| T0839 |
| ID: | 1404241046 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 262 (252) | ||
| Sequences: | 443 (268.4) | ||
| Seq/Len: | 1.758 | ||
| Nf(neff/√len): | 16.9 |
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: 1.758).
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 |
| 43_T | 82_G | 2.870 | 1.00 |
| 202_S | 240_L | 2.320 | 1.00 |
| 202_S | 244_Y | 2.078 | 0.99 |
| 22_K | 35_H | 1.778 | 0.96 |
| 32_K | 35_H | 1.773 | 0.96 |
| 56_L | 59_Q | 1.769 | 0.96 |
| 22_K | 34_K | 1.719 | 0.95 |
| 166_T | 169_D | 1.633 | 0.94 |
| 201_E | 205_I | 1.598 | 0.93 |
| 177_L | 236_Q | 1.596 | 0.93 |
| 20_I | 66_V | 1.530 | 0.90 |
| 52_F | 93_N | 1.511 | 0.90 |
| 71_A | 75_I | 1.489 | 0.89 |
| 170_K | 173_Q | 1.483 | 0.88 |
| 23_A | 35_H | 1.458 | 0.87 |
| 22_K | 32_K | 1.451 | 0.87 |
| 55_G | 59_Q | 1.425 | 0.86 |
| 20_I | 59_Q | 1.420 | 0.85 |
| 69_F | 73_I | 1.417 | 0.85 |
| 206_Y | 242_K | 1.414 | 0.85 |
| 116_I | 175_Q | 1.391 | 0.84 |
| 157_G | 160_T | 1.390 | 0.84 |
| 23_A | 34_K | 1.389 | 0.83 |
| 119_Y | 123_L | 1.370 | 0.82 |
| 32_K | 37_R | 1.359 | 0.82 |
| 206_Y | 239_R | 1.358 | 0.82 |
| 125_A | 131_K | 1.344 | 0.81 |
| 20_I | 33_R | 1.332 | 0.80 |
| 73_I | 193_S | 1.332 | 0.80 |
| 20_I | 23_A | 1.325 | 0.79 |
| 113_G | 117_R | 1.317 | 0.79 |
| 52_F | 238_Y | 1.315 | 0.79 |
| 79_L | 232_R | 1.313 | 0.78 |
| 125_A | 172_D | 1.306 | 0.78 |
| 75_I | 201_E | 1.296 | 0.77 |
| 161_I | 168_Q | 1.290 | 0.77 |
| 252_Y | 256_L | 1.285 | 0.76 |
| 65_E | 103_G | 1.273 | 0.75 |
| 255_S | 258_T | 1.251 | 0.74 |
| 22_K | 37_R | 1.246 | 0.73 |
| 112_Y | 116_I | 1.243 | 0.73 |
| 47_K | 57_K | 1.239 | 0.73 |
| 213_L | 216_M | 1.236 | 0.72 |
| 216_M | 225_A | 1.228 | 0.72 |
| 175_Q | 236_Q | 1.220 | 0.71 |
| 52_F | 56_L | 1.216 | 0.71 |
| 27_E | 232_R | 1.211 | 0.70 |
| 16_L | 168_Q | 1.207 | 0.70 |
| 203_Y | 233_Y | 1.196 | 0.69 |
| 129_F | 192_I | 1.196 | 0.69 |
| 116_I | 120_V | 1.194 | 0.69 |
| 39_C | 44_W | 1.192 | 0.68 |
| 33_R | 37_R | 1.189 | 0.68 |
| 66_V | 94_R | 1.182 | 0.67 |
| 76_H | 119_Y | 1.182 | 0.67 |
| 16_L | 20_I | 1.176 | 0.67 |
| 179_F | 232_R | 1.173 | 0.67 |
| 34_K | 48_S | 1.173 | 0.67 |
| 199_V | 205_I | 1.172 | 0.66 |
| 119_Y | 122_F | 1.153 | 0.65 |
| 58_V | 68_T | 1.150 | 0.64 |
| 69_F | 194_A | 1.147 | 0.64 |
| 209_I | 216_M | 1.146 | 0.64 |
| 47_K | 108_G | 1.144 | 0.64 |
| 216_M | 230_R | 1.136 | 0.63 |
| 51_S | 54_A | 1.134 | 0.63 |
| 164_L | 201_E | 1.132 | 0.62 |
| 83_H | 126_K | 1.130 | 0.62 |
| 35_H | 248_S | 1.128 | 0.62 |
| 165_M | 174_F | 1.125 | 0.62 |
| 157_G | 165_M | 1.125 | 0.62 |
| 168_Q | 175_Q | 1.123 | 0.62 |
| 36_V | 207_K | 1.122 | 0.61 |
| 177_L | 180_S | 1.119 | 0.61 |
