| cdc48_3 |
| ID: | 1487742696 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 289 (282) | ||
| Sequences: | 8833 (4376.5) | ||
| Seq/Len: | 31.323 | ||
| Nf(neff/√len): | 260.6 |
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: 31.323).
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 |
| 219_E | 254_H | 5.207 | 1.00 |
| 172_L | 191_A | 4.416 | 1.00 |
| 175_L | 205_L | 4.077 | 1.00 |
| 172_L | 176_K | 4.062 | 1.00 |
| 168_E | 195_S | 4.028 | 1.00 |
| 167_D | 170_G | 3.228 | 1.00 |
| 165_L | 201_S | 2.964 | 1.00 |
| 93_F | 140_A | 2.899 | 1.00 |
| 121_Q | 125_E | 2.388 | 1.00 |
| 252_K | 256_E | 2.336 | 1.00 |
| 9_E | 218_K | 2.289 | 1.00 |
| 208_I | 259_M | 2.259 | 1.00 |
| 196_K | 256_E | 2.217 | 1.00 |
| 173_S | 176_K | 2.173 | 1.00 |
| 168_E | 194_A | 2.137 | 1.00 |
| 1_E | 173_S | 2.129 | 1.00 |
| 192_Y | 196_K | 2.127 | 1.00 |
| 179_L | 209_T | 1.994 | 1.00 |
| 175_L | 193_I | 1.991 | 1.00 |
| 85_R | 125_E | 1.924 | 1.00 |
| 192_Y | 252_K | 1.906 | 1.00 |
| 179_L | 190_L | 1.899 | 1.00 |
| 179_L | 184_V | 1.870 | 1.00 |
| 3_V | 161_I | 1.850 | 1.00 |
| 103_A | 149_P | 1.841 | 1.00 |
| 209_T | 255_F | 1.805 | 1.00 |
| 197_T | 205_L | 1.779 | 1.00 |
| 189_D | 192_Y | 1.733 | 1.00 |
| 200_F | 208_I | 1.717 | 1.00 |
| 172_L | 190_L | 1.711 | 1.00 |
| 110_D | 113_G | 1.693 | 1.00 |
| 178_Q | 206_A | 1.691 | 1.00 |
| 175_L | 208_I | 1.688 | 1.00 |
| 72_E | 75_S | 1.685 | 1.00 |
| 215_L | 257_E | 1.674 | 1.00 |
| 182_T | 209_T | 1.671 | 1.00 |
| 171_R | 197_T | 1.639 | 1.00 |
| 185_S | 249_E | 1.638 | 1.00 |
| 204_D | 265_S | 1.636 | 1.00 |
| 168_E | 191_A | 1.633 | 1.00 |
| 46_A | 138_I | 1.624 | 1.00 |
| 268_D | 272_R | 1.621 | 1.00 |
| 257_E | 260_R | 1.615 | 1.00 |
| 219_E | 253_R | 1.600 | 1.00 |
| 58_I | 90_C | 1.598 | 1.00 |
| 184_V | 188_V | 1.598 | 1.00 |
| 168_E | 172_L | 1.593 | 1.00 |
| 192_Y | 195_S | 1.586 | 1.00 |
| 36_G | 39_G | 1.563 | 1.00 |
| 253_R | 257_E | 1.555 | 1.00 |
| 139_G | 157_L | 1.537 | 1.00 |
| 182_T | 250_L | 1.517 | 1.00 |
| 96_E | 99_S | 1.504 | 1.00 |
| 75_S | 79_D | 1.504 | 1.00 |
| 49_V | 138_I | 1.498 | 1.00 |
| 166_P | 171_R | 1.477 | 1.00 |
| 105_G | 116_D | 1.470 | 1.00 |
| 74_E | 117_R | 1.470 | 1.00 |
| 97_L | 139_G | 1.457 | 1.00 |
| 206_A | 210_Q | 1.445 | 1.00 |
| 8_K | 12_Q | 1.438 | 1.00 |
| 159_Q | 211_R | 1.438 | 1.00 |
| 196_K | 259_M | 1.435 | 1.00 |
| 253_R | 256_E | 1.424 | 1.00 |
| 174_I | 202_G | 1.396 | 0.99 |
| 73_S | 118_V | 1.364 | 0.99 |
| 82_D | 86_A | 1.355 | 0.99 |
| 152_C | 160_L | 1.345 | 0.99 |
| 96_E | 104_R | 1.342 | 0.99 |
| 58_I | 87_A | 1.340 | 0.99 |
| 57_F | 93_F | 1.333 | 0.99 |
| 266_V | 270_E | 1.325 | 0.99 |
| 12_Q | 16_D | 1.320 | 0.99 |
| 153_R | 156_R | 1.319 | 0.99 |
