| CENPUMIS17 |
| ID: | 1494712819 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 441 (227) | ||
| Sequences: | 28218 (27803.3) | ||
| Seq/Len: | 124.308 | ||
| Nf(neff/√len): | 1845.4 |
Jackhmmer Results: (2016_04)
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: 124.308).
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 |
| 184_F | 188_H | 1.579 | 1.00 |
| 114_V | 117_E | 1.530 | 1.00 |
| 173_R | 176_S | 1.494 | 1.00 |
| 113_A | 117_E | 1.490 | 1.00 |
| 221_Q | 225_L | 1.391 | 0.99 |
| 183_S | 187_E | 1.374 | 0.99 |
| 246_K | 250_V | 1.353 | 0.99 |
| 179_S | 183_S | 1.342 | 0.99 |
| 188_H | 192_V | 1.319 | 0.99 |
| 126_V | 129_N | 1.317 | 0.99 |
| 151_N | 154_T | 1.314 | 0.99 |
| 255_E | 259_I | 1.312 | 0.99 |
| 239_L | 243_S | 1.309 | 0.99 |
| 110_S | 114_V | 1.308 | 0.99 |
| 257_V | 261_L | 1.306 | 0.99 |
| 186_E | 190_G | 1.297 | 0.99 |
| 164_E | 167_P | 1.293 | 0.99 |
| 208_S | 212_T | 1.275 | 0.99 |
| 190_G | 193_T | 1.270 | 0.99 |
| 220_N | 224_S | 1.264 | 0.99 |
| 240_L | 244_T | 1.257 | 0.99 |
| 188_H | 191_N | 1.256 | 0.99 |
| 94_S | 98_V | 1.249 | 0.99 |
| 259_I | 263_K | 1.245 | 0.98 |
| 241_D | 245_E | 1.230 | 0.98 |
| 158_Y | 161_S | 1.230 | 0.98 |
| 251_G | 255_E | 1.228 | 0.98 |
| 223_S | 227_S | 1.227 | 0.98 |
| 254_D | 257_V | 1.226 | 0.98 |
| 241_D | 244_T | 1.225 | 0.98 |
| 219_T | 223_S | 1.217 | 0.98 |
| 109_V | 113_A | 1.215 | 0.98 |
| 145_P | 149_R | 1.215 | 0.98 |
| 173_R | 177_L | 1.215 | 0.98 |
| 254_D | 258_R | 1.212 | 0.98 |
| 251_G | 257_V | 1.209 | 0.98 |
| 170_K | 173_R | 1.202 | 0.98 |
| 65_E | 68_H | 1.202 | 0.98 |
| 130_H | 133_S | 1.199 | 0.98 |
| 178_D | 182_D | 1.198 | 0.98 |
| 97_V | 101_N | 1.195 | 0.98 |
| 80_F | 84_D | 1.195 | 0.98 |
| 211_S | 215_P | 1.194 | 0.98 |
| 199_S | 202_P | 1.191 | 0.98 |
| 227_S | 231_T | 1.189 | 0.98 |
| 170_K | 174_L | 1.180 | 0.98 |
| 253_S | 257_V | 1.178 | 0.98 |
| 109_V | 112_S | 1.177 | 0.98 |
| 219_T | 222_S | 1.176 | 0.98 |
| 171_V | 174_L | 1.170 | 0.97 |
| 63_Q | 67_Y | 1.170 | 0.97 |
| 233_S | 237_R | 1.169 | 0.97 |
| 245_E | 248_I | 1.167 | 0.97 |
| 156_D | 159_S | 1.164 | 0.97 |
| 64_S | 68_H | 1.160 | 0.97 |
| 174_L | 177_L | 1.160 | 0.97 |
| 186_E | 189_P | 1.147 | 0.97 |
| 147_H | 151_N | 1.146 | 0.97 |
| 204_E | 208_S | 1.142 | 0.97 |
| 189_P | 192_V | 1.141 | 0.97 |
| 125_L | 129_N | 1.141 | 0.97 |
| 223_S | 226_Q | 1.132 | 0.97 |
| 162_I | 166_S | 1.131 | 0.97 |
| 121_S | 125_L | 1.131 | 0.97 |
| 144_I | 148_K | 1.130 | 0.97 |
| 180_S | 184_F | 1.127 | 0.97 |
| 238_N | 242_Q | 1.126 | 0.97 |
| 154_T | 158_Y | 1.125 | 0.97 |
| 163_L | 167_P | 1.124 | 0.97 |
| 242_Q | 245_E | 1.123 | 0.97 |
| 128_D | 131_F | 1.122 | 0.97 |
| 171_V | 175_S | 1.117 | 0.96 |
| 172_Q | 176_S | 1.116 | 0.96 |
| 259_I | 262_T | 1.116 | 0.96 |
| 55_Q | 59_E | 1.111 | 0.96 |
| 68_H | 72_D | 1.109 | 0.96 |
| 113_A | 116_R | 1.105 | 0.96 |
| 131_F | 135_K | 1.105 | 0.96 |