| 115_L | 179_F | 1.117 | 0.61 |
| 62_L | 247_C | 1.115 | 0.61 |
| 40_I | 43_T | 1.113 | 0.61 |
| 23_A | 27_E | 1.108 | 0.60 |
| 199_V | 257_I | 1.106 | 0.60 |
| 22_K | 25_S | 1.105 | 0.60 |
| 171_I | 198_L | 1.103 | 0.60 |
| 210_T | 233_Y | 1.102 | 0.59 |
| 37_R | 244_Y | 1.101 | 0.59 |
| 103_G | 117_R | 1.101 | 0.59 |
| 65_E | 98_D | 1.101 | 0.59 |
| 28_E | 195_L | 1.101 | 0.59 |
| 37_R | 202_S | 1.096 | 0.59 |
| 232_R | 236_Q | 1.096 | 0.59 |
| 167_L | 177_L | 1.096 | 0.59 |
| 168_Q | 181_H | 1.089 | 0.58 |
| 32_K | 43_T | 1.088 | 0.58 |
| 32_K | 38_S | 1.087 | 0.58 |
| 97_I | 122_F | 1.085 | 0.58 |
| 16_L | 55_G | 1.084 | 0.58 |
| 206_Y | 243_F | 1.081 | 0.57 |
| 256_L | 260_P | 1.080 | 0.57 |
| 74_T | 236_Q | 1.079 | 0.57 |
| 19_N | 35_H | 1.078 | 0.57 |
| 113_G | 119_Y | 1.078 | 0.57 |
| 116_I | 119_Y | 1.077 | 0.57 |
| 66_V | 128_S | 1.077 | 0.57 |
| 135_E | 149_K | 1.076 | 0.57 |
| 144_E | 148_L | 1.073 | 0.56 |
| 201_E | 230_R | 1.070 | 0.56 |
| 33_R | 211_S | 1.058 | 0.55 |
| 30_A | 235_A | 1.057 | 0.55 |
| 26_P | 62_L | 1.057 | 0.55 |
| 224_E | 228_P | 1.053 | 0.54 |
| 40_I | 78_V | 1.052 | 0.54 |
| 139_T | 149_K | 1.049 | 0.54 |
| 49_S | 52_F | 1.047 | 0.54 |
| 34_K | 37_R | 1.047 | 0.54 |
| 35_H | 241_V | 1.046 | 0.53 |
| 209_I | 233_Y | 1.044 | 0.53 |
| 140_F | 143_E | 1.043 | 0.53 |
| 24_T | 72_L | 1.040 | 0.53 |
| 66_V | 82_G | 1.037 | 0.53 |
| 19_N | 38_S | 1.034 | 0.52 |
| 98_D | 127_L | 1.032 | 0.52 |
| 166_T | 171_I | 1.031 | 0.52 |
| 75_I | 101_S | 1.029 | 0.52 |
| 91_M | 98_D | 1.027 | 0.51 |
| 203_Y | 244_Y | 1.027 | 0.51 |
| 31_P | 198_L | 1.024 | 0.51 |
| 32_K | 42_Y | 1.024 | 0.51 |
| 159_E | 163_D | 1.022 | 0.51 |
| 74_T | 227_E | 1.021 | 0.51 |
| 42_Y | 46_H | 1.018 | 0.50 |
| 78_V | 257_I | 1.017 | 0.50 |
| 62_L | 233_Y | 1.016 | 0.50 |
| 218_S | 225_A | 1.014 | 0.50 |
| 92_A | 178_I | 1.014 | 0.50 |
| 59_Q | 258_T | 1.013 | 0.50 |
| 31_P | 122_F | 1.012 | 0.50 |
| 180_S | 185_I | 1.010 | 0.50 |
| 69_F | 228_P | 1.005 | 0.49 |
| 73_I | 229_L | 1.003 | 0.49 |
| 82_G | 195_L | 1.000 | 0.49 |
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 | |
| 1hx8A | 2 | 0.8702 | 100 | 0.337 | Contact Map |
| 3zylA | 2 | 0.8969 | 100 | 0.357 | Contact Map |
| 3zymA | 3 | 0.8855 | 100 | 0.368 | Contact Map |
| 1eyhA | 1 | 0.5382 | 99.8 | 0.74 | Contact Map |
| 1inzA | 1 | 0.5229 | 99.8 | 0.743 | Contact Map |
| 3onkA | 1 | 0.5076 | 99.7 | 0.777 | Contact Map |
| 4gzcA | 1 | 0.4924 | 99.6 | 0.786 | Contact Map |
| 1xgwA | 1 | 0.5038 | 99.5 | 0.804 | Contact Map |
| 1vdyA | 1 | 0.5153 | 98.7 | 0.863 | Contact Map |
| 1x5bA | 1 | 0.5878 | 90.5 | 0.933 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)