| Landajuela Mrs |
| ID: | 1492710500 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 254 (230) | ||
| Sequences: | 350 (297.1) | ||
| Seq/Len: | 1.522 | ||
| Nf(neff/√len): | 19.6 |
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: 1.522).
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 |
| 85_D | 89_N | 2.477 | 1.00 |
| 96_N | 99_V | 2.335 | 1.00 |
| 171_I | 179_A | 1.838 | 0.96 |
| 89_N | 218_E | 1.759 | 0.95 |
| 53_E | 56_R | 1.729 | 0.94 |
| 174_Y | 179_A | 1.699 | 0.94 |
| 84_S | 90_L | 1.648 | 0.92 |
| 155_V | 194_I | 1.623 | 0.91 |
| 178_N | 181_I | 1.588 | 0.90 |
| 188_E | 203_V | 1.505 | 0.87 |
| 172_K | 180_L | 1.454 | 0.84 |
| 170_K | 182_D | 1.432 | 0.83 |
| 157_F | 194_I | 1.420 | 0.82 |
| 76_M | 178_N | 1.419 | 0.82 |
| 14_L | 19_V | 1.417 | 0.82 |
| 76_M | 181_I | 1.375 | 0.79 |
| 58_A | 141_T | 1.369 | 0.79 |
| 140_V | 219_V | 1.361 | 0.78 |
| 171_I | 212_I | 1.355 | 0.78 |
| 76_M | 171_I | 1.355 | 0.78 |
| 15_P | 19_V | 1.352 | 0.78 |
| 168_K | 186_F | 1.343 | 0.77 |
| 174_Y | 216_Q | 1.338 | 0.77 |
| 138_G | 150_G | 1.336 | 0.76 |
| 51_E | 200_K | 1.336 | 0.76 |
| 171_I | 178_N | 1.314 | 0.75 |
| 97_T | 101_N | 1.312 | 0.75 |
| 161_G | 196_P | 1.309 | 0.74 |
| 42_I | 99_V | 1.303 | 0.74 |
| 51_E | 194_I | 1.302 | 0.74 |
| 131_I | 216_Q | 1.300 | 0.74 |
| 50_G | 151_P | 1.300 | 0.74 |
| 95_F | 171_I | 1.293 | 0.73 |
| 123_G | 129_E | 1.290 | 0.73 |
| 197_F | 209_P | 1.284 | 0.72 |
| 151_P | 176_I | 1.278 | 0.72 |
| 55_K | 190_K | 1.275 | 0.71 |
| 81_Q | 96_N | 1.269 | 0.71 |
| 178_N | 212_I | 1.265 | 0.71 |
| 93_I | 215_V | 1.262 | 0.70 |
| 105_T | 211_S | 1.259 | 0.70 |
| 116_K | 209_P | 1.234 | 0.68 |
| 50_G | 53_E | 1.234 | 0.68 |
| 34_S | 38_I | 1.232 | 0.68 |
| 100_V | 167_V | 1.225 | 0.67 |
| 65_S | 110_Q | 1.222 | 0.67 |
| 70_M | 96_N | 1.219 | 0.67 |
| 16_F | 19_V | 1.212 | 0.66 |
| 129_E | 132_M | 1.196 | 0.64 |
| 13_P | 18_Y | 1.193 | 0.64 |
| 56_R | 211_S | 1.187 | 0.64 |
| 96_N | 191_V | 1.187 | 0.64 |
| 85_D | 90_L | 1.183 | 0.63 |
| 105_T | 172_K | 1.178 | 0.63 |
| 186_F | 207_N | 1.176 | 0.62 |
| 139_Q | 142_G | 1.172 | 0.62 |
| 180_L | 212_I | 1.171 | 0.62 |
| 13_P | 19_V | 1.165 | 0.61 |
| 10_K | 20_M | 1.165 | 0.61 |
| 171_I | 181_I | 1.164 | 0.61 |
| 167_V | 211_S | 1.161 | 0.61 |
| 49_I | 206_N | 1.160 | 0.61 |
| 165_T | 172_K | 1.153 | 0.60 |
| 193_V | 209_P | 1.151 | 0.60 |
| 66_I | 189_I | 1.149 | 0.60 |
| 20_M | 153_I | 1.145 | 0.59 |
| 101_N | 179_A | 1.141 | 0.59 |
| 105_T | 146_L | 1.139 | 0.59 |
| 50_G | 155_V | 1.139 | 0.59 |
