| 10-12 |
| ID: | 1510680458 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 347 (329) | ||
| Sequences: | 672 (433.6) | ||
| Seq/Len: | 2.043 | ||
| Nf(neff/√len): | 23.9 |
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: 2.043).
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 |
| 33_A | 42_Y | 3.048 | 1.00 |
| 152_M | 197_A | 3.046 | 1.00 |
| 55_I | 62_I | 3.008 | 1.00 |
| 179_T | 183_F | 2.844 | 1.00 |
| 124_G | 137_L | 2.701 | 1.00 |
| 171_E | 174_T | 2.456 | 1.00 |
| 141_A | 154_Y | 2.410 | 1.00 |
| 217_N | 220_D | 2.268 | 1.00 |
| 33_A | 60_G | 1.963 | 0.99 |
| 42_Y | 60_G | 1.946 | 0.99 |
| 70_Y | 74_T | 1.919 | 0.99 |
| 64_V | 68_L | 1.907 | 0.99 |
| 112_D | 145_D | 1.855 | 0.98 |
| 109_D | 112_D | 1.740 | 0.97 |
| 71_E | 112_D | 1.680 | 0.96 |
| 170_V | 177_I | 1.676 | 0.96 |
| 70_Y | 191_F | 1.659 | 0.96 |
| 193_F | 211_V | 1.656 | 0.96 |
| 28_V | 62_I | 1.647 | 0.95 |
| 56_N | 59_T | 1.626 | 0.95 |
| 40_I | 82_A | 1.625 | 0.95 |
| 18_V | 68_L | 1.623 | 0.95 |
| 15_P | 29_G | 1.595 | 0.94 |
| 196_I | 208_K | 1.585 | 0.94 |
| 156_L | 170_V | 1.573 | 0.94 |
| 128_E | 186_M | 1.559 | 0.93 |
| 184_H | 219_L | 1.545 | 0.93 |
| 31_I | 62_I | 1.536 | 0.93 |
| 68_L | 76_Y | 1.490 | 0.91 |
| 42_Y | 82_A | 1.481 | 0.91 |
| 8_F | 13_Y | 1.465 | 0.90 |
| 109_D | 113_H | 1.462 | 0.90 |
| 139_V | 177_I | 1.452 | 0.90 |
| 60_G | 82_A | 1.444 | 0.89 |
| 156_L | 178_K | 1.440 | 0.89 |
| 42_Y | 56_N | 1.438 | 0.89 |
| 117_F | 122_Y | 1.434 | 0.89 |
| 220_D | 223_V | 1.405 | 0.87 |
| 71_E | 113_H | 1.390 | 0.87 |
| 137_L | 177_I | 1.383 | 0.86 |
| 69_D | 112_D | 1.378 | 0.86 |
| 35_A | 96_S | 1.370 | 0.86 |
| 109_D | 145_D | 1.367 | 0.85 |
| 114_P | 205_L | 1.358 | 0.85 |
| 44_I | 48_N | 1.354 | 0.85 |
| 139_V | 154_Y | 1.348 | 0.84 |
| 320_E | 325_L | 1.336 | 0.84 |
| 56_N | 63_Y | 1.315 | 0.82 |
| 220_D | 261_S | 1.301 | 0.81 |
| 219_L | 223_V | 1.296 | 0.81 |
| 34_A | 174_T | 1.294 | 0.81 |
| 103_V | 174_T | 1.294 | 0.81 |
| 111_N | 145_D | 1.284 | 0.80 |
| 261_S | 267_H | 1.284 | 0.80 |
| 122_Y | 167_G | 1.281 | 0.80 |
| 28_V | 64_V | 1.272 | 0.79 |
| 53_F | 76_Y | 1.262 | 0.78 |
| 43_S | 55_I | 1.262 | 0.78 |
| 124_G | 136_V | 1.261 | 0.78 |
| 44_I | 47_G | 1.260 | 0.78 |
| 310_I | 313_D | 1.259 | 0.78 |
| 55_I | 60_G | 1.252 | 0.78 |
| 186_M | 217_N | 1.249 | 0.77 |
| 33_A | 56_N | 1.248 | 0.77 |
| 112_D | 199_D | 1.247 | 0.77 |
| 23_A | 26_T | 1.236 | 0.76 |
| 42_Y | 59_T | 1.234 | 0.76 |
| 309_D | 312_K | 1.234 | 0.76 |
| 177_I | 211_V | 1.224 | 0.75 |
| 309_D | 313_D | 1.216 | 0.75 |
| 279_C | 283_V | 1.216 | 0.75 |
| 84_S | 95_P | 1.212 | 0.74 |
| 326_E | 329_T | 1.209 | 0.74 |
| 154_Y | 197_A | 1.208 | 0.74 |
| 305_G | 309_D | 1.205 | 0.74 |
| 27_M | 31_I | 1.204 | 0.74 |
| 47_G | 51_D | 1.201 | 0.73 |
| 84_S | 93_R | 1.200 | 0.73 |
| 128_E | 220_D | 1.198 | 0.73 |
| 193_F | 212_L | 1.195 | 0.73 |
| 220_D | 267_H | 1.194 | 0.73 |
| 113_H | 150_S | 1.189 | 0.72 |
| 185_N | 189_S | 1.184 | 0.72 |
| 146_T | 150_S | 1.180 | 0.72 |
| 198_T | 206_S | 1.180 | 0.72 |
| 59_T | 107_I | 1.172 | 0.71 |
| 157_I | 196_I | 1.169 | 0.71 |
| 112_D | 143_D | 1.159 | 0.70 |
| 118_Q | 140_K | 1.159 | 0.70 |
| 184_H | 217_N | 1.159 | 0.70 |
