| Ufd1 |
| ID: | 1485325044 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 307 (306) | ||
| Sequences: | 340 (210.6) | ||
| Seq/Len: | 1.111 | ||
| Nf(neff/√len): | 12.0 |
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: 1.111).
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 |
| 120_A | 180_V | 3.481 | 1.00 |
| 40_V | 47_I | 2.356 | 0.99 |
| 48_M | 92_C | 2.226 | 0.98 |
| 154_T | 174_T | 1.916 | 0.95 |
| 256_R | 259_P | 1.906 | 0.95 |
| 19_F | 23_Y | 1.829 | 0.93 |
| 71_N | 104_L | 1.715 | 0.90 |
| 151_C | 179_A | 1.664 | 0.88 |
| 185_C | 188_N | 1.663 | 0.88 |
| 50_P | 135_I | 1.641 | 0.87 |
| 76_R | 103_L | 1.635 | 0.87 |
| 60_N | 160_I | 1.635 | 0.87 |
| 117_L | 179_A | 1.621 | 0.86 |
| 29_S | 96_H | 1.614 | 0.86 |
| 60_N | 188_N | 1.608 | 0.85 |
| 24_R | 109_L | 1.570 | 0.83 |
| 19_F | 24_R | 1.541 | 0.82 |
| 19_F | 25_C | 1.532 | 0.81 |
| 123_S | 185_C | 1.523 | 0.81 |
| 102_L | 202_R | 1.514 | 0.80 |
| 48_M | 139_K | 1.513 | 0.80 |
| 78_T | 128_Q | 1.512 | 0.80 |
| 183_I | 231_S | 1.499 | 0.79 |
| 63_Y | 184_E | 1.492 | 0.79 |
| 63_Y | 66_L | 1.483 | 0.78 |
| 101_N | 137_N | 1.483 | 0.78 |
| 33_G | 37_R | 1.482 | 0.78 |
| 50_P | 93_Y | 1.477 | 0.78 |
| 177_D | 190_D | 1.475 | 0.78 |
| 30_M | 149_F | 1.466 | 0.77 |
| 107_G | 156_D | 1.438 | 0.75 |
| 135_I | 167_Y | 1.437 | 0.75 |
| 104_L | 108_G | 1.437 | 0.75 |
| 123_S | 180_V | 1.429 | 0.75 |
| 56_L | 65_M | 1.415 | 0.74 |
| 134_D | 167_Y | 1.361 | 0.69 |
| 62_T | 116_N | 1.359 | 0.69 |
| 172_M | 192_D | 1.352 | 0.69 |
| 50_P | 86_V | 1.342 | 0.68 |
| 56_L | 67_F | 1.338 | 0.68 |
| 158_I | 171_V | 1.329 | 0.67 |
| 125_F | 185_C | 1.325 | 0.66 |
| 61_I | 65_M | 1.309 | 0.65 |
| 60_N | 184_E | 1.309 | 0.65 |
| 185_C | 271_I | 1.307 | 0.65 |
| 131_D | 165_K | 1.295 | 0.64 |
| 266_G | 270_F | 1.295 | 0.64 |
| 147_R | 152_L | 1.281 | 0.63 |
| 125_F | 187_M | 1.278 | 0.62 |
| 47_I | 126_Q | 1.266 | 0.61 |
| 61_I | 200_P | 1.254 | 0.60 |
| 157_V | 196_G | 1.253 | 0.60 |
| 170_R | 196_G | 1.249 | 0.60 |
| 123_S | 151_C | 1.244 | 0.59 |
| 267_K | 271_I | 1.243 | 0.59 |
| 295_G | 300_L | 1.240 | 0.59 |
| 112_V | 149_F | 1.228 | 0.58 |
| 71_N | 108_G | 1.223 | 0.57 |
| 66_L | 114_S | 1.222 | 0.57 |
| 54_D | 151_C | 1.217 | 0.57 |
| 269_T | 272_R | 1.216 | 0.57 |
| 263_F | 272_R | 1.212 | 0.56 |
| 129_S | 133_L | 1.205 | 0.56 |
| 127_P | 138_P | 1.205 | 0.56 |
| 128_Q | 195_L | 1.196 | 0.55 |
| 56_L | 63_Y | 1.195 | 0.55 |
| 48_M | 174_T | 1.187 | 0.54 |
| 197_Y | 200_P | 1.180 | 0.53 |
| 79_H | 112_V | 1.172 | 0.52 |
| 18_R | 190_D | 1.171 | 0.52 |
| 92_C | 151_C | 1.165 | 0.52 |
| 61_I | 307_P | 1.164 | 0.52 |
| 8_D | 12_P | 1.161 | 0.51 |
| 120_A | 271_I | 1.142 | 0.50 |
| 188_N | 209_S | 1.139 | 0.49 |
| 112_V | 229_S | 1.136 | 0.49 |
| 59_L | 184_E | 1.136 | 0.49 |
| 174_T | 198_K | 1.135 | 0.49 |
| 135_I | 184_E | 1.134 | 0.49 |
| 120_A | 164_E | 1.131 | 0.49 |
| 25_C | 109_L | 1.129 | 0.48 |
| 43_G | 46_I | 1.125 | 0.48 |
| 150_A | 187_M | 1.124 | 0.48 |