| 171_I | 182_D | 1.138 | 0.59 |
| 153_I | 166_D | 1.137 | 0.59 |
| 15_P | 27_F | 1.121 | 0.57 |
| 122_T | 129_E | 1.115 | 0.56 |
| 172_K | 182_D | 1.115 | 0.56 |
| 141_T | 149_L | 1.114 | 0.56 |
| 76_M | 215_V | 1.111 | 0.56 |
| 120_T | 129_E | 1.108 | 0.56 |
| 127_A | 131_I | 1.107 | 0.56 |
| 32_T | 86_E | 1.106 | 0.55 |
| 114_H | 218_E | 1.104 | 0.55 |
| 168_K | 207_N | 1.103 | 0.55 |
| 25_V | 62_I | 1.102 | 0.55 |
| 50_G | 209_P | 1.094 | 0.54 |
| 92_T | 104_K | 1.093 | 0.54 |
| 45_V | 210_V | 1.090 | 0.54 |
| 179_A | 212_I | 1.089 | 0.54 |
| 37_M | 187_V | 1.087 | 0.53 |
| 120_T | 131_I | 1.087 | 0.53 |
| 12_G | 15_P | 1.085 | 0.53 |
| 74_E | 111_L | 1.084 | 0.53 |
| 42_I | 187_V | 1.084 | 0.53 |
| 15_P | 23_S | 1.083 | 0.53 |
| 97_T | 165_T | 1.081 | 0.53 |
| 51_E | 202_A | 1.081 | 0.53 |
| 97_T | 209_P | 1.080 | 0.53 |
| 145_L | 199_S | 1.080 | 0.53 |
| 17_R | 21_L | 1.079 | 0.53 |
| 120_T | 132_M | 1.076 | 0.52 |
| 139_Q | 209_P | 1.075 | 0.52 |
| 13_P | 231_V | 1.075 | 0.52 |
| 186_F | 208_V | 1.072 | 0.52 |
| 124_H | 193_V | 1.071 | 0.52 |
| 99_V | 102_S | 1.070 | 0.52 |
| 23_S | 27_F | 1.063 | 0.51 |
| 181_I | 213_K | 1.062 | 0.51 |
| 151_P | 155_V | 1.061 | 0.51 |
| 171_I | 174_Y | 1.059 | 0.51 |
| 153_I | 162_D | 1.057 | 0.50 |
| 39_N | 62_I | 1.055 | 0.50 |
| 15_P | 18_Y | 1.049 | 0.50 |
| 160_I | 166_D | 1.038 | 0.48 |
| 94_D | 209_P | 1.038 | 0.48 |
| 97_T | 100_V | 1.037 | 0.48 |
| 25_V | 153_I | 1.034 | 0.48 |
| 212_I | 216_Q | 1.031 | 0.48 |
| 46_L | 157_F | 1.030 | 0.48 |
| 64_D | 68_D | 1.021 | 0.47 |
| 141_T | 160_I | 1.018 | 0.46 |
| 26_F | 30_S | 1.015 | 0.46 |
| 190_K | 203_V | 1.015 | 0.46 |
| 15_P | 21_L | 1.014 | 0.46 |
| 192_K | 201_T | 1.014 | 0.46 |
| 135_I | 192_K | 1.012 | 0.46 |
| 66_I | 80_F | 1.012 | 0.46 |
| 122_T | 128_S | 1.007 | 0.45 |
| 187_V | 210_V | 1.007 | 0.45 |
| 27_F | 195_I | 1.004 | 0.45 |
| 159_L | 171_I | 1.002 | 0.45 |
| 230_G | 236_Q | 1.000 | 0.44 |
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 | |
| 2m8rA | 1 | 0.1496 | 19.4 | 0.961 | Contact Map |
| 2kogA | 1 | 0.1614 | 13.8 | 0.963 | Contact Map |
| 3fymA | 1 | 0 | 10.6 | 0.965 | Contact Map |
| 1j2pA | 7 | 0.4016 | 6.6 | 0.968 | Contact Map |
| 1q1sA | 2 | 0.0354 | 6.5 | 0.968 | Contact Map |
| 1j8bA | 1 | 0.3465 | 5.8 | 0.969 | Contact Map |
| 1ybxA | 2 | 0.3425 | 5.1 | 0.97 | Contact Map |
| 3hd7A | 2 | 0.1535 | 4.7 | 0.97 | Contact Map |
| 2bs2C | 2 | 0.2283 | 4.7 | 0.97 | Contact Map |
| 1rypC | 2 | 0.4016 | 4.7 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)