| 321_G | 324_I | 1.157 | 0.69 |
| 53_F | 78_L | 1.156 | 0.69 |
| 69_D | 143_D | 1.152 | 0.69 |
| 222_Q | 240_L | 1.149 | 0.69 |
| 33_A | 40_I | 1.149 | 0.69 |
| 111_N | 143_D | 1.138 | 0.68 |
| 275_D | 278_K | 1.137 | 0.68 |
| 35_A | 95_P | 1.133 | 0.67 |
| 20_E | 71_E | 1.129 | 0.67 |
| 71_E | 109_D | 1.123 | 0.66 |
| 124_G | 179_T | 1.121 | 0.66 |
| 21_L | 110_E | 1.117 | 0.66 |
| 26_T | 114_P | 1.116 | 0.65 |
| 318_Y | 322_G | 1.115 | 0.65 |
| 245_D | 254_G | 1.110 | 0.65 |
| 45_V | 81_Q | 1.107 | 0.65 |
| 155_R | 172_T | 1.105 | 0.64 |
| 284_Y | 291_N | 1.104 | 0.64 |
| 92_L | 99_N | 1.104 | 0.64 |
| 128_E | 221_M | 1.100 | 0.64 |
| 48_N | 51_D | 1.100 | 0.64 |
| 154_Y | 174_T | 1.096 | 0.63 |
| 22_A | 26_T | 1.092 | 0.63 |
| 186_M | 221_M | 1.092 | 0.63 |
| 125_G | 214_S | 1.090 | 0.63 |
| 154_Y | 175_G | 1.086 | 0.62 |
| 49_E | 78_L | 1.082 | 0.62 |
| 307_L | 313_D | 1.081 | 0.62 |
| 69_D | 111_N | 1.081 | 0.62 |
| 78_L | 191_F | 1.080 | 0.62 |
| 12_E | 215_V | 1.078 | 0.61 |
| 196_I | 206_S | 1.075 | 0.61 |
| 62_I | 80_V | 1.071 | 0.61 |
| 307_L | 310_I | 1.070 | 0.61 |
| 128_E | 263_G | 1.070 | 0.61 |
| 327_I | 330_P | 1.069 | 0.61 |
| 70_Y | 112_D | 1.067 | 0.60 |
| 108_Q | 113_H | 1.065 | 0.60 |
| 64_V | 286_I | 1.063 | 0.60 |
| 68_L | 107_I | 1.062 | 0.60 |
| 20_E | 69_D | 1.062 | 0.60 |
| 322_G | 326_E | 1.062 | 0.60 |
| 156_L | 193_F | 1.059 | 0.59 |
| 128_E | 184_H | 1.058 | 0.59 |
| 321_G | 327_I | 1.057 | 0.59 |
| 33_A | 82_A | 1.054 | 0.59 |
| 107_I | 121_F | 1.053 | 0.59 |
| 147_G | 150_S | 1.052 | 0.59 |
| 307_L | 312_K | 1.052 | 0.59 |
| 69_D | 113_H | 1.051 | 0.59 |
| 128_E | 217_N | 1.051 | 0.59 |
| 130_A | 183_F | 1.050 | 0.58 |
| 310_I | 323_R | 1.042 | 0.58 |
| 69_D | 109_D | 1.036 | 0.57 |
| 323_R | 326_E | 1.035 | 0.57 |
| 138_R | 211_V | 1.034 | 0.57 |
| 54_G | 65_N | 1.031 | 0.56 |
| 311_N | 322_G | 1.030 | 0.56 |
| 186_M | 219_L | 1.029 | 0.56 |
| 110_E | 114_P | 1.028 | 0.56 |
| 217_N | 263_G | 1.028 | 0.56 |
| 119_K | 213_V | 1.027 | 0.56 |
| 28_V | 31_I | 1.026 | 0.56 |
| 168_F | 188_R | 1.025 | 0.56 |
| 302_F | 314_F | 1.023 | 0.55 |
| 37_N | 95_P | 1.021 | 0.55 |
| 257_V | 294_V | 1.021 | 0.55 |
| 134_A | 181_M | 1.019 | 0.55 |
| 111_N | 115_P | 1.017 | 0.55 |
| 8_F | 33_A | 1.016 | 0.55 |
| 44_I | 178_K | 1.014 | 0.54 |
| 168_F | 193_F | 1.012 | 0.54 |
| 139_V | 212_L | 1.011 | 0.54 |
| 312_K | 322_G | 1.010 | 0.54 |
| 132_M | 181_M | 1.010 | 0.54 |
| 186_M | 220_D | 1.008 | 0.54 |
| 54_G | 63_Y | 1.008 | 0.54 |
| 265_R | 270_A | 1.007 | 0.54 |
| 112_D | 115_P | 1.001 | 0.53 |
| 21_L | 67_P | 1.000 | 0.53 |
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 | |
| 4ux8A | 2 | 0.8588 | 100 | 0.418 | Contact Map |
| 1q55A | 4 | 0.8876 | 100 | 0.423 | Contact Map |
| 1l3wA | 1 | 0.8876 | 100 | 0.448 | Contact Map |
| 3q2wA | 1 | 0.8934 | 100 | 0.45 | Contact Map |
| 2a62A | 1 | 0.8473 | 100 | 0.45 | Contact Map |
| 3mvsA | 1 | 0.5937 | 100 | 0.451 | Contact Map |
| 2x2uA | 1 | 0.585 | 100 | 0.452 | Contact Map |
| 3q2vA | 2 | 0.8905 | 100 | 0.456 | Contact Map |
| 3ubhA | 1 | 0.8732 | 100 | 0.457 | Contact Map |
| 3ubfA | 1 | 0.5735 | 100 | 0.481 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)