| 26_F | 29_S | 1.122 | 0.48 |
| 230_G | 237_G | 1.118 | 0.47 |
| 128_Q | 196_G | 1.117 | 0.47 |
| 104_L | 167_Y | 1.116 | 0.47 |
| 37_R | 189_V | 1.116 | 0.47 |
| 150_A | 169_L | 1.114 | 0.47 |
| 187_M | 272_R | 1.103 | 0.46 |
| 180_V | 238_K | 1.102 | 0.46 |
| 293_F | 300_L | 1.100 | 0.46 |
| 120_A | 169_L | 1.098 | 0.45 |
| 42_K | 88_D | 1.096 | 0.45 |
| 47_I | 181_S | 1.095 | 0.45 |
| 162_Y | 235_L | 1.094 | 0.45 |
| 146_L | 160_I | 1.093 | 0.45 |
| 185_C | 272_R | 1.093 | 0.45 |
| 194_P | 200_P | 1.093 | 0.45 |
| 181_S | 189_V | 1.091 | 0.45 |
| 65_M | 114_S | 1.089 | 0.45 |
| 148_N | 161_N | 1.088 | 0.44 |
| 39_D | 86_V | 1.086 | 0.44 |
| 24_R | 27_S | 1.084 | 0.44 |
| 129_S | 135_I | 1.083 | 0.44 |
| 282_E | 286_A | 1.080 | 0.44 |
| 65_M | 165_K | 1.078 | 0.44 |
| 264_K | 272_R | 1.078 | 0.44 |
| 53_L | 56_L | 1.076 | 0.43 |
| 198_K | 201_E | 1.073 | 0.43 |
| 140_A | 147_R | 1.073 | 0.43 |
| 148_N | 241_G | 1.070 | 0.43 |
| 44_G | 196_G | 1.065 | 0.42 |
| 27_S | 114_S | 1.065 | 0.42 |
| 114_S | 122_Y | 1.064 | 0.42 |
| 116_N | 182_I | 1.062 | 0.42 |
| 172_M | 196_G | 1.058 | 0.42 |
| 120_A | 159_A | 1.057 | 0.42 |
| 15_F | 39_D | 1.057 | 0.42 |
| 71_N | 205_Q | 1.056 | 0.41 |
| 18_R | 114_S | 1.055 | 0.41 |
| 93_Y | 135_I | 1.052 | 0.41 |
| 76_R | 183_I | 1.052 | 0.41 |
| 93_Y | 140_A | 1.052 | 0.41 |
| 18_R | 62_T | 1.052 | 0.41 |
| 128_Q | 187_M | 1.051 | 0.41 |
| 190_D | 231_S | 1.051 | 0.41 |
| 83_L | 98_M | 1.051 | 0.41 |
| 154_T | 198_K | 1.046 | 0.41 |
| 96_H | 103_L | 1.046 | 0.41 |
| 175_K | 190_D | 1.045 | 0.40 |
| 63_Y | 167_Y | 1.045 | 0.40 |
| 1_M | 4_F | 1.044 | 0.40 |
| 120_A | 269_T | 1.044 | 0.40 |
| 32_A | 36_D | 1.038 | 0.40 |
| 19_F | 27_S | 1.037 | 0.40 |
| 140_A | 162_Y | 1.037 | 0.40 |
| 171_V | 232_G | 1.034 | 0.39 |
| 128_Q | 298_Q | 1.029 | 0.39 |
| 133_L | 194_P | 1.027 | 0.39 |
| 20_S | 193_A | 1.024 | 0.39 |
| 60_N | 262_E | 1.022 | 0.38 |
| 261_Y | 272_R | 1.019 | 0.38 |
| 134_D | 140_A | 1.017 | 0.38 |
| 159_A | 190_D | 1.016 | 0.38 |
| 194_P | 199_E | 1.015 | 0.38 |
| 93_Y | 297_G | 1.014 | 0.38 |
| 154_T | 170_R | 1.013 | 0.38 |
| 114_S | 179_A | 1.011 | 0.37 |
| 137_N | 236_D | 1.009 | 0.37 |
| 121_T | 141_V | 1.008 | 0.37 |
| 1_M | 5_N | 1.007 | 0.37 |
| 57_S | 139_K | 1.007 | 0.37 |
| 136_T | 200_P | 1.005 | 0.37 |
| 36_D | 40_V | 1.005 | 0.37 |
| 23_Y | 88_D | 1.004 | 0.37 |
| 93_Y | 153_T | 1.001 | 0.37 |
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 | |
| 1zc1A | 1 | 0.6612 | 100 | 0.358 | Contact Map |
| 2yujA | 1 | 0.6189 | 100 | 0.394 | Contact Map |
| 3tiwA | 2 | 0.5114 | 100 | 0.752 | Contact Map |
| 1cz4A | 1 | 0.5668 | 99.2 | 0.899 | Contact Map |
| 1wlfA | 1 | 0.5147 | 95.6 | 0.952 | Contact Map |
| 4ko8A | 2 | 0.785 | 88.2 | 0.962 | Contact Map |
| 3cf2A | 4 | 0.759 | 82.2 | 0.965 | Contact Map |
| 3j94A | 6 | 0.2117 | 67.2 | 0.969 | Contact Map |
| 2glwA | 1 | 0.2704 | 62.3 | 0.97 | Contact Map |
| 2jv2A | 1 | 0.2443 | 60.5 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)