| mif |
| ID: | 1448269024 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (115) | ||
| Sequences: | 736 (523.6) | ||
| Seq/Len: | 6.400 | ||
| Nf(neff/√len): | 48.8 |
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: 6.400).
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 |
| 6_V | 23_L | 2.660 | 1.00 |
| 22_E | 87_R | 2.524 | 1.00 |
| 37_Y | 114_F | 2.396 | 1.00 |
| 24_T | 35_P | 2.214 | 1.00 |
| 77_S | 108_G | 2.213 | 1.00 |
| 48_M | 57_C | 2.203 | 1.00 |
| 53_S | 94_R | 2.174 | 1.00 |
| 7_N | 43_V | 2.161 | 1.00 |
| 6_V | 60_C | 2.057 | 1.00 |
| 82_G | 86_E | 1.906 | 1.00 |
| 77_S | 99_Y | 1.867 | 1.00 |
| 85_A | 92_P | 1.771 | 1.00 |
| 58_A | 95_V | 1.759 | 1.00 |
| 41_H | 48_M | 1.672 | 1.00 |
| 41_H | 46_Q | 1.609 | 1.00 |
| 56_P | 94_R | 1.509 | 0.99 |
| 69_G | 72_Q | 1.481 | 0.99 |
| 25_Q | 35_P | 1.479 | 0.99 |
| 77_S | 81_C | 1.458 | 0.99 |
| 4_F | 62_L | 1.438 | 0.99 |
| 99_Y | 113_T | 1.434 | 0.99 |
| 57_C | 94_R | 1.365 | 0.98 |
| 109_W | 114_F | 1.313 | 0.97 |
| 78_K | 82_G | 1.311 | 0.97 |
| 39_A | 50_F | 1.293 | 0.97 |
| 102_M | 107_V | 1.290 | 0.97 |
| 25_Q | 29_Q | 1.258 | 0.96 |
| 40_V | 49_A | 1.234 | 0.96 |
| 85_A | 95_V | 1.222 | 0.96 |
| 85_A | 89_R | 1.220 | 0.96 |
| 68_I | 73_N | 1.215 | 0.95 |
| 26_Q | 30_A | 1.210 | 0.95 |
| 29_Q | 79_L | 1.194 | 0.95 |
| 27_L | 38_I | 1.173 | 0.94 |
| 3_M | 41_H | 1.172 | 0.94 |
| 24_T | 38_I | 1.169 | 0.94 |
| 7_N | 41_H | 1.151 | 0.93 |
| 21_S | 35_P | 1.121 | 0.92 |
| 81_C | 95_V | 1.113 | 0.92 |
| 30_A | 79_L | 1.113 | 0.92 |
| 39_A | 59_L | 1.103 | 0.91 |
| 96_Y | 114_F | 1.094 | 0.91 |
| 108_G | 112_S | 1.089 | 0.91 |
| 67_K | 103_N | 1.075 | 0.90 |
| 11_P | 69_G | 1.067 | 0.89 |
| 18_G | 82_G | 1.048 | 0.88 |
| 28_A | 104_A | 1.047 | 0.88 |
| 11_P | 45_D | 1.044 | 0.88 |
| 71_A | 112_S | 1.034 | 0.87 |
| 20_L | 49_A | 1.025 | 0.87 |
| 50_F | 109_W | 1.021 | 0.86 |
| 40_V | 80_L | 1.007 | 0.85 |
| 15_V | 18_G | 1.005 | 0.85 |
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 | |
| 3kanA | 3 | 0.9913 | 100 | 0.222 | Contact Map |
| 3djhA | 3 | 0.9913 | 100 | 0.231 | Contact Map |
| 1hfoA | 6 | 0.9826 | 100 | 0.258 | Contact Map |
| 2wkbA | 6 | 0.9826 | 100 | 0.265 | Contact Map |
| 3b64A | 1 | 0.9652 | 99.9 | 0.285 | Contact Map |
| 3fwuA | 1 | 0.9739 | 99.9 | 0.291 | Contact Map |
| 2os5A | 4 | 0.9913 | 99.9 | 0.294 | Contact Map |
| 1uizA | 4 | 1 | 99.9 | 0.296 | Contact Map |
| 3t5sA | 1 | 0.8261 | 99.9 | 0.301 | Contact Map |
| 3fwtA | 1 | 0.9739 | 99.9 | 0.305 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)