| MinD homodimer |
| ID: | 1430395246 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 268 (242) | ||
| Sequences: | 9457 (6410.8) | ||
| Seq/Len: | 39.079 | ||
| Nf(neff/√len): | 412.1 |
HHblits Results: (2013_03)
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: 39.079).
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 |
| 20_S | 118_I | 4.689 | 1.00 |
| 85_Y | 114_F | 4.471 | 1.00 |
| 205_A | 231_A | 4.296 | 1.00 |
| 6_V | 136_A | 3.676 | 1.00 |
| 19_T | 232_Y | 3.627 | 1.00 |
| 27_L | 116_Y | 3.339 | 1.00 |
| 30_L | 237_R | 3.319 | 1.00 |
| 32_K | 116_Y | 3.064 | 1.00 |
| 219_P | 222_M | 2.948 | 1.00 |
| 3_E | 138_K | 2.795 | 1.00 |
| 35_C | 114_F | 2.687 | 1.00 |
| 29_I | 233_R | 2.624 | 1.00 |
| 20_S | 36_L | 2.578 | 1.00 |
| 7_I | 23_L | 2.498 | 1.00 |
| 36_L | 46_L | 2.415 | 1.00 |
| 26_A | 236_A | 2.137 | 1.00 |
| 24_G | 36_L | 2.135 | 1.00 |
| 33_R | 115_D | 2.130 | 1.00 |
| 209_E | 212_K | 2.128 | 1.00 |
| 27_L | 118_I | 2.105 | 1.00 |
| 24_G | 118_I | 2.033 | 1.00 |
| 21_A | 46_L | 2.017 | 1.00 |
| 175_R | 206_D | 1.978 | 1.00 |
| 190_D | 194_Q | 1.921 | 1.00 |
| 49_V | 148_S | 1.871 | 1.00 |
| 30_L | 233_R | 1.841 | 1.00 |
| 7_I | 140_I | 1.829 | 1.00 |
| 202_G | 238_R | 1.818 | 1.00 |
| 26_A | 221_A | 1.815 | 1.00 |
| 6_V | 121_C | 1.783 | 1.00 |
| 32_K | 115_D | 1.747 | 1.00 |
| 4_A | 119_I | 1.699 | 1.00 |
| 59_D | 62_D | 1.660 | 1.00 |
| 76_K | 85_Y | 1.648 | 1.00 |
| 23_L | 236_A | 1.637 | 1.00 |
| 202_G | 235_I | 1.632 | 1.00 |
| 24_G | 46_L | 1.600 | 1.00 |
| 21_A | 50_M | 1.568 | 1.00 |
| 7_I | 20_S | 1.547 | 1.00 |
| 17_T | 49_V | 1.542 | 1.00 |
| 23_L | 239_I | 1.541 | 1.00 |
| 21_A | 49_V | 1.518 | 1.00 |
| 144_T | 175_R | 1.498 | 1.00 |
| 212_K | 216_H | 1.464 | 1.00 |
| 71_H | 113_E | 1.454 | 1.00 |
| 207_D | 228_A | 1.438 | 1.00 |
| 32_K | 240_L | 1.433 | 1.00 |
| 191_E | 194_Q | 1.409 | 1.00 |
| 190_D | 203_I | 1.398 | 0.99 |
| 35_C | 117_V | 1.361 | 0.99 |
| 234_N | 237_R | 1.343 | 0.99 |
| 230_I | 233_R | 1.337 | 0.99 |
| 39_T | 119_I | 1.332 | 0.99 |
| 48_V | 151_R | 1.323 | 0.99 |
| 204_V | 228_A | 1.323 | 0.99 |
| 18_T | 210_V | 1.316 | 0.99 |
| 70_M | 87_M | 1.315 | 0.99 |
| 30_L | 240_L | 1.315 | 0.99 |
| 191_E | 195_H | 1.308 | 0.99 |
| 69_K | 72_Q | 1.302 | 0.99 |
