| 1pdrd23 |
| ID: | 1430947580 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 228 (202) | ||
| Sequences: | 4832 (3436.3) | ||
| Seq/Len: | 23.921 | ||
| Nf(neff/√len): | 241.8 |
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: 23.921).
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 |
| 55_A | 83_K | 4.872 | 1.00 |
| 38_G | 42_H | 3.442 | 1.00 |
| 84_V | 93_N | 3.243 | 1.00 |
| 32_V | 47_L | 2.538 | 1.00 |
| 47_L | 84_V | 2.490 | 1.00 |
| 179_G | 183_D | 2.393 | 1.00 |
| 83_K | 90_M | 2.385 | 1.00 |
| 54_L | 85_A | 2.278 | 1.00 |
| 37_E | 42_H | 2.244 | 1.00 |
| 173_I | 188_L | 2.203 | 1.00 |
| 56_V | 74_K | 2.154 | 1.00 |
| 81_Y | 92_M | 2.134 | 1.00 |
| 178_A | 183_D | 2.113 | 1.00 |
| 55_A | 58_N | 2.094 | 1.00 |
| 196_S | 199_S | 1.891 | 1.00 |
| 66_H | 70_V | 1.879 | 1.00 |
| 47_L | 82_L | 1.870 | 1.00 |
| 55_A | 60_C | 1.866 | 1.00 |
| 209_Q | 212_A | 1.842 | 1.00 |
| 196_S | 224_V | 1.807 | 1.00 |
| 188_L | 225_A | 1.805 | 1.00 |
| 197_V | 210_A | 1.721 | 1.00 |
| 207_H | 211_A | 1.708 | 1.00 |
| 83_K | 92_M | 1.668 | 1.00 |
| 41_A | 45_G | 1.654 | 1.00 |
| 51_D | 86_K | 1.647 | 1.00 |
| 211_A | 215_K | 1.641 | 1.00 |
| 35_I | 49_I | 1.628 | 1.00 |
| 11_L | 14_S | 1.623 | 1.00 |
| 189_R | 192_D | 1.618 | 1.00 |
| 32_V | 53_L | 1.615 | 1.00 |
| 34_K | 49_I | 1.511 | 1.00 |
| 57_N | 74_K | 1.462 | 1.00 |
| 176_I | 180_G | 1.461 | 1.00 |
| 35_I | 44_D | 1.441 | 1.00 |
| 204_A | 209_Q | 1.440 | 1.00 |
| 54_L | 83_K | 1.435 | 1.00 |
| 182_A | 186_G | 1.432 | 1.00 |
| 75_N | 78_D | 1.426 | 1.00 |
| 41_A | 44_D | 1.421 | 1.00 |
| 176_I | 190_K | 1.392 | 0.99 |
| 30_I | 64_V | 1.390 | 0.99 |
| 175_F | 190_K | 1.376 | 0.99 |
| 84_V | 91_Y | 1.371 | 0.99 |
| 40_A | 43_K | 1.350 | 0.99 |
| 210_A | 214_L | 1.348 | 0.99 |
| 181_P | 185_S | 1.342 | 0.99 |
| 69_A | 73_L | 1.340 | 0.99 |
| 52_K | 85_A | 1.329 | 0.99 |
| 188_L | 192_D | 1.311 | 0.99 |
| 57_N | 80_V | 1.304 | 0.99 |
| 202_L | 210_A | 1.286 | 0.99 |
| 96_Y | 101_I | 1.276 | 0.99 |
| 200_V | 213_A | 1.265 | 0.99 |
| 67_E | 71_T | 1.241 | 0.98 |
| 217_A | 221_V | 1.237 | 0.98 |
| 212_A | 215_K | 1.228 | 0.98 |
| 163_V | 174_S | 1.222 | 0.98 |
| 209_Q | 213_A | 1.210 | 0.98 |
| 54_L | 90_M | 1.209 | 0.98 |
| 162_I | 165_G | 1.201 | 0.98 |
| 98_P | 101_I | 1.192 | 0.98 |
| 208_E | 212_A | 1.183 | 0.98 |
| 198_N | 213_A | 1.167 | 0.97 |
| 173_I | 192_D | 1.152 | 0.97 |
| 52_K | 193_R | 1.152 | 0.97 |
| 196_S | 201_D | 1.139 | 0.97 |
| 96_Y | 99_P | 1.126 | 0.97 |
| 161_N | 175_F | 1.113 | 0.96 |
| 122_T | 126_P | 1.110 | 0.96 |
| 159_G | 162_I | 1.104 | 0.96 |
| 51_D | 54_L | 1.103 | 0.96 |
| 172_F | 193_R | 1.102 | 0.96 |
| 56_V | 82_L | 1.096 | 0.96 |
| 12_G | 15_I | 1.095 | 0.96 |
| 79_F | 94_D | 1.095 | 0.96 |
| 56_V | 80_V | 1.093 | 0.96 |
| 195_I | 226_Q | 1.082 | 0.96 |
| 194_I | 202_L | 1.075 | 0.95 |
| 202_L | 213_A | 1.072 | 0.95 |
| 32_V | 35_I | 1.064 | 0.95 |
| 188_L | 223_I | 1.060 | 0.95 |
| 176_I | 182_A | 1.059 | 0.95 |
| 63_E | 66_H | 1.052 | 0.95 |
| 193_R | 226_Q | 1.050 | 0.94 |
| 182_A | 188_L | 1.047 | 0.94 |
| 11_L | 15_I | 1.042 | 0.94 |
| 35_I | 39_G | 1.039 | 0.94 |
| 69_A | 72_A | 1.035 | 0.94 |
| 31_Y | 40_A | 1.027 | 0.94 |
| 180_G | 186_G | 1.018 | 0.93 |
| 171_I | 202_L | 1.015 | 0.93 |
| 207_H | 210_A | 1.014 | 0.93 |
| 48_Q | 51_D | 1.013 | 0.93 |
| 171_I | 210_A | 1.009 | 0.93 |
| 10_G | 13_F | 1.008 | 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 | |
| 2xkxA | 2 | 1 | 100 | 0.141 | Contact Map |
| 2qt5A | 2 | 0.7851 | 100 | 0.273 | Contact Map |
| 3gslA | 2 | 0.7719 | 100 | 0.31 | Contact Map |
| 3r0hA | 8 | 0.75 | 99.9 | 0.351 | Contact Map |
| 1p1dA | 1 | 0.7851 | 99.9 | 0.388 | Contact Map |
| 3suzA | 1 | 0.3728 | 99.9 | 0.392 | Contact Map |
| 1w9eA | 2 | 0.6886 | 99.9 | 0.425 | Contact Map |
| 3rleA | 1 | 0.6798 | 99.8 | 0.468 | Contact Map |
| 4kfvA | 1 | 0.6535 | 99.8 | 0.469 | Contact Map |
| 1ky9A | 2 | 0.7719 | 99.8 | 0.476 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)