| 44_M | 202_G | 1.319 | 0.99 |
| 7_L | 49_V | 1.317 | 0.99 |
| 215_L | 254_H | 1.310 | 0.99 |
| 211_R | 261_D | 1.309 | 0.99 |
| 169_A | 172_L | 1.294 | 0.99 |
| 189_D | 252_K | 1.287 | 0.99 |
| 172_L | 194_A | 1.282 | 0.99 |
| 127_D | 156_R | 1.278 | 0.99 |
| 254_H | 258_A | 1.277 | 0.99 |
| 34_F | 163_V | 1.259 | 0.99 |
| 33_L | 144_P | 1.259 | 0.99 |
| 179_L | 255_F | 1.258 | 0.99 |
| 5_Q | 218_K | 1.239 | 0.98 |
| 35_Y | 160_L | 1.237 | 0.98 |
| 3_V | 45_L | 1.208 | 0.98 |
| 175_L | 197_T | 1.200 | 0.98 |
| 101_A | 122_L | 1.196 | 0.98 |
| 188_V | 252_K | 1.195 | 0.98 |
| 270_E | 273_R | 1.193 | 0.98 |
| 147_L | 152_C | 1.185 | 0.98 |
| 197_T | 208_I | 1.184 | 0.98 |
| 9_E | 13_Y | 1.183 | 0.98 |
| 192_Y | 256_E | 1.183 | 0.98 |
| 18_P | 21_F | 1.166 | 0.97 |
| 267_S | 270_E | 1.166 | 0.97 |
| 211_R | 214_K | 1.160 | 0.97 |
| 197_T | 259_M | 1.153 | 0.97 |
| 185_S | 188_V | 1.153 | 0.97 |
| 268_D | 273_R | 1.151 | 0.97 |
| 101_A | 151_L | 1.149 | 0.97 |
| 272_R | 276_A | 1.144 | 0.97 |
| 71_G | 74_E | 1.137 | 0.97 |
| 275_E | 279_Q | 1.129 | 0.97 |
| 251_T | 254_H | 1.127 | 0.97 |
| 61_K | 64_E | 1.119 | 0.96 |
| 272_R | 275_E | 1.113 | 0.96 |
| 81_F | 137_V | 1.111 | 0.96 |
| 175_L | 190_L | 1.106 | 0.96 |
| 95_D | 98_D | 1.095 | 0.96 |
| 99_S | 104_R | 1.091 | 0.96 |
| 207_F | 211_R | 1.083 | 0.96 |
| 62_G | 94_L | 1.081 | 0.95 |
| 19_E | 22_L | 1.080 | 0.95 |
| 173_S | 177_A | 1.079 | 0.95 |
| 276_A | 280_Q | 1.058 | 0.95 |
| 13_Y | 21_F | 1.057 | 0.95 |
| 48_A | 52_E | 1.054 | 0.95 |
| 276_A | 279_Q | 1.053 | 0.95 |
| 84_A | 89_P | 1.046 | 0.94 |
| 269_V | 272_R | 1.045 | 0.94 |
| 63_P | 121_Q | 1.045 | 0.94 |
| 212_A | 255_F | 1.044 | 0.94 |
| 112_G | 115_S | 1.040 | 0.94 |
| 216_A | 254_H | 1.035 | 0.94 |
| 194_A | 197_T | 1.034 | 0.94 |
| 65_L | 77_I | 1.027 | 0.94 |
| 45_L | 163_V | 1.021 | 0.93 |
| 77_I | 125_E | 1.018 | 0.93 |
| 88_A | 135_V | 1.014 | 0.93 |
| 271_I | 275_E | 1.013 | 0.93 |
| 95_D | 104_R | 1.011 | 0.93 |
| 150_A | 153_R | 1.010 | 0.93 |
| 20_K | 220_S | 1.007 | 0.93 |
| 79_D | 82_D | 1.006 | 0.93 |
| 168_E | 198_H | 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 | |
| 3cf2A | 4 | 0.6817 | 100 | 0.276 | Contact Map |
| 4ko8A | 2 | 0.872 | 100 | 0.302 | Contact Map |
| 4cr2J | 1 | 0.8408 | 100 | 0.332 | Contact Map |
| 3cmuA | 1 | 0.955 | 100 | 0.334 | Contact Map |
| 3cf0A | 14 | 0.9031 | 100 | 0.364 | Contact Map |
| 4cr2L | 1 | 0.8339 | 100 | 0.367 | Contact Map |
| 2x8aA | 1 | 0.7889 | 100 | 0.368 | Contact Map |
| 4cr2M | 1 | 0.8581 | 100 | 0.373 | Contact Map |
| 4cr2I | 1 | 0.8616 | 100 | 0.381 | Contact Map |
| 2ce7A | 6 | 0.8685 | 100 | 0.386 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)