| Mth_NT_sol |
| ID: | 1485527669 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 162 (149) | ||
| Sequences: | 1684 (1404.4) | ||
| Seq/Len: | 11.302 | ||
| Nf(neff/√len): | 115.1 |
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: 11.302).
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 |
| 77_G | 106_M | 4.361 | 1.00 |
| 16_G | 33_L | 3.374 | 1.00 |
| 91_F | 96_Y | 3.213 | 1.00 |
| 93_Y | 97_L | 2.713 | 1.00 |
| 82_P | 97_L | 2.678 | 1.00 |
| 141_A | 153_A | 2.465 | 1.00 |
| 32_T | 102_I | 2.321 | 1.00 |
| 15_T | 74_R | 2.257 | 1.00 |
| 15_T | 72_V | 2.119 | 1.00 |
| 68_H | 71_D | 1.925 | 1.00 |
| 14_L | 77_G | 1.840 | 1.00 |
| 30_V | 54_V | 1.833 | 1.00 |
| 15_T | 37_E | 1.800 | 1.00 |
| 19_T | 50_N | 1.761 | 1.00 |
| 19_T | 34_A | 1.758 | 1.00 |
| 151_I | 154_A | 1.722 | 1.00 |
| 79_L | 82_P | 1.701 | 1.00 |
| 32_T | 50_N | 1.692 | 1.00 |
| 98_A | 103_Y | 1.624 | 1.00 |
| 82_P | 105_R | 1.568 | 1.00 |
| 145_P | 149_A | 1.568 | 1.00 |
| 147_R | 150_G | 1.533 | 1.00 |
| 144_L | 148_Q | 1.494 | 1.00 |
| 79_L | 104_N | 1.493 | 1.00 |
| 96_Y | 100_R | 1.484 | 1.00 |
| 137_K | 159_D | 1.484 | 1.00 |
| 137_K | 153_A | 1.456 | 1.00 |
| 84_P | 92_D | 1.399 | 0.99 |
| 88_P | 154_A | 1.392 | 0.99 |
| 95_A | 98_A | 1.386 | 0.99 |
| 151_I | 155_L | 1.365 | 0.99 |
| 18_V | 67_Y | 1.356 | 0.99 |
| 97_L | 105_R | 1.345 | 0.99 |
| 95_A | 99_R | 1.325 | 0.99 |
| 97_L | 102_I | 1.300 | 0.99 |
| 92_D | 95_A | 1.257 | 0.99 |
| 132_A | 135_R | 1.221 | 0.98 |
| 87_N | 90_E | 1.212 | 0.98 |
| 16_G | 73_L | 1.205 | 0.98 |
| 17_M | 34_A | 1.197 | 0.98 |
| 141_A | 149_A | 1.170 | 0.97 |
| 31_Y | 53_V | 1.165 | 0.97 |
| 81_A | 94_R | 1.143 | 0.97 |
| 13_D | 76_H | 1.137 | 0.97 |
| 122_G | 125_L | 1.127 | 0.97 |
| 51_V | 79_L | 1.119 | 0.96 |
| 34_A | 50_N | 1.117 | 0.96 |
| 17_M | 72_V | 1.116 | 0.96 |
| 71_D | 114_I | 1.105 | 0.96 |
| 128_L | 131_A | 1.086 | 0.96 |
| 36_R | 72_V | 1.083 | 0.96 |
| 140_I | 157_F | 1.083 | 0.96 |
| 16_G | 75_V | 1.083 | 0.96 |
| 82_P | 104_N | 1.078 | 0.95 |
| 21_E | 136_V | 1.076 | 0.95 |
| 70_G | 127_R | 1.072 | 0.95 |
| 18_V | 33_L | 1.068 | 0.95 |
| 33_L | 75_V | 1.068 | 0.95 |
| 84_P | 94_R | 1.050 | 0.94 |
| 150_G | 154_A | 1.036 | 0.94 |
| 16_G | 77_G | 1.022 | 0.93 |
| 135_R | 139_A | 1.011 | 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 | |
| 4me3A | 1 | 0.5679 | 16.9 | 0.892 | Contact Map |
| 4gnxA | 2 | 0.537 | 11.4 | 0.9 | Contact Map |
| 2pi2E | 4 | 0.6049 | 10.7 | 0.901 | Contact Map |
| 2xgtA | 2 | 0.8704 | 7.8 | 0.907 | Contact Map |
| 3kdfA | 2 | 0.5926 | 7.2 | 0.909 | Contact Map |
| 3ja87 | 1 | 0 | 5.8 | 0.913 | Contact Map |
| 3ja83 | 1 | 0 | 4.6 | 0.917 | Contact Map |
| 4pofA | 6 | 0.6173 | 4.2 | 0.918 | Contact Map |
| 1ltlA | 6 | 0.5741 | 4.1 | 0.919 | Contact Map |
| 3ullA | 2 | 0.5988 | 3.8 | 0.92 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)