| cd81H |
| ID: | 1446722256 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 236 (228) | ||
| Sequences: | 2212 (1439.3) | ||
| Seq/Len: | 9.702 | ||
| Nf(neff/√len): | 95.3 |
HHblits Results: (2015_06)
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: 9.702).
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 |
| 171_K | 174_L | 4.786 | 1.00 |
| 207_I | 211_V | 4.410 | 1.00 |
| 188_E | 193_K | 3.336 | 1.00 |
| 89_C | 93_T | 3.320 | 1.00 |
| 33_L | 37_H | 3.082 | 1.00 |
| 148_K | 151_H | 3.000 | 1.00 |
| 11_K | 86_E | 2.875 | 1.00 |
| 105_E | 216_M | 2.600 | 1.00 |
| 113_F | 206_G | 2.560 | 1.00 |
| 107_A | 111_W | 2.456 | 1.00 |
| 26_G | 30_G | 2.373 | 1.00 |
| 151_H | 165_L | 2.362 | 1.00 |
| 29_L | 33_L | 2.069 | 1.00 |
| 95_F | 220_M | 2.056 | 1.00 |
| 12_Y | 15_F | 2.028 | 1.00 |
| 18_N | 94_F | 2.024 | 1.00 |
| 30_G | 34_W | 2.010 | 1.00 |
| 151_H | 173_N | 1.971 | 1.00 |
| 9_C | 13_L | 1.822 | 1.00 |
| 15_F | 18_N | 1.814 | 1.00 |
| 158_G | 164_A | 1.795 | 1.00 |
| 63_Y | 67_A | 1.767 | 1.00 |
| 170_L | 174_L | 1.729 | 1.00 |
| 22_W | 76_G | 1.721 | 1.00 |
| 92_G | 96_T | 1.711 | 1.00 |
| 219_E | 223_S | 1.677 | 1.00 |
| 111_W | 115_N | 1.675 | 1.00 |
| 219_E | 226_L | 1.668 | 1.00 |
| 32_A | 62_I | 1.625 | 1.00 |
| 171_K | 176_P | 1.584 | 1.00 |
| 203_Y | 207_I | 1.581 | 1.00 |
| 99_V | 220_M | 1.577 | 1.00 |
| 18_N | 21_F | 1.560 | 1.00 |
| 204_L | 208_A | 1.545 | 1.00 |
| 220_M | 224_M | 1.542 | 1.00 |
| 147_V | 151_H | 1.487 | 1.00 |
| 110_I | 114_V | 1.472 | 1.00 |
| 102_F | 220_M | 1.468 | 1.00 |
| 95_F | 99_V | 1.448 | 1.00 |
| 170_L | 176_P | 1.440 | 1.00 |
| 188_E | 196_D | 1.439 | 1.00 |
| 223_S | 226_L | 1.434 | 1.00 |
| 92_G | 227_C | 1.426 | 1.00 |
| 95_F | 224_M | 1.423 | 1.00 |
| 77_F | 81_Y | 1.405 | 0.99 |
| 32_A | 69_G | 1.404 | 0.99 |
| 34_W | 38_D | 1.384 | 0.99 |
| 30_G | 33_L | 1.384 | 0.99 |
| 77_F | 80_C | 1.384 | 0.99 |
| 34_W | 63_Y | 1.363 | 0.99 |
| 18_N | 22_W | 1.346 | 0.99 |
| 29_L | 70_A | 1.343 | 0.99 |
| 147_V | 159_S | 1.341 | 0.99 |
| 136_V | 144_K | 1.338 | 0.99 |
| 108_A | 112_G | 1.299 | 0.99 |
| 11_K | 22_W | 1.286 | 0.99 |
| 25_G | 69_G | 1.281 | 0.99 |
| 32_A | 66_I | 1.269 | 0.99 |
| 36_R | 66_I | 1.262 | 0.99 |
| 95_F | 227_C | 1.261 | 0.99 |
| 222_L | 230_I | 1.259 | 0.99 |
| 26_G | 73_M | 1.250 | 0.98 |
| 155_D | 186_F | 1.246 | 0.98 |
| 77_F | 89_C | 1.228 | 0.98 |
| 22_W | 73_M | 1.205 | 0.98 |
| 79_G | 82_G | 1.203 | 0.98 |
| 109_G | 213_A | 1.198 | 0.98 |
| 224_M | 228_C | 1.191 | 0.98 |
| 126_F | 148_K | 1.178 | 0.97 |
| 14_L | 22_W | 1.172 | 0.97 |
| 78_L | 90_L | 1.160 | 0.97 |
| 88_Q | 91_L | 1.153 | 0.97 |
| 170_L | 173_N | 1.152 | 0.97 |
| 202_L | 205_I | 1.149 | 0.97 |
| 25_G | 72_M | 1.147 | 0.97 |
| 95_F | 228_C | 1.147 | 0.97 |
| 81_Y | 90_L | 1.147 | 0.97 |
| 24_A | 27_V | 1.143 | 0.97 |
| 102_F | 106_V | 1.134 | 0.97 |
| 193_K | 196_D | 1.127 | 0.96 |
| 127_Y | 131_L | 1.112 | 0.96 |
| 159_S | 191_H | 1.111 | 0.96 |
| 166_T | 170_L | 1.111 | 0.96 |
| 176_P | 186_F | 1.091 | 0.96 |
| 78_L | 93_T | 1.085 | 0.95 |
| 131_L | 147_V | 1.076 | 0.95 |
| 22_W | 77_F | 1.073 | 0.95 |
| 81_Y | 87_S | 1.071 | 0.95 |
| 11_K | 15_F | 1.069 | 0.95 |
| 15_F | 80_C | 1.066 | 0.95 |
| 154_L | 197_L | 1.064 | 0.95 |
| 191_H | 195_D | 1.058 | 0.94 |
| 28_I | 32_A | 1.055 | 0.94 |
| 11_K | 14_L | 1.052 | 0.94 |
| 15_F | 19_F | 1.049 | 0.94 |
| 6_C | 9_C | 1.048 | 0.94 |
| 88_Q | 227_C | 1.041 | 0.94 |
| 150_F | 196_D | 1.036 | 0.94 |
| 34_W | 76_G | 1.027 | 0.93 |
| 219_E | 222_L | 1.009 | 0.92 |
| 149_T | 153_T | 1.003 | 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 | |
| 3x0fA | 2 | 0 | 99.7 | 0.653 | Contact Map |
| 2m7zA | 1 | 0.3432 | 99.6 | 0.674 | Contact Map |
| 2ks1B | 1 | 0.1864 | 10 | 0.947 | Contact Map |
| 3pblA | 2 | 0.1483 | 6 | 0.952 | Contact Map |
| 4l6rA | 1 | 0.6229 | 5.6 | 0.953 | Contact Map |
| 4mbsA | 2 | 0.2034 | 4.8 | 0.955 | Contact Map |
| 1fn9A | 2 | 0.4746 | 4.8 | 0.955 | Contact Map |
| 4b1qP | 1 | 0.1144 | 3.8 | 0.957 | Contact Map |
| 4pxzA | 1 | 0.1992 | 3.4 | 0.958 | Contact Map |
| 2mofA | 1 | 0.1653 | 3.2 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)