| matr3 |
| ID: | 1509710377 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 174 (171) | ||
| Sequences: | 17690 (10798) | ||
| Seq/Len: | 103.450 | ||
| Nf(neff/√len): | 825.7 |
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: 103.450).
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 |
| 27_V | 45_A | 3.180 | 1.00 |
| 144_T | 147_D | 3.116 | 1.00 |
| 46_T | 49_D | 2.985 | 1.00 |
| 125_K | 143_E | 2.913 | 1.00 |
| 17_Q | 65_F | 2.272 | 1.00 |
| 10_R | 67_K | 2.219 | 1.00 |
| 25_F | 56_Y | 2.088 | 1.00 |
| 115_A | 163_Q | 2.032 | 1.00 |
| 14_L | 17_Q | 1.945 | 1.00 |
| 52_A | 56_Y | 1.936 | 1.00 |
| 123_Y | 154_H | 1.875 | 1.00 |
| 150_A | 154_H | 1.867 | 1.00 |
| 113_D | 117_L | 1.865 | 1.00 |
| 127_K | 143_E | 1.841 | 1.00 |
| 47_T | 51_Q | 1.823 | 1.00 |
| 51_Q | 73_L | 1.803 | 1.00 |
| 120_A | 140_I | 1.777 | 1.00 |
| 3_V | 54_V | 1.754 | 1.00 |
| 29_S | 45_A | 1.745 | 1.00 |
| 29_S | 43_E | 1.724 | 1.00 |
| 19_L | 23_E | 1.718 | 1.00 |
| 101_I | 152_V | 1.689 | 1.00 |
| 5_I | 22_V | 1.686 | 1.00 |
| 143_E | 147_D | 1.679 | 1.00 |
| 145_R | 149_M | 1.672 | 1.00 |
| 117_L | 121_E | 1.669 | 1.00 |
| 112_S | 115_A | 1.642 | 1.00 |
| 47_T | 73_L | 1.623 | 1.00 |
| 64_V | 69_V | 1.622 | 1.00 |
| 161_W | 166_C | 1.620 | 1.00 |
| 50_A | 73_L | 1.580 | 1.00 |
| 15_R | 19_L | 1.573 | 1.00 |
| 125_K | 147_D | 1.550 | 1.00 |
| 104_S | 168_K | 1.547 | 1.00 |
| 142_M | 151_M | 1.544 | 1.00 |
| 103_L | 120_A | 1.537 | 1.00 |
| 132_M | 137_Q | 1.536 | 1.00 |
| 127_K | 141_E | 1.534 | 1.00 |
| 116_V | 138_A | 1.507 | 1.00 |
| 45_A | 49_D | 1.503 | 1.00 |
| 63_L | 68_P | 1.496 | 1.00 |
| 161_W | 164_G | 1.488 | 1.00 |
| 6_M | 70_R | 1.485 | 1.00 |
| 100_V | 141_E | 1.477 | 1.00 |
| 126_I | 140_I | 1.459 | 1.00 |
| 20_Q | 23_E | 1.450 | 1.00 |
| 34_L | 39_E | 1.442 | 1.00 |
| 52_A | 55_D | 1.416 | 1.00 |
| 22_V | 42_I | 1.396 | 0.99 |
| 27_V | 49_D | 1.381 | 0.99 |
| 119_L | 122_P | 1.378 | 0.99 |
| 118_K | 121_E | 1.370 | 0.99 |
| 63_L | 66_G | 1.367 | 0.99 |
| 108_H | 165_R | 1.366 | 0.99 |
| 11_G | 65_F | 1.341 | 0.99 |
| 119_L | 160_L | 1.331 | 0.99 |
| 51_Q | 55_D | 1.329 | 0.99 |
| 18_L | 40_A | 1.304 | 0.99 |
| 149_M | 171_L | 1.303 | 0.99 |
| 33_I | 40_A | 1.270 | 0.99 |
| 99_R | 141_E | 1.266 | 0.99 |
| 10_R | 38_N | 1.255 | 0.99 |
| 148_A | 171_L | 1.243 | 0.98 |
| 21_L | 62_A | 1.235 | 0.98 |
| 16_Y | 20_Q | 1.224 | 0.98 |
| 149_M | 153_D | 1.222 | 0.98 |
| 44_M | 53_A | 1.209 | 0.98 |
| 150_A | 153_D | 1.196 | 0.98 |
| 104_S | 137_Q | 1.189 | 0.98 |
| 159_A | 166_C | 1.185 | 0.98 |
| 54_V | 73_L | 1.161 | 0.97 |
| 107_P | 110_G | 1.148 | 0.97 |
| 6_M | 39_E | 1.128 | 0.97 |
| 128_N | 141_E | 1.127 | 0.97 |
| 28_I | 42_I | 1.094 | 0.96 |
| 102_H | 137_Q | 1.093 | 0.96 |
| 98_G | 145_R | 1.084 | 0.96 |
| 49_D | 53_A | 1.083 | 0.96 |
| 48_E | 52_A | 1.078 | 0.95 |
| 103_L | 140_I | 1.072 | 0.95 |
| 21_L | 69_V | 1.066 | 0.95 |
| 129_Y | 138_A | 1.061 | 0.95 |
| 146_E | 150_A | 1.059 | 0.95 |
| 162_F | 167_V | 1.058 | 0.95 |
| 25_F | 57_Y | 1.038 | 0.94 |
| 72_H | 75_Q | 1.036 | 0.94 |
| 101_I | 148_A | 1.035 | 0.94 |
| 21_L | 24_P | 1.035 | 0.94 |
| 152_V | 171_L | 1.032 | 0.94 |
| 107_P | 111_Y | 1.028 | 0.94 |
| 16_Y | 19_L | 1.028 | 0.94 |
| 108_H | 136_S | 1.025 | 0.93 |
| 114_S | 118_K | 1.009 | 0.93 |
| 145_R | 171_L | 1.007 | 0.93 |
| 115_A | 118_K | 1.005 | 0.93 |
| 120_A | 169_V | 1.002 | 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 | |
| 2mjnA | 1 | 0.9598 | 100 | 0.053 | Contact Map |
| 4cq1A | 8 | 0.9483 | 100 | 0.054 | Contact Map |
| 2qfjA | 2 | 0.9425 | 100 | 0.061 | Contact Map |
| 2yh0A | 1 | 0.9598 | 100 | 0.078 | Contact Map |
| 3md3A | 1 | 0.8908 | 100 | 0.079 | Contact Map |
| 2adcA | 1 | 0.9655 | 99.9 | 0.084 | Contact Map |
| 4wijA | 2 | 0.8448 | 99.9 | 0.09 | Contact Map |
| 3pgwA | 2 | 0.4713 | 99.9 | 0.095 | Contact Map |
| 4qptA | 1 | 0 | 99.9 | 0.097 | Contact Map |
| 3vajA | 2 | 0.8678 | 99.9 | 0.097 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)