
| 22_I | 102_R | 1.310 | 0.76 |
| 29_W | 32_A | 1.280 | 0.74 |
| 30_V | 126_R | 1.270 | 0.73 |
| 160_F | 258_P | 1.262 | 0.72 |
| 19_A | 25_G | 1.256 | 0.72 |
| 39_D | 163_F | 1.253 | 0.71 |
| 85_D | 214_V | 1.242 | 0.70 |
| 84_L | 272_T | 1.240 | 0.70 |
| 168_R | 251_E | 1.239 | 0.70 |
| 154_H | 200_V | 1.238 | 0.70 |
| 19_A | 28_P | 1.233 | 0.70 |
| 200_V | 264_I | 1.231 | 0.70 |
| 259_G | 263_A | 1.230 | 0.69 |
| 16_W | 46_F | 1.226 | 0.69 |
| 19_A | 27_F | 1.224 | 0.69 |
| 126_R | 232_I | 1.224 | 0.69 |
| 160_F | 259_G | 1.220 | 0.69 |
| 206_G | 236_S | 1.215 | 0.68 |
| 14_N | 50_Q | 1.195 | 0.66 |
| 83_W | 129_Q | 1.194 | 0.66 |
| 9_E | 268_I | 1.193 | 0.66 |
| 232_I | 240_V | 1.180 | 0.65 |
| 19_A | 158_A | 1.175 | 0.64 |
| 12_V | 126_R | 1.172 | 0.64 |
| 20_E | 47_V | 1.171 | 0.64 |
| 214_V | 218_N | 1.166 | 0.63 |
| 196_A | 230_L | 1.165 | 0.63 |
| 107_L | 122_V | 1.165 | 0.63 |
| 80_P | 154_H | 1.159 | 0.63 |
| 11_T | 54_L | 1.158 | 0.63 |
| 80_P | 83_W | 1.153 | 0.62 |
| 213_I | 226_T | 1.152 | 0.62 |
| 175_E | 180_G | 1.147 | 0.62 |
| 157_P | 168_R | 1.142 | 0.61 |
| 35_M | 57_M | 1.135 | 0.60 |
| 215_A | 218_N | 1.127 | 0.60 |
| 159_R | 263_A | 1.126 | 0.59 |
| 105_V | 123_V | 1.122 | 0.59 |
| 183_L | 189_Y | 1.122 | 0.59 |
| 60_L | 66_I | 1.121 | 0.59 |
| 82_R | 140_D | 1.117 | 0.58 |
| 121_G | 126_R | 1.109 | 0.58 |
| 72_D | 268_I | 1.108 | 0.58 |
| 211_V | 232_I | 1.108 | 0.58 |
| 255_T | 268_I | 1.105 | 0.57 |
| 215_A | 221_G | 1.104 | 0.57 |
| 15_A | 149_G | 1.103 | 0.57 |
| 168_R | 268_I | 1.100 | 0.57 |
| 29_W | 232_I | 1.099 | 0.57 |
| 249_D | 253_V | 1.099 | 0.57 |
| 87_R | 232_I | 1.096 | 0.56 |
| 27_F | 254_S | 1.093 | 0.56 |
| 87_R | 102_R | 1.091 | 0.56 |
| 279_Q | 282_P | 1.090 | 0.56 |
| 212_E | 216_G | 1.089 | 0.56 |
| 203_V | 207_P | 1.088 | 0.55 |
| 126_R | 240_V | 1.080 | 0.55 |
| 222_R | 226_T | 1.078 | 0.54 |
| 56_R | 168_R | 1.076 | 0.54 |
| 102_R | 105_V | 1.073 | 0.54 |
| 50_Q | 53_E | 1.068 | 0.53 |
| 213_I | 219_R | 1.060 | 0.53 |
| 39_D | 42_Q | 1.060 | 0.53 |
| 260_T | 267_A | 1.060 | 0.53 |
| 123_V | 158_A | 1.059 | 0.52 |
| 34_T | 37_Y | 1.059 | 0.52 |
| 142_R | 246_R | 1.058 | 0.52 |
| 249_D | 255_T | 1.057 | 0.52 |
| 14_N | 59_L | 1.054 | 0.52 |
| 20_E | 157_P | 1.054 | 0.52 |
| 201_E | 270_T | 1.052 | 0.52 |
| 133_F | 170_G | 1.046 | 0.51 |
| 268_I | 272_T | 1.043 | 0.51 |
| 156_P | 239_R | 1.042 | 0.51 |
| 133_F | 145_V | 1.041 | 0.51 |
| 32_A | 84_L | 1.039 | 0.50 |
| 187_V | 197_R | 1.036 | 0.50 |
| 81_D | 84_L | 1.036 | 0.50 |
| 74_I | 104_I | 1.035 | 0.50 |
| 124_A | 257_S | 1.034 | 0.50 |
| 191_G | 196_A | 1.032 | 0.50 |
| 28_P | 124_A | 1.032 | 0.50 |
| 16_W | 163_F | 1.031 | 0.49 |
| 55_T | 91_P | 1.029 | 0.49 |
| 77_V | 253_V | 1.026 | 0.49 |
| 91_P | 140_D | 1.025 | 0.49 |
| 122_V | 126_R | 1.024 | 0.49 |
| 23_G | 265_A | 1.023 | 0.49 |
| 81_D | 108_R | 1.022 | 0.49 |
| 240_V | 259_G | 1.019 | 0.48 |
| 51_R | 60_L | 1.019 | 0.48 |
| 85_D | 229_G | 1.018 | 0.48 |
| 133_F | 256_F | 1.017 | 0.48 |
| 15_A | 131_V | 1.017 | 0.48 |
| 89_V | 170_G | 1.016 | 0.48 |
| 215_A | 268_I | 1.012 | 0.47 |
| 156_P | 234_D | 1.010 | 0.47 |
| 14_N | 85_D | 1.010 | 0.47 |
| 68_P | 71_A | 1.010 | 0.47 |
| 41_A | 45_A | 1.009 | 0.47 |
| 17_F | 160_F | 1.009 | 0.47 |
| 171_A | 220_D | 1.009 | 0.47 |
| 60_L | 122_V | 1.007 | 0.47 |
| 132_T | 151_G | 1.007 | 0.47 |
| 162_E | 253_V | 1.005 | 0.47 |
| 86_L | 213_I | 1.003 | 0.47 |
| 23_G | 190_L | 1.002 | 0.46 |
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 | |
| 1hgvA | 1 | 0.1559 | 3.7 | 0.969 | Contact Map |
| 4gc5A | 1 | 0.1458 | 2.4 | 0.971 | Contact Map |
| 1q02A | 1 | 0.1525 | 2.3 | 0.972 | Contact Map |
| 3h8dA | 4 | 0.1559 | 2.1 | 0.972 | Contact Map |
| 3tr3A | 2 | 0.1356 | 2.1 | 0.972 | Contact Map |
| 3ci9A | 2 | 0.0915 | 2 | 0.973 | Contact Map |
| 1fvpA | 2 | 0.2034 | 1.9 | 0.973 | Contact Map |
| 1nfpA | 1 | 0.2034 | 1.7 | 0.974 | Contact Map |
| 2x8nA | 1 | 0.2576 | 1.6 | 0.974 | Contact Map |
| 3jstA | 2 | 0.122 | 1.6 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)