| 168_P | 171_L | 1.286 | 0.99 |
| 158_G | 161_E | 1.280 | 0.99 |
| 3_E | 137_D | 1.273 | 0.99 |
| 7_I | 118_I | 1.269 | 0.99 |
| 146_E | 149_A | 1.269 | 0.99 |
| 28_A | 82_D | 1.259 | 0.99 |
| 235_I | 239_I | 1.255 | 0.99 |
| 39_T | 132_A | 1.251 | 0.99 |
| 101_E | 104_K | 1.247 | 0.99 |
| 27_L | 34_V | 1.241 | 0.98 |
| 192_I | 196_L | 1.232 | 0.98 |
| 22_N | 221_A | 1.226 | 0.98 |
| 50_M | 84_L | 1.225 | 0.98 |
| 28_A | 84_L | 1.212 | 0.98 |
| 171_L | 174_N | 1.210 | 0.98 |
| 148_S | 214_S | 1.210 | 0.98 |
| 204_V | 231_A | 1.203 | 0.98 |
| 210_V | 228_A | 1.203 | 0.98 |
| 234_N | 238_R | 1.197 | 0.98 |
| 45_N | 152_D | 1.187 | 0.98 |
| 44_R | 47_D | 1.181 | 0.98 |
| 39_T | 60_L | 1.169 | 0.97 |
| 237_R | 241_G | 1.168 | 0.97 |
| 200_L | 203_I | 1.168 | 0.97 |
| 218_E | 222_M | 1.163 | 0.97 |
| 4_A | 111_K | 1.126 | 0.97 |
| 24_G | 84_L | 1.125 | 0.97 |
| 4_A | 117_V | 1.121 | 0.97 |
| 231_A | 234_N | 1.120 | 0.96 |
| 154_D | 195_H | 1.119 | 0.96 |
| 182_K | 185_D | 1.117 | 0.96 |
| 189_I | 193_V | 1.113 | 0.96 |
| 22_N | 25_T | 1.110 | 0.96 |
| 19_T | 142_V | 1.108 | 0.96 |
| 37_V | 117_V | 1.104 | 0.96 |
| 19_T | 23_L | 1.095 | 0.96 |
| 25_T | 29_I | 1.094 | 0.96 |
| 172_V | 235_I | 1.083 | 0.96 |
| 19_T | 172_V | 1.081 | 0.95 |
| 26_A | 233_R | 1.078 | 0.95 |
| 226_N | 229_S | 1.073 | 0.95 |
| 209_E | 224_P | 1.067 | 0.95 |
| 45_N | 148_S | 1.065 | 0.95 |
| 144_T | 149_A | 1.062 | 0.95 |
| 156_I | 160_L | 1.050 | 0.94 |
| 142_V | 174_N | 1.035 | 0.94 |
| 108_Q | 111_K | 1.032 | 0.94 |
| 114_F | 117_V | 1.028 | 0.94 |
| 233_R | 237_R | 1.027 | 0.94 |
| 8_T | 156_I | 1.026 | 0.94 |
| 27_L | 236_A | 1.019 | 0.93 |
| 2_G | 111_K | 1.003 | 0.93 |
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 | |
| 1hyqA | 1 | 0.8582 | 100 | 0.26 | Contact Map |
| 3q9lA | 2 | 0.9291 | 100 | 0.279 | Contact Map |
| 4v03A | 2 | 0.8769 | 100 | 0.296 | Contact Map |
| 3fwyA | 2 | 0.9291 | 100 | 0.31 | Contact Map |
| 1g3qA | 1 | 0.8769 | 100 | 0.312 | Contact Map |
| 4pfsA | 2 | 0.8694 | 100 | 0.324 | Contact Map |
| 3ea0A | 2 | 0.8619 | 100 | 0.33 | Contact Map |
| 2ynmA | 2 | 0.9254 | 100 | 0.333 | Contact Map |
| 1cp2A | 2 | 0.9328 | 100 | 0.342 | Contact Map |
| 3kjhA | 1 | 0.847 | 100 | 0.35 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)