| 209_P | 212_T | 1.102 | 0.96 |
| 102_S | 105_S | 1.102 | 0.96 |
| 222_S | 228_S | 1.099 | 0.96 |
| 206_I | 210_I | 1.095 | 0.96 |
| 183_S | 186_E | 1.094 | 0.96 |
| 159_S | 163_L | 1.092 | 0.96 |
| 244_T | 247_D | 1.089 | 0.96 |
| 182_D | 186_E | 1.087 | 0.96 |
| 110_S | 113_A | 1.086 | 0.96 |
| 232_S | 236_P | 1.086 | 0.96 |
| 143_S | 147_H | 1.085 | 0.96 |
| 100_E | 106_I | 1.084 | 0.96 |
| 146_F | 149_R | 1.079 | 0.95 |
| 119_Q | 122_A | 1.075 | 0.95 |
| 91_R | 94_S | 1.074 | 0.95 |
| 112_S | 115_A | 1.073 | 0.95 |
| 187_E | 191_N | 1.070 | 0.95 |
| 195_T | 198_S | 1.069 | 0.95 |
| 227_S | 230_Q | 1.066 | 0.95 |
| 196_T | 200_Q | 1.065 | 0.95 |
| 119_Q | 123_N | 1.065 | 0.95 |
| 226_Q | 229_L | 1.064 | 0.95 |
| 124_I | 127_K | 1.064 | 0.95 |
| 153_E | 156_D | 1.062 | 0.95 |
| 198_S | 201_A | 1.061 | 0.95 |
| 225_L | 228_S | 1.058 | 0.95 |
| 132_F | 136_Q | 1.052 | 0.95 |
| 130_H | 134_H | 1.052 | 0.95 |
| 165_N | 168_P | 1.050 | 0.94 |
| 242_Q | 246_K | 1.050 | 0.94 |
| 207_A | 211_S | 1.049 | 0.94 |
| 240_L | 243_S | 1.048 | 0.94 |
| 230_Q | 234_M | 1.047 | 0.94 |
| 233_S | 236_P | 1.047 | 0.94 |
| 184_F | 187_E | 1.046 | 0.94 |
| 215_P | 219_T | 1.046 | 0.94 |
| 187_E | 190_G | 1.044 | 0.94 |
| 107_E | 110_S | 1.040 | 0.94 |
| 240_L | 245_E | 1.039 | 0.94 |
| 243_S | 246_K | 1.037 | 0.94 |
| 194_G | 197_F | 1.037 | 0.94 |
| 128_D | 132_F | 1.037 | 0.94 |
| 199_S | 203_E | 1.034 | 0.94 |
| 44_S | 47_T | 1.034 | 0.94 |
| 245_E | 249_V | 1.034 | 0.94 |
| 216_E | 220_N | 1.033 | 0.94 |
| 126_V | 130_H | 1.031 | 0.94 |
| 144_I | 147_H | 1.030 | 0.94 |
| 129_N | 133_S | 1.025 | 0.93 |
| 155_S | 158_Y | 1.024 | 0.93 |
| 99_R | 103_V | 1.023 | 0.93 |
| 132_F | 135_K | 1.023 | 0.93 |
| 92_R | 96_E | 1.023 | 0.93 |
| 157_A | 161_S | 1.019 | 0.93 |
| 147_H | 150_D | 1.018 | 0.93 |
| 140_Q | 144_I | 1.015 | 0.93 |
| 106_I | 109_V | 1.015 | 0.93 |
| 123_N | 127_K | 1.014 | 0.93 |
| 258_R | 262_T | 1.012 | 0.93 |
| 93_I | 97_V | 1.011 | 0.93 |
| 226_Q | 230_Q | 1.007 | 0.93 |
| 141_R | 145_P | 1.006 | 0.93 |
| 120_S | 123_N | 1.005 | 0.93 |
| 123_N | 126_V | 1.005 | 0.93 |
| 91_R | 95_E | 1.004 | 0.93 |
| 129_N | 132_F | 1.004 | 0.93 |
| 205_R | 209_P | 1.003 | 0.93 |
| 127_K | 130_H | 1.003 | 0.93 |
| 198_S | 202_P | 1.000 | 0.92 |
| 239_L | 242_Q | 1.000 | 0.92 |
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 | |
| 1twfA | 1 | 0 | 94.5 | 0.889 | Contact Map |
| 1deqA | 4 | 0.3424 | 93.6 | 0.893 | Contact Map |
| 4q4gX | 1 | 0 | 92.7 | 0.896 | Contact Map |
| 3ghgA | 4 | 0.3696 | 91 | 0.901 | Contact Map |
| 4rsiB | 1 | 0.3401 | 90.2 | 0.903 | Contact Map |
| 4cgkA | 2 | 0.3152 | 89.4 | 0.904 | Contact Map |
| 4iloA | 2 | 0.3447 | 88.2 | 0.906 | Contact Map |
| 3na7A | 1 | 0.3243 | 88.1 | 0.907 | Contact Map |
| 1c1gA | 4 | 0.3741 | 85.2 | 0.911 | Contact Map |
| 4rsiA | 1 | 0.2018 | 84.2 | 0.912 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)