| d4enza2 |
| ID: | 1448378215 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (146) | ||
| Sequences: | 562 (303.4) | ||
| Seq/Len: | 3.849 | ||
| Nf(neff/√len): | 25.1 |
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: 3.849).
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 |
| 4_R | 68_D | 3.126 | 1.00 |
| 22_E | 37_K | 3.078 | 1.00 |
| 127_C | 132_H | 2.555 | 1.00 |
| 91_Q | 141_F | 2.428 | 1.00 |
| 84_H | 127_C | 2.339 | 1.00 |
| 44_E | 131_N | 2.172 | 1.00 |
| 74_L | 105_L | 2.012 | 1.00 |
| 65_C | 146_C | 1.950 | 1.00 |
| 54_Y | 60_P | 1.764 | 0.99 |
| 117_A | 143_V | 1.720 | 0.99 |
| 22_E | 25_I | 1.665 | 0.99 |
| 15_E | 18_S | 1.647 | 0.99 |
| 16_N | 46_N | 1.632 | 0.99 |
| 6_F | 64_M | 1.623 | 0.99 |
| 87_F | 128_Q | 1.605 | 0.98 |
| 49_Y | 131_N | 1.571 | 0.98 |
| 89_H | 128_Q | 1.529 | 0.98 |
| 127_C | 137_L | 1.457 | 0.97 |
| 73_Y | 112_D | 1.448 | 0.97 |
| 54_Y | 65_C | 1.432 | 0.96 |
| 136_G | 143_V | 1.419 | 0.96 |
| 42_F | 46_N | 1.390 | 0.95 |
| 25_I | 28_Y | 1.375 | 0.95 |
| 8_V | 88_F | 1.362 | 0.95 |
| 32_P | 35_V | 1.357 | 0.95 |
| 87_F | 126_S | 1.340 | 0.94 |
| 89_H | 123_W | 1.288 | 0.92 |
| 72_W | 115_M | 1.284 | 0.92 |
| 53_G | 78_G | 1.281 | 0.92 |
| 16_N | 42_F | 1.278 | 0.92 |
| 12_V | 21_L | 1.269 | 0.92 |
| 117_A | 141_F | 1.243 | 0.90 |
| 122_E | 142_Q | 1.243 | 0.90 |
| 29_C | 35_V | 1.231 | 0.90 |
| 76_G | 80_E | 1.216 | 0.89 |
| 93_L | 100_I | 1.199 | 0.88 |
| 113_A | 116_V | 1.187 | 0.87 |
| 78_G | 107_P | 1.185 | 0.87 |
| 42_F | 45_S | 1.180 | 0.87 |
| 78_G | 82_D | 1.174 | 0.87 |
| 137_L | 143_V | 1.168 | 0.86 |
| 32_P | 38_D | 1.166 | 0.86 |
| 84_H | 132_H | 1.154 | 0.85 |
| 45_S | 48_M | 1.142 | 0.85 |
| 89_H | 126_S | 1.137 | 0.84 |
| 56_F | 67_E | 1.121 | 0.83 |
| 10_F | 105_L | 1.115 | 0.83 |
| 57_G | 79_N | 1.091 | 0.81 |
| 71_K | 114_Y | 1.091 | 0.81 |
| 67_E | 112_D | 1.087 | 0.80 |
| 117_A | 123_W | 1.084 | 0.80 |
| 138_Q | 141_F | 1.083 | 0.80 |
| 60_P | 65_C | 1.081 | 0.80 |
| 129_N | 132_H | 1.079 | 0.80 |
| 48_M | 55_T | 1.067 | 0.79 |
| 16_N | 48_M | 1.067 | 0.79 |
| 80_E | 131_N | 1.059 | 0.78 |
| 39_N | 115_M | 1.049 | 0.77 |
| 72_W | 107_P | 1.048 | 0.77 |
| 16_N | 21_L | 1.045 | 0.77 |
| 67_E | 103_I | 1.038 | 0.76 |
| 71_K | 112_D | 1.038 | 0.76 |
| 12_V | 75_F | 1.025 | 0.75 |
| 121_G | 137_L | 1.012 | 0.73 |
| 132_H | 137_L | 1.006 | 0.73 |
| 16_N | 45_S | 1.005 | 0.73 |
| 92_A | 95_N | 1.003 | 0.72 |
| 93_L | 113_A | 1.001 | 0.72 |
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 | |
| 4enzA | 1 | 1 | 100 | 0.077 | Contact Map |
| 2r7eA | 1 | 0.9932 | 100 | 0.275 | Contact Map |
| 4bxsV | 1 | 1 | 100 | 0.293 | Contact Map |
| 2r7eB | 1 | 1 | 100 | 0.3 | Contact Map |
| 1sddB | 1 | 0.8493 | 100 | 0.353 | Contact Map |
| 1sddA | 1 | 0.7192 | 100 | 0.371 | Contact Map |
| 3t9wA | 1 | 0.7397 | 99.9 | 0.534 | Contact Map |
| 4m3hA | 3 | 0.7397 | 99.9 | 0.536 | Contact Map |
| 3gdcA | 3 | 0.8219 | 99.8 | 0.546 | Contact Map |
| 4e9xA | 3 | 0.8836 | 99.8 | 0.567 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)