| Sec3_Nterm |
| ID: | 1488292824 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 180 (143) | ||
| Sequences: | 398 (255.6) | ||
| Seq/Len: | 2.783 | ||
| Nf(neff/√len): | 21.4 |
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: 2.783).
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 |
| 31_S | 34_Y | 1.831 | 0.99 |
| 39_E | 53_R | 1.720 | 0.98 |
| 23_D | 26_K | 1.715 | 0.98 |
| 90_L | 105_I | 1.712 | 0.98 |
| 56_A | 71_L | 1.645 | 0.97 |
| 123_V | 128_K | 1.620 | 0.97 |
| 22_T | 26_K | 1.579 | 0.97 |
| 70_R | 82_V | 1.579 | 0.97 |
| 145_G | 148_V | 1.557 | 0.96 |
| 39_E | 51_K | 1.526 | 0.96 |
| 5_P | 8_V | 1.484 | 0.95 |
| 59_C | 133_Y | 1.466 | 0.94 |
| 40_E | 50_M | 1.443 | 0.93 |
| 85_W | 90_L | 1.431 | 0.93 |
| 58_T | 69_H | 1.422 | 0.93 |
| 98_D | 119_R | 1.362 | 0.91 |
| 12_I | 15_A | 1.358 | 0.90 |
| 61_D | 88_F | 1.353 | 0.90 |
| 85_W | 111_L | 1.336 | 0.90 |
| 16_V | 54_Y | 1.334 | 0.89 |
| 94_T | 141_T | 1.322 | 0.89 |
| 101_V | 136_R | 1.321 | 0.89 |
| 101_V | 105_I | 1.311 | 0.88 |
| 70_R | 111_L | 1.301 | 0.88 |
| 26_K | 37_V | 1.301 | 0.88 |
| 38_E | 52_P | 1.253 | 0.85 |
| 95_V | 119_R | 1.250 | 0.85 |
| 109_H | 122_F | 1.231 | 0.84 |
| 31_S | 55_I | 1.230 | 0.84 |
| 39_E | 55_I | 1.229 | 0.84 |
| 39_E | 82_V | 1.219 | 0.83 |
| 142_T | 147_K | 1.216 | 0.83 |
| 85_W | 109_H | 1.199 | 0.81 |
| 70_R | 85_W | 1.180 | 0.80 |
| 12_I | 31_S | 1.178 | 0.80 |
| 68_I | 78_G | 1.176 | 0.80 |
| 51_K | 69_H | 1.171 | 0.79 |
| 107_K | 122_F | 1.165 | 0.79 |
| 53_R | 70_R | 1.158 | 0.78 |
| 29_E | 67_Y | 1.156 | 0.78 |
| 25_R | 28_H | 1.145 | 0.77 |
| 57_L | 96_I | 1.140 | 0.77 |
| 146_R | 149_D | 1.134 | 0.76 |
| 6_N | 28_H | 1.132 | 0.76 |
| 78_G | 119_R | 1.131 | 0.76 |
| 5_P | 23_D | 1.124 | 0.75 |
| 59_C | 65_I | 1.123 | 0.75 |
| 21_T | 25_R | 1.117 | 0.75 |
| 83_K | 89_E | 1.116 | 0.74 |
| 86_P | 89_E | 1.114 | 0.74 |
| 14_Q | 20_Q | 1.108 | 0.74 |
| 85_W | 89_E | 1.105 | 0.73 |
| 6_N | 9_E | 1.092 | 0.72 |
| 31_S | 56_A | 1.090 | 0.72 |
| 19_A | 90_L | 1.088 | 0.72 |
| 109_H | 118_A | 1.082 | 0.71 |
| 143_T | 147_K | 1.081 | 0.71 |
| 22_T | 27_A | 1.075 | 0.70 |
| 99_H | 102_T | 1.075 | 0.70 |
| 65_I | 81_V | 1.071 | 0.70 |
| 145_G | 149_D | 1.068 | 0.70 |
| 89_E | 98_D | 1.063 | 0.69 |
| 94_T | 106_N | 1.062 | 0.69 |
| 119_R | 122_F | 1.061 | 0.69 |
| 92_N | 141_T | 1.053 | 0.68 |
| 100_D | 103_M | 1.049 | 0.68 |
| 80_T | 83_K | 1.045 | 0.67 |
| 64_R | 88_F | 1.045 | 0.67 |
| 69_H | 81_V | 1.034 | 0.66 |
| 70_R | 74_N | 1.031 | 0.66 |
| 34_Y | 39_E | 1.028 | 0.65 |
| 21_T | 60_D | 1.020 | 0.65 |
| 27_A | 43_V | 1.014 | 0.64 |
| 54_Y | 91_Q | 1.011 | 0.64 |
| 7_A | 10_Q | 1.008 | 0.63 |
| 138_L | 141_T | 1.004 | 0.63 |
| 83_K | 131_M | 1.003 | 0.63 |
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 | |
| 3a58A | 3 | 0.9111 | 100 | 0.272 | Contact Map |
| 3hieA | 4 | 0.8444 | 100 | 0.276 | Contact Map |
| 4k17A | 4 | 0.8889 | 91.5 | 0.898 | Contact Map |
| 1zc3B | 2 | 0.5778 | 77.4 | 0.916 | Contact Map |
| 1v61A | 1 | 0.6889 | 54.9 | 0.928 | Contact Map |
| 2rovA | 1 | 0.5389 | 51.5 | 0.93 | Contact Map |
| 2dtcA | 2 | 0.5778 | 49.7 | 0.93 | Contact Map |
| 2dhkA | 1 | 0.6333 | 37.6 | 0.935 | Contact Map |
| 2cofA | 1 | 0.5667 | 36 | 0.936 | Contact Map |
| 3rcpA | 1 | 0.5389 | 35 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)